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v1.0.3 ... main

Author SHA1 Message Date
89142f8997 Update version number 2025-07-19 22:47:32 +02:00
17ee6a909a Merge pull request 'Create version 1.2.1' (#40) from ldi into main
Reviewed-on: #40
2025-07-19 20:42:25 +00:00
56d85b1a43 Update test libraries version number 2025-07-19 22:25:17 +02:00
481c702302 Update libraries versions 2025-07-19 22:12:27 +02:00
3e0b790cfe Update Changelog 2025-07-08 18:57:57 +02:00
e2a0c5f4a5 Add Notes to Proposal convergence 2025-07-08 18:50:09 +02:00
aa77745e55 Fix TANLd valid_hyperparameters 2025-07-08 17:28:27 +02:00
e5227c5f4b Add dataset tests to Ld models 2025-07-08 16:07:16 +02:00
ed380b1494 Complete implementation with tests 2025-07-08 11:42:20 +02:00
2c7352ac38 Fix classifier build in proposal 2025-07-07 02:10:08 +02:00
0ce7f664b4 remove unneeded files 2025-07-07 00:38:00 +02:00
62fa85a1b3 Complete proposal 2025-07-07 00:37:16 +02:00
97894cc49c First approach with derived class 2025-07-06 18:49:05 +02:00
090172c6c5 Add Claude local discretization analysis 2025-07-04 12:19:58 +02:00
3048244a27 Add cache clean to conan-clean 2025-07-04 11:56:55 +02:00
c142ff2c4a Compact Makefile and remove unneeded in CMakeLists 2025-07-03 09:55:05 +02:00
a5841000d3 Change optimization flag in Release 2025-07-02 13:56:54 +02:00
e7e80cfa9c Update CHANGELOG 2025-07-02 00:52:53 +02:00
1d58cea276 Add build_type option to sample target in Makefile 2025-07-02 00:51:31 +02:00
189d314990 Fix Conan debug build
Fix smell issues in markdown and python
2025-07-02 00:44:24 +02:00
dfa74056f5 Fix conan debug build 2025-07-02 00:38:47 +02:00
839be5335d Fix smell issues in markdown and python 2025-07-01 19:16:48 +02:00
28be43db02 Update sample target in Makefile 2025-07-01 18:42:20 +02:00
55a24fbaf0 Update optimization flag 2025-07-01 16:49:04 +02:00
3b170324f4 Merge pull request 'conan' (#38) from conan into main
Reviewed-on: #38
2025-07-01 14:33:50 +00:00
8ccc7e263c Update .gitignore 2025-07-01 14:14:38 +02:00
b1e25a7d05 Update Coverage Makefile 2025-07-01 14:13:45 +02:00
3cb454d4aa Fix conan build and remove vcpkg 2025-07-01 13:56:28 +02:00
3178bcbda9 Fix conan build 2025-07-01 12:24:29 +02:00
32d231cdaf Update Makefile 2025-07-01 09:59:29 +02:00
526d036d75 Remove cmake modules unneeded 2025-06-30 22:41:04 +02:00
7a9d4178d9 First profiles
Signed-off-by: Ricardo Montañana Gómez <rmontanana@gmail.com>
2025-06-30 22:40:35 +02:00
3e94d400e2 Fix conan-init 2025-06-30 09:50:27 +02:00
31fa9cd498 First approach 2025-06-29 18:46:11 +02:00
676637fb1b Merge pull request 'Fix vcpkg build and installation' (#36) from fix_vcpkg into main
Reviewed-on: #36
2025-06-29 11:01:08 +00:00
9f3de4d924 Add new hyperparameters to the Ld classifiers
- *ld_algorithm*: algorithm to use for local discretization, with the following options: "MDLP", "BINQ", "BINU".
  - *ld_proposed_cuts*: number of cut points to return.
  - *mdlp_min_length*: minimum length of a partition in MDLP algorithm to be evaluated for partition.
  - *mdlp_max_depth*: maximum level of recursion in MDLP algorithm.
2025-06-29 13:00:34 +02:00
dafd5672bc Add Claude config and report 2025-06-25 14:17:10 +02:00
70545ee0ad Add docs generation and remove 2 code smells 2025-06-24 19:06:41 +02:00
7917a7598b Update json version in vcpkg 2025-06-19 12:17:50 +02:00
bb547a3347 Remove tests/lib 2025-06-04 16:42:01 +02:00
23d74c4643 Add L1FS feature selection 2025-06-04 11:54:36 +02:00
fcccbc15dd Fix iwss selection of second feature 2025-06-02 17:11:20 +02:00
c68b75fcc1 Update version number 2025-06-01 18:28:39 +02:00
ab86dae90d Add tests for Ld models predict_proba 2025-06-01 14:55:31 +02:00
ad72bb355b Fix CFS merit computation error 2025-06-01 13:54:18 +02:00
da357ac5ba remove lib 2025-05-31 20:01:42 +02:00
833455803e Update changelog 2025-05-31 20:01:22 +02:00
74a9d29dc1 Merge pull request 'Fix some issues in FeatureSelect' (#37) from FixSelectFeatures into fix_vcpkg
Reviewed-on: #37
2025-05-31 16:47:03 +00:00
3615a1463c Fix some issues in FeatureSelect 2025-05-31 14:36:51 +02:00
36ce6effe9 Optimize ComputeCPT method with a approx. 30% reducing time 2025-05-19 17:00:07 +02:00
250036f224 ComputeCPT Optimization 2025-05-13 17:43:17 +02:00
b11620bbe8 Add predict_proba to Ld classifiers 2025-05-12 19:47:04 +02:00
8a02a3a5cb Update CHANGELOG 2025-05-08 12:33:48 +02:00
7f6f49b3d0 Update project version to 1.1.1
Fix CMakeLists and different configurations to fix vcpkg build & installation
Fix sample build
Update CHANGELOG
2025-05-08 12:33:11 +02:00
5f95117dd4 Merge pull request 'Replace git submodule dependencies for vcpg dependencies' (#35) from vcpkg into main
Reviewed-on: #35
2025-04-27 20:55:03 +00:00
2f5bc10b8e Update sample project and README 2025-04-27 21:25:21 +02:00
257f519641 Fix update_coverage.py mistake in url 2025-04-27 18:41:34 +02:00
5c5ecef3cf Update vcpkg private repo baseline 2025-04-27 18:37:46 +02:00
d0ebe596f6 Fix json module version in test 2025-04-27 18:34:15 +02:00
670b93d0a1 Remove git modules and add vcpkg configuration 2025-04-27 18:33:23 +02:00
306d3a4b55 Reformat source 2025-03-22 10:31:54 +01:00
bf08b0de89 Change clang-format braces position 2025-03-17 18:02:21 +01:00
b976db53c6 Add models to README 2025-03-17 13:13:06 +01:00
be39d2dedb Add ulm class diagram & update .clang-format 2025-03-17 13:06:15 +01:00
4ca770d16b Update README.md & .clang-format 2025-03-17 12:14:57 +01:00
6bf3b939bc Add items to .clang-format 2025-03-17 11:39:33 +01:00
7076efc2a1 Merge pull request 'Optimize BoostAODE -> XBAODE' (#33) from WA2DE into main
Reviewed-on: #33
2025-03-16 17:58:10 +00:00
9ee388561f Update version, changelog, and Xsp2de clf name 2025-03-16 18:55:24 +01:00
70c7d3dd3d Add test to 99.1% 2025-03-14 18:55:29 +01:00
400967b4e3 Add tests to 90% coverage 2025-03-14 14:53:22 +01:00
c234308701 Add SPnDE n=2 2025-03-13 10:58:43 +01:00
4ded6f51eb TestXBAODE complete, fix XBAODE error in no convergence & 99% coverage 2025-03-13 01:28:48 +01:00
b1d317d8f4 Add format and launch config 2025-03-12 16:29:29 +01:00
7876d1a370 Add test 2025-03-12 16:27:19 +01:00
3bdb14bd65 Tests XSpode & XBAODE 2025-03-12 13:46:04 +01:00
71b05cc1a7 Begin XBAODE tests 2025-03-11 18:16:50 +01:00
a59689272d Fix tests 2025-03-11 01:09:37 +01:00
3d8be79b37 Fix XSpode 2025-03-10 22:18:50 +01:00
619276a5ea Update sample_xpode 2025-03-10 21:44:12 +01:00
e681099360 Add sample_xspode 2025-03-10 21:37:14 +01:00
5919fbfd34 Fix Xspode 2025-03-10 21:29:47 +01:00
a26522e62f Fix XSPode 2025-03-10 15:55:48 +01:00
86cccb6c7b Fix XSpode 2025-03-10 14:23:47 +01:00
d1b235261e Fix XSpode 2025-03-10 14:21:01 +01:00
7a8e0391dc continue fixing xspode 2025-03-10 12:18:10 +01:00
6cfbc482d8 change launch.json 2025-03-10 11:20:36 +01:00
ca54f799ee Fix XSpode predict 2025-03-10 11:18:04 +01:00
06621ea361 Add XBAODE & XSpode classifiers 2025-03-09 19:15:00 +01:00
a70ac3e883 Add namespace to Smoothing.h 2025-03-09 11:21:31 +01:00
b987dcbcc4 Refactor Smoothing type to its own file
Add log to boost
2025-03-08 14:04:08 +01:00
81fd7df7f0 Update CHANGELOG 2025-02-13 01:18:43 +01:00
dd98cf159d ComputeCPT Optimization 2025-02-13 01:17:37 +01:00
f658149977 Add dump_cpt to Ensemble 2025-02-12 20:55:35 +01:00
fb957ac3fe First implemented aproximation 2025-01-31 13:55:46 +01:00
b90e558238 Hyperparameter *maxTolerance* in the BoostAODE class is now in [1, 6] range (it was in [1, 4] range before) 2025-01-23 00:56:18 +01:00
64970cf7f7 Merge pull request 'alphablock' (#32) from alphablock into main
Reviewed-on: #32
Added

- Add a new hyperparameter to the BoostAODE class, alphablock, to control the way α is computed, with the last model or with the ensmble built so far. Default value is false.
- Add a new hyperparameter to the SPODE class, parent, to set the root node of the model. If no value is set the root parameter of the constructor is used.
- Add a new hyperparameter to the TAN class, parent, to set the root node of the model. If not set the first feature is used as root.
2025-01-22 11:48:09 +00:00
b571a4da4d Fix typo in CHANGELOG 2025-01-22 12:43:40 +01:00
8a9f329ff9 Remove typo in README 2024-12-18 14:29:12 +01:00
e2781ee525 Add parent hyperparameter to TAN & SPODE 2024-12-17 10:14:14 +01:00
56a2d3ead0 remove uneeded submodule 2024-12-14 20:27:07 +01:00
dc32a0fc47 Fix tests & update dependencies versions 2024-12-14 14:32:51 +01:00
3d6b4f0614 Implement the functionality of the hyperparameter alpha_block with test 2024-12-14 14:02:45 +01:00
18844c7da7 Add hyperparameter to ChangeLog and Boost class 2024-12-14 14:02:10 +01:00
43ceefd2c9 Fix comment in AODELd 2024-12-10 13:35:23 +01:00
e6501502d1 Update docs and help 2024-11-23 20:28:16 +01:00
d84adf6172 Add model to changelog 2024-11-23 19:13:54 +01:00
268a86cbe0 Actualiza Changelog 2024-11-23 19:11:00 +01:00
fc4c93b299 Fix Mst test 2024-11-23 19:07:35 +01:00
86f2bc44fc libmdlp (#31)
Add mdlp as library in lib/
Fix tests to reach 99.1% of coverage

Reviewed-on: #31
2024-11-23 17:22:41 +00:00
f0f3d9ad6e Fix CUDA and mdlp library issues 2024-11-20 21:02:56 +01:00
9a323cd7a3 Remove mdlp submodule 2024-11-20 20:15:49 +01:00
cb949ac7e5 Update dependecies versions 2024-09-29 13:17:44 +02:00
2c297ea15d Control optional doxygen dependency 2024-09-29 12:48:15 +02:00
4e4b6e67f4 Add env parallel variable to Makefile 2024-09-18 11:05:19 +02:00
82847774ee Update Dockerfile 2024-09-13 09:42:06 +02:00
d0955d9369 Merge pull request 'smoothing' (#30) from smoothing into main
Reviewed-on: #30
2024-09-12 20:28:33 +00:00
2d34eb8c89 Update Makefile to get parallel info from env 2024-08-31 12:43:39 +02:00
0159c397fa Update optimization flag in CMakeLists 2024-07-11 12:29:57 +02:00
0bbc8328a9 Change cpt table type to float 2024-07-08 13:27:55 +02:00
35ca862eca Don't allow add node nor add edge on fitted networks 2024-07-07 21:06:59 +02:00
26eb58b104 Forbids to insert the same edge twice 2024-07-04 18:52:41 +02:00
6fcc15d39a Upgrade mdlp library 2024-06-24 12:38:44 +02:00
9a14133be5 Add thread control to vectors predict 2024-06-23 13:02:40 +02:00
59c1cf5b3b Fix number of threads spawned 2024-06-21 19:56:35 +02:00
8e9090d283 Fix tests 2024-06-21 13:58:42 +02:00
02bcab01be Refactor CountingSemaphore as singleton 2024-06-21 09:30:24 +02:00
716748e18c Add Counting Semaphore class
Fix threading in Network
2024-06-20 10:36:09 +02:00
0b31780d39 Add Thread max spawning to Network 2024-06-18 23:18:24 +02:00
fa26aa80f7 Rename OLD_LAPLACE to ORIGINAL 2024-06-13 15:04:15 +02:00
3eb61905fb Upgrade ArffFiles Module version 2024-06-13 12:33:54 +02:00
ca0ae4dacf Refactor Cestnik smoothin factor assuming m=1 2024-06-13 09:11:47 +02:00
b34869cc61 Set smoothing as fit parameter 2024-06-11 11:40:45 +02:00
27a3e5a5e0 Implement 3 types of smoothing 2024-06-10 15:49:01 +02:00
684443a788 Implement Cestnik & Laplace smoothing 2024-06-09 17:19:38 +02:00
6d9badc33b Merge pull request 'BoostA2DE' (#29) from BoostA2DE into main
Reviewed-on: #29
2024-06-09 10:02:47 +00:00
015b1b0c0f Fix diagram size in manual 2024-05-28 11:43:39 +02:00
7bb8e4df01 Fix back to manual link 2024-05-23 18:59:08 +00:00
53710378de Fix manual generation and deploy 2024-05-23 17:34:48 +00:00
c833e9ba32 Remove coverage report from html folder and integrate in doc 2024-05-23 16:27:02 +02:00
f5cb46ee29 Add doc-install to Makefile 2024-05-22 12:09:58 +02:00
fa35681abe Add documentation link to readme 2024-05-22 11:39:33 +02:00
b0bd0e6eee Create doc target to build documentation 2024-05-22 11:10:21 +02:00
d43be27821 Remove manual and doc pages 2024-05-22 10:17:49 +02:00
a2853dd2e5 Add Doxygen to generate man and manual pages 2024-05-21 23:38:10 +02:00
0341bd5648 Refactor ArffFiles library as a git submodule only for tests 2024-05-21 11:50:19 +00:00
22b742f068 Convert ArffFile library to header only library 2024-05-21 10:11:33 +02:00
2584e8294d Force mutual information methods to be at least 0
There were cases where a tiny negative number was returned (less than -1e-7)
Fix mst glass test that is affected with this change
2024-05-17 11:15:45 +02:00
291ba0fb0e First functional BoostA2DE with its 1st test 2024-05-16 16:33:33 +02:00
80043d5181 First approach to BoostA2DE::trainModel 2024-05-16 14:32:59 +02:00
677ec5613d Add features used to selectKPairs 2024-05-16 14:18:45 +02:00
cccaa6e0af Complete selectKPairs method & test 2024-05-16 13:46:38 +02:00
2e3e0e0fc2 Add selectKParis method 2024-05-16 11:17:21 +02:00
8784a24898 Extract buildModel method to parent class in Boost 2024-05-15 20:00:44 +02:00
54496c68f1 Create Boost class as Boost<x> classifiers parent 2024-05-15 19:49:15 +02:00
1f236a70db Create BoostA2DE base class 2024-05-15 11:53:17 +02:00
ef3c74633c Conditional Entropy test 2024-05-15 11:28:09 +02:00
7efd95095c Merge pull request 'AnDE' (#28) from AnDE into main
Reviewed-on: #28
2024-05-15 09:16:12 +00:00
0e24135d46 Complete Conditional Mutual Information and test 2024-05-15 11:09:23 +02:00
521bfd2a8e Remove unoptimized implementation of conditionalEntropy 2024-05-15 01:24:27 +02:00
e2e0fb0c40 Implement Conditional Mutual Information 2024-05-15 00:48:02 +02:00
56b62a67cc Change BoostAODE tests results because folding upgrade 2024-05-12 20:23:05 +02:00
c0fc107abb Fix catch2 submodule config 2024-05-12 19:05:36 +02:00
d8c44b3b7c Add tests to check the correct version of the mdlp, folding and json libraries 2024-05-12 12:22:44 +02:00
6ab7cd2cbd Remove submodule catch from tests/lib 2024-05-12 11:05:53 +02:00
b578ea8a2d Remove module lib/catch2 2024-05-12 11:04:42 +02:00
9a752d15dc Change build cmake folder names to Debug & Release 2024-05-09 10:51:52 +02:00
4992685e94 Add devcontainer to repository
Fix update_coverage.py with lcov2.1 output
2024-05-08 06:42:19 +00:00
346b693c79 Update pdf coverage report 2024-05-06 18:28:15 +02:00
164c8bd90c Update changelog 2024-05-06 18:02:18 +02:00
ced29a2c2e Refactor coverage report generation
Add some tests to reach 99%
2024-05-06 17:56:00 +02:00
0ec53f405f Fix mistakes in feature selection in SPnDE
Complete the first A2DE test
Update version number
2024-05-05 11:14:01 +02:00
f806015b29 Implement SPnDE and A2DE 2024-05-05 01:35:17 +02:00
8115f25c06 Fix mispell mistake in doc 2024-05-02 10:53:15 +02:00
618a1e539c Return File Library to /lib as it is needed by Local Discretization (factorize) 2024-04-30 20:31:14 +02:00
7aeffba740 Add list of models to README 2024-04-30 18:59:38 +02:00
e79ea63afb Merge pull request 'convergence_best' (#27) from convergence_best into main
Add convergence_best as hyperparameter to allow to take the last or the best accuracy as the accuracy to compare to in convergence

Reviewed-on: #27
2024-04-30 16:22:08 +00:00
3c7382a93a Enhance tests coverage and report output 2024-04-30 14:00:24 +02:00
b4a222b100 Update gcovr configuration 2024-04-30 12:06:32 +02:00
23ef0cc5f7 Remove catch2 as submodule
Add link to pdf coverage report
2024-04-30 11:02:23 +02:00
793b2d3cd5 Refactor TestUtils to allow partial and shuffle dataset load 2024-04-30 02:11:14 +02:00
ae469b8146 Add hyperparameter convergence_best
move test libraries to test folder
2024-04-30 00:52:09 +02:00
f014928411 Update Makefile actions for coverage 2024-04-21 18:54:13 +02:00
c4b563a339 Add link to the coverage report in the README.md coverage label 2024-04-21 16:44:35 +02:00
49bb0582e6 Add Library Logo 2024-04-21 11:31:27 +02:00
b4c5261e01 Delete .github/workflows/main.yml 2024-04-20 17:54:56 +00:00
b956aa3873 Upgrade version number to 1.0.5
Fix dependency graph
Remove loguru library
2024-04-20 18:00:40 +02:00
1f06631f69 Add check dependencies in make diagrams endpoint 2024-04-19 19:47:37 +02:00
6dd589bd61 Add diagram changes to CHANGELOG 2024-04-19 18:29:43 +02:00
6475f10825 Add class and dependency diagrams 2024-04-19 14:33:00 +02:00
7d906b24d1 Merge pull request 'block_update' (#26) from block_update into main
Reviewed-on: #26
2024-04-15 10:26:50 +00:00
464fe029ea Add dump_cpt classifier test 2024-04-11 18:16:06 +02:00
09a1369122 Add copyright header to source files 2024-04-11 18:02:49 +02:00
503ad687dc Add some more tests to 97% coverage 2024-04-11 17:29:46 +02:00
8eeaa1beee Update changelog with the latest changes 2024-04-11 00:35:55 +02:00
a2de1c9522 Implement block update algorithm fix in BoostAODE 2024-04-11 00:02:43 +02:00
cf9b5716ac block_update and install in local folder 2024-04-10 00:55:36 +02:00
1326891d6a Fix previous tests of BoostAODE
Due to the change of default values for hyperparameters in BoostAODE
2024-04-09 00:13:45 +02:00
da2a969686 Create hyperparameter block_update 2024-04-08 23:36:05 +02:00
f9553a38d7 Fix BoostAODE.md doc 2024-04-08 22:45:32 +02:00
8b6121eaf2 Update readme and boostAODE docs 2024-04-08 22:41:23 +02:00
fbbed8ad68 Make some boostAODE tests 2024-04-08 22:30:55 +02:00
a1178554ff Add Ensemble tests 2024-04-08 19:09:51 +02:00
d12a779bd9 Merge pull request 'bisection proposal' (#24) from bisection into main
Reviewed-on: #24
2024-04-08 14:29:25 +00:00
a8fc29e2b2 Create coverage badge 2024-04-08 11:24:25 +02:00
50543e7929 Add tests for Classifier class 2024-04-08 01:25:14 +02:00
9014649a0d Refactor hyperparameters classifier management 2024-04-08 00:55:30 +02:00
0d6a081d01 Add tests to reach 90% coverage 2024-04-08 00:13:59 +02:00
46cb8d30eb Add codacy code quality badge 2024-04-07 12:35:21 +02:00
cb26ef2562 Add some tests and code quality badge 2024-04-07 02:08:37 +02:00
df45fddd45 Update folding library and test result due to change in random engine 2024-04-05 19:17:53 +02:00
a1f9086780 Fix CFS mistake 2024-04-02 22:53:00 +02:00
e55365c41c Update test Models 2024-04-02 17:56:23 +02:00
de23303801 Refactor tests and add FeatureSelection tests 2024-04-02 17:38:48 +02:00
56b5158ff3 Update BoostAODE class structure 2024-04-02 09:52:40 +02:00
a5a29eb66f Update compiler configuration for Mac 2024-04-02 09:48:03 +02:00
d5eba5710a Update pseudocode 2024-04-01 18:37:51 +02:00
8c61840d81 Update tests 2024-04-01 11:51:29 +02:00
bc0b938cfc Remove dataset clone in BoostAODE 2024-03-21 19:35:08 +01:00
58d5a35a35 Update log output size type 2024-03-21 19:24:51 +01:00
45c048f635 Add initial models to log 2024-03-21 11:23:41 +01:00
6e854dfda3 Fix metrics error in BoostAODE Convergence
Update algorithm
2024-03-20 23:33:02 +01:00
5826702fc7 Remove weights backup 2024-03-20 12:01:57 +01:00
42e2be3263 Implement algorithm and add logging 2024-03-20 11:30:02 +01:00
827b0dd893 Add optimization flags to release 2024-03-19 17:24:21 +01:00
882d905a28 First approach to bisection 2024-03-19 14:13:40 +01:00
422129802a Remove predict_single max_models 2024-03-19 11:35:43 +01:00
eb97a5a14b Remove repeatSparent hyperparameter 2024-03-19 09:42:03 +01:00
eb72f13bf0 Make predict_voting default value false in AODE 2024-03-12 00:27:50 +01:00
5db168d87b Make predict_voting default value false in BoostAODE 2024-03-12 00:26:28 +01:00
8f3bb47cfd Fix Initialize worse_model_count if model accuracy is better in BoostAODE 2024-03-11 22:33:50 +01:00
1986d05c34 Initialize worse_model_count if model accuracy is better in BoostAODE 2024-03-11 21:30:01 +01:00
7c98ba9bea Update License & Readme 2024-03-11 10:57:27 +01:00
538af0253b Fix test & sample issue 2024-03-09 12:45:03 +01:00
0b65e34772 Fix config.h location problem 2024-03-09 12:27:05 +01:00
635ef22520 Refactor library structure 2024-03-08 22:20:54 +01:00
1231f4522a Merge pull request 'Create installation process' (#23) from install_lib into main
Reviewed-on: #23
2024-03-08 11:51:59 +00:00
cc34f79b91 Update changelog and readme 2024-03-08 09:02:22 +01:00
6899033806 Change include of library headers 2024-03-08 01:13:30 +01:00
8e2d05e663 Refactor sample to be out of main CMakeLists 2024-03-08 01:09:39 +01:00
eba2095718 Create installation process 2024-03-08 00:37:36 +01:00
199ffc95d2 Update dates on changelog 2024-03-06 23:42:14 +01:00
cbe15e317d Fix FCBF in select_features 2024-03-06 18:24:27 +01:00
debd890519 Update version number in tests 2024-03-06 17:22:45 +01:00
46e929ff4d Merge pull request 'predict_single' (#22) from predict_single into main
Reviewed-on: #22

close #19
2024-03-06 16:16:15 +00:00
d858e26e4b Update version number and Changelog 2024-03-06 17:04:16 +01:00
0ee3eaed53 Update select features models significance 2024-03-05 12:10:58 +01:00
093c197f0a Replace constant strings in BoostAODE 2024-03-05 11:05:11 +01:00
78d7ea7c4d Add predict_single proposal detailed info 2024-03-03 22:56:01 +01:00
d6af1ffe8e Update gcovr config and fix some warnings 2024-02-28 11:51:37 +01:00
20669dd161 Translate BoostAODE.md to English 2024-02-27 20:29:01 +01:00
272dbad4f3 Update README and docs 2024-02-27 17:16:26 +01:00
8bccc3e4bc Update boostaode algorithm explain 2024-02-27 14:24:58 +01:00
903b143338 Refactor library structure and add sample 2024-02-27 13:06:13 +01:00
f10d0daf2e Update test 2024-02-27 10:16:20 +01:00
d39a17089e Begin implementing predict_single hyperparameter in BoostAODE 2024-02-26 20:29:08 +01:00
2e325cd114 Merge pull request 'change boostaode ascending hyperparameter to order {asc,desc,rand}' (#21) from baode_random into main
Reviewed-on: #21

This PR closes #18
2024-02-26 16:28:48 +00:00
fc3d63b7db change boostaode ascending hyperparameter to order {asc,desc,rand} 2024-02-26 17:07:57 +01:00
43dc79a345 Update version number in ChangeLog 2024-02-25 18:07:50 +01:00
160 changed files with 19644 additions and 2710 deletions

10
.clang-format Normal file
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@@ -0,0 +1,10 @@
# .clang-format
---
BasedOnStyle: LLVM
AccessModifierOffset: -4
BreakBeforeBraces: Linux
ColumnLimit: 0
FixNamespaceComments: false
IndentWidth: 4
NamespaceIndentation: All
TabWidth: 4

View File

@@ -5,11 +5,12 @@ Checks: '-*,
cppcoreguidelines-*,
modernize-*,
performance-*,
-modernize-use-nodiscard,
-cppcoreguidelines-pro-type-vararg,
-modernize-use-trailing-return-type,
-bugprone-exception-escape'
HeaderFilterRegex: 'src/*'
HeaderFilterRegex: 'bayesnet/*'
AnalyzeTemporaryDtors: false
WarningsAsErrors: ''
FormatStyle: file

39
.clang-uml Normal file
View File

@@ -0,0 +1,39 @@
compilation_database_dir: build_Debug
output_directory: diagrams
diagrams:
BayesNet:
type: class
glob:
- bayesnet/*.h
- bayesnet/classifiers/*.h
- bayesnet/classifiers/*.cc
- bayesnet/ensembles/*.h
- bayesnet/ensembles/*.cc
- bayesnet/feature_selection/*.h
- bayesnet/feature_selection/*.cc
- bayesnet/network/*.h
- bayesnet/network/*.cc
- bayesnet/utils/*.h
- bayesnet/utils/*.cc
include:
# Only include entities from the following namespaces
namespaces:
- bayesnet
exclude:
access:
- private
plantuml:
style:
# Apply this style to all classes in the diagram
class: "#aliceblue;line:blue;line.dotted;text:blue"
# Apply this style to all packages in the diagram
package: "#back:grey"
# Make all template instantiation relations point upwards and draw them
# as green and dotted lines
instantiation: "up[#green,dotted]"
cmd: "/usr/bin/plantuml -tsvg \"diagrams/{}.puml\""
before:
- 'title clang-uml class diagram model'
mermaid:
before:
- 'classDiagram'

57
.devcontainer/Dockerfile Normal file
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@@ -0,0 +1,57 @@
FROM mcr.microsoft.com/devcontainers/cpp:ubuntu22.04
ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.29.3"
# Optionally install the cmake for vcpkg
COPY ./reinstall-cmake.sh /tmp/
RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
fi \
&& rm -f /tmp/reinstall-cmake.sh
# [Optional] Uncomment this section to install additional vcpkg ports.
# RUN su vscode -c "${VCPKG_ROOT}/vcpkg install <your-port-name-here>"
# [Optional] Uncomment this section to install additional packages.
RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
&& apt-get -y install --no-install-recommends wget software-properties-common libdatetime-perl libcapture-tiny-perl libdatetime-format-dateparse-perl libgd-perl
# Add PPA for GCC 13
RUN add-apt-repository ppa:ubuntu-toolchain-r/test
RUN apt-get update
# Install GCC 13.1
RUN apt-get install -y gcc-13 g++-13 doxygen
# Install lcov 2.1
RUN wget --quiet https://github.com/linux-test-project/lcov/releases/download/v2.1/lcov-2.1.tar.gz && \
tar -xvf lcov-2.1.tar.gz && \
cd lcov-2.1 && \
make install
RUN rm lcov-2.1.tar.gz
RUN rm -fr lcov-2.1
# Install Miniconda
RUN mkdir -p /opt/conda
RUN wget --quiet "https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-aarch64.sh" -O /opt/conda/miniconda.sh && \
bash /opt/conda/miniconda.sh -b -p /opt/miniconda
# Add conda to PATH
ENV PATH=/opt/miniconda/bin:$PATH
# add CXX and CC to the environment with gcc 13
ENV CXX=/usr/bin/g++-13
ENV CC=/usr/bin/gcc-13
# link the last gcov version
RUN rm /usr/bin/gcov
RUN ln -s /usr/bin/gcov-13 /usr/bin/gcov
# change ownership of /opt/miniconda to vscode user
RUN chown -R vscode:vscode /opt/miniconda
USER vscode
RUN conda init
RUN conda install -y -c conda-forge yaml pytorch

View File

@@ -0,0 +1,37 @@
// For format details, see https://aka.ms/devcontainer.json. For config options, see the
// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
{
"name": "C++",
"build": {
"dockerfile": "Dockerfile"
},
// "features": {
// "ghcr.io/devcontainers/features/conda:1": {}
// }
// Features to add to the dev container. More info: https://containers.dev/features.
// "features": {},
// Use 'forwardPorts' to make a list of ports inside the container available locally.
// "forwardPorts": [],
// Use 'postCreateCommand' to run commands after the container is created.
"postCreateCommand": "make release && make debug && echo 'Done!'",
// Configure tool-specific properties.
// "customizations": {},
"customizations": {
// Configure properties specific to VS Code.
"vscode": {
"settings": {},
"extensions": [
"ms-vscode.cpptools",
"ms-vscode.cpptools-extension-pack",
"ms-vscode.cpptools-themes",
"ms-vscode.cmake-tools",
"ms-azuretools.vscode-docker",
"jbenden.c-cpp-flylint",
"matepek.vscode-catch2-test-adapter",
"GitHub.copilot"
]
}
}
// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
// "remoteUser": "root"
}

View File

@@ -0,0 +1,59 @@
#!/usr/bin/env bash
#-------------------------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
#-------------------------------------------------------------------------------------------------------------
#
set -e
CMAKE_VERSION=${1:-"none"}
if [ "${CMAKE_VERSION}" = "none" ]; then
echo "No CMake version specified, skipping CMake reinstallation"
exit 0
fi
# Cleanup temporary directory and associated files when exiting the script.
cleanup() {
EXIT_CODE=$?
set +e
if [[ -n "${TMP_DIR}" ]]; then
echo "Executing cleanup of tmp files"
rm -Rf "${TMP_DIR}"
fi
exit $EXIT_CODE
}
trap cleanup EXIT
echo "Installing CMake..."
apt-get -y purge --auto-remove cmake
mkdir -p /opt/cmake
architecture=$(dpkg --print-architecture)
case "${architecture}" in
arm64)
ARCH=aarch64 ;;
amd64)
ARCH=x86_64 ;;
*)
echo "Unsupported architecture ${architecture}."
exit 1
;;
esac
CMAKE_BINARY_NAME="cmake-${CMAKE_VERSION}-linux-${ARCH}.sh"
CMAKE_CHECKSUM_NAME="cmake-${CMAKE_VERSION}-SHA-256.txt"
TMP_DIR=$(mktemp -d -t cmake-XXXXXXXXXX)
echo "${TMP_DIR}"
cd "${TMP_DIR}"
curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_BINARY_NAME}" -O
curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_CHECKSUM_NAME}" -O
sha256sum -c --ignore-missing "${CMAKE_CHECKSUM_NAME}"
sh "${TMP_DIR}/${CMAKE_BINARY_NAME}" --prefix=/opt/cmake --skip-license
ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
ln -s /opt/cmake/bin/ctest /usr/local/bin/ctest

12
.github/dependabot.yml vendored Normal file
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@@ -0,0 +1,12 @@
# To get started with Dependabot version updates, you'll need to specify which
# package ecosystems to update and where the package manifests are located.
# Please see the documentation for more information:
# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
# https://containers.dev/guide/dependabot
version: 2
updates:
- package-ecosystem: "devcontainers"
directory: "/"
schedule:
interval: weekly

9
.gitignore vendored
View File

@@ -38,3 +38,12 @@ cmake-build*/**
.idea
puml/**
.vscode/settings.json
sample/build
**/.DS_Store
docs/manual
docs/man3
docs/man
docs/Doxyfile
.cache
vcpkg_installed
CMakeUserPresets.json

20
.gitmodules vendored
View File

@@ -1,20 +0,0 @@
[submodule "lib/mdlp"]
path = lib/mdlp
url = https://github.com/rmontanana/mdlp
main = main
update = merge
[submodule "lib/catch2"]
path = lib/catch2
main = v2.x
update = merge
url = https://github.com/catchorg/Catch2.git
[submodule "lib/json"]
path = lib/json
url = https://github.com/nlohmann/json.git
master = master
update = merge
[submodule "lib/folding"]
path = lib/folding
url = https://github.com/rmontanana/folding
main = main
update = merge

View File

@@ -0,0 +1,4 @@
{
"sonarCloudOrganization": "rmontanana",
"projectKey": "rmontanana_BayesNet"
}

View File

@@ -3,15 +3,47 @@
{
"name": "Mac",
"includePath": [
"${workspaceFolder}/**"
"/Users/rmontanana/Code/BayesNet/**"
],
"defines": [],
"macFrameworkPath": [
"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
"/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include"
],
"cStandard": "c17",
"cppStandard": "c++17",
"compileCommands": "${workspaceFolder}/cmake-build-release/compile_commands.json"
"compileCommands": "",
"intelliSenseMode": "macos-clang-arm64",
"mergeConfigurations": false,
"browse": {
"path": [
"/Users/rmontanana/Code/BayesNet/**",
"${workspaceFolder}"
],
"limitSymbolsToIncludedHeaders": true
},
"configurationProvider": "ms-vscode.cmake-tools"
},
{
"name": "Linux",
"includePath": [
"/home/rmontanana/Code/BayesNet/**",
"/home/rmontanana/Code/libtorch/include/torch/csrc/api/include/",
"/home/rmontanana/Code/BayesNet/lib/"
],
"defines": [],
"cStandard": "c17",
"cppStandard": "c++17",
"intelliSenseMode": "linux-gcc-x64",
"mergeConfigurations": false,
"compilerPath": "/usr/bin/g++",
"browse": {
"path": [
"/home/rmontanana/Code/BayesNet/**",
"${workspaceFolder}"
],
"limitSymbolsToIncludedHeaders": true
},
"configurationProvider": "ms-vscode.cmake-tools"
}
],
"version": 4

126
.vscode/launch.json vendored
View File

@@ -5,126 +5,44 @@
"type": "lldb",
"request": "launch",
"name": "sample",
"program": "${workspaceFolder}/build_debug/sample/BayesNetSample",
"program": "${workspaceFolder}/sample/build/bayesnet_sample",
"args": [
"-d",
"iris",
"-m",
"TANLd",
"-s",
"271",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets/",
],
//"cwd": "${workspaceFolder}/build/sample/",
},
{
"type": "lldb",
"request": "launch",
"name": "experimentPy",
"program": "${workspaceFolder}/build_debug/src/Platform/b_main",
"args": [
"-m",
"STree",
"--stratified",
"-d",
"iris",
//"--discretize"
// "--hyperparameters",
// "{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "gridsearch",
"program": "${workspaceFolder}/build_debug/src/Platform/b_grid",
"args": [
"-m",
"KDB",
"--discretize",
"--continue",
"glass",
"--only",
"--compute"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "experimentBayes",
"program": "${workspaceFolder}/build_debug/src/Platform/b_main",
"args": [
"-m",
"TAN",
"--stratified",
"--discretize",
"-d",
"iris",
"--hyperparameters",
"{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "/home/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "best",
"program": "${workspaceFolder}/build_debug/src/Platform/b_best",
"args": [
"-m",
"BoostAODE",
"-s",
"accuracy",
"--build",
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "manage",
"program": "${workspaceFolder}/build_debug/src/Platform/b_manage",
"args": [
"-n",
"20"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "list",
"program": "${workspaceFolder}/build_debug/src/Platform/b_list",
"args": [],
//"cwd": "/Users/rmontanana/Code/discretizbench",
"cwd": "${workspaceFolder}/../discretizbench",
"${workspaceFolder}/tests/data/glass.arff"
]
},
{
"type": "lldb",
"request": "launch",
"name": "test",
"program": "${workspaceFolder}/build_debug/tests/unit_tests_bayesnet",
"program": "${workspaceFolder}/build_Debug/tests/TestBayesNet",
"args": [
//"-c=\"Metrics Test\"",
// "-s",
"[XBAODE]"
],
"cwd": "${workspaceFolder}/build_debug/tests",
"cwd": "${workspaceFolder}/build_Debug/tests"
},
{
"name": "Build & debug active file",
"name": "(gdb) Launch",
"type": "cppdbg",
"request": "launch",
"program": "${workspaceFolder}/build_debug/bayesnet",
"program": "enter program name, for example ${workspaceFolder}/a.out",
"args": [],
"stopAtEntry": false,
"cwd": "${workspaceFolder}",
"cwd": "${fileDirname}",
"environment": [],
"externalConsole": false,
"MIMode": "lldb",
"preLaunchTask": "CMake: build"
"MIMode": "gdb",
"setupCommands": [
{
"description": "Enable pretty-printing for gdb",
"text": "-enable-pretty-printing",
"ignoreFailures": true
},
{
"description": "Set Disassembly Flavor to Intel",
"text": "-gdb-set disassembly-flavor intel",
"ignoreFailures": true
}
]
}
]
}

