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176 Commits

Author SHA1 Message Date
e8d2c9fc0b Set intolerant convergence 2023-11-17 10:26:25 +01:00
d3cb580387 Remove n_jobs from STree 2023-11-17 10:10:31 +01:00
f088df14fd Restore the Creation model position in experiment 2023-11-17 01:10:46 +01:00
e2249eace7 Disable Warning messages in python clfs
Disable removing Python env
2023-11-16 22:38:46 +01:00
408db2aad5 Mark override fit funtcion 2023-11-14 18:59:41 +01:00
f617886133 Add new models to example 2023-11-14 09:12:25 +01:00
69ad660040 Refactor version method in PyClassifier 2023-11-13 13:59:06 +01:00
431b3a3aa5 Fit PyWrap into BayesNet 2023-11-13 11:13:32 +01:00
6a23e2cc26 Add CMakelist integration 2023-11-12 22:14:29 +01:00
f6e00530be Add Pywrap sources 2023-11-12 21:43:07 +01:00
f9258e43b9 Remove using namespace from Library 2023-11-08 18:45:35 +01:00
92820555da Simple fix 2023-10-28 10:56:47 +02:00
5a3af51826 Activate best score in odte 2023-10-25 10:23:42 +02:00
a8f9800631 Fix mistake when no results in manage 2023-10-24 19:44:23 +02:00
84cec0c1e0 Add results files affected in best results excel 2023-10-24 16:18:52 +02:00
130139f644 Update formulas to use letters in ranges in excel 2023-10-24 13:06:31 +02:00
651f84b562 Fix mistake in conditional format in bestresults 2023-10-24 11:18:19 +02:00
553ab0fa22 Add conditional format to BestResults Excel 2023-10-24 10:56:41 +02:00
4975feabff Fix mistake in node count 2023-10-23 22:46:10 +02:00
32293af69f Fix header in manage 2023-10-23 17:04:59 +02:00
858664be2d Add total number of results in manage 2023-10-23 16:22:15 +02:00
1f705f6018 Refactor BestScore and add experiment to .env 2023-10-23 16:12:52 +02:00
7bcd2eed06 Add variable width of dataset name in reports 2023-10-22 22:58:52 +02:00
833acefbb3 Fix index limits mistake in manage 2023-10-22 20:21:50 +02:00
26b649ebae Refactor ManageResults and CommandParser 2023-10-22 20:03:34 +02:00
080eddf9cd Fix hyperparameters output in b_best 2023-10-20 22:52:48 +02:00
04e754b2f5 Adjust filename and hyperparameters in reports 2023-10-20 11:12:46 +02:00
38423048bd Add excel to best report of model 2023-10-19 18:12:55 +02:00
64fc97b892 Rename utilities sources to match final names 2023-10-19 09:57:04 +02:00
2c2159f192 Add quiet mode to b_main
Reduce output when --quiet is set, not showing fold info
2023-10-17 21:51:53 +02:00
6765552a7c Update submodule versions 2023-10-16 19:21:57 +02:00
f72aa5b9a6 Merge pull request 'Create Boost_CFS' (#11) from Boost_CFS into main
Add hyper parameter to BoostAODE. This hyper parameter decides if we select features with cfs/fcbf/iwss before start building models and build a Spode with the selected features.
The hyperparameter is select_features
2023-10-15 09:22:14 +00:00
fa7fe081ad Fix xlsx library finding 2023-10-15 11:19:58 +02:00
660e783517 Update validation for feature selection 2023-10-14 13:32:09 +02:00
b35532dd9e Implement IWSS and FCBF too for BoostAODE 2023-10-14 13:12:04 +02:00
6ef49385ea Remove unneeded method declaration FeatureSelect 2023-10-14 11:30:32 +02:00
6d5a25cdc8 Refactor CFS class creating abstract base class 2023-10-14 11:27:46 +02:00
d00b08cbe8 Fix Header for Linux 2023-10-13 14:26:47 +02:00
977ff6fddb Update CMakeLists for Linux 2023-10-13 14:01:52 +02:00
54b8939f35 Prepare BoostAODE first try 2023-10-13 13:46:22 +02:00
5022a4dc90 Complete CFS tested with Python mufs 2023-10-13 12:29:25 +02:00
40d1dad5d8 Begin CFS implementation 2023-10-11 21:17:26 +02:00
47e2b138c5 Complete first working cfs 2023-10-11 11:33:29 +02:00
e7ded68267 First cfs working version 2023-10-10 23:00:38 +02:00
ca833a34f5 try openssl sha256 2023-10-10 18:16:43 +02:00
df9b4c48d2 Begin CFS initialization 2023-10-10 13:39:11 +02:00
f288bbd6fa Begin adding cfs to BoostAODE 2023-10-10 11:52:39 +02:00
7d8aca4f59 Add Locale shared config to reports 2023-10-09 19:41:29 +02:00
8fdad78a8c Continue Test Network 2023-10-09 11:25:30 +02:00
e3ae073333 Continue test Network 2023-10-08 15:54:58 +02:00