View File

@@ -5,7 +5,162 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
## [Unreleased]
## [1.2.1] - 2025-07-19
### Internal
- Update Libtorch to version 2.7.1
- Update libraries versions:
- mdlp: 2.1.1
- Folding: 1.1.2
- ArffFiles: 1.2.1
## [1.2.0] - 2025-07-08
### Internal
- Add docs generation to CMakeLists.txt.
- Add new hyperparameters to the Ld classifiers:
- *ld_algorithm*: algorithm to use for local discretization, with the following options: "MDLP", "BINQ", "BINU".
- *ld_proposed_cuts*: number of cut points to return.
- *mdlp_min_length*: minimum length of a partition in MDLP algorithm to be evaluated for partition.
- *mdlp_max_depth*: maximum level of recursion in MDLP algorithm.
- *max_iterations*: maximum number of iterations of discretization-build model loop.
- *verbose_convergence*: display status messages during the convergence process.
- Remove vcpkg as a dependency manager, now the library is built with Conan package manager and CMake.
- Add `build_type` option to the sample target in the Makefile to allow building in *Debug* or *Release* mode. Default is *Debug*.
## [1.1.1] - 2025-05-20
### Internal
- Fix CFS metric expression in the FeatureSelection class.
- Fix the vcpkg configuration in building the library.
- Fix the sample app to use the vcpkg configuration.
- Refactor the computeCPT method in the Node class with libtorch vectorized operations.
- Refactor the sample to use local discretization models.
### Added
- Add predict_proba method to all Ld classifiers.
- Add L1FS feature selection methods to the FeatureSelection class.
## [1.1.0] - 2025-04-27
### Internal
- Add changes to .clang-format to adjust to vscode format style thanks to <https://clang-format-configurator.site/>
- Remove all the dependencies as git submodules and add them as vcpkg dependencies.
- Fix the dependencies versions for this specific BayesNet version.
## [1.0.7] 2025-03-16
### Added
- A new hyperparameter to the BoostAODE class, *alphablock*, to control the way &alpha; is computed, with the last model or with the ensmble built so far. Default value is *false*.
- A new hyperparameter to the SPODE class, *parent*, to set the root node of the model. If no value is set the root parameter of the constructor is used.
- A new hyperparameter to the TAN class, *parent*, to set the root node of the model. If not set the first feature is used as root.
- A new model named XSPODE, an optimized for speed averaged one dependence estimator.
- A new model named XSP2DE, an optimized for speed averaged two dependence estimator.
- A new model named XBAODE, an optimized for speed BoostAODE model.
- A new model named XBA2DE, an optimized for speed BoostA2DE model.
### Internal
- Optimize ComputeCPT method in the Node class.
- Add methods getCount and getMaxCount to the CountingSemaphore class, returning the current count and the maximum count of threads respectively.
### Changed
- Hyperparameter *maxTolerance* in the BoostAODE class is now in [1, 6] range (it was in [1, 4] range before).
## [1.0.6] 2024-11-23
### Fixed
- Prevent existing edges to be added to the network in the `add_edge` method.
- Don't allow to add nodes or edges on already fiited networks.
- Number of threads spawned
- Network class tests
### Added
- Library logo generated with <https://openart.ai> to README.md
- Link to the coverage report in the README.md coverage label.
- *convergence_best* hyperparameter to the BoostAODE class, to control the way the prior accuracy is computed if convergence is set. Default value is *false*.
- SPnDE model.
- A2DE model.
- BoostA2DE model.
- A2DE & SPnDE tests.
- Add tests to reach 99% of coverage.
- Add tests to check the correct version of the mdlp, folding and json libraries.
- Library documentation generated with Doxygen.
- Link to documentation in the README.md.
- Three types of smoothing the Bayesian Network ORIGINAL, LAPLACE and CESTNIK.
### Internal
- Fixed doxygen optional dependency
- Add env parallel variable to Makefile
- Add CountingSemaphore class to manage the number of threads spawned.
- Ignore CUDA language in CMake CodeCoverage module.
- Update mdlp library as a git submodule.
- Create library ShuffleArffFile to limit the number of samples with a parameter and shuffle them.
- Refactor catch2 library location to test/lib
- Refactor loadDataset function in tests.
- Remove conditionalEdgeWeights method in BayesMetrics.
- Refactor Coverage Report generation.
- Add devcontainer to work on apple silicon.
- Change build cmake folder names to Debug & Release.
- Add a Makefile target (doc) to generate the documentation.
- Add a Makefile target (doc-install) to install the documentation.
### Libraries versions
- mdlp: 2.0.1
- Folding: 1.1.0
- json: 3.11
- ArffFiles: 1.1.0
## [1.0.5] 2024-04-20
### Added
- Install command and instructions in README.md
- Prefix to install command to install the package in the any location.
- The 'block_update' hyperparameter to the BoostAODE class, to control the way weights/significances are updated. Default value is false.
- Html report of coverage in the coverage folder. It is created with *make viewcoverage*
- Badges of coverage and code quality (codacy) in README.md. Coverage badge is updated with *make viewcoverage*
- Tests to reach 97% of coverage.
- Copyright header to source files.
- Diagrams to README.md: UML class diagram & dependency diagram
- Action to create diagrams to Makefile: *make diagrams*
### Changed
- Sample app now is a separate target in the Makefile and shows how to use the library with a sample dataset
- The worse model count in BoostAODE is reset to 0 every time a new model produces better accuracy, so the tolerance of the model is meant to be the number of **consecutive** models that produce worse accuracy.
- Default hyperparameter values in BoostAODE: bisection is true, maxTolerance is 3, convergence is true
### Removed
- The 'predict_single' hyperparameter from the BoostAODE class.
- The 'repeatSparent' hyperparameter from the BoostAODE class.
## [1.0.4] 2024-03-06
### Added
- Change *ascending* hyperparameter to *order* with these possible values *{"asc", "desc", "rand"}*, Default is *"desc"*.
- Add the *predict_single* hyperparameter to control if only the last model created is used to predict in boost training or the whole ensemble (all the models built so far). Default is true.
- sample app to show how to use the library (make sample)
### Changed
- Change the library structure adding folders for each group of classes (classifiers, ensembles, etc).
- The significances of the models generated under the feature selection algorithm are now computed after all the models have been generated and an &alpha;<sub>t</sub> value is computed and assigned to each model.
## [1.0.3] 2024-02-25
### Added

191
CLAUDE.md Normal file
View File

@@ -0,0 +1,191 @@
# CLAUDE.md
This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
## Project Overview
BayesNet is a C++ library implementing Bayesian Network Classifiers. It provides various algorithms for machine learning classification including TAN, KDB, SPODE, SPnDE, AODE, A2DE, and their ensemble variants (Boost, XB). The library also includes local discretization variants (Ld) and feature selection algorithms.
## Build System & Dependencies
### Dependency Management
The project supports **two package managers**:
#### vcpkg (Default)
- Uses vcpkg with private registry at <https://github.com/rmontanana/vcpkg-stash>
- Core dependencies: libtorch, nlohmann-json, folding, fimdlp, arff-files, catch2
- All dependencies defined in `vcpkg.json` with version overrides
#### Conan (Alternative)
- Modern C++ package manager with better dependency resolution
- Configured via `conanfile.py` for packaging and distribution
- Supports subset of dependencies (libtorch, nlohmann-json, catch2)
- Custom dependencies (folding, fimdlp, arff-files) need custom Conan recipes
### Build Commands
#### Using vcpkg (Default)
```bash
# Initialize dependencies
make init
# Build debug version (with tests and coverage)
make debug
make buildd
# Build release version
make release
make buildr
# Run tests
make test
# Generate coverage report
make coverage
make viewcoverage
# Clean project
make clean
```
#### Using Conan
```bash
# Install Conan first: pip install conan
# Initialize dependencies
make conan-init
# Build debug version (with tests and coverage)
make conan-debug
make buildd
# Build release version
make conan-release
make buildr
# Create and test Conan package
make conan-create
# Upload to Conan remote
make conan-upload remote=myremote
# Clean Conan cache and builds
make conan-clean
```
### CMake Configuration
- Uses CMake 3.27+ with C++17 standard
- Debug builds automatically enable testing and coverage
- Release builds optimize with `-Ofast`
- **Automatic package manager detection**: CMake detects whether Conan or vcpkg is being used
- Supports both static library and package manager installation
- Conditional dependency linking based on availability
## Testing Framework
- **Catch2** testing framework (version 3.8.1)
- Test executable: `TestBayesNet` in `build_Debug/tests/`
- Individual test categories can be run: `./TestBayesNet "[CategoryName]"`
- Coverage reporting with lcov/genhtml
### Test Categories
- A2DE, BoostA2DE, BoostAODE, XSPODE, XSPnDE, XBAODE, XBA2DE
- Classifier, Ensemble, FeatureSelection, Metrics, Models
- Network, Node, MST, Modules
## Code Architecture
### Core Structure
```
bayesnet/
├── BaseClassifier.h # Abstract base for all classifiers
├── classifiers/ # Basic Bayesian classifiers (TAN, KDB, SPODE, etc.)
├── ensembles/ # Ensemble methods (AODE, A2DE, Boost variants)
├── feature_selection/ # Feature selection algorithms (CFS, FCBF, IWSS, L1FS)
├── network/ # Bayesian network structure (Network, Node)
└── utils/ # Utilities (metrics, MST, tensor operations)
```
### Key Design Patterns
- **BaseClassifier** abstract interface for all algorithms
- Template-based design with both std::vector and torch::Tensor support
- Network/Node abstraction for Bayesian network representation
- Feature selection as separate, composable modules
### Data Handling
- Supports both discrete integer data and continuous data with discretization
- ARFF file format support through arff-files library
- Tensor operations via PyTorch C++ (libtorch)
- Local discretization variants use fimdlp library
## Documentation & Tools
- **Doxygen** for API documentation: `make doc`
- **lcov** for coverage reports: `make coverage`
- **plantuml + clang-uml** for UML diagrams: `make diagrams`
- Man pages available in `docs/man3/`
## Sample Applications
Sample code in `sample/` directory demonstrates library usage:
```bash
make sample fname=tests/data/iris.arff model=TANLd
```
## Package Distribution
### Creating Conan Packages
```bash
# Create package locally
make conan-create
# Test package installation
cd test_package
conan create ..
# Upload to remote repository
make conan-upload remote=myremote profile=myprofile
```
### Using the Library
With Conan:
```python
# conanfile.txt or conanfile.py
[requires]
bayesnet/1.1.2@user/channel
[generators]
cmake
```
With vcpkg:
```json
{
"dependencies": ["bayesnet"]
}
```
## Common Development Tasks
- **Add new classifier**: Extend BaseClassifier, implement in appropriate subdirectory
- **Add new test**: Update `tests/CMakeLists.txt` and create test in `tests/`
- **Modify build**: Edit main `CMakeLists.txt` or use Makefile targets
- **Update dependencies**:
- vcpkg: Modify `vcpkg.json` and run `make init`
- Conan: Modify `conanfile.py` and run `make conan-init`
- **Package for distribution**: Use `make conan-create` for Conan packaging

View File

@@ -0,0 +1,5 @@
# Set the default graph title
set(GRAPHVIZ_GRAPH_NAME "BayesNet dependency graph")
set(GRAPHVIZ_SHARED_LIBS OFF)
set(GRAPHVIZ_STATIC_LIBS ON)

View File

@@ -1,21 +1,14 @@
cmake_minimum_required(VERSION 3.20)
cmake_minimum_required(VERSION 3.27)
project(BayesNet
VERSION 1.0.3
project(bayesnet
VERSION 1.2.1
DESCRIPTION "Bayesian Network and basic classifiers Library."
HOMEPAGE_URL "https://github.com/rmontanana/bayesnet"
LANGUAGES CXX
)
if (CODE_COVERAGE AND NOT ENABLE_TESTING)
MESSAGE(FATAL_ERROR "Code coverage requires testing enabled")
endif (CODE_COVERAGE AND NOT ENABLE_TESTING)
find_package(Torch REQUIRED)
if (POLICY CMP0135)
cmake_policy(SET CMP0135 NEW)
endif ()
set(CMAKE_CXX_STANDARD 17)
cmake_policy(SET CMP0135 NEW)
# Global CMake variables
# ----------------------
@@ -25,48 +18,117 @@ set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3")
if (CMAKE_BUILD_TYPE STREQUAL "Debug")
MESSAGE("Debug mode")
else(CMAKE_BUILD_TYPE STREQUAL "Debug")
MESSAGE("Release mode")
endif (CMAKE_BUILD_TYPE STREQUAL "Debug")
# Options
# -------
option(ENABLE_CLANG_TIDY "Enable to add clang tidy." OFF)
option(ENABLE_TESTING "Unit testing build" OFF)
option(CODE_COVERAGE "Collect coverage from test library" OFF)
option(ENABLE_TESTING "Unit testing build" OFF)
find_package(Torch CONFIG REQUIRED)
if(NOT TARGET torch::torch)
add_library(torch::torch INTERFACE IMPORTED GLOBAL)
# expose include paths and libraries that the find-module discovered
set_target_properties(torch::torch PROPERTIES
INTERFACE_INCLUDE_DIRECTORIES "${TORCH_INCLUDE_DIRS}"
INTERFACE_LINK_LIBRARIES "${TORCH_LIBRARIES}")
endif()
# CMakes modules
# --------------
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
include(AddGitSubmodule)
find_package(fimdlp CONFIG REQUIRED)
find_package(folding CONFIG REQUIRED)
find_package(nlohmann_json REQUIRED)
if (CODE_COVERAGE)
enable_testing()
include(CodeCoverage)
MESSAGE("Code coverage enabled")
set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage -O0 -g")
SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
endif (CODE_COVERAGE)
if (ENABLE_CLANG_TIDY)
include(StaticAnalyzers) # clang-tidy
endif (ENABLE_CLANG_TIDY)
# External libraries - dependencies of BayesNet
# ---------------------------------------------
# include(FetchContent)
add_git_submodule("lib/mdlp")
add_git_submodule("lib/json")
# Subdirectories
# --------------
add_subdirectory(config)
add_subdirectory(lib/Files)
add_subdirectory(src)
file(GLOB BayesNet_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/*.cc)
# Add the library
# ---------------
include_directories(
${bayesnet_SOURCE_DIR}
${CMAKE_BINARY_DIR}/configured_files/include
)
file(GLOB_RECURSE Sources "bayesnet/*.cc")
add_library(bayesnet ${Sources})
target_link_libraries(bayesnet
nlohmann_json::nlohmann_json
folding::folding
fimdlp::fimdlp
torch::torch
arff-files::arff-files
)
# Testing
# -------
if (ENABLE_TESTING)
MESSAGE("Testing enabled")
add_git_submodule("lib/catch2")
include(CTest)
add_subdirectory(tests)
MESSAGE(STATUS "Testing enabled")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage -fno-elide-constructors")
if (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fno-default-inline")
endif()
find_package(Catch2 CONFIG REQUIRED)
find_package(arff-files CONFIG REQUIRED)
enable_testing()
include(CTest)
add_subdirectory(tests)
endif (ENABLE_TESTING)
# Installation
# ------------
include(CMakePackageConfigHelpers)
write_basic_package_version_file(
"${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfigVersion.cmake"
VERSION ${PROJECT_VERSION}
COMPATIBILITY AnyNewerVersion
)
configure_package_config_file(
${CMAKE_CURRENT_SOURCE_DIR}/bayesnetConfig.cmake.in
"${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfig.cmake"
INSTALL_DESTINATION share/bayesnet)
install(TARGETS bayesnet
EXPORT bayesnetTargets
ARCHIVE DESTINATION lib
LIBRARY DESTINATION lib)
install(DIRECTORY bayesnet/
DESTINATION include/bayesnet
FILES_MATCHING
PATTERN "*.h")
install(FILES ${CMAKE_BINARY_DIR}/configured_files/include/bayesnet/config.h
DESTINATION include/bayesnet)
install(EXPORT bayesnetTargets
FILE bayesnetTargets.cmake
NAMESPACE bayesnet::
DESTINATION share/bayesnet)
install(FILES
"${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfig.cmake"
"${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfigVersion.cmake"
DESTINATION share/bayesnet
)
# Documentation
# -------------
find_package(Doxygen)
if (Doxygen_FOUND)
set(DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
set(doxyfile_in ${DOC_DIR}/Doxyfile.in)
set(doxyfile ${DOC_DIR}/Doxyfile)
configure_file(${doxyfile_in} ${doxyfile} @ONLY)
doxygen_add_docs(doxygen
WORKING_DIRECTORY ${DOC_DIR}
CONFIG_FILE ${doxyfile})
else (Doxygen_FOUND)
MESSAGE("* Doxygen not found")
endif (Doxygen_FOUND)

86
CONAN_README.md Normal file
View File

@@ -0,0 +1,86 @@
# Using BayesNet with Conan
This document explains how to use Conan as an alternative package manager for BayesNet.
## Prerequisites
```bash
pip install conan
conan remote add Cimmeria https://conan.rmontanana.es/artifactory/api/conan/Cimmeria
conan profile new default --detect
```
## Quick Start
### As a Consumer
1. Create a `conanfile.txt` in your project:
```ini
[requires]
libtorch/2.7.0
bayesnet/1.2.0
[generators]
CMakeDeps
CMakeToolchain
```
1. Install dependencies:
```bash
conan install . --build=missing
```
1. In your CMakeLists.txt:
```cmake
find_package(bayesnet REQUIRED)
target_link_libraries(your_target bayesnet::bayesnet)
```
### Building BayesNet with Conan
```bash
# Install dependencies
make conan-init
# Build debug version
make debug
make buildd
# Build release version
make release
make buildr
# Create package
make conan-create
```
## Current Limitations
- Custom dependencies (folding, fimdlp, arff-files) are not available in ConanCenter
- These need to be built as custom Conan packages or replaced with alternatives
- The conanfile.py currently comments out these dependencies
## Creating Custom Dependency Packages
For the custom dependencies, you'll need to create Conan recipes:
1. **folding**: Cross-validation library
1. **fimdlp**: Discretization library
1. **arff-files**: ARFF file format parser
Contact the maintainer or create custom recipes for these packages.
## Package Distribution
Once custom dependencies are resolved:
```bash
# Create and test package
make conan-create
# Upload to your remote
conan upload bayesnet/1.2.0 -r myremote
```

View File

@@ -1,6 +1,6 @@
MIT License
Copyright (c) <year> <copyright holders>
Copyright (c) 2023 Ricardo Montañana Gómez
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

227
Makefile
View File

@@ -1,12 +1,30 @@
SHELL := /bin/bash
.DEFAULT_GOAL := help
.PHONY: coverage setup help buildr buildd test clean debug release
.PHONY: viewcoverage coverage setup help install uninstall diagrams buildr buildd test clean updatebadge doc doc-install init clean-test debug release conan-create conan-upload conan-clean sample
f_release = build_Release
f_debug = build_Debug
f_diagrams = diagrams
app_targets = bayesnet
test_targets = TestBayesNet
clang-uml = clang-uml
plantuml = plantuml
lcov = lcov
genhtml = genhtml
dot = dot
docsrcdir = docs/manual
mansrcdir = docs/man3
mandestdir = /usr/local/share/man
sed_command_link = 's/e">LCOV -/e"><a href="https:\/\/rmontanana.github.io\/bayesnet">Back to manual<\/a> LCOV -/g'
sed_command_diagram = 's/Diagram"/Diagram" width="100%" height="100%" /g'
# Set the number of parallel jobs to the number of available processors minus 7
CPUS := $(shell getconf _NPROCESSORS_ONLN 2>/dev/null \
|| nproc --all 2>/dev/null \
|| sysctl -n hw.ncpu)
# --- Your desired job count: CPUs 7, but never less than 1 --------------
JOBS := $(shell n=$(CPUS); [ $${n} -gt 7 ] && echo $$((n-7)) || echo 1)
f_release = build_release
f_debug = build_debug
app_targets = BayesNet
test_targets = unit_tests_bayesnet
n_procs = -j 16
define ClearTests
@for t in $(test_targets); do \
@@ -21,6 +39,14 @@ define ClearTests
fi ;
endef
define setup_target
@echo ">>> Setup the project for $(1)..."
@if [ -d $(2) ]; then rm -fr $(2); fi
@conan install . --build=missing -of $(2) -s build_type=$(1)
@cmake -S . -B $(2) -DCMAKE_TOOLCHAIN_FILE=$(2)/build/$(1)/generators/conan_toolchain.cmake -DCMAKE_BUILD_TYPE=$(1) -D$(3)
@echo ">>> Will build using $(JOBS) parallel jobs"
@echo ">>> Done"
endef
setup: ## Install dependencies for tests and coverage
@if [ "$(shell uname)" = "Darwin" ]; then \
@@ -29,57 +55,194 @@ setup: ## Install dependencies for tests and coverage
fi
@if [ "$(shell uname)" = "Linux" ]; then \
pip install gcovr; \
sudo dnf install lcov;\
fi
@echo "* You should install plantuml & graphviz for the diagrams"
dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
@echo ">>> Creating dependency graph diagram of the project...";
$(MAKE) debug
cd $(f_debug) && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png
clean: ## Clean the project
@echo ">>> Cleaning the project..."
@if test -f CMakeCache.txt ; then echo "- Deleting CMakeCache.txt"; rm -f CMakeCache.txt; fimake
@for folder in $(f_release) $(f_debug) vpcpkg_installed install_test ; do \
if test -d "$$folder" ; then \
echo "- Deleting $$folder folder" ; \
rm -rf "$$folder"; \
fi; \
done
@$(MAKE) clean-test
@echo ">>> Done";
# Build targets
# =============
debug: ## Setup debug version using Conan
@$(call setup_target,"Debug","$(f_debug)","ENABLE_TESTING=ON")
release: ## Setup release version using Conan
@$(call setup_target,"Release","$(f_release)","ENABLE_TESTING=OFF")
buildd: ## Build the debug targets
cmake --build $(f_debug) -t $(app_targets) $(n_procs)
cmake --build $(f_debug) --config Debug -t $(app_targets) --parallel $(JOBS)
buildr: ## Build the release targets
cmake --build $(f_release) -t $(app_targets) $(n_procs)
cmake --build $(f_release) --config Release -t $(app_targets) --parallel $(JOBS)
clean: ## Clean the tests info
# Install targets
# ===============
uninstall: ## Uninstall library
@echo ">>> Uninstalling BayesNet...";
xargs rm < $(f_release)/install_manifest.txt
@echo ">>> Done";
prefix = "/usr/local"
install: ## Install library
@echo ">>> Installing BayesNet...";
@cmake --install $(f_release) --prefix $(prefix)
@echo ">>> Done";
# Test targets
# ============
clean-test: ## Clean the tests info
@echo ">>> Cleaning Debug BayesNet tests...";
$(call ClearTests)
@echo ">>> Done";
debug: ## Build a debug version of the project
@echo ">>> Building Debug BayesNet...";
@if [ -d ./$(f_debug) ]; then rm -rf ./$(f_debug); fi
@mkdir $(f_debug);
@cmake -S . -B $(f_debug) -D CMAKE_BUILD_TYPE=Debug -D ENABLE_TESTING=ON -D CODE_COVERAGE=ON
@echo ">>> Done";
release: ## Build a Release version of the project
@echo ">>> Building Release BayesNet...";
@if [ -d ./$(f_release) ]; then rm -rf ./$(f_release); fi
@mkdir $(f_release);
@cmake -S . -B $(f_release) -D CMAKE_BUILD_TYPE=Release
@echo ">>> Done";
opt = ""
test: ## Run tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
@echo ">>> Running BayesNet & Platform tests...";
@$(MAKE) clean
@cmake --build $(f_debug) -t $(test_targets) $(n_procs)
@echo ">>> Running BayesNet tests...";
@$(MAKE) clean-test
@cmake --build $(f_debug) -t $(test_targets) --parallel $(JOBS)
@for t in $(test_targets); do \
echo ">>> Running $$t...";\
if [ -f $(f_debug)/tests/$$t ]; then \
cd $(f_debug)/tests ; \
./$$t $(opt) ; \
cd ../.. ; \
fi ; \
done
@echo ">>> Done";
coverage: ## Run tests and generate coverage report (build/index.html)
@echo ">>> Building tests with coverage..."
@$(MAKE) test
@gcovr $(f_debug)/tests
@which $(lcov) || (echo ">>ease install lcov"; exit 1)
@if [ ! -f $(f_debug)/tests/coverage.info ] ; then $(MAKE) test ; fi
@echo ">>> Building report..."
@cd $(f_debug)/tests; \
$(lcov) --directory CMakeFiles --capture --demangle-cpp --ignore-errors source,source --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info '/usr/*' --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info 'lib/*' --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info 'include/*' --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info 'libtorch/*' --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info 'tests/*' --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info 'bayesnet/utils/loguru.*' --ignore-errors unused --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info '/opt/miniconda/*' --ignore-errors unused --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --remove coverage.info '*/.conan2/*' --ignore-errors unused --output-file coverage.info >/dev/null 2>&1; \
$(lcov) --summary coverage.info
@$(MAKE) updatebadge
@echo ">>> Done";
viewcoverage: ## View the html coverage report
@which $(genhtml) >/dev/null || (echo ">>> Please install lcov (genhtml not found)"; exit 1)
@if [ ! -d $(docsrcdir)/coverage ]; then mkdir -p $(docsrcdir)/coverage; fi
@if [ ! -f $(f_debug)/tests/coverage.info ]; then \
echo ">>> No coverage.info file found. Run make coverage first!"; \
exit 1; \
fi
@$(genhtml) $(f_debug)/tests/coverage.info --demangle-cpp --output-directory $(docsrcdir)/coverage --title "BayesNet Coverage Report" -s -k -f --legend >/dev/null 2>&1;
@xdg-open $(docsrcdir)/coverage/index.html || open $(docsrcdir)/coverage/index.html 2>/dev/null
@echo ">>> Done";
updatebadge: ## Update the coverage badge in README.md
@which python || (echo ">>> Please install python"; exit 1)
@if [ ! -f $(f_debug)/tests/coverage.info ]; then \
echo ">>> No coverage.info file found. Run make coverage first!"; \
exit 1; \
fi
@echo ">>> Updating coverage badge..."
@env python update_coverage.py $(f_debug)/tests
@echo ">>> Done";
# Documentation targets
# =====================
doc: ## Generate documentation
@echo ">>> Generating documentation..."
@cmake --build $(f_release) -t doxygen
@cp -rp diagrams $(docsrcdir)
@
@if [ "$(shell uname)" = "Darwin" ]; then \
sed -i "" $(sed_command_link) $(docsrcdir)/coverage/index.html ; \
sed -i "" $(sed_command_diagram) $(docsrcdir)/index.html ; \
else \
sed -i $(sed_command_link) $(docsrcdir)/coverage/index.html ; \
sed -i $(sed_command_diagram) $(docsrcdir)/index.html ; \
fi
@echo ">>> Done";
diagrams: ## Create an UML class diagram & dependency of the project (diagrams/BayesNet.png)
@echo ">>> Creating diagrams..."
@which $(plantuml) || (echo ">>> Please install plantuml"; exit 1)
@which $(dot) || (echo ">>> Please install graphviz"; exit 1)
@which $(clang-uml) || (echo ">>> Please install clang-uml"; exit 1)
@export PLANTUML_LIMIT_SIZE=16384
@echo ">>> Creating UML class diagram of the project...";
@$(clang-uml) -p
@cd $(f_diagrams); \
$(plantuml) -tsvg BayesNet.puml
@echo ">>> Creating dependency graph diagram of the project...";
$(MAKE) debug
cd $(f_debug) && cmake .. --graphviz=dependency.dot
@$(dot) -Tsvg $(f_debug)/dependency.dot.BayesNet -o $(f_diagrams)/dependency.svg
@echo ">>> Done";
docdir = ""
doc-install: ## Install documentation
@echo ">>> Installing documentation..."
@if [ "$(docdir)" = "" ]; then \
echo "docdir parameter has to be set when calling doc-install, i.e. docdir=../bayesnet_help"; \
exit 1; \
fi
@if [ ! -d $(docdir) ]; then \
@$(MAKE) doc; \
fi
@cp -rp $(docsrcdir)/* $(docdir)
@sudo cp -rp $(mansrcdir) $(mandestdir)
@echo ">>> Done";
# Conan package manager targets
# =============================
conan-create: ## Create Conan package
@echo ">>> Creating Conan package..."
@conan create . --build=missing -tf "" -s:a build_type=Release
@conan create . --build=missing -tf "" -s:a build_type=Debug -o "&:enable_coverage=False" -o "&:enable_testing=False"
@echo ">>> Done"
conan-clean: ## Clean Conan cache and build folders
@echo ">>> Cleaning Conan cache and build folders..."
@conan remove "*" --confirm
@conan cache clean
@if test -d "$(f_release)" ; then rm -rf "$(f_release)"; fi
@if test -d "$(f_debug)" ; then rm -rf "$(f_debug)"; fi
@echo ">>> Done"
fname = "tests/data/iris.arff"
model = "TANLd"
build_type = "Debug"
sample: ## Build sample with Conan
@echo ">>> Building Sample with Conan...";
@if [ -d ./sample/build ]; then rm -rf ./sample/build; fi
@cd sample && conan install . --output-folder=build --build=missing -s build_type=$(build_type) -o "&:enable_coverage=False" -o "&:enable_testing=False"
@cd sample && cmake -B build -S . -DCMAKE_BUILD_TYPE=$(build_type) -DCMAKE_TOOLCHAIN_FILE=build/conan_toolchain.cmake && \
cmake --build build -t bayesnet_sample --parallel $(JOBS)
sample/build/bayesnet_sample $(fname) $(model)
@echo ">>> Done";
# Help target
# ===========
help: ## Show help message
@IFS=$$'\n' ; \

174
README.md
View File

@@ -1,22 +1,170 @@
# BayesNet
# <img src="logo.png" alt="logo" width="50"/> BayesNet
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
![C++](https://img.shields.io/badge/c++-%2300599C.svg?style=flat&logo=c%2B%2B&logoColor=white)
[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](<https://opensource.org/licenses/MIT>)
![Gitea Release](https://img.shields.io/gitea/v/release/rmontanana/bayesnet?gitea_url=https://gitea.rmontanana.es)
[![Codacy Badge](https://app.codacy.com/project/badge/Grade/cf3e0ac71d764650b1bf4d8d00d303b1)](https://app.codacy.com/gh/Doctorado-ML/BayesNet/dashboard?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_grade)
[![Security Rating](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_BayesNet&metric=security_rating)](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
[![Reliability Rating](https://sonarcloud.io/api/project_badges/measure?project=rmontanana_BayesNet&metric=reliability_rating)](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
[![Ask DeepWiki](https://deepwiki.com/badge.svg)](https://deepwiki.com/Doctorado-ML/BayesNet)
![Gitea Last Commit](https://img.shields.io/gitea/last-commit/rmontanana/bayesnet?gitea_url=https://gitea.rmontanana.es&logo=gitea)
[![Coverage Badge](https://img.shields.io/badge/Coverage-99,1%25-green)](https://gitea.rmontanana.es/rmontanana/BayesNet)
[![DOI](https://zenodo.org/badge/667782806.svg)](https://doi.org/10.5281/zenodo.14210344)
Bayesian Network Classifiers using libtorch from scratch
Bayesian Network Classifiers library
### Release
## Using the Library
```bash
make release
make buildr
### Using Conan Package Manager
You can use the library with the [Conan](https://conan.io/) package manager. In your project you need to add the following files:
#### conanfile.txt
```txt
[requires]
bayesnet/1.1.2
[generators]
CMakeDeps
CMakeToolchain
```
### Debug & Tests
#### CMakeLists.txt
```bash
make debug
make test
make coverage
Include the following lines in your `CMakeLists.txt` file:
```cmake
find_package(bayesnet REQUIRED)
add_executable(myapp main.cpp)
target_link_libraries(myapp PRIVATE bayesnet::bayesnet)
```
## 1. Introduction
Then install the dependencies and build your project:
```bash
conan install . --output-folder=build --build=missing
cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=build/conan_toolchain.cmake
cmake --build build
```
**Note: In the `sample` folder you can find a sample application that uses the library. You can use it as a reference to create your own application.**
## Building and Testing
The project uses [Conan](https://conan.io/) for dependency management and provides convenient Makefile targets for common tasks.
### Prerequisites
- [Conan](https://conan.io/) package manager (`pip install conan`)
- CMake 3.27+
- C++17 compatible compiler
### Getting the code
```bash
git clone https://github.com/doctorado-ml/bayesnet
cd bayesnet
```
### Build Commands
#### Release Build
```bash
make release # Configure release build with Conan
make buildr # Build the release version
```
#### Debug Build & Tests
```bash
make debug # Configure debug build with Conan
make buildd # Build the debug version
make test # Run the tests
```
#### Coverage Analysis
```bash
make coverage # Run tests with coverage analysis
make viewcoverage # View coverage report in browser
```
#### Sample Application
Run the sample application with different datasets and models:
```bash
make sample # Run with default settings
make sample fname=tests/data/glass.arff # Use glass dataset
make sample fname=tests/data/iris.arff model=AODE # Use specific model
```
### Available Makefile Targets
- `debug` - Configure debug build using Conan
- `release` - Configure release build using Conan
- `buildd` - Build debug targets
- `buildr` - Build release targets
- `test` - Run all tests (use `opt="-s"` for verbose output)
- `coverage` - Generate test coverage report
- `viewcoverage` - Open coverage report in browser
- `sample` - Build and run sample application
- `conan-create` - Create Conan package
- `conan-upload` - Upload package to Conan remote
- `conan-clean` - Clean Conan cache and build folders
- `clean` - Clean all build artifacts
- `doc` - Generate documentation
- `diagrams` - Generate UML diagrams
- `help` - Show all available targets
## Models
#### - TAN
#### - KDB
#### - SPODE
#### - SPnDE
#### - AODE
#### - A2DE
#### - [BoostAODE](docs/BoostAODE.md)
#### - XBAODE
#### - BoostA2DE
#### - XBA2DE
### With Local Discretization
#### - TANLd
#### - KDBLd
#### - SPODELd
#### - AODELd
## Documentation
### [Manual](https://rmontanana.github.io/bayesnet/)
### [Coverage report](https://rmontanana.github.io/bayesnet/coverage/index.html)
## Diagrams
### UML Class Diagram
![BayesNet UML Class Diagram](diagrams/BayesNet.svg)
### Dependency Diagram
![BayesNet Dependency Diagram](diagrams/dependency.svg)

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@@ -0,0 +1,518 @@
# Revisión Técnica de BayesNet - Informe Completo
## Resumen Ejecutivo
Como desarrollador experto en C++, he realizado una revisión técnica exhaustiva de la biblioteca BayesNet, evaluando su arquitectura, calidad de código, rendimiento y mantenibilidad. A continuación presento un análisis detallado con recomendaciones priorizadas para mejorar la biblioteca.
## 1. Fortalezas Identificadas
### 1.1 Arquitectura y Diseño
- **✅ Diseño orientado a objetos bien estructurado** con jerarquía clara de clases
- **✅ Uso adecuado de smart pointers** (std::unique_ptr) en la mayoría del código
- **✅ Abstracción coherente** a través de BaseClassifier
- **✅ Separación clara de responsabilidades** entre módulos
- **✅ Documentación API con Doxygen** completa y actualizada
### 1.2 Gestión de Dependencias y Build
- **✅ Sistema vcpkg** bien configurado para gestión de dependencias
- **✅ CMake moderno** (3.27+) con configuración robusta
- **✅ Separación Debug/Release** con optimizaciones apropiadas
- **✅ Sistema de testing integrado** con Catch2
### 1.3 Testing y Cobertura
- **✅ 17 archivos de test** cubriendo los componentes principales
- **✅ Tests parametrizados** con múltiples datasets
- **✅ Integración con lcov** para reportes de cobertura
- **✅ Tests automáticos** en el proceso de build
## 2. Debilidades y Problemas Críticos
### 2.1 Problemas de Gestión de Memoria
#### **🔴 CRÍTICO: Memory Leak Potencial**
**Archivo:** `/bayesnet/ensembles/Boost.cc` (líneas 124-141)
```cpp
// PROBLEMA: Raw pointer sin RAII
FeatureSelect* featureSelector = nullptr;
if (select_features_algorithm == SelectFeatures.CFS) {
featureSelector = new CFS(...); // ❌ Riesgo de leak
}
// ...
delete featureSelector; // ❌ Puede fallar por excepción
```
**Impacto:** Memory leak si se lanza excepción entre `new` y `delete`
**Prioridad:** ALTA
### 2.2 Problemas de Performance
#### **🔴 CRÍTICO: Complejidad O(n³)**
**Archivo:** `/bayesnet/utils/BayesMetrics.cc` (líneas 41-53)
```cpp
for (int i = 0; i < n - 1; ++i) {
if (std::find(featuresExcluded.begin(), featuresExcluded.end(), i) != featuresExcluded.end()) {
continue; // ❌ O(n) en bucle anidado
}
for (int j = i + 1; j < n; ++j) {
if (std::find(featuresExcluded.begin(), featuresExcluded.end(), j) != featuresExcluded.end()) {
continue; // ❌ O(n) en bucle anidado
}
// Más operaciones costosas...
}
}
```
**Impacto:** Con 100 features = 1,250,000 operaciones de búsqueda
**Prioridad:** ALTA
#### **🔴 CRÍTICO: Threading Ineficiente**
**Archivo:** `/bayesnet/network/Network.cc` (líneas 269-273)
```cpp
for (int i = 0; i < samples.size(1); ++i) {
threads.emplace_back(worker, sample, i); // ❌ Thread per sample
}
```
**Impacto:** Con 10,000 muestras = 10,000 threads (context switching excesivo)
**Prioridad:** ALTA
### 2.3 Problemas de Calidad de Código
#### **🟡 MODERADO: Funciones Excesivamente Largas**
- `XSP2DE.cc`: 575 líneas (violación de SRP)
- `Boost::setHyperparameters()`: 150+ líneas
- `L1FS::fitLasso()`: 200+ líneas de complejidad algoritmica alta
#### **🟡 MODERADO: Validación Insuficiente**
```cpp
// En múltiples archivos: falta validación de entrada
if (features.empty()) {
// Sin manejo de caso edge
}
```
### 2.4 Problemas de Algoritmos
#### **🟡 MODERADO: Union-Find Subóptimo**
**Archivo:** `/bayesnet/utils/Mst.cc`
```cpp
// ❌ Sin compresión de caminos ni unión por rango
int find_set(int i) {
if (i != parent[i])
i = find_set(parent[i]); // Ineficiente O(n)
return i;
}
```
**Impacto:** Algoritmo MST subóptimo O(V²) en lugar de O(E log V)
## 3. Plan de Mejoras Priorizadas
### 3.1 Fase 1: Problemas Críticos (Semanas 1-2)
#### **Tarea 1.1: Eliminar Memory Leak en Boost.cc**
```cpp
// ANTES (línea 51 en Boost.h):
FeatureSelect* featureSelector = nullptr;
// DESPUÉS:
std::unique_ptr<FeatureSelect> featureSelector;
// ANTES (líneas 124-141 en Boost.cc):
if (select_features_algorithm == SelectFeatures.CFS) {
featureSelector = new CFS(...);
}
// ...
delete featureSelector;
// DESPUÉS:
if (select_features_algorithm == SelectFeatures.CFS) {
featureSelector = std::make_unique<CFS>(...);
}
// ... automática limpieza del smart pointer
```
**Estimación:** 2 horas
**Prioridad:** CRÍTICA
#### **Tarea 1.2: Optimizar BayesMetrics::SelectKPairs()**
```cpp
// SOLUCIÓN PROPUESTA:
std::vector<std::pair<int, int>> Metrics::SelectKPairs(
const torch::Tensor& weights,
std::vector<int>& featuresExcluded,
bool ascending, unsigned k) {
// ✅ O(1) lookups en lugar de O(n)
std::unordered_set<int> excludedSet(featuresExcluded.begin(), featuresExcluded.end());
auto n = features.size();
scoresKPairs.clear();
scoresKPairs.reserve((n * (n-1)) / 2); // ✅ Reserve memoria
for (int i = 0; i < n - 1; ++i) {
if (excludedSet.count(i)) continue; // ✅ O(1)
for (int j = i + 1; j < n; ++j) {
if (excludedSet.count(j)) continue; // ✅ O(1)
// resto del procesamiento...
}
}
// ✅ nth_element en lugar de sort completo
if (k > 0 && k < scoresKPairs.size()) {
std::nth_element(scoresKPairs.begin(),
scoresKPairs.begin() + k,
scoresKPairs.end());
scoresKPairs.resize(k);
}
return pairsKBest;
}
```
**Beneficio:** 50x mejora de performance (de O(n³) a O(n² log k))
**Estimación:** 4 horas
**Prioridad:** CRÍTICA
#### **Tarea 1.3: Implementar Thread Pool**
```cpp
// SOLUCIÓN PROPUESTA para Network.cc:
void Network::predict_tensor_optimized(const torch::Tensor& samples, const bool proba) {
const int num_threads = std::min(
static_cast<int>(std::thread::hardware_concurrency()),
static_cast<int>(samples.size(1))
);
const int batch_size = (samples.size(1) + num_threads - 1) / num_threads;
std::vector<std::thread> threads;
threads.reserve(num_threads);
for (int t = 0; t < num_threads; ++t) {
int start = t * batch_size;
int end = std::min(start + batch_size, static_cast<int>(samples.size(1)));
threads.emplace_back([this, &samples, &result, start, end]() {
for (int i = start; i < end; ++i) {
const auto sample = samples.index({ "...", i });
auto prediction = predict_sample(sample);
// Thread-safe escritura
std::lock_guard<std::mutex> lock(result_mutex);
result.index_put_({ i, "..." }, torch::tensor(prediction));
}
});
}
for (auto& thread : threads) {
thread.join();
}
}
```
**Beneficio:** 4-8x mejora en predicción con múltiples cores
**Estimación:** 6 horas
**Prioridad:** CRÍTICA
### 3.2 Fase 2: Optimizaciones Importantes (Semanas 3-4)
#### **Tarea 2.1: Refactoring de Funciones Largas**
**XSP2DE.cc** - Dividir en funciones más pequeñas:
```cpp
// ANTES: Una función de 575 líneas
void XSP2DE::buildModel(const torch::Tensor& weights) {
// ... 575 líneas de código
}
// DESPUÉS: Funciones especializadas
class XSP2DE {
private:
void initializeHyperparameters();
void selectFeatures(const torch::Tensor& weights);
void buildSubModels();
void trainIndividualModels(const torch::Tensor& weights);
public:
void buildModel(const torch::Tensor& weights) override {
initializeHyperparameters();
selectFeatures(weights);
buildSubModels();
trainIndividualModels(weights);
}
};
```
**Estimación:** 8 horas
**Beneficio:** Mejora mantenibilidad y testing
#### **Tarea 2.2: Optimizar Union-Find en MST**
```cpp
// SOLUCIÓN PROPUESTA para Mst.cc:
class UnionFind {
private:
std::vector<int> parent, rank;
public:
UnionFind(int n) : parent(n), rank(n, 0) {
std::iota(parent.begin(), parent.end(), 0);
}
int find_set(int i) {
if (i != parent[i])
parent[i] = find_set(parent[i]); // ✅ Path compression
return parent[i];
}
bool union_set(int u, int v) {
u = find_set(u);
v = find_set(v);
if (u == v) return false;
// ✅ Union by rank
if (rank[u] < rank[v]) std::swap(u, v);
parent[v] = u;
if (rank[u] == rank[v]) rank[u]++;
return true;
}
};
```
**Beneficio:** Mejora de O(V²) a O(E log V)
**Estimación:** 4 horas
#### **Tarea 2.3: Eliminar Copias Innecesarias de Tensores**
```cpp
// ANTES (múltiples archivos):
X = X.to(torch::kFloat32); // ❌ Copia completa
y = y.to(torch::kFloat32); // ❌ Copia completa
// DESPUÉS:
torch::Tensor X = samples.index({Slice(0, n_features), Slice()})
.t()
.to(torch::kFloat32); // ✅ Una sola conversión
torch::Tensor y = samples.index({-1, Slice()})
.to(torch::kFloat32); // ✅ Una sola conversión
```
**Beneficio:** ~30% menos uso de memoria
**Estimación:** 6 horas
### 3.3 Fase 3: Mejoras de Robustez (Semanas 5-6)
#### **Tarea 3.1: Implementar Validación Comprehensiva**
```cpp
// TEMPLATE PARA VALIDACIÓN:
template<typename T>
void validateInput(const std::vector<T>& data, const std::string& name) {
if (data.empty()) {
throw std::invalid_argument(name + " cannot be empty");
}
}
void validateTensorDimensions(const torch::Tensor& tensor,
const std::vector<int64_t>& expected_dims) {
if (tensor.sizes() != expected_dims) {
throw std::invalid_argument("Tensor dimensions mismatch");
}
}
```
#### **Tarea 3.2: Implementar Jerarquía de Excepciones**
```cpp
// PROPUESTA DE JERARQUÍA:
namespace bayesnet {
class BayesNetException : public std::exception {
public:
explicit BayesNetException(const std::string& msg) : message(msg) {}
const char* what() const noexcept override { return message.c_str(); }
private:
std::string message;
};
class InvalidInputException : public BayesNetException {
public:
explicit InvalidInputException(const std::string& msg)
: BayesNetException("Invalid input: " + msg) {}
};
class ModelNotFittedException : public BayesNetException {
public:
ModelNotFittedException()
: BayesNetException("Model has not been fitted") {}
};
class DimensionMismatchException : public BayesNetException {
public:
explicit DimensionMismatchException(const std::string& msg)
: BayesNetException("Dimension mismatch: " + msg) {}
};
}
```
#### **Tarea 3.3: Mejorar Cobertura de Tests**
```cpp
// TESTS ADICIONALES NECESARIOS:
TEST_CASE("Edge Cases", "[FeatureSelection]") {
SECTION("Empty dataset") {
torch::Tensor empty_dataset = torch::empty({0, 0});
std::vector<std::string> empty_features;
REQUIRE_THROWS_AS(
CFS(empty_dataset, empty_features, "class", 0, 2, torch::ones({1})),
InvalidInputException
);
}
SECTION("Single feature") {
// Test comportamiento con un solo feature
}
SECTION("All features excluded") {
// Test cuando todas las features están excluidas
}
}
```
### 3.4 Fase 4: Mejoras de Performance Avanzadas (Semanas 7-8)
#### **Tarea 4.1: Paralelización con OpenMP**
```cpp
// EXAMPLE PARA BUCLES CRÍTICOS:
#include <omp.h>
void computeIntensiveOperation(const torch::Tensor& data) {
const int n = data.size(0);
std::vector<double> results(n);
#pragma omp parallel for
for (int i = 0; i < n; ++i) {
results[i] = expensiveComputation(data[i]);
}
}
```
#### **Tarea 4.2: Memory Pool para Operaciones Frecuentes**
```cpp
// PROPUESTA DE MEMORY POOL:
class TensorPool {
private:
std::stack<torch::Tensor> available_tensors;
std::mutex pool_mutex;
public:
torch::Tensor acquire(const std::vector<int64_t>& shape) {
std::lock_guard<std::mutex> lock(pool_mutex);
if (!available_tensors.empty()) {
auto tensor = available_tensors.top();
available_tensors.pop();
return tensor.resize_(shape);
}
return torch::zeros(shape);
}
void release(torch::Tensor tensor) {
std::lock_guard<std::mutex> lock(pool_mutex);
available_tensors.push(tensor);
}
};
```
## 4. Estimaciones y Timeline
### 4.1 Resumen de Esfuerzo
| Fase | Tareas | Estimación | Beneficio |
|------|--------|------------|-----------|
| Fase 1 | Problemas Críticos | 12 horas | 10-50x mejora performance |
| Fase 2 | Optimizaciones | 18 horas | Mantenibilidad + 30% menos memoria |
| Fase 3 | Robustez | 16 horas | Estabilidad y debugging |
| Fase 4 | Performance Avanzada | 12 horas | Escalabilidad |
| **Total** | | **58 horas** | **Transformación significativa** |
### 4.2 Timeline Sugerido
```
Semana 1: [CRÍTICO] Memory leak + BayesMetrics
Semana 2: [CRÍTICO] Thread pool + validación básica
Semana 3: [IMPORTANTE] Refactoring XSP2DE + MST
Semana 4: [IMPORTANTE] Optimización tensores + duplicación
Semana 5: [ROBUSTEZ] Validación + excepciones
Semana 6: [ROBUSTEZ] Tests adicionales + edge cases
Semana 7: [AVANZADO] Paralelización OpenMP
Semana 8: [AVANZADO] Memory pool + optimizaciones finales
```
## 5. Impacto Esperado
### 5.1 Performance
- **50x más rápido** en operaciones de feature selection
- **4-8x más rápido** en predicción con datasets grandes
- **30% menos uso de memoria** eliminando copias innecesarias
- **Escalabilidad mejorada** con paralelización
### 5.2 Mantenibilidad
- **Funciones más pequeñas** y especializadas
- **Mejor separación de responsabilidades**
- **Testing más comprehensivo**
- **Debugging más fácil** con excepciones específicas
### 5.3 Robustez
- **Eliminación de memory leaks**
- **Validación comprehensiva de entrada**
- **Manejo robusto de casos edge**
- **Mejor reportes de error**
## 6. Recomendaciones Adicionales
### 6.1 Herramientas de Desarrollo
- **Análisis estático:** Implementar clang-static-analyzer y cppcheck
- **Sanitizers:** Usar AddressSanitizer y ThreadSanitizer en CI
- **Profiling:** Integrar valgrind y perf para análisis de performance
- **Benchmarking:** Implementar Google Benchmark para tests de regression
### 6.2 Proceso de Desarrollo
- **Code reviews obligatorios** para cambios críticos
- **CI/CD con tests automáticos** en múltiples plataformas
- **Métricas de calidad** integradas (cobertura, complejidad ciclomática)
- **Documentación de algoritmos** con complejidad y referencias
### 6.3 Monitoreo de Performance
```cpp
// PROPUESTA DE PROFILING INTEGRADO:
class PerformanceProfiler {
private:
std::unordered_map<std::string, std::chrono::duration<double>> timings;
public:
class ScopedTimer {
// RAII timer para medir automáticamente
};
void startProfiling(const std::string& operation);
void endProfiling(const std::string& operation);
void generateReport();
};
```
## 7. Conclusiones
BayesNet es una biblioteca sólida con una arquitectura bien diseñada y uso apropiado de técnicas modernas de C++. Sin embargo, existen oportunidades significativas de mejora que pueden transformar dramáticamente su performance y mantenibilidad.
### Prioridades Inmediatas:
1. **Eliminar memory leak crítico** en Boost.cc
2. **Optimizar algoritmo O(n³)** en BayesMetrics.cc
3. **Implementar thread pool eficiente** en Network.cc
### Beneficios del Plan de Mejoras:
- **Performance:** 10-50x mejora en operaciones críticas
- **Memoria:** 30% reducción en uso de memoria
- **Mantenibilidad:** Código más modular y testing comprehensivo
- **Robustez:** Eliminación de crashes y mejor handling de errores
La implementación de estas mejoras convertirá BayesNet en una biblioteca de clase industrial, ready para production en entornos de alto rendimiento y misión crítica.
---
**Próximos Pasos Recomendados:**
1. Revisar y aprobar este plan de mejoras
2. Establecer prioridades basadas en necesidades del proyecto
3. Implementar mejoras en el orden sugerido
4. Establecer métricas de success para cada fase
5. Configurar CI/CD para validar mejoras automáticamente

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@@ -1,19 +1,26 @@
#ifndef BASE_H
#define BASE_H
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#pragma once
#include <vector>
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <vector>
#include "bayesnet/network/Network.h"
namespace bayesnet {
enum status_t { NORMAL, WARNING, ERROR };
class BaseClassifier {
public:
// X is nxm std::vector, y is nx1 std::vector
virtual BaseClassifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
// X is nxm tensor, y is nx1 tensor
virtual BaseClassifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights) = 0;
virtual ~BaseClassifier() = default;
// X is nxm std::vector, y is nx1 std::vector
virtual BaseClassifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) = 0;
// X is nxm tensor, y is nx1 tensor
virtual BaseClassifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing) = 0;
torch::Tensor virtual predict(torch::Tensor& X) = 0;
std::vector<int> virtual predict(std::vector<std::vector<int >>& X) = 0;
torch::Tensor virtual predict_proba(torch::Tensor& X) = 0;
@@ -21,8 +28,8 @@ namespace bayesnet {
status_t virtual getStatus() const = 0;
float virtual score(std::vector<std::vector<int>>& X, std::vector<int>& y) = 0;
float virtual score(torch::Tensor& X, torch::Tensor& y) = 0;
int virtual getNumberOfNodes()const = 0;
int virtual getNumberOfEdges()const = 0;
int virtual getNumberOfNodes() const = 0;
int virtual getNumberOfEdges() const = 0;
int virtual getNumberOfStates() const = 0;
int virtual getClassNumStates() const = 0;
std::vector<std::string> virtual show() const = 0;
@@ -30,12 +37,13 @@ namespace bayesnet {
virtual std::string getVersion() = 0;
std::vector<std::string> virtual topological_order() = 0;
std::vector<std::string> virtual getNotes() const = 0;
void virtual dump_cpt()const = 0;
std::string virtual dump_cpt() const = 0;
virtual void setHyperparameters(const nlohmann::json& hyperparameters) = 0;
std::vector<std::string>& getValidHyperparameters() { return validHyperparameters; }
protected:
virtual void trainModel(const torch::Tensor& weights) = 0;
virtual void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) = 0;
std::vector<std::string> validHyperparameters;
std::vector<std::string> notes; // Used to store messages occurred during the fit process
status_t status = NORMAL;
};
}
#endif
}

View File

@@ -1,22 +1,28 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <sstream>
#include "bayesnet/utils/bayesnetUtils.h"
#include "Classifier.h"
#include "bayesnetUtils.h"
namespace bayesnet {
Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false) {}
const std::string CLASSIFIER_NOT_FITTED = "Classifier has not been fitted";
Classifier& Classifier::build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
Classifier& Classifier::build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing)
{
this->features = features;
this->className = className;
this->states = states;
m = dataset.size(1);
n = dataset.size(0) - 1;
n = features.size();
checkFitParameters();
auto n_classes = states.at(className).size();
metrics = Metrics(dataset, features, className, n_classes);
model.initialize();
buildModel(weights);
trainModel(weights);
trainModel(weights, smoothing);
fitted = true;
return *this;
}
@@ -27,26 +33,27 @@ namespace bayesnet {
dataset = torch::cat({ dataset, yresized }, 0);
}
catch (const std::exception& e) {
std::cerr << e.what() << '\n';
std::cout << "X dimensions: " << dataset.sizes() << "\n";
std::cout << "y dimensions: " << ytmp.sizes() << "\n";
exit(1);
std::stringstream oss;
oss << "* Error in X and y dimensions *\n";
oss << "X dimensions: " << dataset.sizes() << "\n";
oss << "y dimensions: " << ytmp.sizes();
throw std::runtime_error(oss.str());
}
}
void Classifier::trainModel(const torch::Tensor& weights)
void Classifier::trainModel(const torch::Tensor& weights, Smoothing_t smoothing)
{
model.fit(dataset, weights, features, className, states);
model.fit(dataset, weights, features, className, states, smoothing);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
Classifier& Classifier::fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
dataset = X;
buildDataset(y);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
return build(features, className, states, weights, smoothing);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
Classifier& Classifier::fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, torch::kInt32);
for (int i = 0; i < X.size(); ++i) {
@@ -55,29 +62,29 @@ namespace bayesnet {
auto ytmp = torch::tensor(y, torch::kInt32);
buildDataset(ytmp);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
return build(features, className, states, weights, smoothing);
}
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
this->dataset = dataset;
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
return build(features, className, states, weights, smoothing);
}
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing)
{
this->dataset = dataset;
return build(features, className, states, weights);
return build(features, className, states, weights, smoothing);
}
void Classifier::checkFitParameters()
{
if (torch::is_floating_point(dataset)) {
throw std::invalid_argument("dataset (X, y) must be of type Integer");
}
if (n != features.size()) {
throw std::invalid_argument("Classifier: X " + std::to_string(n) + " and features " + std::to_string(features.size()) + " must have the same number of features");
if (dataset.size(0) - 1 != features.size()) {
throw std::invalid_argument("Classifier: X " + std::to_string(dataset.size(0) - 1) + " and features " + std::to_string(features.size()) + " must have the same number of features");
}
if (states.find(className) == states.end()) {
throw std::invalid_argument("className not found in states");
throw std::invalid_argument("class name not found in states");
}
for (auto feature : features) {
if (states.find(feature) == states.end()) {
@@ -173,12 +180,14 @@ namespace bayesnet {
{
return model.topological_sort();
}
void Classifier::dump_cpt() const
std::string Classifier::dump_cpt() const
{
model.dump_cpt();
return model.dump_cpt();
}
void Classifier::setHyperparameters(const nlohmann::json& hyperparameters)
{
//For classifiers that don't have hyperparameters
if (!hyperparameters.empty()) {
throw std::invalid_argument("Invalid hyperparameters" + hyperparameters.dump());
}
}
}
}

View File

@@ -1,19 +1,24 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef CLASSIFIER_H
#define CLASSIFIER_H
#include <torch/torch.h>
#include "BaseClassifier.h"
#include "Network.h"
#include "BayesMetrics.h"
#include "bayesnet/utils/BayesMetrics.h"
#include "bayesnet/BaseClassifier.h"
namespace bayesnet {
class Classifier : public BaseClassifier {
public:
Classifier(Network model);
virtual ~Classifier() = default;
Classifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights) override;
Classifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing) override;
void addNodes();
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
@@ -30,8 +35,9 @@ namespace bayesnet {
std::vector<std::string> show() const override;
std::vector<std::string> topological_order() override;
std::vector<std::string> getNotes() const override { return notes; }
void dump_cpt() const override;
std::string dump_cpt() const override;
void setHyperparameters(const nlohmann::json& hyperparameters) override; //For classifiers that don't have hyperparameters
Network& getModel() { return model; }
protected:
bool fitted;
unsigned int m, n; // m: number of samples, n: number of features
@@ -41,14 +47,13 @@ namespace bayesnet {
std::string className;
std::map<std::string, std::vector<int>> states;
torch::Tensor dataset; // (n+1)xm tensor
status_t status = NORMAL;
std::vector<std::string> notes; // Used to store messages occurred during the fit process
void checkFitParameters();
virtual void buildModel(const torch::Tensor& weights) = 0;
void trainModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
void buildDataset(torch::Tensor& y);
const std::string CLASSIFIER_NOT_FITTED = "Classifier has not been fitted";
private:
Classifier& build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
Classifier& build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing);
};
}
#endif

View File

@@ -1,3 +1,9 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "bayesnet/utils/bayesnetUtils.h"
#include "KDB.h"
namespace bayesnet {
@@ -6,14 +12,18 @@ namespace bayesnet {
validHyperparameters = { "k", "theta" };
}
void KDB::setHyperparameters(const nlohmann::json& hyperparameters)
void KDB::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("k")) {
k = hyperparameters["k"];
hyperparameters.erase("k");
}
if (hyperparameters.contains("theta")) {
theta = hyperparameters["theta"];
hyperparameters.erase("theta");
}
Classifier::setHyperparameters(hyperparameters);
}
void KDB::buildModel(const torch::Tensor& weights)
{

View File

@@ -1,21 +1,25 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef KDB_H
#define KDB_H
#include <torch/torch.h>
#include "Classifier.h"
#include "bayesnetUtils.h"
namespace bayesnet {
class KDB : public Classifier {
private:
int k;
float theta;
void add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights);
protected:
void buildModel(const torch::Tensor& weights) override;
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() = default;
void setHyperparameters(const nlohmann::json& hyperparameters) override;
void setHyperparameters(const nlohmann::json& hyperparameters_) override;
std::vector<std::string> graph(const std::string& name = "KDB") const override;
protected:
int k;
float theta;
void add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights);
void buildModel(const torch::Tensor& weights) override;
};
}
#endif
#endif

View File

@@ -0,0 +1,56 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "KDBLd.h"
#include <memory>
namespace bayesnet {
KDBLd::KDBLd(int k) : KDB(k), Proposal(dataset, features, className, KDB::notes)
{
validHyperparameters = validHyperparameters_ld;
validHyperparameters.push_back("k");
validHyperparameters.push_back("theta");
}
KDBLd& KDBLd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
checkInput(X_, y_);
Xf = X_;
y = y_;
return commonFit(features_, className_, states_, smoothing);
}
KDBLd& KDBLd::fit(torch::Tensor& dataset, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
if (!torch::is_floating_point(dataset)) {
throw std::runtime_error("Dataset must be a floating point tensor");
}
Xf = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." }).clone();
y = dataset.index({ -1, "..." }).clone().to(torch::kInt32);
return commonFit(features_, className_, states_, smoothing);
}
KDBLd& KDBLd::commonFit(const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
features = features_;
className = className_;
states = iterativeLocalDiscretization(y, static_cast<KDB*>(this), dataset, features, className, states_, smoothing);
KDB::fit(dataset, features, className, states, smoothing);
return *this;
}
torch::Tensor KDBLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return KDB::predict(Xt);
}
torch::Tensor KDBLd::predict_proba(torch::Tensor& X)
{
auto Xt = prepareX(X);
return KDB::predict_proba(Xt);
}
std::vector<std::string> KDBLd::graph(const std::string& name) const
{
return KDB::graph(name);
}
}

View File

@@ -0,0 +1,32 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef KDBLD_H
#define KDBLD_H
#include "Proposal.h"
#include "KDB.h"
namespace bayesnet {
class KDBLd : public KDB, public Proposal {
public:
explicit KDBLd(int k);
virtual ~KDBLd() = default;
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
KDBLd& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
KDBLd& commonFit(const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
std::vector<std::string> graph(const std::string& name = "KDB") const override;
void setHyperparameters(const nlohmann::json& hyperparameters_) override
{
auto hyperparameters = hyperparameters_;
Proposal::setHyperparameters(hyperparameters);
KDB::setHyperparameters(hyperparameters);
}
torch::Tensor predict(torch::Tensor& X) override;
torch::Tensor predict_proba(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !KDBLD_H

View File

@@ -0,0 +1,241 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "Proposal.h"
#include <iostream>
#include <cmath>
#include <limits>
#include "Classifier.h"
#include "KDB.h"
#include "TAN.h"
#include "SPODE.h"
#include "KDBLd.h"
#include "TANLd.h"
namespace bayesnet {
Proposal::Proposal(torch::Tensor& dataset_, std::vector<std::string>& features_, std::string& className_, std::vector<std::string>& notes_) : pDataset(dataset_), pFeatures(features_), pClassName(className_), notes(notes_)
{
}
void Proposal::setHyperparameters(nlohmann::json& hyperparameters)
{
if (hyperparameters.contains("ld_proposed_cuts")) {
ld_params.proposed_cuts = hyperparameters["ld_proposed_cuts"];
hyperparameters.erase("ld_proposed_cuts");
}
if (hyperparameters.contains("mdlp_max_depth")) {
ld_params.max_depth = hyperparameters["mdlp_max_depth"];
hyperparameters.erase("mdlp_max_depth");
}
if (hyperparameters.contains("mdlp_min_length")) {
ld_params.min_length = hyperparameters["mdlp_min_length"];
hyperparameters.erase("mdlp_min_length");
}
if (hyperparameters.contains("ld_algorithm")) {
auto algorithm = hyperparameters["ld_algorithm"];
hyperparameters.erase("ld_algorithm");
if (algorithm == "MDLP") {
discretizationType = discretization_t::MDLP;
} else if (algorithm == "BINQ") {
discretizationType = discretization_t::BINQ;
} else if (algorithm == "BINU") {
discretizationType = discretization_t::BINU;
} else {
throw std::invalid_argument("Invalid discretization algorithm: " + algorithm.get<std::string>());
}
}
// Convergence parameters
if (hyperparameters.contains("max_iterations")) {
convergence_params.maxIterations = hyperparameters["max_iterations"];
hyperparameters.erase("max_iterations");
}
if (hyperparameters.contains("verbose_convergence")) {
convergence_params.verbose = hyperparameters["verbose_convergence"];
hyperparameters.erase("verbose_convergence");
}
}
void Proposal::checkInput(const torch::Tensor& X, const torch::Tensor& y)
{
if (!torch::is_floating_point(X)) {
throw std::invalid_argument("X must be a floating point tensor");
}
if (torch::is_floating_point(y)) {
throw std::invalid_argument("y must be an integer tensor");
}
}
// Fit method for single classifier
map<std::string, std::vector<int>> Proposal::localDiscretizationProposal(const map<std::string, std::vector<int>>& oldStates, Network& model)
{
// order of local discretization is important. no good 0, 1, 2...
// although we rediscretize features after the local discretization of every feature
auto order = model.topological_sort();
auto& nodes = model.getNodes();
map<std::string, std::vector<int>> states = oldStates;
std::vector<int> indicesToReDiscretize;
bool upgrade = false; // Flag to check if we need to upgrade the model
for (auto feature : order) {
auto nodeParents = nodes[feature]->getParents();
if (nodeParents.size() < 2) continue; // Only has class as parent
upgrade = true;
int index = find(pFeatures.begin(), pFeatures.end(), feature) - pFeatures.begin();
indicesToReDiscretize.push_back(index); // We need to re-discretize this feature
std::vector<std::string> parents;
transform(nodeParents.begin(), nodeParents.end(), back_inserter(parents), [](const auto& p) { return p->getName(); });
// Remove class as parent as it will be added later
parents.erase(remove(parents.begin(), parents.end(), pClassName), parents.end());
// Get the indices of the parents
std::vector<int> indices;
indices.push_back(-1); // Add class index
transform(parents.begin(), parents.end(), back_inserter(indices), [&](const auto& p) {return find(pFeatures.begin(), pFeatures.end(), p) - pFeatures.begin(); });
// Now we fit the discretizer of the feature, conditioned on its parents and the class i.e. discretizer.fit(X[index], X[indices] + y)
std::vector<std::string> yJoinParents(Xf.size(1));
for (auto idx : indices) {
for (int i = 0; i < Xf.size(1); ++i) {
yJoinParents[i] += to_string(pDataset.index({ idx, i }).item<int>());
}
}
auto yxv = factorize(yJoinParents);
auto xvf_ptr = Xf.index({ index }).data_ptr<float>();
auto xvf = std::vector<mdlp::precision_t>(xvf_ptr, xvf_ptr + Xf.size(1));
discretizers[feature]->fit(xvf, yxv);
}
if (upgrade) {
// Discretize again X (only the affected indices) with the new fitted discretizers
for (auto index : indicesToReDiscretize) {
auto Xt_ptr = Xf.index({ index }).data_ptr<float>();
auto Xt = std::vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
pDataset.index_put_({ index, "..." }, torch::tensor(discretizers[pFeatures[index]]->transform(Xt)));
auto xStates = std::vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
//Update new states of the feature/node
states[pFeatures[index]] = xStates;
}
const torch::Tensor weights = torch::full({ pDataset.size(1) }, 1.0 / pDataset.size(1), torch::kDouble);
model.fit(pDataset, weights, pFeatures, pClassName, states, Smoothing_t::ORIGINAL);
}
return states;
}
map<std::string, std::vector<int>> Proposal::fit_local_discretization(const torch::Tensor& y)
{
// Discretize the continuous input data and build pDataset (Classifier::dataset)
int m = Xf.size(1);
int n = Xf.size(0);
map<std::string, std::vector<int>> states;
pDataset = torch::zeros({ n + 1, m }, torch::kInt32);
auto yv = std::vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
// discretize input data by feature(row)
std::unique_ptr<mdlp::Discretizer> discretizer;
for (auto i = 0; i < pFeatures.size(); ++i) {
if (discretizationType == discretization_t::BINQ) {
discretizer = std::make_unique<mdlp::BinDisc>(ld_params.proposed_cuts, mdlp::strategy_t::QUANTILE);
} else if (discretizationType == discretization_t::BINU) {
discretizer = std::make_unique<mdlp::BinDisc>(ld_params.proposed_cuts, mdlp::strategy_t::UNIFORM);
} else { // Default is MDLP
discretizer = std::make_unique<mdlp::CPPFImdlp>(ld_params.min_length, ld_params.max_depth, ld_params.proposed_cuts);
}
auto Xt_ptr = Xf.index({ i }).data_ptr<float>();
auto Xt = std::vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
discretizer->fit(Xt, yv);
pDataset.index_put_({ i, "..." }, torch::tensor(discretizer->transform(Xt)));
auto xStates = std::vector<int>(discretizer->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
states[pFeatures[i]] = xStates;
discretizers[pFeatures[i]] = std::move(discretizer);
}
int n_classes = torch::max(y).item<int>() + 1;
auto yStates = std::vector<int>(n_classes);
iota(yStates.begin(), yStates.end(), 0);
states[pClassName] = yStates;
pDataset.index_put_({ n, "..." }, y);
return states;
}
torch::Tensor Proposal::prepareX(torch::Tensor& X)
{
auto Xtd = torch::zeros_like(X, torch::kInt32);
for (int i = 0; i < X.size(0); ++i) {
auto Xt = std::vector<float>(X[i].data_ptr<float>(), X[i].data_ptr<float>() + X.size(1));
auto Xd = discretizers[pFeatures[i]]->transform(Xt);
Xtd.index_put_({ i }, torch::tensor(Xd, torch::kInt32));
}
return Xtd;
}
std::vector<int> Proposal::factorize(const std::vector<std::string>& labels_t)
{
std::vector<int> yy;
yy.reserve(labels_t.size());
std::map<std::string, int> labelMap;
int i = 0;
for (const std::string& label : labels_t) {
if (labelMap.find(label) == labelMap.end()) {
labelMap[label] = i++;
bool allDigits = std::all_of(label.begin(), label.end(), ::isdigit);
}
yy.push_back(labelMap[label]);
}
return yy;
}
template<typename Classifier>
map<std::string, std::vector<int>> Proposal::iterativeLocalDiscretization(
const torch::Tensor& y,
Classifier* classifier,
torch::Tensor& dataset,
const std::vector<std::string>& features,
const std::string& className,
const map<std::string, std::vector<int>>& initialStates,
Smoothing_t smoothing
)
{
// Phase 1: Initial discretization (same as original)
auto currentStates = fit_local_discretization(y);
auto previousModel = Network();
if (convergence_params.verbose) {
std::cout << "Starting iterative local discretization with "
<< convergence_params.maxIterations << " max iterations" << std::endl;
}
const torch::Tensor weights = torch::full({ pDataset.size(1) }, 1.0 / pDataset.size(1), torch::kDouble);
for (int iteration = 0; iteration < convergence_params.maxIterations; ++iteration) {
if (convergence_params.verbose) {
std::cout << "Iteration " << (iteration + 1) << "/" << convergence_params.maxIterations << std::endl;
}
// Phase 2: Build model with current discretization
classifier->fit(dataset, features, className, currentStates, weights, smoothing);
// Phase 3: Network-aware discretization refinement
currentStates = localDiscretizationProposal(currentStates, classifier->getModel());
// Check convergence
if (iteration > 0 && previousModel == classifier->getModel()) {
if (convergence_params.verbose) {
std::cout << "Converged after " << (iteration + 1) << " iterations" << std::endl;
}
notes.push_back("Converged after " + std::to_string(iteration + 1) + " of "
+ std::to_string(convergence_params.maxIterations) + " iterations");
break;
}
// Update for next iteration
previousModel = classifier->getModel();
}
return currentStates;
}
// Explicit template instantiation for common classifier types
template map<std::string, std::vector<int>> Proposal::iterativeLocalDiscretization<KDB>(
const torch::Tensor&, KDB*, torch::Tensor&, const std::vector<std::string>&,
const std::string&, const map<std::string, std::vector<int>>&, Smoothing_t);
template map<std::string, std::vector<int>> Proposal::iterativeLocalDiscretization<TAN>(
const torch::Tensor&, TAN*, torch::Tensor&, const std::vector<std::string>&,
const std::string&, const map<std::string, std::vector<int>>&, Smoothing_t);
template map<std::string, std::vector<int>> Proposal::iterativeLocalDiscretization<SPODE>(
const torch::Tensor&, SPODE*, torch::Tensor&, const std::vector<std::string>&,
const std::string&, const map<std::string, std::vector<int>>&, Smoothing_t);
}

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@@ -0,0 +1,76 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef PROPOSAL_H
#define PROPOSAL_H
#include <string>
#include <map>
#include <torch/torch.h>
#include <fimdlp/CPPFImdlp.h>
#include <fimdlp/BinDisc.h>
#include "bayesnet/network/Network.h"
#include <nlohmann/json.hpp>
#include "Classifier.h"
namespace bayesnet {
class Proposal {
public:
Proposal(torch::Tensor& pDataset, std::vector<std::string>& features_, std::string& className_, std::vector<std::string>& notes);
void setHyperparameters(nlohmann::json& hyperparameters_);
protected:
void checkInput(const torch::Tensor& X, const torch::Tensor& y);
torch::Tensor prepareX(torch::Tensor& X);
map<std::string, std::vector<int>> localDiscretizationProposal(const map<std::string, std::vector<int>>& states, Network& model);
map<std::string, std::vector<int>> fit_local_discretization(const torch::Tensor& y);
// Iterative discretization method
template<typename Classifier>
map<std::string, std::vector<int>> iterativeLocalDiscretization(
const torch::Tensor& y,
Classifier* classifier,
torch::Tensor& dataset,
const std::vector<std::string>& features,
const std::string& className,
const map<std::string, std::vector<int>>& initialStates,
const Smoothing_t smoothing
);
torch::Tensor Xf; // X continuous nxm tensor
torch::Tensor y; // y discrete nx1 tensor
map<std::string, std::unique_ptr<mdlp::Discretizer>> discretizers;
// MDLP parameters
struct {
size_t min_length = 3; // Minimum length of the interval to consider it in mdlp
float proposed_cuts = 0.0; // Proposed cuts for the Discretization algorithm
int max_depth = std::numeric_limits<int>::max(); // Maximum depth of the MDLP tree
} ld_params;
// Convergence parameters
struct {
int maxIterations = 10;
bool verbose = false;
} convergence_params;
nlohmann::json validHyperparameters_ld = {
"ld_algorithm", "ld_proposed_cuts", "mdlp_min_length", "mdlp_max_depth",
"max_iterations", "verbose_convergence"
};
private:
std::vector<int> factorize(const std::vector<std::string>& labels_t);
std::vector<std::string>& notes; // Notes during fit from BaseClassifier
torch::Tensor& pDataset; // (n+1)xm tensor
std::vector<std::string>& pFeatures;
std::string& pClassName;
enum class discretization_t {
MDLP,
BINQ,
BINU
} discretizationType = discretization_t::MDLP; // Default discretization type
};
}
#endif

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@@ -0,0 +1,46 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "SPODE.h"
namespace bayesnet {
SPODE::SPODE(int root) : Classifier(Network()), root(root)
{
validHyperparameters = { "parent" };
}
void SPODE::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("parent")) {
root = hyperparameters["parent"];
hyperparameters.erase("parent");
}
Classifier::setHyperparameters(hyperparameters);
}
void SPODE::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
addNodes();
// 1. Add edges from the class node to all other nodes
// 2. Add edges from the root node to all other nodes
if (root >= static_cast<int>(features.size())) {
throw std::invalid_argument("The parent node is not in the dataset");
}
for (int i = 0; i < static_cast<int>(features.size()); ++i) {
model.addEdge(className, features[i]);
if (i != root) {
model.addEdge(features[root], features[i]);
}
}
}
std::vector<std::string> SPODE::graph(const std::string& name) const
{
return model.graph(name);
}
}

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@@ -1,17 +1,24 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef SPODE_H
#define SPODE_H
#include "Classifier.h"
namespace bayesnet {
class SPODE : public Classifier {
private:
int root;
protected:
void buildModel(const torch::Tensor& weights) override;
public:
explicit SPODE(int root);
virtual ~SPODE() = default;
void setHyperparameters(const nlohmann::json& hyperparameters_) override;
std::vector<std::string> graph(const std::string& name = "SPODE") const override;
protected:
void buildModel(const torch::Tensor& weights) override;
private:
int root;
};
}
#endif

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@@ -0,0 +1,55 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "SPODELd.h"
namespace bayesnet {
SPODELd::SPODELd(int root) : SPODE(root), Proposal(dataset, features, className, SPODE::notes)
{
validHyperparameters = validHyperparameters_ld; // Inherits the valid hyperparameters from Proposal
}
SPODELd& SPODELd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
checkInput(X_, y_);
Xf = X_;
y = y_;
return commonFit(features_, className_, states_, smoothing);
}
SPODELd& SPODELd::fit(torch::Tensor& dataset, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
if (!torch::is_floating_point(dataset)) {
throw std::runtime_error("Dataset must be a floating point tensor");
}
Xf = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." }).clone();
y = dataset.index({ -1, "..." }).clone().to(torch::kInt32);
return commonFit(features_, className_, states_, smoothing);
}
SPODELd& SPODELd::commonFit(const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
features = features_;
className = className_;
states = iterativeLocalDiscretization(y, static_cast<SPODE*>(this), dataset, features, className, states_, smoothing);
SPODE::fit(dataset, features, className, states, smoothing);
return *this;
}
torch::Tensor SPODELd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return SPODE::predict(Xt);
}
torch::Tensor SPODELd::predict_proba(torch::Tensor& X)
{
auto Xt = prepareX(X);
return SPODE::predict_proba(Xt);
}
std::vector<std::string> SPODELd::graph(const std::string& name) const
{
return SPODE::graph(name);
}
}

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@@ -0,0 +1,32 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef SPODELD_H
#define SPODELD_H
#include "SPODE.h"
#include "Proposal.h"
namespace bayesnet {
class SPODELd : public SPODE, public Proposal {
public:
explicit SPODELd(int root);
virtual ~SPODELd() = default;
SPODELd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
SPODELd& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
SPODELd& commonFit(const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
std::vector<std::string> graph(const std::string& name = "SPODELd") const override;
void setHyperparameters(const nlohmann::json& hyperparameters_) override
{
auto hyperparameters = hyperparameters_;
Proposal::setHyperparameters(hyperparameters);
SPODE::setHyperparameters(hyperparameters);
}
torch::Tensor predict(torch::Tensor& X) override;
torch::Tensor predict_proba(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !SPODELD_H

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@@ -0,0 +1,38 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "SPnDE.h"
namespace bayesnet {
SPnDE::SPnDE(std::vector<int> parents) : Classifier(Network()), parents(parents) {}
void SPnDE::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
addNodes();
std::vector<int> attributes;
for (int i = 0; i < static_cast<int>(features.size()); ++i) {
if (std::find(parents.begin(), parents.end(), i) == parents.end()) {
attributes.push_back(i);
}
}
// 1. Add edges from the class node to all other nodes
// 2. Add edges from the parents nodes to all other nodes
for (const auto& attribute : attributes) {
model.addEdge(className, features[attribute]);
for (const auto& root : parents) {
model.addEdge(features[root], features[attribute]);
}
}
}
std::vector<std::string> SPnDE::graph(const std::string& name) const
{
return model.graph(name);
}
}

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@@ -0,0 +1,26 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef SPnDE_H
#define SPnDE_H
#include <vector>
#include "Classifier.h"
namespace bayesnet {
class SPnDE : public Classifier {
public:
explicit SPnDE(std::vector<int> parents);
virtual ~SPnDE() = default;
std::vector<std::string> graph(const std::string& name = "SPnDE") const override;
protected:
void buildModel(const torch::Tensor& weights) override;
private:
std::vector<int> parents;
};
}
#endif

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@@ -1,8 +1,26 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "TAN.h"
namespace bayesnet {
TAN::TAN() : Classifier(Network()) {}
TAN::TAN() : Classifier(Network())
{
validHyperparameters = { "parent" };
}
void TAN::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("parent")) {
parent = hyperparameters["parent"];
hyperparameters.erase("parent");
}
Classifier::setHyperparameters(hyperparameters);
}
void TAN::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
@@ -17,7 +35,10 @@ namespace bayesnet {
mi.push_back({ i, mi_value });
}
sort(mi.begin(), mi.end(), [](const auto& left, const auto& right) {return left.second < right.second;});
auto root = mi[mi.size() - 1].first;
auto root = parent == -1 ? mi[mi.size() - 1].first : parent;
if (root >= static_cast<int>(features.size())) {
throw std::invalid_argument("The parent node is not in the dataset");
}
// 2. Compute mutual information between each feature and the class
auto weights_matrix = metrics.conditionalEdge(weights);
// 3. Compute the maximum spanning tree

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@@ -0,0 +1,23 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef TAN_H
#define TAN_H
#include "Classifier.h"
namespace bayesnet {
class TAN : public Classifier {
public:
TAN();
virtual ~TAN() = default;
void setHyperparameters(const nlohmann::json& hyperparameters_) override;
std::vector<std::string> graph(const std::string& name = "TAN") const override;
protected:
void buildModel(const torch::Tensor& weights) override;
private:
int parent = -1;
};
}
#endif

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@@ -0,0 +1,54 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "TANLd.h"
#include <memory>
namespace bayesnet {
TANLd::TANLd() : TAN(), Proposal(dataset, features, className, TAN::notes)
{
validHyperparameters = validHyperparameters_ld; // Inherits the valid hyperparameters from Proposal
}
TANLd& TANLd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
checkInput(X_, y_);
Xf = X_;
y = y_;
return commonFit(features_, className_, states_, smoothing);
}
TANLd& TANLd::fit(torch::Tensor& dataset, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
if (!torch::is_floating_point(dataset)) {
throw std::runtime_error("Dataset must be a floating point tensor");
}
Xf = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." }).clone();
y = dataset.index({ -1, "..." }).clone().to(torch::kInt32);
return commonFit(features_, className_, states_, smoothing);
}
TANLd& TANLd::commonFit(const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
features = features_;
className = className_;
states = iterativeLocalDiscretization(y, static_cast<TAN*>(this), dataset, features, className, states_, smoothing);
TAN::fit(dataset, features, className, states, smoothing);
return *this;
}
torch::Tensor TANLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return TAN::predict(Xt);
}
torch::Tensor TANLd::predict_proba(torch::Tensor& X)
{
auto Xt = prepareX(X);
return TAN::predict_proba(Xt);
}
std::vector<std::string> TANLd::graph(const std::string& name) const
{
return TAN::graph(name);
}
}

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@@ -0,0 +1,32 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef TANLD_H
#define TANLD_H
#include "TAN.h"
#include "Proposal.h"
namespace bayesnet {
class TANLd : public TAN, public Proposal {
private:
public:
TANLd();
virtual ~TANLd() = default;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
TANLd& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing) override;
TANLd& commonFit(const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
std::vector<std::string> graph(const std::string& name = "TANLd") const override;
void setHyperparameters(const nlohmann::json& hyperparameters_) override
{
auto hyperparameters = hyperparameters_;
Proposal::setHyperparameters(hyperparameters);
TAN::setHyperparameters(hyperparameters);
}
torch::Tensor predict(torch::Tensor& X) override;
torch::Tensor predict_proba(torch::Tensor& X) override;
};
}
#endif // !TANLD_H