4b732e76c2 MST change unordered_set to list 2023-10-07 19:08:13 +02:00
fe5fead27e Begin Fix Test MST 2023-10-07 01:43:26 +02:00
8c3864f3c8 Complete Folding Test 2023-10-07 01:23:36 +02:00
1287160c47 Refactor makefile to use variables 2023-10-07 00:16:25 +02:00
2f58807322 Begin refactor CMakeLists debug/release paths 2023-10-06 19:32:29 +02:00
17e079edd5 Begin Test Folding 2023-10-06 17:08:54 +02:00
b9e0028e9d Refactor Makefile 2023-10-06 01:28:27 +02:00
e0d39fe631 Fix BayesMetrics Test 2023-10-06 01:14:55 +02:00
36b0277576 Add Maximum Spanning Tree test 2023-10-05 15:45:36 +02:00
da8d018ec4 Refactor Makefile 2023-10-05 11:45:00 +02:00
5f0676691c Add First BayesMetrics Tests 2023-10-05 01:14:16 +02:00
3448fb1299 Refactor Tests and add BayesMetrics test 2023-10-04 23:19:23 +02:00
5e938d5cca Add ranks sheet to excel best results 2023-10-04 16:26:57 +02:00
55e742438f Add constant references to Statistics 2023-10-04 13:40:45 +02:00
c4ae3fe429 Add Control model rank info to report 2023-10-04 12:42:35 +02:00
93e4ff94db Add significance level as parameter in best 2023-10-02 15:46:40 +02:00
57c27f739c Remove unused code in BestResults 2023-10-02 15:31:02 +02:00
a434d7f1ae Add a Linux config in launch.json 2023-09-30 18:44:21 +02:00
294666c516 Fix a Linux problem in Datasets 2023-09-30 18:43:47 +02:00
fd04e78ad9 Restore sample.cc 2023-09-29 18:50:25 +02:00
66ec1b343b Remove platformUtils and split Datasets & Dataset 2023-09-29 18:20:46 +02:00
bb423da42f Add csv and R_dat files to platform 2023-09-29 13:52:50 +02:00
db17c14042 Change names of executables to b_... 2023-09-29 09:17:50 +02:00
a4401cb78f Linux CMakeLists.txt adjustment 2023-09-29 00:30:47 +02:00
9d3d9cc6c6 Complete Excel output for bestResults with Friedman test 2023-09-28 18:52:37 +02:00
cfcf3c16df Add best results Excel 2023-09-28 17:12:04 +02:00
85202260f3 Separate specific Excel methods to ExcelFile 2023-09-28 13:07:11 +02:00
82acb3cab5 Enhance output of Best results reports 2023-09-28 12:08:56 +02:00
623ceed396 Merge pull request 'Add Friedman Test & post hoc tests to BestResults' (#10) from boost into main
Reviewed-on: #10
2023-09-28 07:44:55 +00:00
926de2bebd Add boost info to README 2023-09-28 09:44:33 +02:00
71704e3547 Enhance output info in Statistics 2023-09-28 01:27:18 +02:00
3b06534327 Remove duplicated code in BestResults 2023-09-28 00:59:34 +02:00
ac89a451e3 Duplicate statistics tests in class 2023-09-28 00:45:15 +02:00
00c6cf663b Fix order of output in posthoc 2023-09-27 19:11:47 +02:00
5043c12be8 Complete posthoc with Holm adjust 2023-09-27 18:34:16 +02:00
11320e2cc7 Complete friedman test as in exreport 2023-09-27 12:36:03 +02:00
ce66483b65 Update boost version requirement for Linux 2023-09-26 14:12:53 +02:00
cab8e14b2d Add friedman hyperparameter 2023-09-26 11:26:59 +02:00
f0d0abe891 Add boost library link to linux build 2023-09-26 01:07:50 +02:00
dcba146e12 Begin adding Friedman test to BestResults 2023-09-26 01:04:59 +02:00
3ea0285119 Fix ranks to match friedman test ranks 2023-09-25 18:38:12 +02:00
e3888e1503 Merge pull request 'bestResults' (#9) from bestResults into main
Reviewed-on: https://gitea.rmontanana.es:3000/rmontanana/BayesNet/pulls/9

Add best results management, build, report, build all & report all
2023-09-25 12:02:17 +00:00
06de13df98 Add date/time to header of report best 2023-09-25 10:04:53 +02:00
de4fa6a04f Add color to totals 2023-09-23 10:30:39 +02:00
3a7bf4e672 Fix ranking order mistake 2023-09-23 01:33:23 +02:00
cd0bc02a74 Add report/build all with totals and ranks 2023-09-23 01:14:02 +02:00
c8597a794e Begin report all models 2023-09-22 18:13:32 +02:00
b30416364d Fix mistake in best results file name 2023-09-22 14:14:39 +02:00
3a16589220 Add best config for debug in vscode 2023-09-22 01:04:36 +02:00
c4f9187e2a Complete best build and report 2023-09-22 01:03:55 +02:00
c4d0a5b4e6 Split Result from Results 2023-09-21 23:30:17 +02:00
7bfafe555f Begin BestResults build 2023-09-21 23:04:11 +02:00
337b6f7e79 Rename BestResult to BestScore 2023-09-21 19:30:07 +02:00