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@@ -0,0 +1,575 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "XSP2DE.h"
#include <pthread.h> // for pthread_setname_np on linux
#include <cassert>
#include <cmath>
#include <limits>
#include <stdexcept>
#include <iostream>
#include "bayesnet/utils/TensorUtils.h"
namespace bayesnet {
// --------------------------------------
// Constructor
// --------------------------------------
XSp2de::XSp2de(int spIndex1, int spIndex2)
: superParent1_{ spIndex1 }
, superParent2_{ spIndex2 }
, nFeatures_{0}
, statesClass_{0}
, alpha_{1.0}
, initializer_{1.0}
, semaphore_{ CountingSemaphore::getInstance() }
, Classifier(Network())
{
validHyperparameters = { "parent1", "parent2" };
}
// --------------------------------------
// setHyperparameters
// --------------------------------------
void XSp2de::setHyperparameters(const nlohmann::json &hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("parent1")) {
superParent1_ = hyperparameters["parent1"];
hyperparameters.erase("parent1");
}
if (hyperparameters.contains("parent2")) {
superParent2_ = hyperparameters["parent2"];
hyperparameters.erase("parent2");
}
// Hand off anything else to base Classifier
Classifier::setHyperparameters(hyperparameters);
}
// --------------------------------------
// fitx
// --------------------------------------
void XSp2de::fitx(torch::Tensor & X, torch::Tensor & y,
torch::Tensor & weights_, const Smoothing_t smoothing)
{
m = X.size(1); // number of samples
n = X.size(0); // number of features
dataset = X;
// Build the dataset in your environment if needed:
buildDataset(y);
// Construct the data structures needed for counting
buildModel(weights_);
// Accumulate counts & convert to probabilities
trainModel(weights_, smoothing);
fitted = true;
}
// --------------------------------------
// buildModel
// --------------------------------------
void XSp2de::buildModel(const torch::Tensor &weights)
{
nFeatures_ = n;
// Derive the number of states for each feature from the dataset
// states_[f] = max value in dataset[f] + 1.
states_.resize(nFeatures_);
for (int f = 0; f < nFeatures_; f++) {
// This is naive: we take max in feature f. You might adapt for real data.
states_[f] = dataset[f].max().item<int>() + 1;
}
// Class states:
statesClass_ = dataset[-1].max().item<int>() + 1;
// Initialize the class counts
classCounts_.resize(statesClass_, 0.0);
// For sp1 -> p(sp1Val| c)
sp1FeatureCounts_.resize(states_[superParent1_] * statesClass_, 0.0);
// For sp2 -> p(sp2Val| c)
sp2FeatureCounts_.resize(states_[superParent2_] * statesClass_, 0.0);
// For child features, we store p(childVal | c, sp1Val, sp2Val).
// childCounts_ will hold raw counts. Well gather them in one big vector.
// We need an offset for each feature.
childOffsets_.resize(nFeatures_, -1);
int totalSize = 0;
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent1_ || f == superParent2_) {
// skip the superparents
childOffsets_[f] = -1;
continue;
}
childOffsets_[f] = totalSize;
// block size for a single child f: states_[f] * statesClass_
// * states_[superParent1_]
// * states_[superParent2_].
totalSize += (states_[f] * statesClass_
* states_[superParent1_]
* states_[superParent2_]);
}
childCounts_.resize(totalSize, 0.0);
}
// --------------------------------------
// trainModel
// --------------------------------------
void XSp2de::trainModel(const torch::Tensor &weights,
const bayesnet::Smoothing_t smoothing)
{
// Accumulate raw counts
for (int i = 0; i < m; i++) {
std::vector<int> instance(nFeatures_ + 1);
for (int f = 0; f < nFeatures_; f++) {
instance[f] = dataset[f][i].item<int>();
}
instance[nFeatures_] = dataset[-1][i].item<int>(); // class
double w = weights[i].item<double>();
addSample(instance, w);
}
// Choose alpha based on smoothing:
switch (smoothing) {
case bayesnet::Smoothing_t::ORIGINAL:
alpha_ = 1.0 / m;
break;
case bayesnet::Smoothing_t::LAPLACE:
alpha_ = 1.0;
break;
default:
alpha_ = 0.0; // no smoothing
}
// Large initializer factor for numerical stability
initializer_ = std::numeric_limits<double>::max() / (nFeatures_ * nFeatures_);
// Convert raw counts to probabilities
computeProbabilities();
}
// --------------------------------------
// addSample
// --------------------------------------
void XSp2de::addSample(const std::vector<int> &instance, double weight)
{
if (weight <= 0.0)
return;
int c = instance.back();
// increment classCounts
classCounts_[c] += weight;
int sp1Val = instance[superParent1_];
int sp2Val = instance[superParent2_];
// p(sp1|c)
sp1FeatureCounts_[sp1Val * statesClass_ + c] += weight;
// p(sp2|c)
sp2FeatureCounts_[sp2Val * statesClass_ + c] += weight;
// p(childVal| c, sp1Val, sp2Val)
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent1_ || f == superParent2_)
continue;
int childVal = instance[f];
int offset = childOffsets_[f];
// block layout:
// offset + (sp1Val*(states_[sp2_]* states_[f]* statesClass_))
// + (sp2Val*(states_[f]* statesClass_))
// + childVal*(statesClass_)
// + c
int blockSizeSp2 = states_[superParent2_]
* states_[f]
* statesClass_;
int blockSizeChild = states_[f] * statesClass_;
int idx = offset
+ sp1Val*blockSizeSp2
+ sp2Val*blockSizeChild
+ childVal*statesClass_
+ c;
childCounts_[idx] += weight;
}
}
// --------------------------------------
// computeProbabilities
// --------------------------------------
void XSp2de::computeProbabilities()
{
double totalCount = std::accumulate(classCounts_.begin(),
classCounts_.end(), 0.0);
// classPriors_
classPriors_.resize(statesClass_, 0.0);
if (totalCount <= 0.0) {
// fallback => uniform
double unif = 1.0 / static_cast<double>(statesClass_);
for (int c = 0; c < statesClass_; c++) {
classPriors_[c] = unif;
}
} else {
for (int c = 0; c < statesClass_; c++) {
classPriors_[c] =
(classCounts_[c] + alpha_)
/ (totalCount + alpha_ * statesClass_);
}
}
// p(sp1Val| c)
sp1FeatureProbs_.resize(sp1FeatureCounts_.size());
int sp1Card = states_[superParent1_];
for (int spVal = 0; spVal < sp1Card; spVal++) {
for (int c = 0; c < statesClass_; c++) {
double denom = classCounts_[c] + alpha_ * sp1Card;
double num = sp1FeatureCounts_[spVal * statesClass_ + c] + alpha_;
sp1FeatureProbs_[spVal * statesClass_ + c] =
(denom <= 0.0 ? 0.0 : num / denom);
}
}
// p(sp2Val| c)
sp2FeatureProbs_.resize(sp2FeatureCounts_.size());
int sp2Card = states_[superParent2_];
for (int spVal = 0; spVal < sp2Card; spVal++) {
for (int c = 0; c < statesClass_; c++) {
double denom = classCounts_[c] + alpha_ * sp2Card;
double num = sp2FeatureCounts_[spVal * statesClass_ + c] + alpha_;
sp2FeatureProbs_[spVal * statesClass_ + c] =
(denom <= 0.0 ? 0.0 : num / denom);
}
}
// p(childVal| c, sp1Val, sp2Val)
childProbs_.resize(childCounts_.size());
int offset = 0;
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent1_ || f == superParent2_)
continue;
int fCard = states_[f];
int sp1Card_ = states_[superParent1_];
int sp2Card_ = states_[superParent2_];
int childBlockSizeSp2 = sp2Card_ * fCard * statesClass_;
int childBlockSizeF = fCard * statesClass_;
int blockSize = fCard * sp1Card_ * sp2Card_ * statesClass_;
for (int sp1Val = 0; sp1Val < sp1Card_; sp1Val++) {
for (int sp2Val = 0; sp2Val < sp2Card_; sp2Val++) {
for (int childVal = 0; childVal < fCard; childVal++) {
for (int c = 0; c < statesClass_; c++) {
// index in childCounts_
int idx = offset
+ sp1Val*childBlockSizeSp2
+ sp2Val*childBlockSizeF
+ childVal*statesClass_
+ c;
double num = childCounts_[idx] + alpha_;
// denominator is the count of (sp1Val,sp2Val,c) plus alpha * fCard
// We can find that by summing childVal dimension, but we already
// have it in childCounts_[...] or we can re-check the superparent
// counts if your approach is purely hierarchical.
// Here we'll do it like the XSpode approach: sp1&sp2 are
// conditionally independent given c, so denominators come from
// summing the relevant block or we treat sp1,sp2 as "parents."
// A simpler approach:
double sumSp1Sp2C = 0.0;
// sum over all childVal:
for (int cv = 0; cv < fCard; cv++) {
int idx2 = offset
+ sp1Val*childBlockSizeSp2
+ sp2Val*childBlockSizeF
+ cv*statesClass_ + c;
sumSp1Sp2C += childCounts_[idx2];
}
double denom = sumSp1Sp2C + alpha_ * fCard;
childProbs_[idx] = (denom <= 0.0 ? 0.0 : num / denom);
}
}
}
}
offset += blockSize;
}
}
// --------------------------------------
// predict_proba (single instance)
// --------------------------------------
std::vector<double> XSp2de::predict_proba(const std::vector<int> &instance) const
{
if (!fitted) {
throw std::logic_error(CLASSIFIER_NOT_FITTED);
}
std::vector<double> probs(statesClass_, 0.0);
int sp1Val = instance[superParent1_];
int sp2Val = instance[superParent2_];
// Start with p(c) * p(sp1Val| c) * p(sp2Val| c)
for (int c = 0; c < statesClass_; c++) {
double pC = classPriors_[c];
double pSp1C = sp1FeatureProbs_[sp1Val * statesClass_ + c];
double pSp2C = sp2FeatureProbs_[sp2Val * statesClass_ + c];
probs[c] = pC * pSp1C * pSp2C * initializer_;
}
// Multiply by each child feature f
int offset = 0;
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent1_ || f == superParent2_)
continue;
int valF = instance[f];
int fCard = states_[f];
int sp1Card = states_[superParent1_];
int sp2Card = states_[superParent2_];
int blockSizeSp2 = sp2Card * fCard * statesClass_;
int blockSizeF = fCard * statesClass_;
// base index for childProbs_ for this child and sp1Val, sp2Val
int base = offset
+ sp1Val*blockSizeSp2
+ sp2Val*blockSizeF
+ valF*statesClass_;
for (int c = 0; c < statesClass_; c++) {
probs[c] *= childProbs_[base + c];
}
offset += (fCard * sp1Card * sp2Card * statesClass_);
}
// Normalize
normalize(probs);
return probs;
}
// --------------------------------------
// predict_proba (batch)
// --------------------------------------
std::vector<std::vector<double>> XSp2de::predict_proba(std::vector<std::vector<int>> &test_data)
{
int test_size = test_data[0].size(); // each feature is test_data[f], size = #samples
int sample_size = test_data.size(); // = nFeatures_
std::vector<std::vector<double>> probabilities(
test_size, std::vector<double>(statesClass_, 0.0));
// same concurrency approach
int chunk_size = std::min(150, int(test_size / semaphore_.getMaxCount()) + 1);
std::vector<std::thread> threads;
auto worker = [&](const std::vector<std::vector<int>> &samples,
int begin,
int chunk,
int sample_size,
std::vector<std::vector<double>> &predictions) {
std::string threadName =
"XSp2de-" + std::to_string(begin) + "-" + std::to_string(chunk);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
std::vector<int> instance(sample_size);
for (int sample = begin; sample < begin + chunk; ++sample) {
for (int feature = 0; feature < sample_size; ++feature) {
instance[feature] = samples[feature][sample];
}
predictions[sample] = predict_proba(instance);
}
semaphore_.release();
};
for (int begin = 0; begin < test_size; begin += chunk_size) {
int chunk = std::min(chunk_size, test_size - begin);
semaphore_.acquire();
threads.emplace_back(worker, test_data, begin, chunk, sample_size,
std::ref(probabilities));
}
for (auto &th : threads) {
th.join();
}
return probabilities;
}
// --------------------------------------
// predict (single instance)
// --------------------------------------
int XSp2de::predict(const std::vector<int> &instance) const
{
auto p = predict_proba(instance);
return static_cast<int>(
std::distance(p.begin(), std::max_element(p.begin(), p.end()))
);
}
// --------------------------------------
// predict (batch of data)
// --------------------------------------
std::vector<int> XSp2de::predict(std::vector<std::vector<int>> &test_data)
{
auto probabilities = predict_proba(test_data);
std::vector<int> predictions(probabilities.size(), 0);
for (size_t i = 0; i < probabilities.size(); i++) {
predictions[i] = static_cast<int>(
std::distance(probabilities[i].begin(),
std::max_element(probabilities[i].begin(),
probabilities[i].end()))
);
}
return predictions;
}
// --------------------------------------
// predict (torch::Tensor version)
// --------------------------------------
torch::Tensor XSp2de::predict(torch::Tensor &X)
{
auto X_ = TensorUtils::to_matrix(X);
auto result_v = predict(X_);
return torch::tensor(result_v, torch::kInt32);
}
// --------------------------------------
// predict_proba (torch::Tensor version)
// --------------------------------------
torch::Tensor XSp2de::predict_proba(torch::Tensor &X)
{
auto X_ = TensorUtils::to_matrix(X);
auto result_v = predict_proba(X_);
int n_samples = X.size(1);
torch::Tensor result =
torch::zeros({ n_samples, statesClass_ }, torch::kDouble);
for (int i = 0; i < (int)result_v.size(); ++i) {
result.index_put_({ i, "..." }, torch::tensor(result_v[i]));
}
return result;
}
// --------------------------------------
// score (torch::Tensor version)
// --------------------------------------
float XSp2de::score(torch::Tensor &X, torch::Tensor &y)
{
torch::Tensor y_pred = predict(X);
return (y_pred == y).sum().item<float>() / y.size(0);
}
// --------------------------------------
// score (vector version)
// --------------------------------------
float XSp2de::score(std::vector<std::vector<int>> &X, std::vector<int> &y)
{
auto y_pred = predict(X);
int correct = 0;
for (size_t i = 0; i < y_pred.size(); ++i) {
if (y_pred[i] == y[i]) {
correct++;
}
}
return static_cast<float>(correct) / static_cast<float>(y_pred.size());
}
// --------------------------------------
// Utility: normalize
// --------------------------------------
void XSp2de::normalize(std::vector<double> &v) const
{
double sum = 0.0;
for (auto &val : v) {
sum += val;
}
if (sum > 0.0) {
for (auto &val : v) {
val /= sum;
}
}
}
// --------------------------------------
// to_string
// --------------------------------------
std::string XSp2de::to_string() const
{
std::ostringstream oss;
oss << "----- XSp2de Model -----\n"
<< "nFeatures_ = " << nFeatures_ << "\n"
<< "superParent1_ = " << superParent1_ << "\n"
<< "superParent2_ = " << superParent2_ << "\n"
<< "statesClass_ = " << statesClass_ << "\n\n";
oss << "States: [";
for (auto s : states_) oss << s << " ";
oss << "]\n";
oss << "classCounts_:\n";
for (auto v : classCounts_) oss << v << " ";
oss << "\nclassPriors_:\n";
for (auto v : classPriors_) oss << v << " ";
oss << "\nsp1FeatureCounts_ (size=" << sp1FeatureCounts_.size() << ")\n";
for (auto v : sp1FeatureCounts_) oss << v << " ";
oss << "\nsp2FeatureCounts_ (size=" << sp2FeatureCounts_.size() << ")\n";
for (auto v : sp2FeatureCounts_) oss << v << " ";
oss << "\nchildCounts_ (size=" << childCounts_.size() << ")\n";
for (auto v : childCounts_) oss << v << " ";
oss << "\nchildOffsets_:\n";
for (auto c : childOffsets_) oss << c << " ";
oss << "\n----------------------------------------\n";
return oss.str();
}
// --------------------------------------
// Some introspection about the graph
// --------------------------------------
int XSp2de::getNumberOfNodes() const
{
// nFeatures + 1 class node
return nFeatures_ + 1;
}
int XSp2de::getClassNumStates() const
{
return statesClass_;
}
int XSp2de::getNFeatures() const
{
return nFeatures_;
}
int XSp2de::getNumberOfStates() const
{
// purely an example. Possibly you want to sum up actual
// cardinalities or something else.
return std::accumulate(states_.begin(), states_.end(), 0) * nFeatures_;
}
int XSp2de::getNumberOfEdges() const
{
// In an SPNDE with n=2, for each feature we have edges from class, sp1, sp2.
// So thats 3*(nFeatures_) edges, minus the ones for the superparents themselves,
// plus the edges from class->superparent1, class->superparent2.
// For a quick approximation:
// - class->sp1, class->sp2 => 2 edges
// - class->child => (nFeatures -2) edges
// - sp1->child, sp2->child => 2*(nFeatures -2) edges
// total = 2 + (nFeatures-2) + 2*(nFeatures-2) = 2 + 3*(nFeatures-2)
// = 3nFeatures - 4 (just an example).
// You can adapt to your liking:
return 3 * nFeatures_ - 4;
}
} // namespace bayesnet

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// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef XSP2DE_H
#define XSP2DE_H
#include "Classifier.h"
#include "bayesnet/utils/CountingSemaphore.h"
#include <torch/torch.h>
#include <vector>
namespace bayesnet {
class XSp2de : public Classifier {
public:
XSp2de(int spIndex1, int spIndex2);
void setHyperparameters(const nlohmann::json &hyperparameters_) override;
void fitx(torch::Tensor &X, torch::Tensor &y, torch::Tensor &weights_, const Smoothing_t smoothing);
std::vector<double> predict_proba(const std::vector<int> &instance) const;
std::vector<std::vector<double>> predict_proba(std::vector<std::vector<int>> &test_data) override;
int predict(const std::vector<int> &instance) const;
std::vector<int> predict(std::vector<std::vector<int>> &test_data) override;
torch::Tensor predict(torch::Tensor &X) override;
torch::Tensor predict_proba(torch::Tensor &X) override;
float score(torch::Tensor &X, torch::Tensor &y) override;
float score(std::vector<std::vector<int>> &X, std::vector<int> &y) override;
std::string to_string() const;
std::vector<std::string> graph(const std::string &title) const override {
return std::vector<std::string>({title});
}
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNFeatures() const;
int getClassNumStates() const override;
int getNumberOfStates() const override;
protected:
void buildModel(const torch::Tensor &weights) override;
void trainModel(const torch::Tensor &weights, const bayesnet::Smoothing_t smoothing) override;
private:
void addSample(const std::vector<int> &instance, double weight);
void normalize(std::vector<double> &v) const;
void computeProbabilities();
int superParent1_;
int superParent2_;
int nFeatures_;
int statesClass_;
double alpha_;
double initializer_;
std::vector<int> states_;
std::vector<double> classCounts_;
std::vector<double> classPriors_;
std::vector<double> sp1FeatureCounts_, sp1FeatureProbs_;
std::vector<double> sp2FeatureCounts_, sp2FeatureProbs_;
// childOffsets_[f] will be the offset into childCounts_ for feature f.
// If f is either superParent1 or superParent2, childOffsets_[f] = -1
std::vector<int> childOffsets_;
// For each child f, we store p(x_f | c, sp1Val, sp2Val). We'll store the raw
// counts in childCounts_, and the probabilities in childProbs_, with a
// dimension block of size: states_[f]* statesClass_* states_[sp1]* states_[sp2].
std::vector<double> childCounts_;
std::vector<double> childProbs_;
CountingSemaphore &semaphore_;
};
} // namespace bayesnet
#endif // XSP2DE_H

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// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <algorithm>
#include <cmath>
#include <limits>
#include <numeric>
#include <sstream>
#include <stdexcept>
#include "XSPODE.h"
#include "bayesnet/utils/TensorUtils.h"
namespace bayesnet {
// --------------------------------------
// Constructor
// --------------------------------------
XSpode::XSpode(int spIndex)
: superParent_{ spIndex }, nFeatures_{ 0 }, statesClass_{ 0 }, alpha_{ 1.0 },
initializer_{ 1.0 }, semaphore_{ CountingSemaphore::getInstance() },
Classifier(Network())
{
validHyperparameters = { "parent" };
}
void XSpode::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("parent")) {
superParent_ = hyperparameters["parent"];
hyperparameters.erase("parent");
}
Classifier::setHyperparameters(hyperparameters);
}
void XSpode::fitx(torch::Tensor & X, torch::Tensor& y, torch::Tensor& weights_, const Smoothing_t smoothing)
{
m = X.size(1);
n = X.size(0);
dataset = X;
buildDataset(y);
buildModel(weights_);
trainModel(weights_, smoothing);
fitted = true;
}
// --------------------------------------
// trainModel
// --------------------------------------
// Initialize storage needed for the super-parent and child features counts and
// probs.
// --------------------------------------
void XSpode::buildModel(const torch::Tensor& weights)
{
int numInstances = m;
nFeatures_ = n;
// Derive the number of states for each feature and for the class.
// (This is just one approach; adapt to match your environment.)
// Here, we assume the user also gave us the total #states per feature in e.g.
// statesMap. We'll simply reconstruct the integer states_ array. The last
// entry is statesClass_.
states_.resize(nFeatures_);
for (int f = 0; f < nFeatures_; f++) {
// Suppose you look up in “statesMap” by the feature name, or read directly
// from X. We'll assume states_[f] = max value in X[f] + 1.
states_[f] = dataset[f].max().item<int>() + 1;
}
// For the class: states_.back() = max(y)+1
statesClass_ = dataset[-1].max().item<int>() + 1;
// Initialize counts
classCounts_.resize(statesClass_, 0.0);
// p(x_sp = spVal | c)
// We'll store these counts in spFeatureCounts_[spVal * statesClass_ + c].
spFeatureCounts_.resize(states_[superParent_] * statesClass_, 0.0);
// For each child ≠ sp, we store p(childVal| c, spVal) in a separate block of
// childCounts_. childCounts_ will be sized as sum_{child≠sp} (states_[child]
// * statesClass_ * states_[sp]). We also need an offset for each child to
// index into childCounts_.
childOffsets_.resize(nFeatures_, -1);
int totalSize = 0;
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent_)
continue; // skip sp
childOffsets_[f] = totalSize;
// block size for this child's counts: states_[f] * statesClass_ *
// states_[superParent_]
totalSize += (states_[f] * statesClass_ * states_[superParent_]);
}
childCounts_.resize(totalSize, 0.0);
}
// --------------------------------------
// buildModel
// --------------------------------------
//
// We only store conditional probabilities for:
// p(x_sp| c) (the super-parent feature)
// p(x_child| c, x_sp) for all child ≠ sp
//
// --------------------------------------
void XSpode::trainModel(const torch::Tensor& weights,
const bayesnet::Smoothing_t smoothing)
{
// Accumulate raw counts
for (int i = 0; i < m; i++) {
std::vector<int> instance(nFeatures_ + 1);
for (int f = 0; f < nFeatures_; f++) {
instance[f] = dataset[f][i].item<int>();
}
instance[nFeatures_] = dataset[-1][i].item<int>();
addSample(instance, weights[i].item<double>());
}
switch (smoothing) {
case bayesnet::Smoothing_t::ORIGINAL:
alpha_ = 1.0 / m;
break;
case bayesnet::Smoothing_t::LAPLACE:
alpha_ = 1.0;
break;
default:
alpha_ = 0.0; // No smoothing
}
initializer_ = std::numeric_limits<double>::max() /
(nFeatures_ * nFeatures_); // for numerical stability
// Convert raw counts to probabilities
computeProbabilities();
}
// --------------------------------------
// addSample
// --------------------------------------
//
// instance has size nFeatures_ + 1, with the class at the end.
// We add 1 to the appropriate counters for each (c, superParentVal, childVal).
//
void XSpode::addSample(const std::vector<int>& instance, double weight)
{
if (weight <= 0.0)
return;
int c = instance.back();
// (A) increment classCounts
classCounts_[c] += weight;
// (B) increment super-parent counts => p(x_sp | c)
int spVal = instance[superParent_];
spFeatureCounts_[spVal * statesClass_ + c] += weight;
// (C) increment child counts => p(childVal | c, x_sp)
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent_)
continue;
int childVal = instance[f];
int offset = childOffsets_[f];
// Compute index in childCounts_.
// Layout: [ offset + (spVal * states_[f] + childVal) * statesClass_ + c ]
int blockSize = states_[f] * statesClass_;
int idx = offset + spVal * blockSize + childVal * statesClass_ + c;
childCounts_[idx] += weight;
}
}
// --------------------------------------
// computeProbabilities
// --------------------------------------
//
// Once all samples are added in COUNTS mode, call this to:
// p(c)
// p(x_sp = spVal | c)
// p(x_child = v | c, x_sp = s_sp)
//
// --------------------------------------
void XSpode::computeProbabilities()
{
double totalCount =
std::accumulate(classCounts_.begin(), classCounts_.end(), 0.0);
// p(c) => classPriors_
classPriors_.resize(statesClass_, 0.0);
if (totalCount <= 0.0) {
// fallback => uniform
double unif = 1.0 / static_cast<double>(statesClass_);
for (int c = 0; c < statesClass_; c++) {
classPriors_[c] = unif;
}
} else {
for (int c = 0; c < statesClass_; c++) {
classPriors_[c] =
(classCounts_[c] + alpha_) / (totalCount + alpha_ * statesClass_);
}
}
// p(x_sp | c)
spFeatureProbs_.resize(spFeatureCounts_.size());
// denominator for spVal * statesClass_ + c is just classCounts_[c] + alpha_ *
// (#states of sp)
int spCard = states_[superParent_];
for (int spVal = 0; spVal < spCard; spVal++) {
for (int c = 0; c < statesClass_; c++) {
double denom = classCounts_[c] + alpha_ * spCard;
double num = spFeatureCounts_[spVal * statesClass_ + c] + alpha_;
spFeatureProbs_[spVal * statesClass_ + c] = (denom <= 0.0 ? 0.0 : num / denom);
}
}
// p(x_child | c, x_sp)
childProbs_.resize(childCounts_.size());
for (int f = 0; f < nFeatures_; f++) {
if (f == superParent_)
continue;
int offset = childOffsets_[f];
int childCard = states_[f];
// For each spVal, c, childVal in childCounts_:
for (int spVal = 0; spVal < spCard; spVal++) {
for (int childVal = 0; childVal < childCard; childVal++) {
for (int c = 0; c < statesClass_; c++) {
int idx = offset + spVal * (childCard * statesClass_) +
childVal * statesClass_ + c;
double num = childCounts_[idx] + alpha_;
// denominator = spFeatureCounts_[spVal * statesClass_ + c] + alpha_ *
// (#states of child)
double denom =
spFeatureCounts_[spVal * statesClass_ + c] + alpha_ * childCard;
childProbs_[idx] = (denom <= 0.0 ? 0.0 : num / denom);
}
}
}
}
}
// --------------------------------------
// predict_proba
// --------------------------------------
//
// For a single instance x of dimension nFeatures_:
// P(c | x) ∝ p(c) × p(x_sp | c) × ∏(child ≠ sp) p(x_child | c, x_sp).
//
// --------------------------------------
std::vector<double> XSpode::predict_proba(const std::vector<int>& instance) const
{
if (!fitted) {
throw std::logic_error(CLASSIFIER_NOT_FITTED);
}
std::vector<double> probs(statesClass_, 0.0);
// Multiply p(c) × p(x_sp | c)
int spVal = instance[superParent_];
for (int c = 0; c < statesClass_; c++) {
double pc = classPriors_[c];
double pSpC = spFeatureProbs_[spVal * statesClass_ + c];
probs[c] = pc * pSpC * initializer_;
}
// Multiply by each childs probability p(x_child | c, x_sp)
for (int feature = 0; feature < nFeatures_; feature++) {
if (feature == superParent_)
continue; // skip sp
int sf = instance[feature];
int offset = childOffsets_[feature];
int childCard = states_[feature]; // not used directly, but for clarity
// Index into childProbs_ = offset + spVal*(childCard*statesClass_) +
// childVal*statesClass_ + c
int base = offset + spVal * (childCard * statesClass_) + sf * statesClass_;
for (int c = 0; c < statesClass_; c++) {
probs[c] *= childProbs_[base + c];
}
}
// Normalize
normalize(probs);
return probs;
}
std::vector<std::vector<double>> XSpode::predict_proba(std::vector<std::vector<int>>& test_data)
{
int test_size = test_data[0].size();
int sample_size = test_data.size();
auto probabilities = std::vector<std::vector<double>>(
test_size, std::vector<double>(statesClass_));
int chunk_size = std::min(150, int(test_size / semaphore_.getMaxCount()) + 1);
std::vector<std::thread> threads;
auto worker = [&](const std::vector<std::vector<int>>& samples, int begin,
int chunk, int sample_size,
std::vector<std::vector<double>>& predictions) {
std::string threadName =
"(V)PWorker-" + std::to_string(begin) + "-" + std::to_string(chunk);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
std::vector<int> instance(sample_size);
for (int sample = begin; sample < begin + chunk; ++sample) {
for (int feature = 0; feature < sample_size; ++feature) {
instance[feature] = samples[feature][sample];
}
predictions[sample] = predict_proba(instance);
}
semaphore_.release();
};
for (int begin = 0; begin < test_size; begin += chunk_size) {
int chunk = std::min(chunk_size, test_size - begin);
semaphore_.acquire();
threads.emplace_back(worker, test_data, begin, chunk, sample_size, std::ref(probabilities));
}
for (auto& thread : threads) {
thread.join();
}
return probabilities;
}
// --------------------------------------
// Utility: normalize
// --------------------------------------
void XSpode::normalize(std::vector<double>& v) const
{
double sum = 0.0;
for (auto val : v) {
sum += val;
}
if (sum <= 0.0) {
return;
}
for (auto& val : v) {
val /= sum;
}
}
// --------------------------------------
// representation of the model
// --------------------------------------
std::string XSpode::to_string() const
{
std::ostringstream oss;
oss << "----- XSpode Model -----" << std::endl
<< "nFeatures_ = " << nFeatures_ << std::endl
<< "superParent_ = " << superParent_ << std::endl
<< "statesClass_ = " << statesClass_ << std::endl
<< std::endl;
oss << "States: [";
for (int s : states_)
oss << s << " ";
oss << "]" << std::endl;
oss << "classCounts_: [";
for (double c : classCounts_)
oss << c << " ";
oss << "]" << std::endl;
oss << "classPriors_: [";
for (double c : classPriors_)
oss << c << " ";
oss << "]" << std::endl;
oss << "spFeatureCounts_: size = " << spFeatureCounts_.size() << std::endl
<< "[";
for (double c : spFeatureCounts_)
oss << c << " ";
oss << "]" << std::endl;
oss << "spFeatureProbs_: size = " << spFeatureProbs_.size() << std::endl
<< "[";
for (double c : spFeatureProbs_)
oss << c << " ";
oss << "]" << std::endl;
oss << "childCounts_: size = " << childCounts_.size() << std::endl << "[";
for (double cc : childCounts_)
oss << cc << " ";
oss << "]" << std::endl;
for (double cp : childProbs_)
oss << cp << " ";
oss << "]" << std::endl;
oss << "childOffsets_: [";
for (int co : childOffsets_)
oss << co << " ";
oss << "]" << std::endl;
oss << std::string(40,'-') << std::endl;
return oss.str();
}
int XSpode::getNumberOfNodes() const { return nFeatures_ + 1; }
int XSpode::getClassNumStates() const { return statesClass_; }
int XSpode::getNFeatures() const { return nFeatures_; }
int XSpode::getNumberOfStates() const
{
return std::accumulate(states_.begin(), states_.end(), 0) * nFeatures_;
}
int XSpode::getNumberOfEdges() const
{
return 2 * nFeatures_ + 1;
}
// ------------------------------------------------------
// Predict overrides (classifier interface)
// ------------------------------------------------------
int XSpode::predict(const std::vector<int>& instance) const
{
auto p = predict_proba(instance);
return static_cast<int>(std::distance(p.begin(), std::max_element(p.begin(), p.end())));
}
std::vector<int> XSpode::predict(std::vector<std::vector<int>>& test_data)
{
auto probabilities = predict_proba(test_data);
std::vector<int> predictions(probabilities.size(), 0);
for (size_t i = 0; i < probabilities.size(); i++) {
predictions[i] = std::distance(
probabilities[i].begin(),
std::max_element(probabilities[i].begin(), probabilities[i].end()));
}
return predictions;
}
torch::Tensor XSpode::predict(torch::Tensor& X)
{
auto X_ = TensorUtils::to_matrix(X);
auto result_v = predict(X_);
return torch::tensor(result_v, torch::kInt32);
}
torch::Tensor XSpode::predict_proba(torch::Tensor& X)
{
auto X_ = TensorUtils::to_matrix(X);
auto result_v = predict_proba(X_);
int n_samples = X.size(1);
torch::Tensor result =
torch::zeros({ n_samples, statesClass_ }, torch::kDouble);
for (int i = 0; i < result_v.size(); ++i) {
result.index_put_({ i, "..." }, torch::tensor(result_v[i]));
}
return result;
}
float XSpode::score(torch::Tensor& X, torch::Tensor& y)
{
torch::Tensor y_pred = predict(X);
return (y_pred == y).sum().item<float>() / y.size(0);
}
float XSpode::score(std::vector<std::vector<int>>& X, std::vector<int>& y)
{
auto y_pred = this->predict(X);
int correct = 0;
for (int i = 0; i < y_pred.size(); ++i) {
if (y_pred[i] == y[i]) {
correct++;
}
}
return (double)correct / y_pred.size();
}
} // namespace bayesnet

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@@ -0,0 +1,76 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef XSPODE_H
#define XSPODE_H
#include <vector>
#include <torch/torch.h>
#include "Classifier.h"
#include "bayesnet/utils/CountingSemaphore.h"
namespace bayesnet {
class XSpode : public Classifier {
public:
explicit XSpode(int spIndex);
std::vector<double> predict_proba(const std::vector<int>& instance) const;
std::vector<std::vector<double>> predict_proba(std::vector<std::vector<int>>& X) override;
int predict(const std::vector<int>& instance) const;
void normalize(std::vector<double>& v) const;
std::string to_string() const;
int getNFeatures() const;
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
int getClassNumStates() const override;
std::vector<int>& getStates();
std::vector<std::string> graph(const std::string& title) const override { return std::vector<std::string>({ title }); }
void fitx(torch::Tensor& X, torch::Tensor& y, torch::Tensor& weights_, const Smoothing_t smoothing);
void setHyperparameters(const nlohmann::json& hyperparameters_) override;
//
// Classifier interface
//
torch::Tensor predict(torch::Tensor& X) override;
std::vector<int> predict(std::vector<std::vector<int>>& X) override;
torch::Tensor predict_proba(torch::Tensor& X) override;
float score(torch::Tensor& X, torch::Tensor& y) override;
float score(std::vector<std::vector<int>>& X, std::vector<int>& y) override;
protected:
void buildModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights, const bayesnet::Smoothing_t smoothing) override;
private:
void addSample(const std::vector<int>& instance, double weight);
void computeProbabilities();
int superParent_;
int nFeatures_;
int statesClass_;
std::vector<int> states_; // [states_feat0, ..., states_feat(N-1)] (class not included in this array)
// Class counts
std::vector<double> classCounts_; // [c], accumulative
std::vector<double> classPriors_; // [c], after normalization
// For p(x_sp = spVal | c)
std::vector<double> spFeatureCounts_; // [spVal * statesClass_ + c]
std::vector<double> spFeatureProbs_; // same shape, after normalization
// For p(x_child = childVal | x_sp = spVal, c)
// childCounts_ is big enough to hold all child features except sp:
// For each child f, we store childOffsets_[f] as the start index, then
// childVal, spVal, c => the data.
std::vector<double> childCounts_;
std::vector<double> childProbs_;
std::vector<int> childOffsets_;
double alpha_ = 1.0;
double initializer_; // for numerical stability
CountingSemaphore& semaphore_;
};
}
#endif // XSPODE_H

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@@ -0,0 +1,40 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "A2DE.h"
namespace bayesnet {
A2DE::A2DE(bool predict_voting) : Ensemble(predict_voting)
{
validHyperparameters = { "predict_voting" };
}
void A2DE::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("predict_voting")) {
predict_voting = hyperparameters["predict_voting"];
hyperparameters.erase("predict_voting");
}
Classifier::setHyperparameters(hyperparameters);
}
void A2DE::buildModel(const torch::Tensor& weights)
{
models.clear();
significanceModels.clear();
for (int i = 0; i < features.size() - 1; ++i) {
for (int j = i + 1; j < features.size(); ++j) {
auto model = std::make_unique<SPnDE>(std::vector<int>({ i, j }));
models.push_back(std::move(model));
}
}
n_models = static_cast<unsigned>(models.size());
significanceModels = std::vector<double>(n_models, 1.0);
}
std::vector<std::string> A2DE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}
}

22
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@@ -0,0 +1,22 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef A2DE_H
#define A2DE_H
#include "bayesnet/classifiers/SPnDE.h"
#include "Ensemble.h"
namespace bayesnet {
class A2DE : public Ensemble {
public:
A2DE(bool predict_voting = false);
virtual ~A2DE() {};
void setHyperparameters(const nlohmann::json& hyperparameters) override;
std::vector<std::string> graph(const std::string& title = "A2DE") const override;
protected:
void buildModel(const torch::Tensor& weights) override;
};
}
#endif

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@@ -1,3 +1,9 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "AODE.h"
namespace bayesnet {
@@ -13,9 +19,7 @@ namespace bayesnet {
predict_voting = hyperparameters["predict_voting"];
hyperparameters.erase("predict_voting");
}
if (!hyperparameters.empty()) {
throw std::invalid_argument("Invalid hyperparameters" + hyperparameters.dump());
}
Classifier::setHyperparameters(hyperparameters);
}
void AODE::buildModel(const torch::Tensor& weights)
{

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@@ -1,11 +1,17 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef AODE_H
#define AODE_H
#include "bayesnet/classifiers/SPODE.h"
#include "Ensemble.h"
#include "SPODE.h"
namespace bayesnet {
class AODE : public Ensemble {
public:
AODE(bool predict_voting = true);
AODE(bool predict_voting = false);
virtual ~AODE() {};
void setHyperparameters(const nlohmann::json& hyperparameters) override;
std::vector<std::string> graph(const std::string& title = "AODE") const override;

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@@ -1,23 +1,17 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "AODELd.h"
namespace bayesnet {
AODELd::AODELd(bool predict_voting) : Ensemble(predict_voting), Proposal(dataset, features, className)
AODELd::AODELd(bool predict_voting) : Ensemble(predict_voting), Proposal(dataset, features, className, Ensemble::notes)
{
validHyperparameters = { "predict_voting" };
validHyperparameters = validHyperparameters_ld; // Inherits the valid hyperparameters from Proposal
}
void AODELd::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("predict_voting")) {
predict_voting = hyperparameters["predict_voting"];
hyperparameters.erase("predict_voting");
}
if (!hyperparameters.empty()) {
throw std::invalid_argument("Invalid hyperparameters" + hyperparameters.dump());
}
}
AODELd& AODELd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
AODELd& AODELd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing)
{
checkInput(X_, y_);
features = features_;
@@ -27,8 +21,9 @@ namespace bayesnet {
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal TAN structure, TAN::fit initializes the base Bayesian network
Ensemble::fit(dataset, features, className, states);
// 1st we need to fit the model to build the normal AODE structure, Ensemble::fit
// calls buildModel to initialize the base models
Ensemble::fit(dataset, features, className, states, smoothing);
return *this;
}
@@ -37,14 +32,15 @@ namespace bayesnet {
models.clear();
for (int i = 0; i < features.size(); ++i) {
models.push_back(std::make_unique<SPODELd>(i));
models.back()->setHyperparameters(hyperparameters);
}
n_models = models.size();
significanceModels = std::vector<double>(n_models, 1.0);
}
void AODELd::trainModel(const torch::Tensor& weights)
void AODELd::trainModel(const torch::Tensor& weights, const Smoothing_t smoothing)
{
for (const auto& model : models) {
model->fit(Xf, y, features, className, states);
model->fit(Xf, y, features, className, states, smoothing);
}
}
std::vector<std::string> AODELd::graph(const std::string& name) const

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@@ -0,0 +1,31 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef AODELD_H
#define AODELD_H
#include "bayesnet/classifiers/Proposal.h"
#include "bayesnet/classifiers/SPODELd.h"
#include "Ensemble.h"
namespace bayesnet {
class AODELd : public Ensemble, public Proposal {
public:
AODELd(bool predict_voting = true);
virtual ~AODELd() = default;
AODELd& fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_, const Smoothing_t smoothing) override;
std::vector<std::string> graph(const std::string& name = "AODELd") const override;
void setHyperparameters(const nlohmann::json& hyperparameters_) override
{
hyperparameters = hyperparameters_;
}
protected:
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
void buildModel(const torch::Tensor& weights) override;
private:
nlohmann::json hyperparameters = {}; // Hyperparameters for the model
};
}
#endif // !AODELD_H

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@@ -0,0 +1,268 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "Boost.h"
#include "bayesnet/feature_selection/CFS.h"
#include "bayesnet/feature_selection/FCBF.h"
#include "bayesnet/feature_selection/IWSS.h"
#include <folding.hpp>
namespace bayesnet {
Boost::Boost(bool predict_voting) : Ensemble(predict_voting) {
validHyperparameters = {"alpha_block", "order", "convergence", "convergence_best", "bisection",
"threshold", "maxTolerance", "predict_voting", "select_features", "block_update"};
}
void Boost::setHyperparameters(const nlohmann::json &hyperparameters_) {
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("order")) {
std::vector<std::string> algos = {Orders.ASC, Orders.DESC, Orders.RAND};
order_algorithm = hyperparameters["order"];
if (std::find(algos.begin(), algos.end(), order_algorithm) == algos.end()) {
throw std::invalid_argument("Invalid order algorithm, valid values [" + Orders.ASC + ", " + Orders.DESC +
", " + Orders.RAND + "]");
}
hyperparameters.erase("order");
}
if (hyperparameters.contains("alpha_block")) {
alpha_block = hyperparameters["alpha_block"];
hyperparameters.erase("alpha_block");
}
if (hyperparameters.contains("convergence")) {
convergence = hyperparameters["convergence"];
hyperparameters.erase("convergence");
}
if (hyperparameters.contains("convergence_best")) {
convergence_best = hyperparameters["convergence_best"];
hyperparameters.erase("convergence_best");
}
if (hyperparameters.contains("bisection")) {
bisection = hyperparameters["bisection"];
hyperparameters.erase("bisection");
}
if (hyperparameters.contains("threshold")) {
threshold = hyperparameters["threshold"];
hyperparameters.erase("threshold");
}
if (hyperparameters.contains("maxTolerance")) {
maxTolerance = hyperparameters["maxTolerance"];
if (maxTolerance < 1 || maxTolerance > 6)
throw std::invalid_argument("Invalid maxTolerance value, must be greater in [1, 6]");
hyperparameters.erase("maxTolerance");
}
if (hyperparameters.contains("predict_voting")) {
predict_voting = hyperparameters["predict_voting"];
hyperparameters.erase("predict_voting");
}
if (hyperparameters.contains("select_features")) {
auto selectedAlgorithm = hyperparameters["select_features"];
std::vector<std::string> algos = {SelectFeatures.IWSS, SelectFeatures.CFS, SelectFeatures.FCBF};
selectFeatures = true;
select_features_algorithm = selectedAlgorithm;
if (std::find(algos.begin(), algos.end(), selectedAlgorithm) == algos.end()) {
throw std::invalid_argument("Invalid selectFeatures value, valid values [" + SelectFeatures.IWSS + ", " +
SelectFeatures.CFS + ", " + SelectFeatures.FCBF + "]");
}
hyperparameters.erase("select_features");
}
if (hyperparameters.contains("block_update")) {
block_update = hyperparameters["block_update"];
hyperparameters.erase("block_update");
}
if (block_update && alpha_block) {
throw std::invalid_argument("alpha_block and block_update cannot be true at the same time");
}
if (block_update && !bisection) {
throw std::invalid_argument("block_update needs bisection to be true");
}
Classifier::setHyperparameters(hyperparameters);
}
void Boost::add_model(std::unique_ptr<Classifier> model, double significance) {
models.push_back(std::move(model));
n_models++;
significanceModels.push_back(significance);
}
void Boost::remove_last_model() {
models.pop_back();
significanceModels.pop_back();
n_models--;
}
void Boost::buildModel(const torch::Tensor &weights) {
// Models shall be built in trainModel
models.clear();
significanceModels.clear();
n_models = 0;
// Prepare the validation dataset
auto y_ = dataset.index({-1, "..."});
if (convergence) {
// Prepare train & validation sets from train data
auto fold = folding::StratifiedKFold(5, y_, 271);
auto [train, test] = fold.getFold(0);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
// Get train and validation sets
X_train = dataset.index({torch::indexing::Slice(0, dataset.size(0) - 1), train_t});
y_train = dataset.index({-1, train_t});
X_test = dataset.index({torch::indexing::Slice(0, dataset.size(0) - 1), test_t});
y_test = dataset.index({-1, test_t});
dataset = X_train;
m = X_train.size(1);
auto n_classes = states.at(className).size();
// Build dataset with train data
buildDataset(y_train);
metrics = Metrics(dataset, features, className, n_classes);
} else {
// Use all data to train
X_train = dataset.index({torch::indexing::Slice(0, dataset.size(0) - 1), "..."});
y_train = y_;
}
}
std::vector<int> Boost::featureSelection(torch::Tensor &weights_) {
int maxFeatures = 0;
if (select_features_algorithm == SelectFeatures.CFS) {
featureSelector = new CFS(dataset, features, className, maxFeatures, states.at(className).size(), weights_);
} else if (select_features_algorithm == SelectFeatures.IWSS) {
if (threshold < 0 || threshold > 0.5) {
throw std::invalid_argument("Invalid threshold value for " + SelectFeatures.IWSS + " [0, 0.5]");
}
featureSelector =
new IWSS(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
} else if (select_features_algorithm == SelectFeatures.FCBF) {
if (threshold < 1e-7 || threshold > 1) {
throw std::invalid_argument("Invalid threshold value for " + SelectFeatures.FCBF + " [1e-7, 1]");
}
featureSelector =
new FCBF(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
}
featureSelector->fit();
auto featuresUsed = featureSelector->getFeatures();
delete featureSelector;
return featuresUsed;
}
std::tuple<torch::Tensor &, double, bool> Boost::update_weights(torch::Tensor &ytrain, torch::Tensor &ypred,
torch::Tensor &weights) {
bool terminate = false;
double alpha_t = 0;
auto mask_wrong = ypred != ytrain;
auto mask_right = ypred == ytrain;
auto masked_weights = weights * mask_wrong.to(weights.dtype());
double epsilon_t = masked_weights.sum().item<double>();
// std::cout << "epsilon_t: " << epsilon_t << " count wrong: " << mask_wrong.sum().item<int>() << " count right: "
// << mask_right.sum().item<int>() << std::endl;
if (epsilon_t > 0.5) {
// Inverse the weights policy (plot ln(wt))
// "In each round of AdaBoost, there is a sanity check to ensure that the current base
// learner is better than random guess" (Zhi-Hua Zhou, 2012)
terminate = true;
} else {
double wt = (1 - epsilon_t) / epsilon_t;
alpha_t = epsilon_t == 0 ? 1 : 0.5 * log(wt);
// Step 3.2: Update weights for next classifier
// Step 3.2.1: Update weights of wrong samples
weights += mask_wrong.to(weights.dtype()) * exp(alpha_t) * weights;
// Step 3.2.2: Update weights of right samples
weights += mask_right.to(weights.dtype()) * exp(-alpha_t) * weights;
// Step 3.3: Normalise the weights
double totalWeights = torch::sum(weights).item<double>();
weights = weights / totalWeights;
}
return {weights, alpha_t, terminate};
}
std::tuple<torch::Tensor &, double, bool> Boost::update_weights_block(int k, torch::Tensor &ytrain,
torch::Tensor &weights) {
/* Update Block algorithm
k = # of models in block
n_models = # of models in ensemble to make predictions
n_models_bak = # models saved
models = vector of models to make predictions
models_bak = models not used to make predictions
significances_bak = backup of significances vector
Case list
A) k = 1, n_models = 1 => n = 0 , n_models = n + k
B) k = 1, n_models = n + 1 => n_models = n + k
C) k > 1, n_models = k + 1 => n= 1, n_models = n + k
D) k > 1, n_models = k => n = 0, n_models = n + k
E) k > 1, n_models = k + n => n_models = n + k
A, D) n=0, k > 0, n_models == k
1. n_models_bak <- n_models
2. significances_bak <- significances
3. significances = vector(k, 1)
4. Dont move any classifiers out of models
5. n_models <- k
6. Make prediction, compute alpha, update weights
7. Dont restore any classifiers to models
8. significances <- significances_bak
9. Update last k significances
10. n_models <- n_models_bak
B, C, E) n > 0, k > 0, n_models == n + k
1. n_models_bak <- n_models
2. significances_bak <- significances
3. significances = vector(k, 1)
4. Move first n classifiers to models_bak
5. n_models <- k
6. Make prediction, compute alpha, update weights
7. Insert classifiers in models_bak to be the first n models
8. significances <- significances_bak
9. Update last k significances
10. n_models <- n_models_bak
*/
//
// Make predict with only the last k models
//
std::unique_ptr<Classifier> model;
std::vector<std::unique_ptr<Classifier>> models_bak;
// 1. n_models_bak <- n_models 2. significances_bak <- significances
auto significance_bak = significanceModels;
auto n_models_bak = n_models;
// 3. significances = vector(k, 1)
significanceModels = std::vector<double>(k, 1.0);
// 4. Move first n classifiers to models_bak
// backup the first n_models - k models (if n_models == k, don't backup any)
for (int i = 0; i < n_models - k; ++i) {
model = std::move(models[0]);
models.erase(models.begin());
models_bak.push_back(std::move(model));
}
assert(models.size() == k);
// 5. n_models <- k
n_models = k;
// 6. Make prediction, compute alpha, update weights
auto ypred = predict(X_train);
//
// Update weights
//
double alpha_t;
bool terminate;
std::tie(weights, alpha_t, terminate) = update_weights(y_train, ypred, weights);
//
// Restore the models if needed
//
// 7. Insert classifiers in models_bak to be the first n models
// if n_models_bak == k, don't restore any, because none of them were moved
if (k != n_models_bak) {
// Insert in the same order as they were extracted
int bak_size = models_bak.size();
for (int i = 0; i < bak_size; ++i) {
model = std::move(models_bak[bak_size - 1 - i]);
models_bak.erase(models_bak.end() - 1);
models.insert(models.begin(), std::move(model));
}
}
// 8. significances <- significances_bak
significanceModels = significance_bak;
//
// Update the significance of the last k models
//
// 9. Update last k significances
for (int i = 0; i < k; ++i) {
significanceModels[n_models_bak - k + i] = alpha_t;
}
// 10. n_models <- n_models_bak
n_models = n_models_bak;
return {weights, alpha_t, terminate};
}
} // namespace bayesnet

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@@ -0,0 +1,57 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef BOOST_H
#define BOOST_H
#include <string>
#include <tuple>
#include <vector>
#include <nlohmann/json.hpp>
#include <torch/torch.h>
#include "Ensemble.h"
#include "bayesnet/feature_selection/FeatureSelect.h"
namespace bayesnet {
const struct {
std::string CFS = "CFS";
std::string FCBF = "FCBF";
std::string IWSS = "IWSS";
}SelectFeatures;
const struct {
std::string ASC = "asc";
std::string DESC = "desc";
std::string RAND = "rand";
}Orders;
class Boost : public Ensemble {
public:
explicit Boost(bool predict_voting = false);
virtual ~Boost() override = default;
void setHyperparameters(const nlohmann::json& hyperparameters_) override;
protected:
std::vector<int> featureSelection(torch::Tensor& weights_);
void buildModel(const torch::Tensor& weights) override;
std::tuple<torch::Tensor&, double, bool> update_weights(torch::Tensor& ytrain, torch::Tensor& ypred, torch::Tensor& weights);
std::tuple<torch::Tensor&, double, bool> update_weights_block(int k, torch::Tensor& ytrain, torch::Tensor& weights);
void add_model(std::unique_ptr<Classifier> model, double significance);
void remove_last_model();
//
// Attributes
//
torch::Tensor X_train, y_train, X_test, y_test;
// Hyperparameters
bool bisection = true; // if true, use bisection stratety to add k models at once to the ensemble
int maxTolerance = 3;
std::string order_algorithm = Orders.DESC; // order to process the KBest features asc, desc, rand
bool convergence = true; //if true, stop when the model does not improve
bool convergence_best = false; // wether to keep the best accuracy to the moment or the last accuracy as prior accuracy
bool selectFeatures = false; // if true, use feature selection
std::string select_features_algorithm; // Selected feature selection algorithm
FeatureSelect* featureSelector = nullptr;
double threshold = -1;
bool block_update = false; // if true, use block update algorithm, only meaningful if bisection is true
bool alpha_block = false; // if true, the alpha is computed with the ensemble built so far and the new model
};
}
#endif

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@@ -0,0 +1,165 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <limits.h>
#include <tuple>
#include <folding.hpp>
#include "BoostA2DE.h"
namespace bayesnet {
BoostA2DE::BoostA2DE(bool predict_voting) : Boost(predict_voting)
{
}
std::vector<int> BoostA2DE::initializeModels(const Smoothing_t smoothing)
{
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
std::vector<int> featuresSelected = featureSelection(weights_);
if (featuresSelected.size() < 2) {
notes.push_back("No features selected in initialization");
status = ERROR;
return std::vector<int>();
}
for (int i = 0; i < featuresSelected.size() - 1; i++) {
for (int j = i + 1; j < featuresSelected.size(); j++) {
auto parents = { featuresSelected[i], featuresSelected[j] };
std::unique_ptr<Classifier> model = std::make_unique<SPnDE>(parents);
model->fit(dataset, features, className, states, weights_, smoothing);
models.push_back(std::move(model));
significanceModels.push_back(1.0); // They will be updated later in trainModel
n_models++;
}
}
notes.push_back("Used features in initialization: " + std::to_string(featuresSelected.size()) + " of " + std::to_string(features.size()) + " with " + select_features_algorithm);
return featuresSelected;
}
void BoostA2DE::trainModel(const torch::Tensor& weights, const Smoothing_t smoothing)
{
//
// Logging setup
//
// loguru::set_thread_name("BoostA2DE");
// loguru::g_stderr_verbosity = loguru::Verbosity_OFF;
// loguru::add_file("boostA2DE.log", loguru::Truncate, loguru::Verbosity_MAX);
// Algorithm based on the adaboost algorithm for classification
// as explained in Ensemble methods (Zhi-Hua Zhou, 2012)
fitted = true;
double alpha_t = 0;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
bool finished = false;
std::vector<int> featuresUsed;
if (selectFeatures) {
featuresUsed = initializeModels(smoothing);
if (featuresUsed.size() == 0) {
return;
}
auto ypred = predict(X_train);
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
// Update significance of the models
for (int i = 0; i < n_models; ++i) {
significanceModels[i] = alpha_t;
}
if (finished) {
return;
}
}
int numItemsPack = 0; // The counter of the models inserted in the current pack
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double improvement = 1.0;
double convergence_threshold = 1e-4;
int tolerance = 0; // number of times the accuracy is lower than the convergence_threshold
// Step 0: Set the finish condition
// epsilon sub t > 0.5 => inverse the weights policy
// validation error is not decreasing
// run out of features
bool ascending = order_algorithm == Orders.ASC;
std::mt19937 g{ 173 };
std::vector<std::pair<int, int>> pairSelection;
while (!finished) {
// Step 1: Build ranking with mutual information
pairSelection = metrics.SelectKPairs(weights_, featuresUsed, ascending, 0); // Get all the pairs sorted
if (order_algorithm == Orders.RAND) {
std::shuffle(pairSelection.begin(), pairSelection.end(), g);
}
int k = bisection ? pow(2, tolerance) : 1;
int counter = 0; // The model counter of the current pack
// VLOG_SCOPE_F(1, "counter=%d k=%d featureSelection.size: %zu", counter, k, featureSelection.size());
while (counter++ < k && pairSelection.size() > 0) {
auto feature_pair = pairSelection[0];
pairSelection.erase(pairSelection.begin());
std::unique_ptr<Classifier> model;
model = std::make_unique<SPnDE>(std::vector<int>({ feature_pair.first, feature_pair.second }));
model->fit(dataset, features, className, states, weights_, smoothing);
alpha_t = 0.0;
if (!block_update) {
auto ypred = model->predict(X_train);
// Step 3.1: Compute the classifier amout of say
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
}
// Step 3.4: Store classifier and its accuracy to weigh its future vote
numItemsPack++;
models.push_back(std::move(model));
significanceModels.push_back(alpha_t);
n_models++;
// VLOG_SCOPE_F(2, "numItemsPack: %d n_models: %d featuresUsed: %zu", numItemsPack, n_models, featuresUsed.size());
}
if (block_update) {
std::tie(weights_, alpha_t, finished) = update_weights_block(k, y_train, weights_);
}
if (convergence && !finished) {
auto y_val_predict = predict(X_test);
double accuracy = (y_val_predict == y_test).sum().item<double>() / (double)y_test.size(0);
if (priorAccuracy == 0) {
priorAccuracy = accuracy;
} else {
improvement = accuracy - priorAccuracy;
}
if (improvement < convergence_threshold) {
// VLOG_SCOPE_F(3, " (improvement<threshold) tolerance: %d numItemsPack: %d improvement: %f prior: %f current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance++;
} else {
// VLOG_SCOPE_F(3, "* (improvement>=threshold) Reset. tolerance: %d numItemsPack: %d improvement: %f prior: %f current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance = 0; // Reset the counter if the model performs better
numItemsPack = 0;
}
if (convergence_best) {
// Keep the best accuracy until now as the prior accuracy
priorAccuracy = std::max(accuracy, priorAccuracy);
} else {
// Keep the last accuray obtained as the prior accuracy
priorAccuracy = accuracy;
}
}
// VLOG_SCOPE_F(1, "tolerance: %d featuresUsed.size: %zu features.size: %zu", tolerance, featuresUsed.size(), features.size());
finished = finished || tolerance > maxTolerance || pairSelection.size() == 0;
}
if (tolerance > maxTolerance) {
if (numItemsPack < n_models) {
notes.push_back("Convergence threshold reached & " + std::to_string(numItemsPack) + " models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & %d models eliminated of %d", numItemsPack, n_models);
for (int i = 0; i < numItemsPack; ++i) {
significanceModels.pop_back();
models.pop_back();
n_models--;
}
} else {
notes.push_back("Convergence threshold reached & 0 models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & 0 models eliminated n_models=%d numItemsPack=%d", n_models, numItemsPack);
}
}
if (pairSelection.size() > 0) {
notes.push_back("Pairs not used in train: " + std::to_string(pairSelection.size()));
status = WARNING;
}
notes.push_back("Number of models: " + std::to_string(n_models));
}
std::vector<std::string> BoostA2DE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}
}

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@@ -0,0 +1,25 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef BOOSTA2DE_H
#define BOOSTA2DE_H
#include <string>
#include <vector>
#include "bayesnet/classifiers/SPnDE.h"
#include "Boost.h"
namespace bayesnet {
class BoostA2DE : public Boost {
public:
explicit BoostA2DE(bool predict_voting = false);
virtual ~BoostA2DE() = default;
std::vector<std::string> graph(const std::string& title = "BoostA2DE") const override;
protected:
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
private:
std::vector<int> initializeModels(const Smoothing_t smoothing);
};
}
#endif

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@@ -0,0 +1,181 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "BoostAODE.h"
#include "bayesnet/classifiers/SPODE.h"
#include <limits.h>
// #include <loguru.cpp>
// #include <loguru.hpp>
#include <random>
#include <set>
#include <tuple>
namespace bayesnet {
BoostAODE::BoostAODE(bool predict_voting) : Boost(predict_voting)
{
}
std::vector<int> BoostAODE::initializeModels(const Smoothing_t smoothing)
{
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
std::vector<int> featuresSelected = featureSelection(weights_);
for (const int& feature : featuresSelected) {
std::unique_ptr<Classifier> model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_, smoothing);
models.push_back(std::move(model));
significanceModels.push_back(1.0); // They will be updated later in trainModel
n_models++;
}
notes.push_back("Used features in initialization: " + std::to_string(featuresSelected.size()) + " of " + std::to_string(features.size()) + " with " + select_features_algorithm);
return featuresSelected;
}
void BoostAODE::trainModel(const torch::Tensor& weights, const Smoothing_t smoothing)
{
//
// Logging setup
//
// loguru::set_thread_name("BoostAODE");
// loguru::g_stderr_verbosity = loguru::Verbosity_OFF;
// loguru::add_file("boostAODE.log", loguru::Truncate, loguru::Verbosity_MAX);
// Algorithm based on the adaboost algorithm for classification
// as explained in Ensemble methods (Zhi-Hua Zhou, 2012)
fitted = true;
double alpha_t = 0;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
bool finished = false;
std::vector<int> featuresUsed;
n_models = 0;
if (selectFeatures) {
featuresUsed = initializeModels(smoothing);
auto ypred = predict(X_train);
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
// Update significance of the models
for (int i = 0; i < n_models; ++i) {
significanceModels.push_back(alpha_t);
}
// VLOG_SCOPE_F(1, "SelectFeatures. alpha_t: %f n_models: %d", alpha_t, n_models);
if (finished) {
return;
}
}
int numItemsPack = 0; // The counter of the models inserted in the current pack
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double improvement = 1.0;
double convergence_threshold = 1e-4;
int tolerance = 0; // number of times the accuracy is lower than the convergence_threshold
// Step 0: Set the finish condition
// epsilon sub t > 0.5 => inverse the weights policy
// validation error is not decreasing
// run out of features
bool ascending = order_algorithm == Orders.ASC;
std::mt19937 g{ 173 };
while (!finished) {
// Step 1: Build ranking with mutual information
auto featureSelection = metrics.SelectKBestWeighted(weights_, ascending, n); // Get all the features sorted
if (order_algorithm == Orders.RAND) {
std::shuffle(featureSelection.begin(), featureSelection.end(), g);
}
// Remove used features
featureSelection.erase(remove_if(begin(featureSelection), end(featureSelection), [&](auto x) { return std::find(begin(featuresUsed), end(featuresUsed), x) != end(featuresUsed); }),
end(featureSelection));
int k = bisection ? pow(2, tolerance) : 1;
int counter = 0; // The model counter of the current pack
// VLOG_SCOPE_F(1, "counter=%d k=%d featureSelection.size: %zu", counter, k, featureSelection.size());
while (counter++ < k && featureSelection.size() > 0) {
auto feature = featureSelection[0];
featureSelection.erase(featureSelection.begin());
std::unique_ptr<Classifier> model;
model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_, smoothing);
alpha_t = 0.0;
if (!block_update) {
torch::Tensor ypred;
if (alpha_block) {
//
// Compute the prediction with the current ensemble + model
//
// Add the model to the ensemble
n_models++;
models.push_back(std::move(model));
significanceModels.push_back(1);
// Compute the prediction
ypred = predict(X_train);
// Remove the model from the ensemble
model = std::move(models.back());
models.pop_back();
significanceModels.pop_back();
n_models--;
} else {
ypred = model->predict(X_train);
}
// Step 3.1: Compute the classifier amout of say
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
}
// Step 3.4: Store classifier and its accuracy to weigh its future vote
numItemsPack++;
featuresUsed.push_back(feature);
models.push_back(std::move(model));
significanceModels.push_back(alpha_t);
n_models++;
// VLOG_SCOPE_F(2, "finished: %d numItemsPack: %d n_models: %d featuresUsed: %zu", finished, numItemsPack, n_models, featuresUsed.size());
}
if (block_update) {
std::tie(weights_, alpha_t, finished) = update_weights_block(k, y_train, weights_);
}
if (convergence && !finished) {
auto y_val_predict = predict(X_test);
double accuracy = (y_val_predict == y_test).sum().item<double>() / (double)y_test.size(0);
if (priorAccuracy == 0) {
priorAccuracy = accuracy;
} else {
improvement = accuracy - priorAccuracy;
}
if (improvement < convergence_threshold) {
// VLOG_SCOPE_F(3, " (improvement<threshold) tolerance: %d numItemsPack: %d improvement: %f prior: %f current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance++;
} else {
// VLOG_SCOPE_F(3, "* (improvement>=threshold) Reset. tolerance: %d numItemsPack: %d improvement: %f prior: %f current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance = 0; // Reset the counter if the model performs better
numItemsPack = 0;
}
if (convergence_best) {
// Keep the best accuracy until now as the prior accuracy
priorAccuracy = std::max(accuracy, priorAccuracy);
} else {
// Keep the last accuray obtained as the prior accuracy
priorAccuracy = accuracy;
}
}
// VLOG_SCOPE_F(1, "tolerance: %d featuresUsed.size: %zu features.size: %zu", tolerance, featuresUsed.size(), features.size());
finished = finished || tolerance > maxTolerance || featuresUsed.size() == features.size();
}
if (tolerance > maxTolerance) {
if (numItemsPack < n_models) {
notes.push_back("Convergence threshold reached & " + std::to_string(numItemsPack) + " models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & %d models eliminated of %d", numItemsPack, n_models);
for (int i = 0; i < numItemsPack; ++i) {
significanceModels.pop_back();
models.pop_back();
n_models--;
}
} else {
notes.push_back("Convergence threshold reached & 0 models eliminated");
// VLG_SCOPE_F(4, "Convergence threshold reached & 0 models eliminated n_models=%d numItemsPack=%d", n_models, numItemsPack);
}
}
if (featuresUsed.size() != features.size()) {
notes.push_back("Used features in train: " + std::to_string(featuresUsed.size()) + " of " + std::to_string(features.size()));
status = WARNING;
}
notes.push_back("Number of models: " + std::to_string(n_models));
}
std::vector<std::string> BoostAODE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}
}

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@@ -0,0 +1,25 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef BOOSTAODE_H
#define BOOSTAODE_H
#include <string>
#include <vector>
#include "Boost.h"
namespace bayesnet {
class BoostAODE : public Boost {
public:
explicit BoostAODE(bool predict_voting = false);
virtual ~BoostAODE() = default;
std::vector<std::string> graph(const std::string& title = "BoostAODE") const override;
protected:
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
private:
std::vector<int> initializeModels(const Smoothing_t smoothing);
};
}
#endif

View File

@@ -1,18 +1,22 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "Ensemble.h"
namespace bayesnet {
Ensemble::Ensemble(bool predict_voting) : Classifier(Network()), n_models(0), predict_voting(predict_voting)
{
};
const std::string ENSEMBLE_NOT_FITTED = "Ensemble has not been fitted";
void Ensemble::trainModel(const torch::Tensor& weights)
void Ensemble::trainModel(const torch::Tensor& weights, const Smoothing_t smoothing)
{
n_models = models.size();
for (auto i = 0; i < n_models; ++i) {
// fit with std::vectors
models[i]->fit(dataset, features, className, states);
models[i]->fit(dataset, features, className, states, smoothing);
}
}
std::vector<int> Ensemble::compute_arg_max(std::vector<std::vector<double>>& X)
@@ -79,17 +83,10 @@ namespace bayesnet {
{
auto n_states = models[0]->getClassNumStates();
torch::Tensor y_pred = torch::zeros({ X.size(1), n_states }, torch::kFloat32);
auto threads{ std::vector<std::thread>() };
std::mutex mtx;
for (auto i = 0; i < n_models; ++i) {
threads.push_back(std::thread([&, i]() {
auto ypredict = models[i]->predict_proba(X);
std::lock_guard<std::mutex> lock(mtx);
y_pred += ypredict * significanceModels[i];
}));
}
for (auto& thread : threads) {
thread.join();
auto ypredict = models[i]->predict_proba(X);
/*std::cout << "model " << i << " prediction: " << ypredict << " significance " << significanceModels[i] << std::endl;*/
y_pred += ypredict * significanceModels[i];
}
auto sum = std::reduce(significanceModels.begin(), significanceModels.end());
y_pred /= sum;
@@ -99,23 +96,15 @@ namespace bayesnet {
{
auto n_states = models[0]->getClassNumStates();
std::vector<std::vector<double>> y_pred(X[0].size(), std::vector<double>(n_states, 0.0));
auto threads{ std::vector<std::thread>() };
std::mutex mtx;
for (auto i = 0; i < n_models; ++i) {
threads.push_back(std::thread([&, i]() {
auto ypredict = models[i]->predict_proba(X);
assert(ypredict.size() == y_pred.size());
assert(ypredict[0].size() == y_pred[0].size());
std::lock_guard<std::mutex> lock(mtx);
// Multiply each prediction by the significance of the model and then add it to the final prediction
for (auto j = 0; j < ypredict.size(); ++j) {
std::transform(y_pred[j].begin(), y_pred[j].end(), ypredict[j].begin(), y_pred[j].begin(),
[significanceModels = significanceModels[i]](double x, double y) { return x + y * significanceModels; });
}
}));
}
for (auto& thread : threads) {
thread.join();
auto ypredict = models[i]->predict_proba(X);
assert(ypredict.size() == y_pred.size());
assert(ypredict[0].size() == y_pred[0].size());
// Multiply each prediction by the significance of the model and then add it to the final prediction
for (auto j = 0; j < ypredict.size(); ++j) {
std::transform(y_pred[j].begin(), y_pred[j].end(), ypredict[j].begin(), y_pred[j].begin(),
[significanceModels = significanceModels[i]](double x, double y) { return x + y * significanceModels; });
}
}
auto sum = std::reduce(significanceModels.begin(), significanceModels.end());
//Divide each element of the prediction by the sum of the significances
@@ -135,17 +124,9 @@ namespace bayesnet {
{
// Build a m x n_models tensor with the predictions of each model
torch::Tensor y_pred = torch::zeros({ X.size(1), n_models }, torch::kInt32);
auto threads{ std::vector<std::thread>() };
std::mutex mtx;
for (auto i = 0; i < n_models; ++i) {
threads.push_back(std::thread([&, i]() {
auto ypredict = models[i]->predict(X);
std::lock_guard<std::mutex> lock(mtx);
y_pred.index_put_({ "...", i }, ypredict);
}));
}
for (auto& thread : threads) {
thread.join();
auto ypredict = models[i]->predict(X);
y_pred.index_put_({ "...", i }, ypredict);
}
return voting(y_pred);
}
@@ -213,4 +194,4 @@ namespace bayesnet {
}
return nstates;
}
}
}

View File

@@ -1,9 +1,15 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef ENSEMBLE_H
#define ENSEMBLE_H
#include <torch/torch.h>
#include "Classifier.h"
#include "BayesMetrics.h"
#include "bayesnetUtils.h"
#include "bayesnet/utils/BayesMetrics.h"
#include "bayesnet/utils/bayesnetUtils.h"
#include "bayesnet/classifiers/Classifier.h"
namespace bayesnet {
class Ensemble : public Classifier {
@@ -25,10 +31,17 @@ namespace bayesnet {
{
return std::vector<std::string>();
}
void dump_cpt() const override
std::string dump_cpt() const override
{
std::string output;
for (auto& model : models) {
output += model->dump_cpt();
output += std::string(80, '-') + "\n";
}
return output;
}
protected:
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
torch::Tensor predict_average_voting(torch::Tensor& X);
std::vector<std::vector<double>> predict_average_voting(std::vector<std::vector<int>>& X);
torch::Tensor predict_average_proba(torch::Tensor& X);
@@ -36,10 +49,10 @@ namespace bayesnet {
torch::Tensor compute_arg_max(torch::Tensor& X);
std::vector<int> compute_arg_max(std::vector<std::vector<double>>& X);
torch::Tensor voting(torch::Tensor& votes);
// Attributes
unsigned n_models;
std::vector<std::unique_ptr<Classifier>> models;
std::vector<double> significanceModels;
void trainModel(const torch::Tensor& weights) override;
bool predict_voting;
};
}

View File

@@ -0,0 +1,168 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2025 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <folding.hpp>
#include <limits.h>
#include "XBA2DE.h"
#include "bayesnet/classifiers/XSP2DE.h"
#include "bayesnet/utils/TensorUtils.h"
namespace bayesnet {
XBA2DE::XBA2DE(bool predict_voting) : Boost(predict_voting) {}
std::vector<int> XBA2DE::initializeModels(const Smoothing_t smoothing) {
torch::Tensor weights_ = torch::full({m}, 1.0 / m, torch::kFloat64);
std::vector<int> featuresSelected = featureSelection(weights_);
if (featuresSelected.size() < 2) {
notes.push_back("No features selected in initialization");
status = ERROR;
return std::vector<int>();
}
for (int i = 0; i < featuresSelected.size() - 1; i++) {
for (int j = i + 1; j < featuresSelected.size(); j++) {
std::unique_ptr<Classifier> model = std::make_unique<XSp2de>(featuresSelected[i], featuresSelected[j]);
model->fit(dataset, features, className, states, weights_, smoothing);
add_model(std::move(model), 1.0);
}
}
notes.push_back("Used features in initialization: " + std::to_string(featuresSelected.size()) + " of " +
std::to_string(features.size()) + " with " + select_features_algorithm);
return featuresSelected;
}
void XBA2DE::trainModel(const torch::Tensor &weights, const Smoothing_t smoothing) {
//
// Logging setup
//
// loguru::set_thread_name("XBA2DE");
// loguru::g_stderr_verbosity = loguru::Verbosity_OFF;
// loguru::add_file("boostA2DE.log", loguru::Truncate, loguru::Verbosity_MAX);
// Algorithm based on the adaboost algorithm for classification
// as explained in Ensemble methods (Zhi-Hua Zhou, 2012)
X_train_ = TensorUtils::to_matrix(X_train);
y_train_ = TensorUtils::to_vector<int>(y_train);
if (convergence) {
X_test_ = TensorUtils::to_matrix(X_test);
y_test_ = TensorUtils::to_vector<int>(y_test);
}
fitted = true;
double alpha_t = 0;
torch::Tensor weights_ = torch::full({m}, 1.0 / m, torch::kFloat64);
bool finished = false;
std::vector<int> featuresUsed;
if (selectFeatures) {
featuresUsed = initializeModels(smoothing);
if (featuresUsed.size() == 0) {
return;
}
auto ypred = predict(X_train);
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
// Update significance of the models
for (int i = 0; i < n_models; ++i) {
significanceModels[i] = alpha_t;
}
if (finished) {
return;
}
}
int numItemsPack = 0; // The counter of the models inserted in the current pack
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double improvement = 1.0;
double convergence_threshold = 1e-4;
int tolerance = 0; // number of times the accuracy is lower than the convergence_threshold
// Step 0: Set the finish condition
// epsilon sub t > 0.5 => inverse the weights policy
// validation error is not decreasing
// run out of features
bool ascending = order_algorithm == Orders.ASC;
std::mt19937 g{173};
std::vector<std::pair<int, int>> pairSelection;
while (!finished) {
// Step 1: Build ranking with mutual information
pairSelection = metrics.SelectKPairs(weights_, featuresUsed, ascending, 0); // Get all the pairs sorted
if (order_algorithm == Orders.RAND) {
std::shuffle(pairSelection.begin(), pairSelection.end(), g);
}
int k = bisection ? pow(2, tolerance) : 1;
int counter = 0; // The model counter of the current pack
// VLOG_SCOPE_F(1, "counter=%d k=%d featureSelection.size: %zu", counter, k, featureSelection.size());
while (counter++ < k && pairSelection.size() > 0) {
auto feature_pair = pairSelection[0];
pairSelection.erase(pairSelection.begin());
std::unique_ptr<Classifier> model;
model = std::make_unique<XSp2de>(feature_pair.first, feature_pair.second);
model->fit(dataset, features, className, states, weights_, smoothing);
alpha_t = 0.0;
if (!block_update) {
auto ypred = model->predict(X_train);
// Step 3.1: Compute the classifier amout of say
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
}
// Step 3.4: Store classifier and its accuracy to weigh its future vote
numItemsPack++;
models.push_back(std::move(model));
significanceModels.push_back(alpha_t);
n_models++;
// VLOG_SCOPE_F(2, "numItemsPack: %d n_models: %d featuresUsed: %zu", numItemsPack, n_models,
// featuresUsed.size());
}
if (block_update) {
std::tie(weights_, alpha_t, finished) = update_weights_block(k, y_train, weights_);
}
if (convergence && !finished) {
auto y_val_predict = predict(X_test);
double accuracy = (y_val_predict == y_test).sum().item<double>() / (double)y_test.size(0);
if (priorAccuracy == 0) {
priorAccuracy = accuracy;
} else {
improvement = accuracy - priorAccuracy;
}
if (improvement < convergence_threshold) {
// VLOG_SCOPE_F(3, " (improvement<threshold) tolerance: %d numItemsPack: %d improvement: %f prior: %f
// current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance++;
} else {
// VLOG_SCOPE_F(3, "* (improvement>=threshold) Reset. tolerance: %d numItemsPack: %d improvement: %f
// prior: %f current: %f", tolerance, numItemsPack, improvement, priorAccuracy, accuracy);
tolerance = 0; // Reset the counter if the model performs better
numItemsPack = 0;
}
if (convergence_best) {
// Keep the best accuracy until now as the prior accuracy
priorAccuracy = std::max(accuracy, priorAccuracy);
} else {
// Keep the last accuray obtained as the prior accuracy
priorAccuracy = accuracy;
}
}
// VLOG_SCOPE_F(1, "tolerance: %d featuresUsed.size: %zu features.size: %zu", tolerance, featuresUsed.size(),
// features.size());
finished = finished || tolerance > maxTolerance || pairSelection.size() == 0;
}
if (tolerance > maxTolerance) {
if (numItemsPack < n_models) {
notes.push_back("Convergence threshold reached & " + std::to_string(numItemsPack) + " models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & %d models eliminated of %d", numItemsPack, n_models);
for (int i = 0; i < numItemsPack; ++i) {
significanceModels.pop_back();
models.pop_back();
n_models--;
}
} else {
notes.push_back("Convergence threshold reached & 0 models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & 0 models eliminated n_models=%d numItemsPack=%d",
// n_models, numItemsPack);
}
}
if (pairSelection.size() > 0) {
notes.push_back("Pairs not used in train: " + std::to_string(pairSelection.size()));
status = WARNING;
}
notes.push_back("Number of models: " + std::to_string(n_models));
}
std::vector<std::string> XBA2DE::graph(const std::string &title) const { return Ensemble::graph(title); }
} // namespace bayesnet

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@@ -0,0 +1,28 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2025 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef XBA2DE_H
#define XBA2DE_H
#include <string>
#include <vector>
#include "Boost.h"
namespace bayesnet {
class XBA2DE : public Boost {
public:
explicit XBA2DE(bool predict_voting = false);
virtual ~XBA2DE() = default;
std::vector<std::string> graph(const std::string& title = "XBA2DE") const override;
std::string getVersion() override { return version; };
protected:
void trainModel(const torch::Tensor& weights, const Smoothing_t smoothing) override;
private:
std::vector<int> initializeModels(const Smoothing_t smoothing);
std::vector<std::vector<int>> X_train_, X_test_;
std::vector<int> y_train_, y_test_;
std::string version = "0.9.7";
};
}
#endif

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@@ -0,0 +1,184 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2025 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "XBAODE.h"
#include "bayesnet/classifiers/XSPODE.h"
#include "bayesnet/utils/TensorUtils.h"
#include <limits.h>
#include <random>
#include <tuple>
namespace bayesnet
{
XBAODE::XBAODE() : Boost(false) {}
std::vector<int> XBAODE::initializeModels(const Smoothing_t smoothing)
{
torch::Tensor weights_ = torch::full({m}, 1.0 / m, torch::kFloat64);
std::vector<int> featuresSelected = featureSelection(weights_);
for (const int &feature : featuresSelected) {
std::unique_ptr<Classifier> model = std::make_unique<XSpode>(feature);
model->fit(dataset, features, className, states, weights_, smoothing);
add_model(std::move(model), 1.0);
}
notes.push_back("Used features in initialization: " + std::to_string(featuresSelected.size()) + " of " +
std::to_string(features.size()) + " with " + select_features_algorithm);
return featuresSelected;
}
void XBAODE::trainModel(const torch::Tensor &weights, const bayesnet::Smoothing_t smoothing)
{
X_train_ = TensorUtils::to_matrix(X_train);
y_train_ = TensorUtils::to_vector<int>(y_train);
if (convergence) {
X_test_ = TensorUtils::to_matrix(X_test);
y_test_ = TensorUtils::to_vector<int>(y_test);
}
fitted = true;
double alpha_t;
torch::Tensor weights_ = torch::full({m}, 1.0 / m, torch::kFloat64);
bool finished = false;
std::vector<int> featuresUsed;
n_models = 0;
if (selectFeatures) {
featuresUsed = initializeModels(smoothing);
auto ypred = predict(X_train_);
auto ypred_t = torch::tensor(ypred);
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred_t, weights_);
// Update significance of the models
for (const int &feature : featuresUsed) {
significanceModels.pop_back();
}
for (const int &feature : featuresUsed) {
significanceModels.push_back(alpha_t);
}
// VLOG_SCOPE_F(1, "SelectFeatures. alpha_t: %f n_models: %d", alpha_t,
// n_models);
if (finished) {
return;
}
}
int numItemsPack = 0; // The counter of the models inserted in the current pack
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double improvement = 1.0;
double convergence_threshold = 1e-4;
int tolerance = 0; // number of times the accuracy is lower than the convergence_threshold
// Step 0: Set the finish condition
// epsilon sub t > 0.5 => inverse the weights_ policy
// validation error is not decreasing
// run out of features
bool ascending = order_algorithm == bayesnet::Orders.ASC;
std::mt19937 g{173};
while (!finished) {
// Step 1: Build ranking with mutual information
auto featureSelection = metrics.SelectKBestWeighted(weights_, ascending, n); // Get all the features sorted
if (order_algorithm == bayesnet::Orders.RAND) {
std::shuffle(featureSelection.begin(), featureSelection.end(), g);
}
// Remove used features
featureSelection.erase(remove_if(featureSelection.begin(), featureSelection.end(),
[&](auto x) {
return std::find(featuresUsed.begin(), featuresUsed.end(), x) !=
featuresUsed.end();
}),
featureSelection.end());
int k = bisection ? pow(2, tolerance) : 1;
int counter = 0; // The model counter of the current pack
// VLOG_SCOPE_F(1, "counter=%d k=%d featureSelection.size: %zu", counter, k,
// featureSelection.size());
while (counter++ < k && featureSelection.size() > 0) {
auto feature = featureSelection[0];
featureSelection.erase(featureSelection.begin());
std::unique_ptr<Classifier> model;
model = std::make_unique<XSpode>(feature);
model->fit(dataset, features, className, states, weights_, smoothing);
/*dynamic_cast<XSpode*>(model.get())->fitx(X_train, y_train, weights_,
* smoothing); // using exclusive XSpode fit method*/
// DEBUG
/*std::cout << dynamic_cast<XSpode*>(model.get())->to_string() <<
* std::endl;*/
// DEBUG
std::vector<int> ypred;
if (alpha_block) {
//
// Compute the prediction with the current ensemble + model
//
// Add the model to the ensemble
add_model(std::move(model), 1.0);
// Compute the prediction
ypred = predict(X_train_);
model = std::move(models.back());
// Remove the model from the ensemble
remove_last_model();
} else {
ypred = model->predict(X_train_);
}
// Step 3.1: Compute the classifier amout of say
auto ypred_t = torch::tensor(ypred);
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred_t, weights_);
// Step 3.4: Store classifier and its accuracy to weigh its future vote
numItemsPack++;
featuresUsed.push_back(feature);
add_model(std::move(model), alpha_t);
// VLOG_SCOPE_F(2, "finished: %d numItemsPack: %d n_models: %d
// featuresUsed: %zu", finished, numItemsPack, n_models,
// featuresUsed.size());
} // End of the pack
if (convergence && !finished) {
auto y_val_predict = predict(X_test);
double accuracy = (y_val_predict == y_test).sum().item<double>() / (double)y_test.size(0);
if (priorAccuracy == 0) {
priorAccuracy = accuracy;
} else {
improvement = accuracy - priorAccuracy;
}
if (improvement < convergence_threshold) {
// VLOG_SCOPE_F(3, " (improvement<threshold) tolerance: %d
// numItemsPack: %d improvement: %f prior: %f current: %f", tolerance,
// numItemsPack, improvement, priorAccuracy, accuracy);
tolerance++;
} else {
// VLOG_SCOPE_F(3, "* (improvement>=threshold) Reset. tolerance: %d
// numItemsPack: %d improvement: %f prior: %f current: %f", tolerance,
// numItemsPack, improvement, priorAccuracy, accuracy);
tolerance = 0; // Reset the counter if the model performs better
numItemsPack = 0;
}
if (convergence_best) {
// Keep the best accuracy until now as the prior accuracy
priorAccuracy = std::max(accuracy, priorAccuracy);
} else {
// Keep the last accuray obtained as the prior accuracy
priorAccuracy = accuracy;
}
}
// VLOG_SCOPE_F(1, "tolerance: %d featuresUsed.size: %zu features.size:
// %zu", tolerance, featuresUsed.size(), features.size());
finished = finished || tolerance > maxTolerance || featuresUsed.size() == features.size();
}
if (tolerance > maxTolerance) {
if (numItemsPack < n_models) {
notes.push_back("Convergence threshold reached & " + std::to_string(numItemsPack) + " models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & %d models eliminated
// of %d", numItemsPack, n_models);
for (int i = featuresUsed.size() - 1; i >= featuresUsed.size() - numItemsPack; --i) {
remove_last_model();
}
// VLOG_SCOPE_F(4, "*Convergence threshold %d models left & %d features
// used.", n_models, featuresUsed.size());
} else {
notes.push_back("Convergence threshold reached & 0 models eliminated");
// VLOG_SCOPE_F(4, "Convergence threshold reached & 0 models eliminated
// n_models=%d numItemsPack=%d", n_models, numItemsPack);
}
}
if (featuresUsed.size() != features.size()) {
notes.push_back("Used features in train: " + std::to_string(featuresUsed.size()) + " of " +
std::to_string(features.size()));
status = bayesnet::WARNING;
}
notes.push_back("Number of models: " + std::to_string(n_models));
return;
}
} // namespace bayesnet