5fa0b957dd Fix mistake in idx range in manage 2023-09-20 19:12:07 +02:00
67252fc41d Fix CMakeLists libxlsxwriter for Linux 2023-09-20 19:02:53 +02:00
94ae9456a0 Fix libxslxwriter linking problem 2023-09-20 18:50:11 +02:00
781993e326 Resolve some warnings 2023-09-20 17:54:15 +02:00
8257a6ae39 Add message of not exist Best Results 2023-09-20 13:50:34 +02:00
fc81730dfc Merge pull request 'Exchange OpenXLSX to libxlsxwriter' (#8) from libxlsxwriter into main
Add multiple sheets to excel file
Add format and color to sheets
Add comparison with ZeroR
Add comparison with Best Results
Separate contextual menu from general in manage
2023-09-20 11:17:16 +00:00
d8734ff082 Separate contextual menu from general 2023-09-20 13:15:33 +02:00
03533461c8 Add compare to best results in manage 2023-09-20 12:51:19 +02:00
68f22a673d Add comparison to report console 2023-09-20 11:40:01 +02:00
b9bc0088f3 Add format to unique dataset results summary 2023-09-20 10:30:45 +02:00
c280e254ca Remove OpenXLSX submodule 2023-09-20 01:09:58 +02:00
3d0f29fda3 Remove .vscode/settings.json from repository 2023-09-20 01:01:40 +02:00
20a6ebab7c Support to add any number of sheets to excel 2023-09-20 00:58:01 +02:00
925f71166c Fix mistake in comparison 2023-09-19 23:46:49 +02:00
f69f415b92 Complete comparison with ZeroR 2023-09-19 17:55:03 +02:00
1bdfbd1620 Complete adding color to format 2023-09-19 14:07:41 +02:00
06fb135526 First approach 2023-09-18 23:26:22 +02:00
501ea0ab4e Fix CMakeList manage build with Linux 2023-09-18 19:27:40 +02:00
847c6761d7 Add Linux specific link library to cmake 2023-09-17 10:42:19 +02:00
6030885fc3 Add partial result filter to manage 2023-09-16 17:27:18 +02:00
89df7f4db0 Add library to manage link 2023-09-14 01:41:49 +02:00
41257ed566 If ! convergence don't predict test 2023-09-10 19:50:36 +02:00
506369e46b Add Convergence hyperparameter 2023-09-07 11:27:35 +02:00
d908f389f5 Begin using validation as finish condition 2023-09-06 10:51:07 +02:00
5a7c8f1818 Add status to classifier and Experiment 2023-09-05 13:39:43 +02:00
64fc7bd9dd Add show dataset detail in report 2023-09-05 09:26:49 +02:00
0b7beda78c Add threads without limit to network fit 2023-09-04 21:24:11 +02:00
05b670dfc0 Add detail to fold progress in main 2023-09-03 16:33:48 +02:00
de62d42b74 Fix make debug command 2023-09-03 14:13:10 +02:00
edb957d22e Add filter complete results to manage 2023-09-03 14:07:11 +02:00
4de5cb4c6c Merge pull request 'Solve Ensemble models exceptions on certain datasets' (#7) from solveexceptions into main
Reviewed-on: #7
2023-09-02 15:29:33 +00:00
c35030f137 Upgrade models version and Add class diagram 2023-09-02 14:39:43 +02:00
182b07ed90 Solve voting vector error 2023-09-02 13:58:12 +02:00
7806f961e2 Remove threads 2023-08-31 20:30:28 +02:00
7c3e315ae7 Add Linux specific options to compile 2023-08-29 18:20:55 +02:00
284ef6dfd1 Add significanceModels to AODELd 2023-08-24 12:58:53 +02:00
1c6af619b5 Exception if hyperparameters not valid 2023-08-24 12:09:35 +02:00
86ffdfd6f3 Add const feature and className to fit models 2023-08-23 23:15:39 +02:00
d82148079d Add KDB hyperparameters K and theta 2023-08-23 00:44:10 +02:00
067430fd1b Add xlsxopen submodule 2023-08-22 23:45:11 +02:00
f5d0d16365 Merge pull request 'Add excel report to manage results' (#6) from xlsx into main
Reviewed-on: https://gitea.rmontanana.es:11000/rmontanana/BayesNet/pulls/6
2023-08-22 21:40:11 +00:00
97ca8ac084 Move check valid hyperparameters to Classifier 2023-08-22 22:12:20 +02:00
1c1385b768 Fix maxModels mistake in BoostAODE if !repeatSp
Throw exception if wrong hyperparmeter is supplied
2023-08-22 21:55:17 +02:00
35432b6294 Fix time std was not saved in experiment 2023-08-22 12:30:27 +02:00
c59dd30e53 Complete Excel Report with data 2023-08-22 11:55:15 +02:00
d2da0ddb88 Create ReportExcel eq to ReportConsole 2023-08-21 17:51:49 +02:00
8066701c3c Refactor Report class into ReportBase & ReportCons 2023-08-21 17:16:29 +02:00
0f66ac73d0 Revert "Refactor Report into ReportBase & ReportConsole"
This reverts commit 4370bf51d7.