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@@ -0,0 +1,27 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2025 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef XBAODE_H
#define XBAODE_H
#include <vector>
#include <cmath>
#include "Boost.h"
namespace bayesnet {
class XBAODE : public Boost {
public:
XBAODE();
std::string getVersion() override { return version; };
protected:
void trainModel(const torch::Tensor& weights, const bayesnet::Smoothing_t smoothing) override;
private:
std::vector<int> initializeModels(const Smoothing_t smoothing);
std::vector<std::vector<int>> X_train_, X_test_;
std::vector<int> y_train_, y_test_;
std::string version = "0.9.7";
};
}
#endif // XBAODE_H

View File

@@ -1,6 +1,12 @@
#include "CFS.h"
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <limits>
#include "bayesnetUtils.h"
#include "bayesnet/utils/bayesnetUtils.h"
#include "CFS.h"
namespace bayesnet {
void CFS::fit()
{
@@ -11,7 +17,7 @@ namespace bayesnet {
auto feature = featureOrder[0];
selectedFeatures.push_back(feature);
selectedScores.push_back(suLabels[feature]);
selectedFeatures.erase(selectedFeatures.begin());
featureOrder.erase(featureOrder.begin());
while (continueCondition) {
double merit = std::numeric_limits<double>::lowest();
int bestFeature = -1;

View File

@@ -1,8 +1,14 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef CFS_H
#define CFS_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
#include "bayesnet/feature_selection/FeatureSelect.h"
namespace bayesnet {
class CFS : public FeatureSelect {
public:

View File

@@ -1,4 +1,10 @@
#include "bayesnetUtils.h"
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "bayesnet/utils/bayesnetUtils.h"
#include "FCBF.h"
namespace bayesnet {

View File

@@ -1,8 +1,14 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef FCBF_H
#define FCBF_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
#include "bayesnet/feature_selection/FeatureSelect.h"
namespace bayesnet {
class FCBF : public FeatureSelect {
public:

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@@ -0,0 +1,139 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "bayesnet/utils/bayesnetUtils.h"
#include "FeatureSelect.h"
namespace bayesnet {
using namespace torch::indexing; // for Ellipsis constant
//---------------------------------------------------------------------
// ctor
//---------------------------------------------------------------------
FeatureSelect::FeatureSelect(const torch::Tensor& samples,
const std::vector<std::string>& features,
const std::string& className,
int maxFeatures,
int classNumStates,
const torch::Tensor& weights)
: Metrics(samples, features, className, classNumStates),
maxFeatures(maxFeatures == 0 ? samples.size(0) - 1 : maxFeatures),
weights(weights)
{
}
//---------------------------------------------------------------------
// public helpers
//---------------------------------------------------------------------
void FeatureSelect::initialize()
{
selectedFeatures.clear();
selectedScores.clear();
suLabels.clear();
suFeatures.clear();
fitted = false;
}
//---------------------------------------------------------------------
// Symmetrical Uncertainty (SU)
//---------------------------------------------------------------------
double FeatureSelect::symmetricalUncertainty(int a, int b)
{
/*
* Compute symmetrical uncertainty. Normalises the information gain
* (mutual information) with the entropies of the variables to compensate
* the bias due to highcardinality features. Range: [0, 1]
* See: https://www.sciencedirect.com/science/article/pii/S0020025519303603
*/
auto x = samples.index({ a, Ellipsis }); // row a => feature a
auto y = (b >= 0) ? samples.index({ b, Ellipsis }) // row b (>=0) => feature b
: samples.index({ -1, Ellipsis }); // 1 treated as last row = labels
double mu = mutualInformation(x, y, weights);
double hx = entropy(x, weights);
double hy = entropy(y, weights);
const double denom = hx + hy;
if (denom == 0.0) return 0.0; // perfectly pure variables
return 2.0 * mu / denom;
}
//---------------------------------------------------------------------
// SU featureclass
//---------------------------------------------------------------------
void FeatureSelect::computeSuLabels()
{
// Compute Symmetrical Uncertainty between each feature and the class labels
// https://en.wikipedia.org/wiki/Symmetric_uncertainty
const int classIdx = static_cast<int>(samples.size(0)) - 1; // labels in last row
suLabels.reserve(features.size());
for (int i = 0; i < static_cast<int>(features.size()); ++i) {
suLabels.emplace_back(symmetricalUncertainty(i, classIdx));
}
}
//---------------------------------------------------------------------
// SU featurefeature with cache
//---------------------------------------------------------------------
double FeatureSelect::computeSuFeatures(int firstFeature, int secondFeature)
{
// Order the pair to exploit symmetry => only one entry in the map
auto ordered = std::minmax(firstFeature, secondFeature);
const std::pair<int, int> key{ ordered.first, ordered.second };
auto it = suFeatures.find(key);
if (it != suFeatures.end()) return it->second;
double result = symmetricalUncertainty(key.first, key.second);
suFeatures[key] = result; // store once (symmetry handled by ordering)
return result;
}
//---------------------------------------------------------------------
// Correlationbased Feature Selection (CFS) merit
//---------------------------------------------------------------------
double FeatureSelect::computeMeritCFS()
{
const int n = static_cast<int>(selectedFeatures.size());
if (n == 0) return 0.0;
// average r_cf (featureclass)
double rcf_sum = 0.0;
for (int f : selectedFeatures) rcf_sum += suLabels[f];
const double rcf_avg = rcf_sum / n;
// average r_ff (featurefeature)
double rff_sum = 0.0;
const auto& pairs = doCombinations(selectedFeatures); // generates each unordered pair once
for (const auto& p : pairs) rff_sum += computeSuFeatures(p.first, p.second);
const double numPairs = n * (n - 1) * 0.5;
const double rff_avg = (numPairs > 0) ? rff_sum / numPairs : 0.0;
// Merit_S = k * r_cf / sqrt( k + k*(k1) * r_ff ) (Hall, 1999)
const double k = static_cast<double>(n);
return (k * rcf_avg) / std::sqrt(k + k * (k - 1) * rff_avg);
}
//---------------------------------------------------------------------
// getters
//---------------------------------------------------------------------
std::vector<int> FeatureSelect::getFeatures() const
{
if (!fitted) throw std::runtime_error("FeatureSelect not fitted");
return selectedFeatures;
}
std::vector<double> FeatureSelect::getScores() const
{
if (!fitted) throw std::runtime_error("FeatureSelect not fitted");
return selectedScores;
}
}

View File

@@ -1,8 +1,14 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef FEATURE_SELECT_H
#define FEATURE_SELECT_H
#include <torch/torch.h>
#include <vector>
#include "BayesMetrics.h"
#include "bayesnet/utils/BayesMetrics.h"
namespace bayesnet {
class FeatureSelect : public Metrics {
public:

View File

@@ -1,6 +1,12 @@
#include "IWSS.h"
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <limits>
#include "bayesnetUtils.h"
#include "bayesnet/utils/bayesnetUtils.h"
#include "IWSS.h"
namespace bayesnet {
IWSS::IWSS(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights, const double threshold) :
FeatureSelect(samples, features, className, maxFeatures, classNumStates, weights), threshold(threshold)
@@ -20,15 +26,31 @@ namespace bayesnet {
auto first_feature = pop_first(featureOrderCopy);
selectedFeatures.push_back(first_feature);
selectedScores.push_back(suLabels.at(first_feature));
// Second with the score of the candidates
selectedFeatures.push_back(pop_first(featureOrderCopy));
auto merit = computeMeritCFS();
selectedScores.push_back(merit);
// Select second feature that maximizes merit with first
double maxMerit = 0.0;
int secondFeature = -1;
for (const auto& candidate : featureOrderCopy) {
selectedFeatures.push_back(candidate);
double candidateMerit = computeMeritCFS();
if (candidateMerit > maxMerit) {
maxMerit = candidateMerit;
secondFeature = candidate;
}
selectedFeatures.pop_back();
}
if (secondFeature != -1) {
selectedFeatures.push_back(secondFeature);
selectedScores.push_back(maxMerit);
// Remove from featureOrderCopy
featureOrderCopy.erase(std::remove(featureOrderCopy.begin(), featureOrderCopy.end(), secondFeature), featureOrderCopy.end());
}
double merit = maxMerit;
for (const auto feature : featureOrderCopy) {
selectedFeatures.push_back(feature);
// Compute merit with selectedFeatures
auto meritNew = computeMeritCFS();
double delta = merit != 0.0 ? abs(merit - meritNew) / merit : 0.0;
double delta = merit != 0.0 ? std::abs(merit - meritNew) / merit : 0.0;
if (meritNew > merit || delta < threshold) {
if (meritNew > merit) {
merit = meritNew;

View File

@@ -1,7 +1,13 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef IWSS_H
#define IWSS_H
#include <torch/torch.h>
#include <vector>
#include <torch/torch.h>
#include "FeatureSelect.h"
namespace bayesnet {
class IWSS : public FeatureSelect {

View File

@@ -0,0 +1,279 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <algorithm>
#include <cmath>
#include <numeric>
#include "bayesnet/utils/bayesnetUtils.h"
#include "L1FS.h"
namespace bayesnet {
using namespace torch::indexing;
L1FS::L1FS(const torch::Tensor& samples,
const std::vector<std::string>& features,
const std::string& className,
const int maxFeatures,
const int classNumStates,
const torch::Tensor& weights,
const double alpha,
const int maxIter,
const double tolerance,
const bool fitIntercept)
: FeatureSelect(samples, features, className, maxFeatures, classNumStates, weights),
alpha(alpha), maxIter(maxIter), tolerance(tolerance), fitIntercept(fitIntercept)
{
if (alpha < 0) {
throw std::invalid_argument("Alpha (regularization strength) must be non-negative");
}
if (maxIter < 1) {
throw std::invalid_argument("Maximum iterations must be positive");
}
if (tolerance <= 0) {
throw std::invalid_argument("Tolerance must be positive");
}
// Determine if this is a regression or classification task
// For simplicity, assume binary classification if classNumStates == 2
// and regression otherwise (this can be refined based on your needs)
isRegression = (classNumStates > 2 || classNumStates == 0);
}
void L1FS::fit()
{
initialize();
// Prepare data
int n_samples = samples.size(1);
int n_features = features.size();
// Extract features (all rows except last)
auto X = samples.index({ Slice(0, n_features), Slice() }).t().contiguous();
// Extract labels (last row)
auto y = samples.index({ -1, Slice() }).contiguous();
// Convert to float for numerical operations
X = X.to(torch::kFloat32);
y = y.to(torch::kFloat32);
// Normalize features for better convergence
auto X_mean = X.mean(0);
auto X_std = X.std(0);
X_std = torch::where(X_std == 0, torch::ones_like(X_std), X_std);
X = (X - X_mean) / X_std;
if (isRegression) {
// Normalize y for regression
auto y_mean = y.mean();
auto y_std = y.std();
if (y_std.item<double>() > 0) {
y = (y - y_mean) / y_std;
}
fitLasso(X, y, weights);
} else {
// For binary classification
fitL1Logistic(X, y, weights);
}
// Select features based on non-zero coefficients
std::vector<std::pair<int, double>> featureImportance;
for (int i = 0; i < n_features; ++i) {
double coef_magnitude = std::abs(coefficients[i]);
if (coef_magnitude > 1e-10) { // Threshold for numerical zero
featureImportance.push_back({ i, coef_magnitude });
}
}
// If all coefficients are zero (high regularization), select based on original feature-class correlation
if (featureImportance.empty() && maxFeatures > 0) {
// Compute SU with labels as fallback
computeSuLabels();
auto featureOrder = argsort(suLabels);
// Select top features by SU score
int numToSelect = std::min(static_cast<int>(featureOrder.size()),
std::min(maxFeatures, 3)); // At most 3 features as fallback
for (int i = 0; i < numToSelect; ++i) {
selectedFeatures.push_back(featureOrder[i]);
selectedScores.push_back(suLabels[featureOrder[i]]);
}
} else {
// Sort by importance (absolute coefficient value)
std::sort(featureImportance.begin(), featureImportance.end(),
[](const auto& a, const auto& b) { return a.second > b.second; });
// Select top features up to maxFeatures
int numToSelect = std::min(static_cast<int>(featureImportance.size()),
maxFeatures);
for (int i = 0; i < numToSelect; ++i) {
selectedFeatures.push_back(featureImportance[i].first);
selectedScores.push_back(featureImportance[i].second);
}
}
fitted = true;
}
void L1FS::fitLasso(const torch::Tensor& X, const torch::Tensor& y,
const torch::Tensor& sampleWeights)
{
int n_samples = X.size(0);
int n_features = X.size(1);
// Initialize coefficients
coefficients.resize(n_features, 0.0);
double intercept = 0.0;
// Ensure consistent types
torch::Tensor weights = sampleWeights.to(torch::kFloat32);
// Coordinate descent for Lasso
torch::Tensor residuals = y.clone();
if (fitIntercept) {
intercept = (y * weights).sum().item<float>() / weights.sum().item<float>();
residuals = y - intercept;
}
// Precompute feature norms
std::vector<double> featureNorms(n_features);
for (int j = 0; j < n_features; ++j) {
auto Xj = X.index({ Slice(), j });
featureNorms[j] = (Xj * Xj * weights).sum().item<float>();
}
// Coordinate descent iterations
for (int iter = 0; iter < maxIter; ++iter) {
double maxChange = 0.0;
// Update each coordinate
for (int j = 0; j < n_features; ++j) {
auto Xj = X.index({ Slice(), j });
// Compute partial residuals (excluding feature j)
torch::Tensor partialResiduals = residuals + coefficients[j] * Xj;
// Compute rho (correlation with residuals)
double rho = (Xj * partialResiduals * weights).sum().item<float>();
// Soft thresholding
double oldCoef = coefficients[j];
coefficients[j] = softThreshold(rho, alpha) / featureNorms[j];
// Update residuals
residuals = partialResiduals - coefficients[j] * Xj;
maxChange = std::max(maxChange, std::abs(coefficients[j] - oldCoef));
}
// Update intercept if needed
if (fitIntercept) {
double oldIntercept = intercept;
intercept = (residuals * weights).sum().item<float>() /
weights.sum().item<float>();
residuals = residuals - (intercept - oldIntercept);
maxChange = std::max(maxChange, std::abs(intercept - oldIntercept));
}
// Check convergence
if (maxChange < tolerance) {
break;
}
}
}
void L1FS::fitL1Logistic(const torch::Tensor& X, const torch::Tensor& y,
const torch::Tensor& sampleWeights)
{
int n_samples = X.size(0);
int n_features = X.size(1);
// Initialize coefficients
torch::Tensor coef = torch::zeros({ n_features }, torch::kFloat32);
double intercept = 0.0;
// Ensure consistent types
torch::Tensor weights = sampleWeights.to(torch::kFloat32);
// Learning rate (can be adaptive)
double learningRate = 0.01;
// Proximal gradient descent
for (int iter = 0; iter < maxIter; ++iter) {
// Compute predictions
torch::Tensor linearPred = X.matmul(coef);
if (fitIntercept) {
linearPred = linearPred + intercept;
}
torch::Tensor pred = sigmoid(linearPred);
// Compute gradient
torch::Tensor diff = pred - y;
torch::Tensor grad = X.t().matmul(diff * weights) / n_samples;
// Gradient descent step
torch::Tensor coef_new = coef - learningRate * grad;
// Proximal step (soft thresholding)
for (int j = 0; j < n_features; ++j) {
coef_new[j] = softThreshold(coef_new[j].item<float>(),
learningRate * alpha);
}
// Update intercept if needed
if (fitIntercept) {
double grad_intercept = (diff * weights).sum().item<float>() / n_samples;
intercept -= learningRate * grad_intercept;
}
// Check convergence
double change = (coef_new - coef).abs().max().item<float>();
coef = coef_new;
if (change < tolerance) {
break;
}
// Adaptive learning rate (optional)
if (iter % 100 == 0) {
learningRate *= 0.9;
}
}
// Store final coefficients
coefficients.resize(n_features);
for (int j = 0; j < n_features; ++j) {
coefficients[j] = coef[j].item<float>();
}
}
double L1FS::softThreshold(double x, double lambda) const
{
if (x > lambda) {
return x - lambda;
} else if (x < -lambda) {
return x + lambda;
} else {
return 0.0;
}
}
torch::Tensor L1FS::sigmoid(const torch::Tensor& z) const
{
return 1.0 / (1.0 + torch::exp(-z));
}
std::vector<double> L1FS::getCoefficients() const
{
if (!fitted) {
throw std::runtime_error("L1FS not fitted");
}
return coefficients;
}
} // namespace bayesnet

View File

@@ -0,0 +1,83 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2025 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef L1FS_H
#define L1FS_H
#include <torch/torch.h>
#include <vector>
#include "bayesnet/feature_selection/FeatureSelect.h"
namespace bayesnet {
/**
* L1-Regularized Feature Selection (L1FS)
*
* This class implements feature selection using L1-regularized linear models.
* For classification tasks, it uses one-vs-rest logistic regression with L1 penalty.
* For regression tasks, it uses Lasso regression.
*
* The L1 penalty induces sparsity in the model coefficients, effectively
* performing feature selection by setting irrelevant feature weights to zero.
*/
class L1FS : public FeatureSelect {
public:
/**
* Constructor for L1FS
* @param samples n+1xm tensor where samples[-1] is the target variable
* @param features vector of feature names
* @param className name of the class/target variable
* @param maxFeatures maximum number of features to select (0 = all)
* @param classNumStates number of states for classification (ignored for regression)
* @param weights sample weights
* @param alpha L1 regularization strength (higher = more sparsity)
* @param maxIter maximum iterations for optimization
* @param tolerance convergence tolerance
* @param fitIntercept whether to fit an intercept term
*/
L1FS(const torch::Tensor& samples,
const std::vector<std::string>& features,
const std::string& className,
const int maxFeatures,
const int classNumStates,
const torch::Tensor& weights,
const double alpha = 1.0,
const int maxIter = 1000,
const double tolerance = 1e-4,
const bool fitIntercept = true);
virtual ~L1FS() {};
void fit() override;
// Get the learned coefficients for each feature
std::vector<double> getCoefficients() const;
private:
double alpha; // L1 regularization strength
int maxIter; // Maximum iterations for optimization
double tolerance; // Convergence tolerance
bool fitIntercept; // Whether to fit intercept
bool isRegression; // Task type (regression vs classification)
std::vector<double> coefficients; // Learned coefficients
// Coordinate descent for Lasso regression
void fitLasso(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& sampleWeights);
// Proximal gradient descent for L1-regularized logistic regression
void fitL1Logistic(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& sampleWeights);
// Soft thresholding operator for L1 regularization
double softThreshold(double x, double lambda) const;
// Logistic function
torch::Tensor sigmoid(const torch::Tensor& z) const;
// Compute logistic loss
double logisticLoss(const torch::Tensor& X, const torch::Tensor& y,
const torch::Tensor& coef, const torch::Tensor& sampleWeights) const;
};
}
#endif

View File

@@ -1,36 +1,125 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <thread>
#include <mutex>
#include <sstream>
#include <numeric>
#include <algorithm>
#include "Network.h"
#include "bayesnetUtils.h"
#include "bayesnet/utils/bayesnetUtils.h"
#include "bayesnet/utils/CountingSemaphore.h"
#include <pthread.h>
#include <fstream>
namespace bayesnet {
Network::Network() : features(std::vector<std::string>()), className(""), classNumStates(0), fitted(false), laplaceSmoothing(0) {}
Network::Network(float maxT) : features(std::vector<std::string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false), laplaceSmoothing(0) {}
Network::Network(Network& other) : laplaceSmoothing(other.laplaceSmoothing), features(other.features), className(other.className), classNumStates(other.getClassNumStates()), maxThreads(other.
getmaxThreads()), fitted(other.fitted)
Network::Network() : fitted{ false }, classNumStates{ 0 }
{
}
Network::Network(const Network& other)
: features(other.features), className(other.className), classNumStates(other.classNumStates),
fitted(other.fitted)
{
// Deep copy the samples tensor
if (other.samples.defined()) {
samples = other.samples.clone();
}
// First, create all nodes (without relationships)
for (const auto& node : other.nodes) {
nodes[node.first] = std::make_unique<Node>(*node.second);
}
// Second, reconstruct the relationships between nodes
for (const auto& node : other.nodes) {
const std::string& nodeName = node.first;
Node* originalNode = node.second.get();
Node* newNode = nodes[nodeName].get();
// Reconstruct parent relationships
for (Node* parent : originalNode->getParents()) {
const std::string& parentName = parent->getName();
if (nodes.find(parentName) != nodes.end()) {
newNode->addParent(nodes[parentName].get());
}
}
// Reconstruct child relationships
for (Node* child : originalNode->getChildren()) {
const std::string& childName = child->getName();
if (nodes.find(childName) != nodes.end()) {
newNode->addChild(nodes[childName].get());
}
}
}
}
Network& Network::operator=(const Network& other)
{
if (this != &other) {
// Clear existing state
nodes.clear();
features = other.features;
className = other.className;
classNumStates = other.classNumStates;
fitted = other.fitted;
// Deep copy the samples tensor
if (other.samples.defined()) {
samples = other.samples.clone();
} else {
samples = torch::Tensor();
}
// First, create all nodes (without relationships)
for (const auto& node : other.nodes) {
nodes[node.first] = std::make_unique<Node>(*node.second);
}
// Second, reconstruct the relationships between nodes
for (const auto& node : other.nodes) {
const std::string& nodeName = node.first;
Node* originalNode = node.second.get();
Node* newNode = nodes[nodeName].get();
// Reconstruct parent relationships
for (Node* parent : originalNode->getParents()) {
const std::string& parentName = parent->getName();
if (nodes.find(parentName) != nodes.end()) {
newNode->addParent(nodes[parentName].get());
}
}
// Reconstruct child relationships
for (Node* child : originalNode->getChildren()) {
const std::string& childName = child->getName();
if (nodes.find(childName) != nodes.end()) {
newNode->addChild(nodes[childName].get());
}
}
}
}
return *this;
}
void Network::initialize()
{
features = std::vector<std::string>();
features.clear();
className = "";
classNumStates = 0;
fitted = false;
nodes.clear();
samples = torch::Tensor();
}
float Network::getmaxThreads()
{
return maxThreads;
}
torch::Tensor& Network::getSamples()
{
return samples;
}
void Network::addNode(const std::string& name)
{
if (fitted) {
throw std::invalid_argument("Cannot add node to a fitted network. Initialize first.");
}
if (name == "") {
throw std::invalid_argument("Node name cannot be empty");
}
@@ -71,7 +160,7 @@ namespace bayesnet {
for (Node* child : nodes[nodeId]->getChildren()) {
if (visited.find(child->getName()) == visited.end() && isCyclic(child->getName(), visited, recStack))
return true;
else if (recStack.find(child->getName()) != recStack.end())
if (recStack.find(child->getName()) != recStack.end())
return true;
}
}
@@ -80,12 +169,21 @@ namespace bayesnet {
}
void Network::addEdge(const std::string& parent, const std::string& child)
{
if (fitted) {
throw std::invalid_argument("Cannot add edge to a fitted network. Initialize first.");
}
if (nodes.find(parent) == nodes.end()) {
throw std::invalid_argument("Parent node " + parent + " does not exist");
}
if (nodes.find(child) == nodes.end()) {
throw std::invalid_argument("Child node " + child + " does not exist");
}
// Check if the edge is already in the graph
for (auto& node : nodes[parent]->getChildren()) {
if (node->getName() == child) {
throw std::invalid_argument("Edge " + parent + " -> " + child + " already exists");
}
}
// Temporarily add edge to check for cycles
nodes[parent]->addChild(nodes[child].get());
nodes[child]->addParent(nodes[parent].get());
@@ -114,11 +212,14 @@ namespace bayesnet {
if (n_features != featureNames.size()) {
throw std::invalid_argument("X and features must have the same number of features in Network::fit (" + std::to_string(n_features) + " != " + std::to_string(featureNames.size()) + ")");
}
if (features.size() == 0) {
throw std::invalid_argument("The network has not been initialized. You must call addNode() before calling fit()");
}
if (n_features != features.size() - 1) {
throw std::invalid_argument("X and local features must have the same number of features in Network::fit (" + std::to_string(n_features) + " != " + std::to_string(features.size() - 1) + ")");
}
if (find(features.begin(), features.end(), className) == features.end()) {
throw std::invalid_argument("className not found in Network::features");
throw std::invalid_argument("Class Name not found in Network::features");
}
for (auto& feature : featureNames) {
if (find(features.begin(), features.end(), feature) == features.end()) {
@@ -138,7 +239,7 @@ namespace bayesnet {
classNumStates = nodes.at(className)->getNumStates();
}
// X comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
void Network::fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
checkFitData(X.size(1), X.size(0), y.size(0), featureNames, className, states, weights);
this->className = className;
@@ -147,17 +248,17 @@ namespace bayesnet {
for (int i = 0; i < featureNames.size(); ++i) {
auto row_feature = X.index({ i, "..." });
}
completeFit(states, weights);
completeFit(states, weights, smoothing);
}
void Network::fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
void Network::fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
checkFitData(samples.size(1), samples.size(0) - 1, samples.size(1), featureNames, className, states, weights);
this->className = className;
this->samples = samples;
completeFit(states, weights);
completeFit(states, weights, smoothing);
}
// input_data comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights_, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
void Network::fit(const std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights_, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing)
{
const torch::Tensor weights = torch::tensor(weights_, torch::kFloat64);
checkFitData(input_data[0].size(), input_data.size(), labels.size(), featureNames, className, states, weights);
@@ -168,17 +269,43 @@ namespace bayesnet {
samples.index_put_({ i, "..." }, torch::tensor(input_data[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
completeFit(states, weights);
completeFit(states, weights, smoothing);
}
void Network::completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
void Network::completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing)
{
setStates(states);
laplaceSmoothing = 1.0 / samples.size(1); // To use in CPT computation
std::vector<std::thread> threads;
auto& semaphore = CountingSemaphore::getInstance();
const double n_samples = static_cast<double>(samples.size(1));
auto worker = [&](std::pair<const std::string, std::unique_ptr<Node>>& node, int i) {
std::string threadName = "FitWorker-" + std::to_string(i);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
double numStates = static_cast<double>(node.second->getNumStates());
double smoothing_factor;
switch (smoothing) {
case Smoothing_t::ORIGINAL:
smoothing_factor = 1.0 / n_samples;
break;
case Smoothing_t::LAPLACE:
smoothing_factor = 1.0;
break;
case Smoothing_t::CESTNIK:
smoothing_factor = 1 / numStates;
break;
default:
smoothing_factor = 0.0; // No smoothing
}
node.second->computeCPT(samples, features, smoothing_factor, weights);
semaphore.release();
};
int i = 0;
for (auto& node : nodes) {
threads.emplace_back([this, &node, &weights]() {
node.second->computeCPT(samples, features, laplaceSmoothing, weights);
});
semaphore.acquire();
threads.emplace_back(worker, std::ref(node), i++);
}
for (auto& thread : threads) {
thread.join();
@@ -190,14 +317,38 @@ namespace bayesnet {
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict()");
}
// Ensure the sample size is equal to the number of features
if (samples.size(0) != features.size() - 1) {
throw std::invalid_argument("(T) Sample size (" + std::to_string(samples.size(0)) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
torch::Tensor result;
std::vector<std::thread> threads;
std::mutex mtx;
auto& semaphore = CountingSemaphore::getInstance();
result = torch::zeros({ samples.size(1), classNumStates }, torch::kFloat64);
for (int i = 0; i < samples.size(1); ++i) {
const torch::Tensor sample = samples.index({ "...", i });
auto worker = [&](const torch::Tensor& sample, int i) {
std::string threadName = "PredictWorker-" + std::to_string(i);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
auto psample = predict_sample(sample);
auto temp = torch::tensor(psample, torch::kFloat64);
// result.index_put_({ i, "..." }, torch::tensor(predict_sample(sample), torch::kFloat64));
result.index_put_({ i, "..." }, temp);
{
std::lock_guard<std::mutex> lock(mtx);
result.index_put_({ i, "..." }, temp);
}
semaphore.release();
};
for (int i = 0; i < samples.size(1); ++i) {
semaphore.acquire();
const torch::Tensor sample = samples.index({ "...", i });
threads.emplace_back(worker, sample, i);
}
for (auto& thread : threads) {
thread.join();
}
if (proba)
return result;
@@ -222,18 +373,38 @@ namespace bayesnet {
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict()");
}
std::vector<int> predictions;
// Ensure the sample size is equal to the number of features
if (tsamples.size() != features.size() - 1) {
throw std::invalid_argument("(V) Sample size (" + std::to_string(tsamples.size()) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
std::vector<int> predictions(tsamples[0].size(), 0);
std::vector<int> sample;
std::vector<std::thread> threads;
auto& semaphore = CountingSemaphore::getInstance();
auto worker = [&](const std::vector<int>& sample, const int row, int& prediction) {
std::string threadName = "(V)PWorker-" + std::to_string(row);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
auto classProbabilities = predict_sample(sample);
auto maxElem = max_element(classProbabilities.begin(), classProbabilities.end());
int predictedClass = distance(classProbabilities.begin(), maxElem);
prediction = predictedClass;
semaphore.release();
};
for (int row = 0; row < tsamples[0].size(); ++row) {
sample.clear();
for (int col = 0; col < tsamples.size(); ++col) {
sample.push_back(tsamples[col][row]);
}
std::vector<double> classProbabilities = predict_sample(sample);
// Find the class with the maximum posterior probability
auto maxElem = max_element(classProbabilities.begin(), classProbabilities.end());
int predictedClass = distance(classProbabilities.begin(), maxElem);
predictions.push_back(predictedClass);
semaphore.acquire();
threads.emplace_back(worker, sample, row, std::ref(predictions[row]));
}
for (auto& thread : threads) {
thread.join();
}
return predictions;
}
@@ -244,14 +415,36 @@ namespace bayesnet {
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict_proba()");
}
std::vector<std::vector<double>> predictions;
// Ensure the sample size is equal to the number of features
if (tsamples.size() != features.size() - 1) {
throw std::invalid_argument("(V) Sample size (" + std::to_string(tsamples.size()) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
std::vector<std::vector<double>> predictions(tsamples[0].size(), std::vector<double>(classNumStates, 0.0));
std::vector<int> sample;
std::vector<std::thread> threads;
auto& semaphore = CountingSemaphore::getInstance();
auto worker = [&](const std::vector<int>& sample, int row, std::vector<double>& predictions) {
std::string threadName = "(V)PWorker-" + std::to_string(row);
#if defined(__linux__)
pthread_setname_np(pthread_self(), threadName.c_str());
#else
pthread_setname_np(threadName.c_str());
#endif
std::vector<double> classProbabilities = predict_sample(sample);
predictions = classProbabilities;
semaphore.release();
};
for (int row = 0; row < tsamples[0].size(); ++row) {
sample.clear();
for (int col = 0; col < tsamples.size(); ++col) {
sample.push_back(tsamples[col][row]);
}
predictions.push_back(predict_sample(sample));
semaphore.acquire();
threads.emplace_back(worker, sample, row, std::ref(predictions[row]));
}
for (auto& thread : threads) {
thread.join();
}
return predictions;
}
@@ -269,11 +462,6 @@ namespace bayesnet {
// Return 1xn std::vector of probabilities
std::vector<double> Network::predict_sample(const std::vector<int>& sample)
{
// Ensure the sample size is equal to the number of features
if (sample.size() != features.size() - 1) {
throw std::invalid_argument("Sample size (" + std::to_string(sample.size()) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
std::map<std::string, int> evidence;
for (int i = 0; i < sample.size(); ++i) {
evidence[features[i]] = sample[i];
@@ -283,44 +471,26 @@ namespace bayesnet {
// Return 1xn std::vector of probabilities
std::vector<double> Network::predict_sample(const torch::Tensor& sample)
{
// Ensure the sample size is equal to the number of features
if (sample.size(0) != features.size() - 1) {
throw std::invalid_argument("Sample size (" + std::to_string(sample.size(0)) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
std::map<std::string, int> evidence;
for (int i = 0; i < sample.size(0); ++i) {
evidence[features[i]] = sample[i].item<int>();
}
return exactInference(evidence);
}
double Network::computeFactor(std::map<std::string, int>& completeEvidence)
{
double result = 1.0;
for (auto& node : getNodes()) {
result *= node.second->getFactorValue(completeEvidence);
}
return result;
}
std::vector<double> Network::exactInference(std::map<std::string, int>& evidence)
{
std::vector<double> result(classNumStates, 0.0);
std::vector<std::thread> threads;
std::mutex mtx;
auto completeEvidence = std::map<std::string, int>(evidence);
for (int i = 0; i < classNumStates; ++i) {
threads.emplace_back([this, &result, &evidence, i, &mtx]() {
auto completeEvidence = std::map<std::string, int>(evidence);
completeEvidence[getClassName()] = i;
double factor = computeFactor(completeEvidence);
std::lock_guard<std::mutex> lock(mtx);
result[i] = factor;
});
}
for (auto& thread : threads) {
thread.join();
completeEvidence[getClassName()] = i;
double partial = 1.0;
for (auto& node : getNodes()) {
partial *= node.second->getFactorValue(completeEvidence);
}
result[i] = partial;
}
// Normalize result
double sum = accumulate(result.begin(), result.end(), 0.0);
double sum = std::accumulate(result.begin(), result.end(), 0.0);
transform(result.begin(), result.end(), result.begin(), [sum](const double& value) { return value / sum; });
return result;
}
@@ -393,22 +563,57 @@ namespace bayesnet {
result.insert(it2, fatherName);
ending = false;
}
} else {
throw std::logic_error("Error in topological sort because of node " + feature + " is not in result");
}
} else {
throw std::logic_error("Error in topological sort because of node father " + fatherName + " is not in result");
}
}
}
}
return result;
}
void Network::dump_cpt() const
std::string Network::dump_cpt() const
{
std::stringstream oss;
for (auto& node : nodes) {
std::cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << std::endl;
std::cout << node.second->getCPT() << std::endl;
oss << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << std::endl;
oss << node.second->getCPT() << std::endl;
}
return oss.str();
}
bool Network::operator==(const Network& other) const
{
// Compare number of nodes
if (nodes.size() != other.nodes.size()) {
return false;
}
// Compare if all node names exist in both networks
for (const auto& node : nodes) {
if (other.nodes.find(node.first) == other.nodes.end()) {
return false;
}
}
// Compare edges (topology)
auto thisEdges = getEdges();
auto otherEdges = other.getEdges();
// Compare number of edges
if (thisEdges.size() != otherEdges.size()) {
return false;
}
// Sort both edge lists for comparison
std::sort(thisEdges.begin(), thisEdges.end());
std::sort(otherEdges.begin(), otherEdges.end());
// Compare each edge
for (size_t i = 0; i < thisEdges.size(); ++i) {
if (thisEdges[i] != otherEdges[i]) {
return false;
}
}
return true;
}
}

View File

@@ -1,19 +1,26 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef NETWORK_H
#define NETWORK_H
#include "Node.h"
#include <map>
#include <vector>
#include "config.h"
#include "bayesnet/config.h"
#include "Node.h"
#include "Smoothing.h"
namespace bayesnet {
class Network {
public:
Network();
explicit Network(float);
explicit Network(Network&);
Network(const Network& other);
Network& operator=(const Network& other);
~Network() = default;
torch::Tensor& getSamples();
float getmaxThreads();
void addNode(const std::string&);
void addEdge(const std::string&, const std::string&);
std::map<std::string, std::unique_ptr<Node>>& getNodes();
@@ -26,9 +33,9 @@ namespace bayesnet {
/*
Notice: Nodes have to be inserted in the same order as they are in the dataset, i.e., first node is first column and so on.
*/
void fit(const std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
void fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
void fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
void fit(const std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
void fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
void fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const Smoothing_t smoothing);
std::vector<int> predict(const std::vector<std::vector<int>>&); // Return mx1 std::vector of predictions
torch::Tensor predict(const torch::Tensor&); // Return mx1 tensor of predictions
torch::Tensor predict_tensor(const torch::Tensor& samples, const bool proba);
@@ -39,24 +46,22 @@ namespace bayesnet {
std::vector<std::string> show() const;
std::vector<std::string> graph(const std::string& title) const; // Returns a std::vector of std::strings representing the graph in graphviz format
void initialize();
void dump_cpt() const;
std::string dump_cpt() const;
inline std::string version() { return { project_version.begin(), project_version.end() }; }
bool operator==(const Network& other) const;
private:
std::map<std::string, std::unique_ptr<Node>> nodes;
bool fitted;
float maxThreads = 0.95;
int classNumStates;
std::vector<std::string> features; // Including classname
std::string className;
double laplaceSmoothing;
torch::Tensor samples; // nxm tensor used to fit the model
torch::Tensor samples; // n+1xm tensor used to fit the model
bool isCyclic(const std::string&, std::unordered_set<std::string>&, std::unordered_set<std::string>&);
std::vector<double> predict_sample(const std::vector<int>&);
std::vector<double> predict_sample(const torch::Tensor&);
std::vector<double> exactInference(std::map<std::string, int>&);
double computeFactor(std::map<std::string, int>&);
void completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
void checkFitData(int n_features, int n_samples, int n_samples_y, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
void completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing);
void checkFitData(int n_samples, int n_features, int n_samples_y, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
void setStates(const std::map<std::string, std::vector<int>>&);
};
}

197
bayesnet/network/Node.cc Normal file
View File

@@ -0,0 +1,197 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "Node.h"
#include <iterator>
namespace bayesnet {
Node::Node(const std::string& name)
: name(name)
{
}
Node::Node(const Node& other)
: name(other.name), numStates(other.numStates), dimensions(other.dimensions)
{
// Deep copy the CPT tensor
if (other.cpTable.defined()) {
cpTable = other.cpTable.clone();
}
// Note: parent and children pointers are NOT copied here
// They will be reconstructed by the Network copy constructor
// to maintain proper object relationships
}
Node& Node::operator=(const Node& other)
{
if (this != &other) {
name = other.name;
numStates = other.numStates;
dimensions = other.dimensions;
// Deep copy the CPT tensor
if (other.cpTable.defined()) {
cpTable = other.cpTable.clone();
} else {
cpTable = torch::Tensor();
}
// Clear existing relationships
parents.clear();
children.clear();
// Note: parent and children pointers are NOT copied here
// They must be reconstructed to maintain proper object relationships
}
return *this;
}
void Node::clear()
{
parents.clear();
children.clear();
cpTable = torch::Tensor();
dimensions.clear();
numStates = 0;
}
std::string Node::getName() const
{
return name;
}
void Node::addParent(Node* parent)
{
parents.push_back(parent);
}
void Node::removeParent(Node* parent)
{
parents.erase(std::remove(parents.begin(), parents.end(), parent), parents.end());
}
void Node::removeChild(Node* child)
{
children.erase(std::remove(children.begin(), children.end(), child), children.end());
}
void Node::addChild(Node* child)
{
children.push_back(child);
}
std::vector<Node*>& Node::getParents()
{
return parents;
}
std::vector<Node*>& Node::getChildren()
{
return children;
}
int Node::getNumStates() const
{
return numStates;
}
void Node::setNumStates(int numStates)
{
this->numStates = numStates;
}
torch::Tensor& Node::getCPT()
{
return cpTable;
}
/*
The MinFill criterion is a heuristic for variable elimination.
The variable that minimizes the number of edges that need to be added to the graph to make it triangulated.
This is done by counting the number of edges that need to be added to the graph if the variable is eliminated.
The variable with the minimum number of edges is chosen.
Here this is done computing the length of the combinations of the node neighbors taken 2 by 2.
*/
unsigned Node::minFill()
{
std::unordered_set<std::string> neighbors;
for (auto child : children) {
neighbors.emplace(child->getName());
}
for (auto parent : parents) {
neighbors.emplace(parent->getName());
}
auto source = std::vector<std::string>(neighbors.begin(), neighbors.end());
return combinations(source).size();
}
std::vector<std::pair<std::string, std::string>> Node::combinations(const std::vector<std::string>& source)
{
std::vector<std::pair<std::string, std::string>> result;
for (int i = 0; i < source.size(); ++i) {
std::string temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
}
}
return result;
}
void Node::computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double smoothing, const torch::Tensor& weights)
{
dimensions.clear();
dimensions.reserve(parents.size() + 1);
dimensions.push_back(numStates);
for (const auto& parent : parents) {
dimensions.push_back(parent->getNumStates());
}
cpTable = torch::full(dimensions, smoothing, torch::kDouble);
// Build feature index map
std::unordered_map<std::string, int> featureIndexMap;
for (size_t i = 0; i < features.size(); ++i) {
featureIndexMap[features[i]] = i;
}
// Gather indices for node and parents
std::vector<int64_t> all_indices;
all_indices.push_back(featureIndexMap[name]);
for (const auto& parent : parents) {
all_indices.push_back(featureIndexMap[parent->getName()]);
}
// Extract relevant columns: shape (num_features, num_samples)
auto indices_tensor = dataset.index_select(0, torch::tensor(all_indices, torch::kLong));
indices_tensor = indices_tensor.transpose(0, 1).to(torch::kLong); // (num_samples, num_features)
// Manual flattening of indices
std::vector<int64_t> strides(all_indices.size(), 1);
for (int i = strides.size() - 2; i >= 0; --i) {
strides[i] = strides[i + 1] * cpTable.size(i + 1);
}
auto indices_tensor_cpu = indices_tensor.cpu();
auto indices_accessor = indices_tensor_cpu.accessor<int64_t, 2>();
std::vector<int64_t> flat_indices(indices_tensor.size(0));
for (int64_t i = 0; i < indices_tensor.size(0); ++i) {
int64_t idx = 0;
for (size_t j = 0; j < strides.size(); ++j) {
idx += indices_accessor[i][j] * strides[j];
}
flat_indices[i] = idx;
}
// Accumulate weights into flat CPT
auto flat_cpt = cpTable.flatten();
auto flat_indices_tensor = torch::from_blob(flat_indices.data(), { (int64_t)flat_indices.size() }, torch::kLong).clone();
flat_cpt.index_add_(0, flat_indices_tensor, weights.cpu());
cpTable = flat_cpt.view(cpTable.sizes());
// Normalize the counts (dividing each row by the sum of the row)
cpTable /= cpTable.sum(0, true);
}
double Node::getFactorValue(std::map<std::string, int>& evidence)
{
c10::List<c10::optional<at::Tensor>> coordinates;
// following predetermined order of indices in the cpTable (see Node.h)
coordinates.push_back(at::tensor(evidence[name]));
transform(parents.begin(), parents.end(), std::back_inserter(coordinates), [&evidence](const auto& parent) { return at::tensor(evidence[parent->getName()]); });
return cpTable.index({ coordinates }).item<double>();
}
std::vector<std::string> Node::graph(const std::string& className)
{
auto output = std::vector<std::string>();
auto suffix = name == className ? ", fontcolor=red, fillcolor=lightblue, style=filled " : "";
output.push_back("\"" + name + "\" [shape=circle" + suffix + "] \n");
transform(children.begin(), children.end(), back_inserter(output), [this](const auto& child) { return "\"" + name + "\" -> \"" + child->getName() + "\""; });
return output;
}
}

View File

@@ -1,21 +1,22 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef NODE_H
#define NODE_H
#include <torch/torch.h>
#include <unordered_set>
#include <vector>
#include <string>
#include <torch/torch.h>
namespace bayesnet {
class Node {
private:
std::string name;
std::vector<Node*> parents;
std::vector<Node*> children;
int numStates; // number of states of the variable
torch::Tensor cpTable; // Order of indices is 0-> node variable, 1-> 1st parent, 2-> 2nd parent, ...
std::vector<int64_t> dimensions; // dimensions of the cpTable
std::vector<std::pair<std::string, std::string>> combinations(const std::vector<std::string>&);
public:
explicit Node(const std::string&);
Node(const Node& other);
Node& operator=(const Node& other);
~Node() = default;
void clear();
void addParent(Node*);
void addChild(Node*);
@@ -25,12 +26,20 @@ namespace bayesnet {
std::vector<Node*>& getParents();
std::vector<Node*>& getChildren();
torch::Tensor& getCPT();
void computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double laplaceSmoothing, const torch::Tensor& weights);
void computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double smoothing, const torch::Tensor& weights);
int getNumStates() const;
void setNumStates(int);
unsigned minFill();
std::vector<std::string> graph(const std::string& clasName); // Returns a std::vector of std::strings representing the graph in graphviz format
float getFactorValue(std::map<std::string, int>&);
double getFactorValue(std::map<std::string, int>&);
private:
std::string name;
std::vector<Node*> parents;
std::vector<Node*> children;
int numStates = 0; // number of states of the variable
torch::Tensor cpTable; // Order of indices is 0-> node variable, 1-> 1st parent, 2-> 2nd parent, ...
std::vector<int64_t> dimensions; // dimensions of the cpTable
std::vector<std::pair<std::string, std::string>> combinations(const std::vector<std::string>&);
};
}
#endif

View File

@@ -0,0 +1,17 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef SMOOTHING_H
#define SMOOTHING_H
namespace bayesnet {
enum class Smoothing_t {
NONE = -1,
ORIGINAL = 0,
LAPLACE,
CESTNIK
};
}
#endif // SMOOTHING_H

View File

@@ -1,30 +1,86 @@
#include "BayesMetrics.h"
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <map>
#include <unordered_map>
#include <tuple>
#include "Mst.h"
#include "BayesMetrics.h"
namespace bayesnet {
//samples is n+1xm tensor used to fit the model
Metrics::Metrics(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int classNumStates)
: samples(samples)
, features(features)
, className(className)
, features(features)
, classNumStates(classNumStates)
{
}
//samples is nxm std::vector used to fit the model
//samples is n+1xm std::vector used to fit the model
Metrics::Metrics(const std::vector<std::vector<int>>& vsamples, const std::vector<int>& labels, const std::vector<std::string>& features, const std::string& className, const int classNumStates)
: features(features)
: samples(torch::zeros({ static_cast<int>(vsamples.size() + 1), static_cast<int>(vsamples[0].size()) }, torch::kInt32))
, className(className)
, features(features)
, classNumStates(classNumStates)
, samples(torch::zeros({ static_cast<int>(vsamples[0].size()), static_cast<int>(vsamples.size() + 1) }, torch::kInt32))
{
for (int i = 0; i < vsamples.size(); ++i) {
samples.index_put_({ i, "..." }, torch::tensor(vsamples[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
}
std::vector<std::pair<int, int>> Metrics::SelectKPairs(const torch::Tensor& weights, std::vector<int>& featuresExcluded, bool ascending, unsigned k)
{
// Return the K Best features
auto n = features.size();
// compute scores
scoresKPairs.clear();
pairsKBest.clear();
auto labels = samples.index({ -1, "..." });
for (int i = 0; i < n - 1; ++i) {
if (std::find(featuresExcluded.begin(), featuresExcluded.end(), i) != featuresExcluded.end()) {
continue;
}
for (int j = i + 1; j < n; ++j) {
if (std::find(featuresExcluded.begin(), featuresExcluded.end(), j) != featuresExcluded.end()) {
continue;
}
auto key = std::make_pair(i, j);
auto value = conditionalMutualInformation(samples.index({ i, "..." }), samples.index({ j, "..." }), labels, weights);
scoresKPairs.push_back({ key, value });
}
}
// sort scores
if (ascending) {
sort(scoresKPairs.begin(), scoresKPairs.end(), [](auto& a, auto& b)
{ return a.second < b.second; });
} else {
sort(scoresKPairs.begin(), scoresKPairs.end(), [](auto& a, auto& b)
{ return a.second > b.second; });
}
for (auto& [pairs, score] : scoresKPairs) {
pairsKBest.push_back(pairs);
}
if (k != 0 && k < pairsKBest.size()) {
if (ascending) {
int limit = pairsKBest.size() - k;
for (int i = 0; i < limit; i++) {
pairsKBest.erase(pairsKBest.begin());
scoresKPairs.erase(scoresKPairs.begin());
}
} else {
pairsKBest.resize(k);
scoresKPairs.resize(k);
}
}
return pairsKBest;
}
std::vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, bool ascending, unsigned k)
{
// Return the K Best features
auto n = samples.size(0) - 1;
auto n = features.size();
if (k == 0) {
k = n;
}
@@ -60,7 +116,10 @@ namespace bayesnet {
{
return scoresKBest;
}
std::vector<std::pair<std::pair<int, int>, double>> Metrics::getScoresKPairs() const
{
return scoresKPairs;
}
torch::Tensor Metrics::conditionalEdge(const torch::Tensor& weights)
{
auto result = std::vector<double>();
@@ -99,14 +158,8 @@ namespace bayesnet {
}
return matrix;
}
// To use in Python
std::vector<float> Metrics::conditionalEdgeWeights(std::vector<float>& weights_)
{
const torch::Tensor weights = torch::tensor(weights_);
auto matrix = conditionalEdge(weights);
std::vector<float> v(matrix.data_ptr<float>(), matrix.data_ptr<float>() + matrix.numel());
return v;
}
// Measured in nats (natural logarithm (log) base e)
// Elements of Information Theory, 2nd Edition, Thomas M. Cover, Joy A. Thomas p. 14
double Metrics::entropy(const torch::Tensor& feature, const torch::Tensor& weights)
{
torch::Tensor counts = feature.bincount(weights);
@@ -145,10 +198,54 @@ namespace bayesnet {
}
return entropyValue;
}
// I(X;Y) = H(Y) - H(Y|X)
// H(X|Y,C) = sum_{y in Y, c in C} p(x,c) H(X|Y=y,C=c)
double Metrics::conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& labels, const torch::Tensor& weights)
{
// Ensure the tensors are of the same length
assert(firstFeature.size(0) == secondFeature.size(0) && firstFeature.size(0) == labels.size(0) && firstFeature.size(0) == weights.size(0));
// Convert tensors to vectors for easier processing
auto firstFeatureData = firstFeature.accessor<int, 1>();
auto secondFeatureData = secondFeature.accessor<int, 1>();
auto labelsData = labels.accessor<int, 1>();
auto weightsData = weights.accessor<double, 1>();
int numSamples = firstFeature.size(0);
// Maps for joint and marginal probabilities
std::map<std::tuple<int, int, int>, double> jointCount;
std::map<std::tuple<int, int>, double> marginalCount;
// Compute joint and marginal counts
for (int i = 0; i < numSamples; ++i) {
auto keyJoint = std::make_tuple(firstFeatureData[i], labelsData[i], secondFeatureData[i]);
auto keyMarginal = std::make_tuple(firstFeatureData[i], labelsData[i]);
jointCount[keyJoint] += weightsData[i];
marginalCount[keyMarginal] += weightsData[i];
}
// Total weight sum
double totalWeight = torch::sum(weights).item<double>();
if (totalWeight == 0)
return 0;
// Compute the conditional entropy
double conditionalEntropy = 0.0;
for (const auto& [keyJoint, jointFreq] : jointCount) {
auto [x, c, y] = keyJoint;
auto keyMarginal = std::make_tuple(x, c);
//double p_xc = marginalCount[keyMarginal] / totalWeight;
double p_y_given_xc = jointFreq / marginalCount[keyMarginal];
if (p_y_given_xc > 0) {
conditionalEntropy -= (jointFreq / totalWeight) * std::log(p_y_given_xc);
}
}
return conditionalEntropy;
}
// I(X;Y) = H(Y) - H(Y|X) ; I(X;Y) >= 0
double Metrics::mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights)
{
return entropy(firstFeature, weights) - conditionalEntropy(firstFeature, secondFeature, weights);
return std::max(entropy(firstFeature, weights) - conditionalEntropy(firstFeature, secondFeature, weights), 0.0);
}
// I(X;Y|C) = H(X|C) - H(X|Y,C) >= 0
double Metrics::conditionalMutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& labels, const torch::Tensor& weights)
{
return std::max(conditionalEntropy(firstFeature, labels, weights) - conditionalEntropy(firstFeature, secondFeature, labels, weights), 0.0);
}
/*
Compute the maximum spanning tree considering the weights as distances

View File

@@ -1,25 +1,41 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef BAYESNET_METRICS_H
#define BAYESNET_METRICS_H
#include <torch/torch.h>
#include <vector>
#include <string>
#include <torch/torch.h>
namespace bayesnet {
class Metrics {
private:
int classNumStates = 0;
std::vector<double> scoresKBest;
std::vector<int> featuresKBest; // sorted indices of the features
double conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
public:
Metrics() = default;
Metrics(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
Metrics(const std::vector<std::vector<int>>& vsamples, const std::vector<int>& labels, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
std::vector<int> SelectKBestWeighted(const torch::Tensor& weights, bool ascending = false, unsigned k = 0);
std::vector<std::pair<int, int>> SelectKPairs(const torch::Tensor& weights, std::vector<int>& featuresExcluded, bool ascending = false, unsigned k = 0);
std::vector<double> getScoresKBest() const;
std::vector<std::pair<std::pair<int, int>, double>> getScoresKPairs() const;
double mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
double conditionalMutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& labels, const torch::Tensor& weights);
torch::Tensor conditionalEdge(const torch::Tensor& weights);
std::vector<std::pair<int, int>> maximumSpanningTree(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
// Measured in nats (natural logarithm (log) base e)
// Elements of Information Theory, 2nd Edition, Thomas M. Cover, Joy A. Thomas p. 14
double entropy(const torch::Tensor& feature, const torch::Tensor& weights);
double conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& labels, const torch::Tensor& weights);
protected:
torch::Tensor samples; // n+1xm torch::Tensor used to fit the model where samples[-1] is the y std::vector
std::string className;
double entropy(const torch::Tensor& feature, const torch::Tensor& weights);
std::vector<std::string> features;
template <class T>
std::vector<std::pair<T, T>> doCombinations(const std::vector<T>& source)
{
std::vector<std::pair<T, T>> result;
for (int i = 0; i < source.size(); ++i) {
for (int i = 0; i < source.size() - 1; ++i) {
T temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
@@ -34,16 +50,13 @@ namespace bayesnet {
v.erase(v.begin());
return temp;
}
public:
Metrics() = default;
Metrics(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
Metrics(const std::vector<std::vector<int>>& vsamples, const std::vector<int>& labels, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
std::vector<int> SelectKBestWeighted(const torch::Tensor& weights, bool ascending = false, unsigned k = 0);
std::vector<double> getScoresKBest() const;
double mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
std::vector<float> conditionalEdgeWeights(std::vector<float>& weights); // To use in Python
torch::Tensor conditionalEdge(const torch::Tensor& weights);
std::vector<std::pair<int, int>> maximumSpanningTree(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
private:
int classNumStates = 0;
std::vector<double> scoresKBest;
std::vector<int> featuresKBest; // sorted indices of the features
std::vector<std::pair<int, int>> pairsKBest; // sorted indices of the pairs
std::vector<std::pair<std::pair<int, int>, double>> scoresKPairs;
double conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
};
}
#endif

View File

@@ -0,0 +1,51 @@
#ifndef COUNTING_SEMAPHORE_H
#define COUNTING_SEMAPHORE_H
#include <mutex>
#include <condition_variable>
#include <algorithm>
#include <thread>
class CountingSemaphore {
public:
static CountingSemaphore& getInstance()
{
static CountingSemaphore instance;
return instance;
}
// Delete copy constructor and assignment operator
CountingSemaphore(const CountingSemaphore&) = delete;
CountingSemaphore& operator=(const CountingSemaphore&) = delete;
void acquire()
{
std::unique_lock<std::mutex> lock(mtx_);
cv_.wait(lock, [this]() { return count_ > 0; });
--count_;
}
void release()
{
std::lock_guard<std::mutex> lock(mtx_);
++count_;
if (count_ <= max_count_) {
cv_.notify_one();
}
}
uint getCount() const
{
return count_;
}
uint getMaxCount() const
{
return max_count_;
}
private:
CountingSemaphore()
: max_count_(std::max(1u, static_cast<uint>(0.95 * std::thread::hardware_concurrency()))),
count_(max_count_)
{
}
std::mutex mtx_;
std::condition_variable cv_;
const uint max_count_;
uint count_;
};
#endif

View File

@@ -1,6 +1,13 @@
#include "Mst.h"
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include <sstream>
#include <vector>
#include <list>
#include "Mst.h"
/*
Based on the code from https://www.softwaretestinghelp.com/minimum-spanning-tree-tutorial/
@@ -45,24 +52,15 @@ namespace bayesnet {
}
}
}
void Graph::display_mst()
{
std::cout << "Edge :" << " Weight" << std::endl;
for (int i = 0; i < T.size(); i++) {
std::cout << T[i].second.first << " - " << T[i].second.second << " : "
<< T[i].first;
std::cout << std::endl;
}
}
void insertElement(std::list<int>& variables, int variable)
void MST::insertElement(std::list<int>& variables, int variable)
{
if (std::find(variables.begin(), variables.end(), variable) == variables.end()) {
variables.push_front(variable);
}
}
std::vector<std::pair<int, int>> reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original)
std::vector<std::pair<int, int>> MST::reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original)
{
// Create the edges of a DAG from the MST
// replacing unordered_set with list because unordered_set cannot guarantee the order of the elements inserted

View File

@@ -1,33 +1,40 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef MST_H
#define MST_H
#include <torch/torch.h>
#include <vector>
#include <string>
#include <torch/torch.h>
namespace bayesnet {
class MST {
public:
MST() = default;
MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
void insertElement(std::list<int>& variables, int variable);
std::vector<std::pair<int, int>> reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original);
std::vector<std::pair<int, int>> maximumSpanningTree();
private:
torch::Tensor weights;
std::vector<std::string> features;
int root = 0;
public:
MST() = default;
MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
std::vector<std::pair<int, int>> maximumSpanningTree();
};
class Graph {
private:
int V; // number of nodes in graph
std::vector <std::pair<float, std::pair<int, int>>> G; // std::vector for graph
std::vector <std::pair<float, std::pair<int, int>>> T; // std::vector for mst
std::vector<int> parent;
public:
explicit Graph(int V);
void addEdge(int u, int v, float wt);
int find_set(int i);
void union_set(int u, int v);
void kruskal_algorithm();
void display_mst();
std::vector <std::pair<float, std::pair<int, int>>> get_mst() { return T; }
private:
int V; // number of nodes in graph
std::vector <std::pair<float, std::pair<int, int>>> G; // std::vector for graph
std::vector <std::pair<float, std::pair<int, int>>> T; // std::vector for mst
std::vector<int> parent;
};
}
#endif

View File

@@ -0,0 +1,51 @@
#ifndef TENSORUTILS_H
#define TENSORUTILS_H
#include <torch/torch.h>
#include <vector>
namespace bayesnet {
class TensorUtils {
public:
static std::vector<std::vector<int>> to_matrix(const torch::Tensor& X)
{
// Ensure tensor is contiguous in memory
auto X_contig = X.contiguous();
// Access tensor data pointer directly
auto data_ptr = X_contig.data_ptr<int>();
// IF you are using int64_t as the data type, use the following line
//auto data_ptr = X_contig.data_ptr<int64_t>();
//std::vector<std::vector<int64_t>> data(X.size(0), std::vector<int64_t>(X.size(1)));
// Prepare output container
std::vector<std::vector<int>> data(X.size(0), std::vector<int>(X.size(1)));
// Fill the 2D vector in a single loop using pointer arithmetic
int rows = X.size(0);
int cols = X.size(1);
for (int i = 0; i < rows; ++i) {
std::copy(data_ptr + i * cols, data_ptr + (i + 1) * cols, data[i].begin());
}
return data;
}
template <typename T>
static std::vector<T> to_vector(const torch::Tensor& y)
{
// Ensure the tensor is contiguous in memory
auto y_contig = y.contiguous();
// Access data pointer
auto data_ptr = y_contig.data_ptr<T>();
// Prepare output container
std::vector<T> data(y.size(0));
// Copy data efficiently
std::copy(data_ptr, data_ptr + y.size(0), data.begin());
return data;
}
};
}
#endif // TENSORUTILS_H

View File

@@ -1,3 +1,9 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#include "bayesnetUtils.h"
namespace bayesnet {
@@ -10,18 +16,6 @@ namespace bayesnet {
sort(indices.begin(), indices.end(), [&nums](int i, int j) {return nums[i] > nums[j];});
return indices;
}
std::vector<std::vector<int>> tensorToVector(torch::Tensor& dtensor)
{
// convert mxn tensor to nxm std::vector
std::vector<std::vector<int>> result;
// Iterate over cols
for (int i = 0; i < dtensor.size(1); ++i) {
auto col_tensor = dtensor.index({ "...", i });
auto col = std::vector<int>(col_tensor.data_ptr<int>(), col_tensor.data_ptr<int>() + dtensor.size(0));
result.push_back(col);
}
return result;
}
std::vector<std::vector<double>> tensorToVectorDouble(torch::Tensor& dtensor)
{
// convert mxn tensor to mxn std::vector

View File

@@ -1,10 +1,15 @@
// ***************************************************************
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
// SPDX-FileType: SOURCE
// SPDX-License-Identifier: MIT
// ***************************************************************
#ifndef BAYESNET_UTILS_H
#define BAYESNET_UTILS_H
#include <torch/torch.h>
#include <vector>
#include <torch/torch.h>
namespace bayesnet {
std::vector<int> argsort(std::vector<double>& nums);
std::vector<std::vector<int>> tensorToVector(torch::Tensor& dtensor);
std::vector<std::vector<double>> tensorToVectorDouble(torch::Tensor& dtensor);
torch::Tensor vectorToTensor(std::vector<std::vector<int>>& vector, bool transpose = true);
}

4
bayesnetConfig.cmake.in Normal file
View File

@@ -0,0 +1,4 @@
@PACKAGE_INIT@
include("${CMAKE_CURRENT_LIST_DIR}/bayesnetTargets.cmake")

View File

@@ -1,12 +0,0 @@
function(add_git_submodule dir)
find_package(Git REQUIRED)
if(NOT EXISTS ${dir}/CMakeLists.txt)
message(STATUS "🚨 Adding git submodule => ${dir}")
execute_process(COMMAND ${GIT_EXECUTABLE}
submodule update --init --recursive -- ${dir}
WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
endif()
add_subdirectory(${dir})
endfunction(add_git_submodule)

View File

@@ -1,742 +0,0 @@
# Copyright (c) 2012 - 2017, Lars Bilke
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification,
# are permitted provided that the following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this
# list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice,
# this list of conditions and the following disclaimer in the documentation
# and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors
# may be used to endorse or promote products derived from this software without
# specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
# CHANGES:
#
# 2012-01-31, Lars Bilke
# - Enable Code Coverage
#
# 2013-09-17, Joakim Söderberg
# - Added support for Clang.
# - Some additional usage instructions.
#
# 2016-02-03, Lars Bilke
# - Refactored functions to use named parameters
#
# 2017-06-02, Lars Bilke
# - Merged with modified version from github.com/ufz/ogs
#
# 2019-05-06, Anatolii Kurotych
# - Remove unnecessary --coverage flag
#
# 2019-12-13, FeRD (Frank Dana)
# - Deprecate COVERAGE_LCOVR_EXCLUDES and COVERAGE_GCOVR_EXCLUDES lists in favor
# of tool-agnostic COVERAGE_EXCLUDES variable, or EXCLUDE setup arguments.
# - CMake 3.4+: All excludes can be specified relative to BASE_DIRECTORY
# - All setup functions: accept BASE_DIRECTORY, EXCLUDE list
# - Set lcov basedir with -b argument
# - Add automatic --demangle-cpp in lcovr, if 'c++filt' is available (can be
# overridden with NO_DEMANGLE option in setup_target_for_coverage_lcovr().)
# - Delete output dir, .info file on 'make clean'
# - Remove Python detection, since version mismatches will break gcovr
# - Minor cleanup (lowercase function names, update examples...)
#
# 2019-12-19, FeRD (Frank Dana)
# - Rename Lcov outputs, make filtered file canonical, fix cleanup for targets
#
# 2020-01-19, Bob Apthorpe
# - Added gfortran support
#
# 2020-02-17, FeRD (Frank Dana)
# - Make all add_custom_target()s VERBATIM to auto-escape wildcard characters
# in EXCLUDEs, and remove manual escaping from gcovr targets
#
# 2021-01-19, Robin Mueller
# - Add CODE_COVERAGE_VERBOSE option which will allow to print out commands which are run
# - Added the option for users to set the GCOVR_ADDITIONAL_ARGS variable to supply additional
# flags to the gcovr command
#
# 2020-05-04, Mihchael Davis
# - Add -fprofile-abs-path to make gcno files contain absolute paths
# - Fix BASE_DIRECTORY not working when defined
# - Change BYPRODUCT from folder to index.html to stop ninja from complaining about double defines
#
# 2021-05-10, Martin Stump
# - Check if the generator is multi-config before warning about non-Debug builds
#
# 2022-02-22, Marko Wehle
# - Change gcovr output from -o <filename> for --xml <filename> and --html <filename> output respectively.
# This will allow for Multiple Output Formats at the same time by making use of GCOVR_ADDITIONAL_ARGS, e.g. GCOVR_ADDITIONAL_ARGS "--txt".
#
# 2022-09-28, Sebastian Mueller
# - fix append_coverage_compiler_flags_to_target to correctly add flags
# - replace "-fprofile-arcs -ftest-coverage" with "--coverage" (equivalent)
#
# USAGE:
#
# 1. Copy this file into your cmake modules path.
#
# 2. Add the following line to your CMakeLists.txt (best inside an if-condition
# using a CMake option() to enable it just optionally):
# include(CodeCoverage)
#
# 3. Append necessary compiler flags for all supported source files:
# append_coverage_compiler_flags()
# Or for specific target:
# append_coverage_compiler_flags_to_target(YOUR_TARGET_NAME)
#
# 3.a (OPTIONAL) Set appropriate optimization flags, e.g. -O0, -O1 or -Og
#
# 4. If you need to exclude additional directories from the report, specify them
# using full paths in the COVERAGE_EXCLUDES variable before calling
# setup_target_for_coverage_*().
# Example:
# set(COVERAGE_EXCLUDES
# '${PROJECT_SOURCE_DIR}/src/dir1/*'
# '/path/to/my/src/dir2/*')
# Or, use the EXCLUDE argument to setup_target_for_coverage_*().
# Example:
# setup_target_for_coverage_lcov(
# NAME coverage
# EXECUTABLE testrunner
# EXCLUDE "${PROJECT_SOURCE_DIR}/src/dir1/*" "/path/to/my/src/dir2/*")
#
# 4.a NOTE: With CMake 3.4+, COVERAGE_EXCLUDES or EXCLUDE can also be set
# relative to the BASE_DIRECTORY (default: PROJECT_SOURCE_DIR)
# Example:
# set(COVERAGE_EXCLUDES "dir1/*")
# setup_target_for_coverage_gcovr_html(
# NAME coverage
# EXECUTABLE testrunner
# BASE_DIRECTORY "${PROJECT_SOURCE_DIR}/src"
# EXCLUDE "dir2/*")
#
# 5. Use the functions described below to create a custom make target which
# runs your test executable and produces a code coverage report.
#
# 6. Build a Debug build:
# cmake -DCMAKE_BUILD_TYPE=Debug ..
# make
# make my_coverage_target
#
include(CMakeParseArguments)
option(CODE_COVERAGE_VERBOSE "Verbose information" FALSE)
# Check prereqs
find_program( GCOV_PATH gcov )
find_program( LCOV_PATH NAMES lcov lcov.bat lcov.exe lcov.perl)
find_program( FASTCOV_PATH NAMES fastcov fastcov.py )
find_program( GENHTML_PATH NAMES genhtml genhtml.perl genhtml.bat )
find_program( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/scripts/test)
find_program( CPPFILT_PATH NAMES c++filt )
if(NOT GCOV_PATH)
message(FATAL_ERROR "gcov not found! Aborting...")
endif() # NOT GCOV_PATH
# Check supported compiler (Clang, GNU and Flang)
get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
foreach(LANG ${LANGUAGES})
if("${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(Apple)?[Cc]lang")
if("${CMAKE_${LANG}_COMPILER_VERSION}" VERSION_LESS 3)
message(FATAL_ERROR "Clang version must be 3.0.0 or greater! Aborting...")
endif()
elseif(NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "GNU"
AND NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(LLVM)?[Ff]lang")
message(FATAL_ERROR "Compiler is not GNU or Flang! Aborting...")
endif()
endforeach()
set(COVERAGE_COMPILER_FLAGS "-g --coverage"
CACHE INTERNAL "")
if(CMAKE_CXX_COMPILER_ID MATCHES "(GNU|Clang)")
include(CheckCXXCompilerFlag)
check_cxx_compiler_flag(-fprofile-abs-path HAVE_fprofile_abs_path)
if(HAVE_fprofile_abs_path)
set(COVERAGE_COMPILER_FLAGS "${COVERAGE_COMPILER_FLAGS} -fprofile-abs-path")
endif()
endif()
set(CMAKE_Fortran_FLAGS_COVERAGE
${COVERAGE_COMPILER_FLAGS}
CACHE STRING "Flags used by the Fortran compiler during coverage builds."
FORCE )
set(CMAKE_CXX_FLAGS_COVERAGE
${COVERAGE_COMPILER_FLAGS}
CACHE STRING "Flags used by the C++ compiler during coverage builds."
FORCE )
set(CMAKE_C_FLAGS_COVERAGE
${COVERAGE_COMPILER_FLAGS}
CACHE STRING "Flags used by the C compiler during coverage builds."
FORCE )
set(CMAKE_EXE_LINKER_FLAGS_COVERAGE
""
CACHE STRING "Flags used for linking binaries during coverage builds."
FORCE )
set(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
""
CACHE STRING "Flags used by the shared libraries linker during coverage builds."
FORCE )
mark_as_advanced(
CMAKE_Fortran_FLAGS_COVERAGE
CMAKE_CXX_FLAGS_COVERAGE
CMAKE_C_FLAGS_COVERAGE
CMAKE_EXE_LINKER_FLAGS_COVERAGE
CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
get_property(GENERATOR_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
if(NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR GENERATOR_IS_MULTI_CONFIG))
message(WARNING "Code coverage results with an optimised (non-Debug) build may be misleading")
endif() # NOT (CMAKE_BUILD_TYPE STREQUAL "Debug" OR GENERATOR_IS_MULTI_CONFIG)
if(CMAKE_C_COMPILER_ID STREQUAL "GNU" OR CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
link_libraries(gcov)
endif()
# Defines a target for running and collection code coverage information
# Builds dependencies, runs the given executable and outputs reports.
# NOTE! The executable should always have a ZERO as exit code otherwise
# the coverage generation will not complete.
#
# setup_target_for_coverage_lcov(
# NAME testrunner_coverage # New target name
# EXECUTABLE testrunner -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
# DEPENDENCIES testrunner # Dependencies to build first
# BASE_DIRECTORY "../" # Base directory for report
# # (defaults to PROJECT_SOURCE_DIR)
# EXCLUDE "src/dir1/*" "src/dir2/*" # Patterns to exclude (can be relative
# # to BASE_DIRECTORY, with CMake 3.4+)
# NO_DEMANGLE # Don't demangle C++ symbols
# # even if c++filt is found
# )
function(setup_target_for_coverage_lcov)
set(options NO_DEMANGLE SONARQUBE)
set(oneValueArgs BASE_DIRECTORY NAME)
set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES LCOV_ARGS GENHTML_ARGS)
cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
if(NOT LCOV_PATH)
message(FATAL_ERROR "lcov not found! Aborting...")
endif() # NOT LCOV_PATH
if(NOT GENHTML_PATH)
message(FATAL_ERROR "genhtml not found! Aborting...")
endif() # NOT GENHTML_PATH
# Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
if(DEFINED Coverage_BASE_DIRECTORY)
get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
else()
set(BASEDIR ${PROJECT_SOURCE_DIR})
endif()
# Collect excludes (CMake 3.4+: Also compute absolute paths)
set(LCOV_EXCLUDES "")
foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_LCOV_EXCLUDES})
if(CMAKE_VERSION VERSION_GREATER 3.4)
get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
endif()
list(APPEND LCOV_EXCLUDES "${EXCLUDE}")
endforeach()
list(REMOVE_DUPLICATES LCOV_EXCLUDES)
# Conditional arguments
if(CPPFILT_PATH AND NOT ${Coverage_NO_DEMANGLE})
set(GENHTML_EXTRA_ARGS "--demangle-cpp")
endif()
# Setting up commands which will be run to generate coverage data.
# Cleanup lcov
set(LCOV_CLEAN_CMD
${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -directory .
-b ${BASEDIR} --zerocounters
)
# Create baseline to make sure untouched files show up in the report
set(LCOV_BASELINE_CMD
${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -c -i -d . -b
${BASEDIR} -o ${Coverage_NAME}.base
)
# Run tests
set(LCOV_EXEC_TESTS_CMD
${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
)
# Capturing lcov counters and generating report
set(LCOV_CAPTURE_CMD
${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --directory . -b
${BASEDIR} --capture --output-file ${Coverage_NAME}.capture
)
# add baseline counters
set(LCOV_BASELINE_COUNT_CMD
${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} -a ${Coverage_NAME}.base
-a ${Coverage_NAME}.capture --output-file ${Coverage_NAME}.total
)
# filter collected data to final coverage report
set(LCOV_FILTER_CMD
${LCOV_PATH} ${Coverage_LCOV_ARGS} --gcov-tool ${GCOV_PATH} --remove
${Coverage_NAME}.total ${LCOV_EXCLUDES} --output-file ${Coverage_NAME}.info
)
# Generate HTML output
set(LCOV_GEN_HTML_CMD
${GENHTML_PATH} ${GENHTML_EXTRA_ARGS} ${Coverage_GENHTML_ARGS} -o
${Coverage_NAME} ${Coverage_NAME}.info
)
if(${Coverage_SONARQUBE})
# Generate SonarQube output
set(GCOVR_XML_CMD
${GCOVR_PATH} --sonarqube ${Coverage_NAME}_sonarqube.xml -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
)
set(GCOVR_XML_CMD_COMMAND
COMMAND ${GCOVR_XML_CMD}
)
set(GCOVR_XML_CMD_BYPRODUCTS ${Coverage_NAME}_sonarqube.xml)
set(GCOVR_XML_CMD_COMMENT COMMENT "SonarQube code coverage info report saved in ${Coverage_NAME}_sonarqube.xml.")
endif()
if(CODE_COVERAGE_VERBOSE)
message(STATUS "Executed command report")
message(STATUS "Command to clean up lcov: ")
string(REPLACE ";" " " LCOV_CLEAN_CMD_SPACED "${LCOV_CLEAN_CMD}")
message(STATUS "${LCOV_CLEAN_CMD_SPACED}")
message(STATUS "Command to create baseline: ")
string(REPLACE ";" " " LCOV_BASELINE_CMD_SPACED "${LCOV_BASELINE_CMD}")
message(STATUS "${LCOV_BASELINE_CMD_SPACED}")
message(STATUS "Command to run the tests: ")
string(REPLACE ";" " " LCOV_EXEC_TESTS_CMD_SPACED "${LCOV_EXEC_TESTS_CMD}")
message(STATUS "${LCOV_EXEC_TESTS_CMD_SPACED}")
message(STATUS "Command to capture counters and generate report: ")
string(REPLACE ";" " " LCOV_CAPTURE_CMD_SPACED "${LCOV_CAPTURE_CMD}")
message(STATUS "${LCOV_CAPTURE_CMD_SPACED}")
message(STATUS "Command to add baseline counters: ")
string(REPLACE ";" " " LCOV_BASELINE_COUNT_CMD_SPACED "${LCOV_BASELINE_COUNT_CMD}")
message(STATUS "${LCOV_BASELINE_COUNT_CMD_SPACED}")
message(STATUS "Command to filter collected data: ")
string(REPLACE ";" " " LCOV_FILTER_CMD_SPACED "${LCOV_FILTER_CMD}")
message(STATUS "${LCOV_FILTER_CMD_SPACED}")
message(STATUS "Command to generate lcov HTML output: ")
string(REPLACE ";" " " LCOV_GEN_HTML_CMD_SPACED "${LCOV_GEN_HTML_CMD}")
message(STATUS "${LCOV_GEN_HTML_CMD_SPACED}")
if(${Coverage_SONARQUBE})
message(STATUS "Command to generate SonarQube XML output: ")
string(REPLACE ";" " " GCOVR_XML_CMD_SPACED "${GCOVR_XML_CMD}")
message(STATUS "${GCOVR_XML_CMD_SPACED}")
endif()
endif()
# Setup target
add_custom_target(${Coverage_NAME}
COMMAND ${LCOV_CLEAN_CMD}
COMMAND ${LCOV_BASELINE_CMD}
COMMAND ${LCOV_EXEC_TESTS_CMD}
COMMAND ${LCOV_CAPTURE_CMD}
COMMAND ${LCOV_BASELINE_COUNT_CMD}
COMMAND ${LCOV_FILTER_CMD}
COMMAND ${LCOV_GEN_HTML_CMD}
${GCOVR_XML_CMD_COMMAND}
# Set output files as GENERATED (will be removed on 'make clean')
BYPRODUCTS
${Coverage_NAME}.base
${Coverage_NAME}.capture
${Coverage_NAME}.total
${Coverage_NAME}.info
${GCOVR_XML_CMD_BYPRODUCTS}
${Coverage_NAME}/index.html
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
DEPENDS ${Coverage_DEPENDENCIES}
VERBATIM # Protect arguments to commands
COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
)
# Show where to find the lcov info report
add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
COMMAND ;
COMMENT "Lcov code coverage info report saved in ${Coverage_NAME}.info."
${GCOVR_XML_CMD_COMMENT}
)
# Show info where to find the report
add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
COMMAND ;
COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
)
endfunction() # setup_target_for_coverage_lcov
# Defines a target for running and collection code coverage information
# Builds dependencies, runs the given executable and outputs reports.
# NOTE! The executable should always have a ZERO as exit code otherwise
# the coverage generation will not complete.
#
# setup_target_for_coverage_gcovr_xml(
# NAME ctest_coverage # New target name
# EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
# DEPENDENCIES executable_target # Dependencies to build first
# BASE_DIRECTORY "../" # Base directory for report
# # (defaults to PROJECT_SOURCE_DIR)
# EXCLUDE "src/dir1/*" "src/dir2/*" # Patterns to exclude (can be relative
# # to BASE_DIRECTORY, with CMake 3.4+)
# )
# The user can set the variable GCOVR_ADDITIONAL_ARGS to supply additional flags to the
# GCVOR command.
function(setup_target_for_coverage_gcovr_xml)
set(options NONE)
set(oneValueArgs BASE_DIRECTORY NAME)
set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
if(NOT GCOVR_PATH)
message(FATAL_ERROR "gcovr not found! Aborting...")
endif() # NOT GCOVR_PATH
# Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
if(DEFINED Coverage_BASE_DIRECTORY)
get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
else()
set(BASEDIR ${PROJECT_SOURCE_DIR})
endif()
# Collect excludes (CMake 3.4+: Also compute absolute paths)
set(GCOVR_EXCLUDES "")
foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_GCOVR_EXCLUDES})
if(CMAKE_VERSION VERSION_GREATER 3.4)
get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
endif()
list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
endforeach()
list(REMOVE_DUPLICATES GCOVR_EXCLUDES)
# Combine excludes to several -e arguments
set(GCOVR_EXCLUDE_ARGS "")
foreach(EXCLUDE ${GCOVR_EXCLUDES})
list(APPEND GCOVR_EXCLUDE_ARGS "-e")
list(APPEND GCOVR_EXCLUDE_ARGS "${EXCLUDE}")
endforeach()
# Set up commands which will be run to generate coverage data
# Run tests
set(GCOVR_XML_EXEC_TESTS_CMD
${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
)
# Running gcovr
set(GCOVR_XML_CMD
${GCOVR_PATH} --xml ${Coverage_NAME}.xml -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
)
if(CODE_COVERAGE_VERBOSE)
message(STATUS "Executed command report")
message(STATUS "Command to run tests: ")
string(REPLACE ";" " " GCOVR_XML_EXEC_TESTS_CMD_SPACED "${GCOVR_XML_EXEC_TESTS_CMD}")
message(STATUS "${GCOVR_XML_EXEC_TESTS_CMD_SPACED}")
message(STATUS "Command to generate gcovr XML coverage data: ")
string(REPLACE ";" " " GCOVR_XML_CMD_SPACED "${GCOVR_XML_CMD}")
message(STATUS "${GCOVR_XML_CMD_SPACED}")
endif()
add_custom_target(${Coverage_NAME}
COMMAND ${GCOVR_XML_EXEC_TESTS_CMD}
COMMAND ${GCOVR_XML_CMD}
BYPRODUCTS ${Coverage_NAME}.xml
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
DEPENDS ${Coverage_DEPENDENCIES}
VERBATIM # Protect arguments to commands
COMMENT "Running gcovr to produce Cobertura code coverage report."
)
# Show info where to find the report
add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
COMMAND ;
COMMENT "Cobertura code coverage report saved in ${Coverage_NAME}.xml."
)
endfunction() # setup_target_for_coverage_gcovr_xml
# Defines a target for running and collection code coverage information
# Builds dependencies, runs the given executable and outputs reports.
# NOTE! The executable should always have a ZERO as exit code otherwise
# the coverage generation will not complete.
#
# setup_target_for_coverage_gcovr_html(
# NAME ctest_coverage # New target name
# EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
# DEPENDENCIES executable_target # Dependencies to build first
# BASE_DIRECTORY "../" # Base directory for report
# # (defaults to PROJECT_SOURCE_DIR)
# EXCLUDE "src/dir1/*" "src/dir2/*" # Patterns to exclude (can be relative
# # to BASE_DIRECTORY, with CMake 3.4+)
# )
# The user can set the variable GCOVR_ADDITIONAL_ARGS to supply additional flags to the
# GCVOR command.
function(setup_target_for_coverage_gcovr_html)
set(options NONE)
set(oneValueArgs BASE_DIRECTORY NAME)
set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
if(NOT GCOVR_PATH)
message(FATAL_ERROR "gcovr not found! Aborting...")
endif() # NOT GCOVR_PATH
# Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
if(DEFINED Coverage_BASE_DIRECTORY)
get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
else()
set(BASEDIR ${PROJECT_SOURCE_DIR})
endif()
# Collect excludes (CMake 3.4+: Also compute absolute paths)
set(GCOVR_EXCLUDES "")
foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_GCOVR_EXCLUDES})
if(CMAKE_VERSION VERSION_GREATER 3.4)
get_filename_component(EXCLUDE ${EXCLUDE} ABSOLUTE BASE_DIR ${BASEDIR})
endif()
list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
endforeach()
list(REMOVE_DUPLICATES GCOVR_EXCLUDES)
# Combine excludes to several -e arguments
set(GCOVR_EXCLUDE_ARGS "")
foreach(EXCLUDE ${GCOVR_EXCLUDES})
list(APPEND GCOVR_EXCLUDE_ARGS "-e")
list(APPEND GCOVR_EXCLUDE_ARGS "${EXCLUDE}")
endforeach()
# Set up commands which will be run to generate coverage data
# Run tests
set(GCOVR_HTML_EXEC_TESTS_CMD
${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS}
)
# Create folder
set(GCOVR_HTML_FOLDER_CMD
${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/${Coverage_NAME}
)
# Running gcovr
set(GCOVR_HTML_CMD
${GCOVR_PATH} --html ${Coverage_NAME}/index.html --html-details -r ${BASEDIR} ${GCOVR_ADDITIONAL_ARGS}
${GCOVR_EXCLUDE_ARGS} --object-directory=${PROJECT_BINARY_DIR}
)
if(CODE_COVERAGE_VERBOSE)
message(STATUS "Executed command report")
message(STATUS "Command to run tests: ")
string(REPLACE ";" " " GCOVR_HTML_EXEC_TESTS_CMD_SPACED "${GCOVR_HTML_EXEC_TESTS_CMD}")
message(STATUS "${GCOVR_HTML_EXEC_TESTS_CMD_SPACED}")
message(STATUS "Command to create a folder: ")
string(REPLACE ";" " " GCOVR_HTML_FOLDER_CMD_SPACED "${GCOVR_HTML_FOLDER_CMD}")
message(STATUS "${GCOVR_HTML_FOLDER_CMD_SPACED}")
message(STATUS "Command to generate gcovr HTML coverage data: ")
string(REPLACE ";" " " GCOVR_HTML_CMD_SPACED "${GCOVR_HTML_CMD}")
message(STATUS "${GCOVR_HTML_CMD_SPACED}")
endif()
add_custom_target(${Coverage_NAME}
COMMAND ${GCOVR_HTML_EXEC_TESTS_CMD}
COMMAND ${GCOVR_HTML_FOLDER_CMD}
COMMAND ${GCOVR_HTML_CMD}
BYPRODUCTS ${PROJECT_BINARY_DIR}/${Coverage_NAME}/index.html # report directory
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
DEPENDS ${Coverage_DEPENDENCIES}
VERBATIM # Protect arguments to commands
COMMENT "Running gcovr to produce HTML code coverage report."
)
# Show info where to find the report
add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
COMMAND ;
COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
)
endfunction() # setup_target_for_coverage_gcovr_html
# Defines a target for running and collection code coverage information
# Builds dependencies, runs the given executable and outputs reports.
# NOTE! The executable should always have a ZERO as exit code otherwise
# the coverage generation will not complete.
#
# setup_target_for_coverage_fastcov(
# NAME testrunner_coverage # New target name
# EXECUTABLE testrunner -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
# DEPENDENCIES testrunner # Dependencies to build first
# BASE_DIRECTORY "../" # Base directory for report
# # (defaults to PROJECT_SOURCE_DIR)
# EXCLUDE "src/dir1/" "src/dir2/" # Patterns to exclude.
# NO_DEMANGLE # Don't demangle C++ symbols
# # even if c++filt is found
# SKIP_HTML # Don't create html report
# POST_CMD perl -i -pe s!${PROJECT_SOURCE_DIR}/!!g ctest_coverage.json # E.g. for stripping source dir from file paths
# )
function(setup_target_for_coverage_fastcov)
set(options NO_DEMANGLE SKIP_HTML)
set(oneValueArgs BASE_DIRECTORY NAME)
set(multiValueArgs EXCLUDE EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES FASTCOV_ARGS GENHTML_ARGS POST_CMD)
cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
if(NOT FASTCOV_PATH)
message(FATAL_ERROR "fastcov not found! Aborting...")
endif()
if(NOT Coverage_SKIP_HTML AND NOT GENHTML_PATH)
message(FATAL_ERROR "genhtml not found! Aborting...")
endif()
# Set base directory (as absolute path), or default to PROJECT_SOURCE_DIR
if(Coverage_BASE_DIRECTORY)
get_filename_component(BASEDIR ${Coverage_BASE_DIRECTORY} ABSOLUTE)
else()
set(BASEDIR ${PROJECT_SOURCE_DIR})
endif()
# Collect excludes (Patterns, not paths, for fastcov)
set(FASTCOV_EXCLUDES "")
foreach(EXCLUDE ${Coverage_EXCLUDE} ${COVERAGE_EXCLUDES} ${COVERAGE_FASTCOV_EXCLUDES})
list(APPEND FASTCOV_EXCLUDES "${EXCLUDE}")
endforeach()
list(REMOVE_DUPLICATES FASTCOV_EXCLUDES)
# Conditional arguments
if(CPPFILT_PATH AND NOT ${Coverage_NO_DEMANGLE})
set(GENHTML_EXTRA_ARGS "--demangle-cpp")
endif()
# Set up commands which will be run to generate coverage data
set(FASTCOV_EXEC_TESTS_CMD ${Coverage_EXECUTABLE} ${Coverage_EXECUTABLE_ARGS})
set(FASTCOV_CAPTURE_CMD ${FASTCOV_PATH} ${Coverage_FASTCOV_ARGS} --gcov ${GCOV_PATH}
--search-directory ${BASEDIR}
--process-gcno
--output ${Coverage_NAME}.json
--exclude ${FASTCOV_EXCLUDES}
)
set(FASTCOV_CONVERT_CMD ${FASTCOV_PATH}
-C ${Coverage_NAME}.json --lcov --output ${Coverage_NAME}.info
)
if(Coverage_SKIP_HTML)
set(FASTCOV_HTML_CMD ";")
else()
set(FASTCOV_HTML_CMD ${GENHTML_PATH} ${GENHTML_EXTRA_ARGS} ${Coverage_GENHTML_ARGS}
-o ${Coverage_NAME} ${Coverage_NAME}.info
)
endif()
set(FASTCOV_POST_CMD ";")
if(Coverage_POST_CMD)
set(FASTCOV_POST_CMD ${Coverage_POST_CMD})
endif()
if(CODE_COVERAGE_VERBOSE)
message(STATUS "Code coverage commands for target ${Coverage_NAME} (fastcov):")
message(" Running tests:")
string(REPLACE ";" " " FASTCOV_EXEC_TESTS_CMD_SPACED "${FASTCOV_EXEC_TESTS_CMD}")
message(" ${FASTCOV_EXEC_TESTS_CMD_SPACED}")
message(" Capturing fastcov counters and generating report:")
string(REPLACE ";" " " FASTCOV_CAPTURE_CMD_SPACED "${FASTCOV_CAPTURE_CMD}")
message(" ${FASTCOV_CAPTURE_CMD_SPACED}")
message(" Converting fastcov .json to lcov .info:")
string(REPLACE ";" " " FASTCOV_CONVERT_CMD_SPACED "${FASTCOV_CONVERT_CMD}")
message(" ${FASTCOV_CONVERT_CMD_SPACED}")
if(NOT Coverage_SKIP_HTML)
message(" Generating HTML report: ")
string(REPLACE ";" " " FASTCOV_HTML_CMD_SPACED "${FASTCOV_HTML_CMD}")
message(" ${FASTCOV_HTML_CMD_SPACED}")
endif()
if(Coverage_POST_CMD)
message(" Running post command: ")
string(REPLACE ";" " " FASTCOV_POST_CMD_SPACED "${FASTCOV_POST_CMD}")
message(" ${FASTCOV_POST_CMD_SPACED}")
endif()
endif()
# Setup target
add_custom_target(${Coverage_NAME}
# Cleanup fastcov
COMMAND ${FASTCOV_PATH} ${Coverage_FASTCOV_ARGS} --gcov ${GCOV_PATH}
--search-directory ${BASEDIR}
--zerocounters
COMMAND ${FASTCOV_EXEC_TESTS_CMD}
COMMAND ${FASTCOV_CAPTURE_CMD}
COMMAND ${FASTCOV_CONVERT_CMD}
COMMAND ${FASTCOV_HTML_CMD}
COMMAND ${FASTCOV_POST_CMD}
# Set output files as GENERATED (will be removed on 'make clean')
BYPRODUCTS
${Coverage_NAME}.info
${Coverage_NAME}.json
${Coverage_NAME}/index.html # report directory
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
DEPENDS ${Coverage_DEPENDENCIES}
VERBATIM # Protect arguments to commands
COMMENT "Resetting code coverage counters to zero. Processing code coverage counters and generating report."
)
set(INFO_MSG "fastcov code coverage info report saved in ${Coverage_NAME}.info and ${Coverage_NAME}.json.")
if(NOT Coverage_SKIP_HTML)
string(APPEND INFO_MSG " Open ${PROJECT_BINARY_DIR}/${Coverage_NAME}/index.html in your browser to view the coverage report.")
endif()
# Show where to find the fastcov info report
add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
COMMAND ${CMAKE_COMMAND} -E echo ${INFO_MSG}
)
endfunction() # setup_target_for_coverage_fastcov
function(append_coverage_compiler_flags)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} ${COVERAGE_COMPILER_FLAGS}" PARENT_SCOPE)
message(STATUS "Appending code coverage compiler flags: ${COVERAGE_COMPILER_FLAGS}")
endfunction() # append_coverage_compiler_flags
# Setup coverage for specific library
function(append_coverage_compiler_flags_to_target name)
separate_arguments(_flag_list NATIVE_COMMAND "${COVERAGE_COMPILER_FLAGS}")
target_compile_options(${name} PRIVATE ${_flag_list})
if(CMAKE_C_COMPILER_ID STREQUAL "GNU" OR CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
target_link_libraries(${name} PRIVATE gcov)
endif()
endfunction()

View File

@@ -1,22 +0,0 @@
if(ENABLE_CLANG_TIDY)
find_program(CLANG_TIDY_COMMAND NAMES clang-tidy)
if(NOT CLANG_TIDY_COMMAND)
message(WARNING "🔴 CMake_RUN_CLANG_TIDY is ON but clang-tidy is not found!")
set(CMAKE_CXX_CLANG_TIDY "" CACHE STRING "" FORCE)
else()
message(STATUS "🟢 CMake_RUN_CLANG_TIDY is ON")
set(CLANGTIDY_EXTRA_ARGS
"-extra-arg=-Wno-unknown-warning-option"
)
set(CMAKE_CXX_CLANG_TIDY "${CLANG_TIDY_COMMAND};-p=${CMAKE_BINARY_DIR};${CLANGTIDY_EXTRA_ARGS}" CACHE STRING "" FORCE)
add_custom_target(clang-tidy
COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target ${CMAKE_PROJECT_NAME}
COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target clang-tidy
COMMENT "Running clang-tidy..."
)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
endif()
endif(ENABLE_CLANG_TIDY)

10
conandata.yml Normal file
View File

@@ -0,0 +1,10 @@
sources:
"1.1.2":
url: "https://github.com/rmontanana/BayesNet/archive/v1.1.2.tar.gz"
sha256: "placeholder_sha256" # Replace with actual SHA256 when releasing
"1.0.7":
url: "https://github.com/rmontanana/BayesNet/archive/v1.0.7.tar.gz"
sha256: "placeholder_sha256" # Replace with actual SHA256 when releasing
patches:
# Add patches here if needed for specific versions

108
conanfile.py Normal file
View File

@@ -0,0 +1,108 @@
import os, re, pathlib
from conan import ConanFile
from conan.tools.cmake import CMakeToolchain, CMake, cmake_layout, CMakeDeps
from conan.tools.files import copy
class BayesNetConan(ConanFile):
name = "bayesnet"
settings = "os", "compiler", "build_type", "arch"
options = {
"shared": [True, False],
"fPIC": [True, False],
"enable_testing": [True, False],
"enable_coverage": [True, False],
}
default_options = {
"shared": False,
"fPIC": True,
"enable_testing": False,
"enable_coverage": False,
}
# Sources are located in the same place as this recipe, copy them to the recipe
exports_sources = (
"CMakeLists.txt",
"bayesnet/*",
"config/*",
"cmake/*",
"docs/*",
"tests/*",
"bayesnetConfig.cmake.in",
)
def set_version(self) -> None:
cmake = pathlib.Path(self.recipe_folder) / "CMakeLists.txt"
text = cmake.read_text(encoding="utf-8")
# Accept either: project(foo VERSION 1.2.3) or set(foo_VERSION 1.2.3)
match = re.search(
r"""project\s*\([^\)]*VERSION\s+([0-9]+\.[0-9]+\.[0-9]+)""",
text,
re.IGNORECASE | re.VERBOSE,
)
if match:
self.version = match.group(1)
else:
raise Exception("Version not found in CMakeLists.txt")
self.version = match.group(1)
def config_options(self):
if self.settings.os == "Windows":
del self.options.fPIC
def configure(self):
if self.options.shared:
self.options.rm_safe("fPIC")
def requirements(self):
# Core dependencies
self.requires("libtorch/2.7.1")
self.requires("nlohmann_json/3.11.3")
self.requires("folding/1.1.2") # Custom package
self.requires("fimdlp/2.1.1") # Custom package
def build_requirements(self):
self.build_requires("cmake/[>=3.27]")
self.test_requires("arff-files/1.2.1") # Custom package
self.test_requires("catch2/3.8.1")
def layout(self):
cmake_layout(self)
def generate(self):
deps = CMakeDeps(self)
deps.generate()
tc = CMakeToolchain(self)
tc.variables["ENABLE_TESTING"] = self.options.enable_testing
tc.variables["CODE_COVERAGE"] = self.options.enable_coverage
tc.generate()
def build(self):
cmake = CMake(self)
cmake.configure()
cmake.build()
if self.options.enable_testing:
# Run tests only if we're building with testing enabled
self.run("ctest --output-on-failure", cwd=self.build_folder)
def package(self):
copy(
self,
"LICENSE",
src=self.source_folder,
dst=os.path.join(self.package_folder, "licenses"),
)
cmake = CMake(self)
cmake.install()
def package_info(self):
self.cpp_info.libs = ["bayesnet"]
self.cpp_info.includedirs = ["include"]
self.cpp_info.set_property("cmake_find_mode", "both")
self.cpp_info.set_property("cmake_target_name", "bayesnet::bayesnet")
# Add compiler flags that might be needed
if self.settings.os == "Linux":
self.cpp_info.system_libs = ["pthread"]

View File

@@ -1,4 +1,4 @@
configure_file(
"config.h.in"
"${CMAKE_BINARY_DIR}/configured_files/include/config.h" ESCAPE_QUOTES
"${CMAKE_BINARY_DIR}/configured_files/include/bayesnet/config.h" ESCAPE_QUOTES
)

View File

@@ -3,12 +3,8 @@
#include <string>
#include <string_view>
#define PROJECT_VERSION_MAJOR @PROJECT_VERSION_MAJOR @
#define PROJECT_VERSION_MINOR @PROJECT_VERSION_MINOR @
#define PROJECT_VERSION_PATCH @PROJECT_VERSION_PATCH @
static constexpr std::string_view project_name = "@PROJECT_NAME@";
static constexpr std::string_view project_version = "@PROJECT_VERSION@";
static constexpr std::string_view project_description = "@PROJECT_DESCRIPTION@";
static constexpr std::string_view git_sha = "@GIT_SHA@";
static constexpr std::string_view data_path = "@BayesNet_SOURCE_DIR@/tests/data/";
static constexpr std::string_view data_path = "@bayesnet_SOURCE_DIR@/tests/data/";

Binary file not shown.

676
diagrams/BayesNet.puml Normal file
View File

@@ -0,0 +1,676 @@
@startuml
title clang-uml class diagram model
class "bayesnet::Node" as C_0010428199432536647474
class C_0010428199432536647474 #aliceblue;line:blue;line.dotted;text:blue {
+Node(const std::string &) : void
..
+addChild(Node *) : void
+addParent(Node *) : void
+clear() : void
+computeCPT(const torch::Tensor & dataset, const std::vector<std::string> & features, const double smoothing, const torch::Tensor & weights) : void
+getCPT() : torch::Tensor &
+getChildren() : std::vector<Node *> &
+getFactorValue(std::map<std::string,int> &) : double
+getName() const : std::string
+getNumStates() const : int
+getParents() : std::vector<Node *> &
+graph(const std::string & clasName) : std::vector<std::string>
+minFill() : unsigned int
+removeChild(Node *) : void
+removeParent(Node *) : void
+setNumStates(int) : void
__
}
enum "bayesnet::Smoothing_t" as C_0013393078277439680282
enum C_0013393078277439680282 {
NONE
ORIGINAL
LAPLACE
CESTNIK
}
class "bayesnet::Network" as C_0009493661199123436603
class C_0009493661199123436603 #aliceblue;line:blue;line.dotted;text:blue {
+Network() : void
+Network(const Network &) : void
+~Network() = default : void
..
+addEdge(const std::string &, const std::string &) : void
+addNode(const std::string &) : void
+dump_cpt() const : std::string
+fit(const torch::Tensor & samples, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
+fit(const torch::Tensor & X, const torch::Tensor & y, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
+fit(const std::vector<std::vector<int>> & input_data, const std::vector<int> & labels, const std::vector<double> & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
+getClassName() const : std::string
+getClassNumStates() const : int
+getEdges() const : std::vector<std::pair<std::string,std::string>>
+getFeatures() const : std::vector<std::string>
+getNodes() : std::map<std::string,std::unique_ptr<Node>> &
+getNumEdges() const : int
+getSamples() : torch::Tensor &
+getStates() const : int
+graph(const std::string & title) const : std::vector<std::string>
+initialize() : void
+predict(const std::vector<std::vector<int>> &) : std::vector<int>
+predict(const torch::Tensor &) : torch::Tensor
+predict_proba(const std::vector<std::vector<int>> &) : std::vector<std::vector<double>>
+predict_proba(const torch::Tensor &) : torch::Tensor
+predict_tensor(const torch::Tensor & samples, const bool proba) : torch::Tensor
+score(const std::vector<std::vector<int>> &, const std::vector<int> &) : double
+show() const : std::vector<std::string>
+topological_sort() : std::vector<std::string>
+version() : std::string
__
}
enum "bayesnet::status_t" as C_0005907365846270811004
enum C_0005907365846270811004 {
NORMAL
WARNING
ERROR
}
abstract "bayesnet::BaseClassifier" as C_0002617087915615796317
abstract C_0002617087915615796317 #aliceblue;line:blue;line.dotted;text:blue {
+~BaseClassifier() = default : void
..
{abstract} +dump_cpt() const = 0 : std::string
{abstract} +fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights, const Smoothing_t smoothing) = 0 : BaseClassifier &
{abstract} +fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
{abstract} +getClassNumStates() const = 0 : int
{abstract} +getNotes() const = 0 : std::vector<std::string>
{abstract} +getNumberOfEdges() const = 0 : int
{abstract} +getNumberOfNodes() const = 0 : int
{abstract} +getNumberOfStates() const = 0 : int
{abstract} +getStatus() const = 0 : status_t
+getValidHyperparameters() : std::vector<std::string> &
{abstract} +getVersion() = 0 : std::string
{abstract} +graph(const std::string & title = "") const = 0 : std::vector<std::string>
{abstract} +predict(std::vector<std::vector<int>> & X) = 0 : std::vector<int>
{abstract} +predict(torch::Tensor & X) = 0 : torch::Tensor
{abstract} +predict_proba(std::vector<std::vector<int>> & X) = 0 : std::vector<std::vector<double>>
{abstract} +predict_proba(torch::Tensor & X) = 0 : torch::Tensor
{abstract} +score(std::vector<std::vector<int>> & X, std::vector<int> & y) = 0 : float
{abstract} +score(torch::Tensor & X, torch::Tensor & y) = 0 : float
{abstract} +setHyperparameters(const nlohmann::json & hyperparameters) = 0 : void
{abstract} +show() const = 0 : std::vector<std::string>
{abstract} +topological_order() = 0 : std::vector<std::string>
{abstract} #trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) = 0 : void
__
#notes : std::vector<std::string>
#status : status_t
#validHyperparameters : std::vector<std::string>
}
class "bayesnet::Metrics" as C_0005895723015084986588
class C_0005895723015084986588 #aliceblue;line:blue;line.dotted;text:blue {
+Metrics() = default : void
+Metrics(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
+Metrics(const std::vector<std::vector<int>> & vsamples, const std::vector<int> & labels, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
..
+SelectKBestWeighted(const torch::Tensor & weights, bool ascending = false, unsigned int k = 0) : std::vector<int>
+SelectKPairs(const torch::Tensor & weights, std::vector<int> & featuresExcluded, bool ascending = false, unsigned int k = 0) : std::vector<std::pair<int,int>>
+conditionalEdge(const torch::Tensor & weights) : torch::Tensor
+conditionalEntropy(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & labels, const torch::Tensor & weights) : double
+conditionalMutualInformation(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & labels, const torch::Tensor & weights) : double
#doCombinations<T>(const std::vector<T> & source) : std::vector<std::pair<T, T> >
+entropy(const torch::Tensor & feature, const torch::Tensor & weights) : double
+getScoresKBest() const : std::vector<double>
+getScoresKPairs() const : std::vector<std::pair<std::pair<int,int>,double>>
+maximumSpanningTree(const std::vector<std::string> & features, const torch::Tensor & weights, const int root) : std::vector<std::pair<int,int>>
+mutualInformation(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & weights) : double
#pop_first<T>(std::vector<T> & v) : T
__
#className : std::string
#features : std::vector<std::string>
#samples : torch::Tensor
}
abstract "bayesnet::Classifier" as C_0016351972983202413152
abstract C_0016351972983202413152 #aliceblue;line:blue;line.dotted;text:blue {
+Classifier(Network model) : void
+~Classifier() = default : void
..
+addNodes() : void
#buildDataset(torch::Tensor & y) : void
{abstract} #buildModel(const torch::Tensor & weights) = 0 : void
#checkFitParameters() : void
+dump_cpt() const : std::string
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
+fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights, const Smoothing_t smoothing) : Classifier &
+getClassNumStates() const : int
+getNotes() const : std::vector<std::string>
+getNumberOfEdges() const : int
+getNumberOfNodes() const : int
+getNumberOfStates() const : int
+getStatus() const : status_t
+getVersion() : std::string
+predict(std::vector<std::vector<int>> & X) : std::vector<int>
+predict(torch::Tensor & X) : torch::Tensor
+predict_proba(std::vector<std::vector<int>> & X) : std::vector<std::vector<double>>
+predict_proba(torch::Tensor & X) : torch::Tensor
+score(torch::Tensor & X, torch::Tensor & y) : float
+score(std::vector<std::vector<int>> & X, std::vector<int> & y) : float
+setHyperparameters(const nlohmann::json & hyperparameters) : void
+show() const : std::vector<std::string>
+topological_order() : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
__
#CLASSIFIER_NOT_FITTED : const std::string
#className : std::string
#dataset : torch::Tensor
#features : std::vector<std::string>
#fitted : bool
#m : unsigned int
#metrics : Metrics
#model : Network
#n : unsigned int
#states : std::map<std::string,std::vector<int>>
}
class "bayesnet::Proposal" as C_0017759964713298103839
class C_0017759964713298103839 #aliceblue;line:blue;line.dotted;text:blue {
+Proposal(torch::Tensor & pDataset, std::vector<std::string> & features_, std::string & className_) : void
+~Proposal() : void
..
#checkInput(const torch::Tensor & X, const torch::Tensor & y) : void
#fit_local_discretization(const torch::Tensor & y) : std::map<std::string,std::vector<int>>
#localDiscretizationProposal(const std::map<std::string,std::vector<int>> & states, Network & model) : std::map<std::string,std::vector<int>>
#prepareX(torch::Tensor & X) : torch::Tensor
__
#Xf : torch::Tensor
#discretizers : map<std::string,mdlp::CPPFImdlp *>
#y : torch::Tensor
}
class "bayesnet::KDB" as C_0008902920152122000044
class C_0008902920152122000044 #aliceblue;line:blue;line.dotted;text:blue {
+KDB(int k, float theta = 0.03) : void
+~KDB() = default : void
..
#add_m_edges(int idx, std::vector<int> & S, torch::Tensor & weights) : void
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & name = "KDB") const : std::vector<std::string>
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
__
}
class "bayesnet::KDBLd" as C_0002756018222998454702
class C_0002756018222998454702 #aliceblue;line:blue;line.dotted;text:blue {
+KDBLd(int k) : void
+~KDBLd() = default : void
..
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : KDBLd &
+graph(const std::string & name = "KDB") const : std::vector<std::string>
+predict(torch::Tensor & X) : torch::Tensor
{static} +version() : std::string
__
}
class "bayesnet::SPODE" as C_0004096182510460307610
class C_0004096182510460307610 #aliceblue;line:blue;line.dotted;text:blue {
+SPODE(int root) : void
+~SPODE() = default : void
..
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & name = "SPODE") const : std::vector<std::string>
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
__
}
class "bayesnet::SPODELd" as C_0010957245114062042836
class C_0010957245114062042836 #aliceblue;line:blue;line.dotted;text:blue {
+SPODELd(int root) : void
+~SPODELd() = default : void
..
+commonFit(const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
+graph(const std::string & name = "SPODELd") const : std::vector<std::string>
+predict(torch::Tensor & X) : torch::Tensor
{static} +version() : std::string
__
}
class "bayesnet::SPnDE" as C_0016268916386101512883
class C_0016268916386101512883 #aliceblue;line:blue;line.dotted;text:blue {
+SPnDE(std::vector<int> parents) : void
+~SPnDE() = default : void
..
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & name = "SPnDE") const : std::vector<std::string>
__
}
class "bayesnet::TAN" as C_0014087955399074584137
class C_0014087955399074584137 #aliceblue;line:blue;line.dotted;text:blue {
+TAN() : void
+~TAN() = default : void
..
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & name = "TAN") const : std::vector<std::string>
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
__
}
class "bayesnet::TANLd" as C_0013350632773616302678
class C_0013350632773616302678 #aliceblue;line:blue;line.dotted;text:blue {
+TANLd() : void
+~TANLd() = default : void
..
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : TANLd &
+graph(const std::string & name = "TANLd") const : std::vector<std::string>
+predict(torch::Tensor & X) : torch::Tensor
__
}
class "bayesnet::XSp2de" as C_0007640742442325463418
class C_0007640742442325463418 #aliceblue;line:blue;line.dotted;text:blue {
+XSp2de(int spIndex1, int spIndex2) : void
..
#buildModel(const torch::Tensor & weights) : void
+fitx(torch::Tensor & X, torch::Tensor & y, torch::Tensor & weights_, const Smoothing_t smoothing) : void
+getClassNumStates() const : int
+getNFeatures() const : int
+getNumberOfEdges() const : int
+getNumberOfNodes() const : int
+getNumberOfStates() const : int
+graph(const std::string & title) const : std::vector<std::string>
+predict(const std::vector<int> & instance) const : int
+predict(std::vector<std::vector<int>> & test_data) : std::vector<int>
+predict(torch::Tensor & X) : torch::Tensor
+predict_proba(const std::vector<int> & instance) const : std::vector<double>
+predict_proba(std::vector<std::vector<int>> & test_data) : std::vector<std::vector<double>>
+predict_proba(torch::Tensor & X) : torch::Tensor
+score(std::vector<std::vector<int>> & X, std::vector<int> & y) : float
+score(torch::Tensor & X, torch::Tensor & y) : float
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
+to_string() const : std::string
#trainModel(const torch::Tensor & weights, const bayesnet::Smoothing_t smoothing) : void
__
}
class "bayesnet::XSpode" as C_0015654113248178830206
class C_0015654113248178830206 #aliceblue;line:blue;line.dotted;text:blue {
+XSpode(int spIndex) : void
..
#buildModel(const torch::Tensor & weights) : void
+fitx(torch::Tensor & X, torch::Tensor & y, torch::Tensor & weights_, const Smoothing_t smoothing) : void
+getClassNumStates() const : int
+getNFeatures() const : int
+getNumberOfEdges() const : int
+getNumberOfNodes() const : int
+getNumberOfStates() const : int
+getStates() : std::vector<int> &
+graph(const std::string & title) const : std::vector<std::string>
+normalize(std::vector<double> & v) const : void
+predict(const std::vector<int> & instance) const : int
+predict(std::vector<std::vector<int>> & X) : std::vector<int>
+predict(torch::Tensor & X) : torch::Tensor
+predict_proba(std::vector<std::vector<int>> & X) : std::vector<std::vector<double>>
+predict_proba(torch::Tensor & X) : torch::Tensor
+predict_proba(const std::vector<int> & instance) const : std::vector<double>
+score(torch::Tensor & X, torch::Tensor & y) : float
+score(std::vector<std::vector<int>> & X, std::vector<int> & y) : float
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
+to_string() const : std::string
#trainModel(const torch::Tensor & weights, const bayesnet::Smoothing_t smoothing) : void
__
}
class "bayesnet::TensorUtils" as C_0010304804115474100819
class C_0010304804115474100819 #aliceblue;line:blue;line.dotted;text:blue {
{static} +to_matrix(const torch::Tensor & X) : std::vector<std::vector<int>>
{static} +to_vector<T>(const torch::Tensor & y) : std::vector<T>
__
}
class "bayesnet::Ensemble" as C_0015881931090842884611
class C_0015881931090842884611 #aliceblue;line:blue;line.dotted;text:blue {
+Ensemble(bool predict_voting = true) : void
+~Ensemble() = default : void
..
#compute_arg_max(std::vector<std::vector<double>> & X) : std::vector<int>
#compute_arg_max(torch::Tensor & X) : torch::Tensor
+dump_cpt() const : std::string
+getNumberOfEdges() const : int
+getNumberOfNodes() const : int
+getNumberOfStates() const : int
+graph(const std::string & title) const : std::vector<std::string>
+predict(std::vector<std::vector<int>> & X) : std::vector<int>
+predict(torch::Tensor & X) : torch::Tensor
#predict_average_proba(torch::Tensor & X) : torch::Tensor
#predict_average_proba(std::vector<std::vector<int>> & X) : std::vector<std::vector<double>>
#predict_average_voting(torch::Tensor & X) : torch::Tensor
#predict_average_voting(std::vector<std::vector<int>> & X) : std::vector<std::vector<double>>
+predict_proba(std::vector<std::vector<int>> & X) : std::vector<std::vector<double>>
+predict_proba(torch::Tensor & X) : torch::Tensor
+score(std::vector<std::vector<int>> & X, std::vector<int> & y) : float
+score(torch::Tensor & X, torch::Tensor & y) : float
+show() const : std::vector<std::string>
+topological_order() : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
#voting(torch::Tensor & votes) : torch::Tensor
__
#models : std::vector<std::unique_ptr<Classifier>>
#n_models : unsigned int
#predict_voting : bool
#significanceModels : std::vector<double>
}
class "bayesnet::A2DE" as C_0001410789567057647859
class C_0001410789567057647859 #aliceblue;line:blue;line.dotted;text:blue {
+A2DE(bool predict_voting = false) : void
+~A2DE() : void
..
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & title = "A2DE") const : std::vector<std::string>
+setHyperparameters(const nlohmann::json & hyperparameters) : void
__
}
class "bayesnet::AODE" as C_0006288892608974306258
class C_0006288892608974306258 #aliceblue;line:blue;line.dotted;text:blue {
+AODE(bool predict_voting = false) : void
+~AODE() : void
..
#buildModel(const torch::Tensor & weights) : void
+graph(const std::string & title = "AODE") const : std::vector<std::string>
+setHyperparameters(const nlohmann::json & hyperparameters) : void
__
}
class "bayesnet::AODELd" as C_0003898187834670349177
class C_0003898187834670349177 #aliceblue;line:blue;line.dotted;text:blue {
+AODELd(bool predict_voting = true) : void
+~AODELd() = default : void
..
#buildModel(const torch::Tensor & weights) : void
+fit(torch::Tensor & X_, torch::Tensor & y_, const std::vector<std::string> & features_, const std::string & className_, std::map<std::string,std::vector<int>> & states_, const Smoothing_t smoothing) : AODELd &
+graph(const std::string & name = "AODELd") const : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
__
}
abstract "bayesnet::FeatureSelect" as C_0013562609546004646591
abstract C_0013562609546004646591 #aliceblue;line:blue;line.dotted;text:blue {
+FeatureSelect(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights) : void
+~FeatureSelect() : void
..
#computeMeritCFS() : double
#computeSuFeatures(const int a, const int b) : double
#computeSuLabels() : void
{abstract} +fit() = 0 : void
+getFeatures() const : std::vector<int>
+getScores() const : std::vector<double>
#initialize() : void
#symmetricalUncertainty(int a, int b) : double
__
#fitted : bool
#maxFeatures : int
#selectedFeatures : std::vector<int>
#selectedScores : std::vector<double>
#suFeatures : std::map<std::pair<int,int>,double>
#suLabels : std::vector<double>
#weights : const torch::Tensor &
}
class "bayesnet::(anonymous_60357672)" as C_0006397015156479549697
class C_0006397015156479549697 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60358326)" as C_0013066254331852347304
class C_0013066254331852347304 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::Boost" as C_0009819322948617116148
class C_0009819322948617116148 #aliceblue;line:blue;line.dotted;text:blue {
+Boost(bool predict_voting = false) : void
+~Boost() = default : void
..
#add_model(std::unique_ptr<Classifier> model, double significance) : void
#buildModel(const torch::Tensor & weights) : void
#featureSelection(torch::Tensor & weights_) : std::vector<int>
#remove_last_model() : void
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
#update_weights(torch::Tensor & ytrain, torch::Tensor & ypred, torch::Tensor & weights) : std::tuple<torch::Tensor &,double,bool>
#update_weights_block(int k, torch::Tensor & ytrain, torch::Tensor & weights) : std::tuple<torch::Tensor &,double,bool>
__
#X_test : torch::Tensor
#X_train : torch::Tensor
#alpha_block : bool
#bisection : bool
#block_update : bool
#convergence : bool
#convergence_best : bool
#featureSelector : FeatureSelect *
#maxTolerance : int
#order_algorithm : std::string
#selectFeatures : bool
#select_features_algorithm : std::string
#threshold : double
#y_test : torch::Tensor
#y_train : torch::Tensor
}
class "bayesnet::BoostA2DE" as C_0000272055465257861326
class C_0000272055465257861326 #aliceblue;line:blue;line.dotted;text:blue {
+BoostA2DE(bool predict_voting = false) : void
+~BoostA2DE() = default : void
..
+graph(const std::string & title = "BoostA2DE") const : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
__
}
class "bayesnet::(anonymous_60425028)" as C_0000461144706913711531
class C_0000461144706913711531 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60425682)" as C_0014849589915262463453
class C_0014849589915262463453 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::BoostAODE" as C_0002867772739198819061
class C_0002867772739198819061 #aliceblue;line:blue;line.dotted;text:blue {
+BoostAODE(bool predict_voting = false) : void
+~BoostAODE() = default : void
..
+graph(const std::string & title = "BoostAODE") const : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
__
}
class "bayesnet::XBA2DE" as C_0008480973840710001141
class C_0008480973840710001141 #aliceblue;line:blue;line.dotted;text:blue {
+XBA2DE(bool predict_voting = false) : void
+~XBA2DE() = default : void
..
+getVersion() : std::string
+graph(const std::string & title = "XBA2DE") const : std::vector<std::string>
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
__
}
class "bayesnet::(anonymous_60414016)" as C_0008746994658440620779
class C_0008746994658440620779 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60414670)" as C_0008030559132212449356
class C_0008030559132212449356 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::XBAODE" as C_0005198482342493966768
class C_0005198482342493966768 #aliceblue;line:blue;line.dotted;text:blue {
+XBAODE() : void
..
+getVersion() : std::string
#trainModel(const torch::Tensor & weights, const bayesnet::Smoothing_t smoothing) : void
__
}
class "bayesnet::CFS" as C_0000093018845530739957
class C_0000093018845530739957 #aliceblue;line:blue;line.dotted;text:blue {
+CFS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights) : void
+~CFS() : void
..
+fit() : void
__
}
class "bayesnet::FCBF" as C_0001157456122733975432
class C_0001157456122733975432 #aliceblue;line:blue;line.dotted;text:blue {
+FCBF(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
+~FCBF() : void
..
+fit() : void
__
}
class "bayesnet::IWSS" as C_0000066148117395428429
class C_0000066148117395428429 #aliceblue;line:blue;line.dotted;text:blue {
+IWSS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
+~IWSS() : void
..
+fit() : void
__
}
class "bayesnet::(anonymous_60810808)" as C_0012002108046995621535
class C_0012002108046995621535 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60811462)" as C_0004735044229422764240
class C_0004735044229422764240 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::(anonymous_60804220)" as C_0007082100550474633839
class C_0007082100550474633839 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60804874)" as C_0003669430095936529648
class C_0003669430095936529648 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::(anonymous_60809706)" as C_0012336951062058157227
class C_0012336951062058157227 #aliceblue;line:blue;line.dotted;text:blue {
__
+CFS : std::string
+FCBF : std::string
+IWSS : std::string
}
class "bayesnet::(anonymous_60810360)" as C_0002435892998884329673
class C_0002435892998884329673 #aliceblue;line:blue;line.dotted;text:blue {
__
+ASC : std::string
+DESC : std::string
+RAND : std::string
}
class "bayesnet::MST" as C_0001054867409378333602
class C_0001054867409378333602 #aliceblue;line:blue;line.dotted;text:blue {
+MST() = default : void
+MST(const std::vector<std::string> & features, const torch::Tensor & weights, const int root) : void
..
+insertElement(std::list<int> & variables, int variable) : void
+maximumSpanningTree() : std::vector<std::pair<int,int>>
+reorder(std::vector<std::pair<float,std::pair<int,int>>> T, int root_original) : std::vector<std::pair<int,int>>
__
}
class "bayesnet::Graph" as C_0009576333456015187741
class C_0009576333456015187741 #aliceblue;line:blue;line.dotted;text:blue {
+Graph(int V) : void
..
+addEdge(int u, int v, float wt) : void
+find_set(int i) : int
+get_mst() : std::vector<std::pair<float,std::pair<int,int>>>
+kruskal_algorithm() : void
+union_set(int u, int v) : void
__
}
C_0010428199432536647474 --> C_0010428199432536647474 : -parents
C_0010428199432536647474 --> C_0010428199432536647474 : -children
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C_0009493661199123436603 o-- C_0010428199432536647474 : -nodes
C_0002617087915615796317 ..> C_0013393078277439680282
C_0002617087915615796317 o-- C_0005907365846270811004 : #status
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C_0016351972983202413152 ..> C_0005907365846270811004
C_0016351972983202413152 o-- C_0009493661199123436603 : #model
C_0016351972983202413152 o-- C_0005895723015084986588 : #metrics
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C_0013350632773616302678 ..> C_0013393078277439680282
C_0014087955399074584137 <|-- C_0013350632773616302678
C_0017759964713298103839 <|-- C_0013350632773616302678
C_0007640742442325463418 ..> C_0013393078277439680282
C_0016351972983202413152 <|-- C_0007640742442325463418
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C_0016351972983202413152 <|-- C_0015654113248178830206
C_0015881931090842884611 ..> C_0013393078277439680282
C_0015881931090842884611 o-- C_0016351972983202413152 : #models
C_0016351972983202413152 <|-- C_0015881931090842884611
C_0015881931090842884611 <|-- C_0001410789567057647859
C_0015881931090842884611 <|-- C_0006288892608974306258
C_0003898187834670349177 ..> C_0013393078277439680282
C_0015881931090842884611 <|-- C_0003898187834670349177
C_0017759964713298103839 <|-- C_0003898187834670349177
C_0005895723015084986588 <|-- C_0013562609546004646591
C_0009819322948617116148 ..> C_0016351972983202413152
C_0009819322948617116148 --> C_0013562609546004646591 : #featureSelector
C_0015881931090842884611 <|-- C_0009819322948617116148
C_0000272055465257861326 ..> C_0013393078277439680282
C_0009819322948617116148 <|-- C_0000272055465257861326
C_0002867772739198819061 ..> C_0013393078277439680282
C_0009819322948617116148 <|-- C_0002867772739198819061
C_0008480973840710001141 ..> C_0013393078277439680282
C_0009819322948617116148 <|-- C_0008480973840710001141
C_0005198482342493966768 ..> C_0013393078277439680282
C_0009819322948617116148 <|-- C_0005198482342493966768
C_0013562609546004646591 <|-- C_0000093018845530739957
C_0013562609546004646591 <|-- C_0001157456122733975432
C_0013562609546004646591 <|-- C_0000066148117395428429
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# BoostAODE Algorithm Operation
## Hyperparameters
The hyperparameters defined in the algorithm are:
- ***bisection*** (*boolean*): If set to true allows the algorithm to add *k* models at once (as specified in the algorithm) to the ensemble. Default value: *true*.
- ***bisection_best*** (*boolean*): If set to *true*, the algorithm will take as *priorAccuracy* the best accuracy computed. If set to *false⁺ it will take the last accuracy as *priorAccuracy*. Default value: *false*.
- ***order*** (*{"asc", "desc", "rand"}*): Sets the order (ascending/descending/random) in which dataset variables will be processed to choose the parents of the *SPODEs*. Default value: *"desc"*.
- ***block_update*** (*boolean*): Sets whether the algorithm will update the weights of the models in blocks. If set to false, the algorithm will update the weights of the models one by one. Default value: *false*.
- ***convergence*** (*boolean*): Sets whether the convergence of the result will be used as a termination condition. If this hyperparameter is set to true, the training dataset passed to the model is divided into two sets, one serving as training data and the other as a test set (so the original test partition will become a validation partition in this case). The partition is made by taking the first partition generated by a process of generating a 5 fold partition with stratification using a predetermined seed. The exit condition used in this *convergence* is that the difference between the accuracy obtained by the current model and that obtained by the previous model is greater than *1e-4*; otherwise, one will be added to the number of models that worsen the result (see next hyperparameter). Default value: *true*.
- ***maxTolerance*** (*int*): Sets the maximum number of models that can worsen the result without constituting a termination condition. if ***bisection*** is set to *true*, the value of this hyperparameter will be exponent of base 2 to compute the number of models to insert at once. Default value: *3*
- ***select_features*** (*{"IWSS", "FCBF", "CFS", ""}*): Selects the variable selection method to be used to build initial models for the ensemble that will be included without considering any of the other exit conditions. Once the models of the selected variables are built, the algorithm will update the weights using the ensemble and set the significance of all the models built with the same &alpha;<sub>t</sub>. Default value: *""*.
- ***threshold*** (*double*): Sets the necessary value for the IWSS and FCBF algorithms to function. Accepted values are:
- IWSS: $threshold \in [0, 0.5]$
- FCBF: $threshold \in [10^{-7}, 1]$
Default value is *-1* so every time any of those algorithms are called, the threshold has to be set to the desired value.
- ***predict_voting*** (*boolean*): Sets whether the algorithm will use *model voting* to predict the result. If set to false, the weighted average of the probabilities of each model's prediction will be used. Default value: *false*.
## Operation
### [Base Algorithm](./algorithm.md)

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