2023-08-21 17:15:14 +02:00
4370bf51d7 Refactor Report into ReportBase & ReportConsole 2023-08-21 17:14:23 +02:00
2b7353b9e0 Add default sorting by date in manage 2023-08-21 16:30:10 +02:00
b686b3c9c3 Enhance copy in Makefile 2023-08-21 12:18:23 +02:00
2dd04a6c44 enhance saving results and add Makefile copy 2023-08-21 11:57:45 +02:00
1da83662d0 Always save results 2023-08-21 10:55:20 +02:00
3ac9593c65 Fix mistake in sample 2023-08-20 20:36:46 +02:00
6b317accf1 Add hyperparameters and processing order to Boost 2023-08-20 20:31:23 +02:00
4964aab722 Add hyperparameters management in experiments 2023-08-20 17:57:38 +02:00
7a6ec73d63 Merge pull request 'boostAode' (#5) from boostAode into main
Reviewed-on: https://gitea.rmontanana.es:11000/rmontanana/BayesNet/pulls/5
Implement boostAODE
add list datasets
add manage results
2023-08-20 09:02:07 +00:00
1a534888d6 Fix report format 2023-08-19 23:30:44 +02:00
59ffd179f4 Fix report format 2023-08-19 21:26:48 +02:00
9972738deb Add list datasets and add locale format 2023-08-19 19:05:16 +02:00
bafcb26bb6 Add manage to build target 2023-08-18 13:43:53 +02:00
2d7999d5f2 Add manage to release targets 2023-08-18 13:43:13 +02:00
a6bb22dfb5 Complete first BoostAODE 2023-08-18 11:50:34 +02:00
704dc937be Remove FeatureSel, add SelectKBest to BayesMetrics 2023-08-16 19:05:18 +02:00
a3e665eed6 make weights double 2023-08-16 12:46:09 +02:00
918a7b4180 Remove unneeded output 2023-08-16 12:36:38 +02:00
80b20f35b4 Fix weights mistakes in computation 2023-08-16 12:32:51 +02:00
4d4780c1d5 Add BoostAODE model based on AODE 2023-08-15 16:16:04 +02:00
fa612c531e Complete Adding weights to Models 2023-08-15 15:59:56 +02:00
24b68f9ae2 Add weigths as parameter 2023-08-15 15:04:56 +02:00
a062ebf445 Merge pull request 'reports' (#4) from reports into boostAode
Reviewed-on: https://gitea.rmontanana.es:11000/rmontanana/BayesNet/pulls/4
2023-08-14 16:58:48 +00:00
f26ea1f0ac Add weights to BayesMetrics 2023-08-13 12:56:06 +02:00
af0419c9da First approx with const 1 weights 2023-08-13 00:59:02 +02:00
143 changed files with 6198 additions and 1979 deletions

31
.clang-uml Normal file
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@@ -0,0 +1,31 @@
compilation_database_dir: build
output_directory: puml
diagrams:
BayesNet:
type: class
glob:
- src/BayesNet/*.cc
- src/Platform/*.cc
using_namespace: bayesnet
include:
namespaces:
- bayesnet
- platform
plantuml:
after:
- "note left of {{ alias(\"MyProjectMain\") }}: Main class of myproject library."
sequence:
type: sequence
glob:
- src/Platform/main.cc
combine_free_functions_into_file_participants: true
using_namespace:
- std
- bayesnet
- platform
include:
paths:
- src/BayesNet
- src/Platform
start_from:
- function: main(int,const char **)

6
.gitignore vendored
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@@ -31,7 +31,11 @@
*.exe
*.out
*.app
build/
build/**
build_debug/**
build_release/**
*.dSYM/**
cmake-build*/**
.idea
puml/**
.vscode/settings.json

3
.gitmodules vendored
View File

@@ -10,3 +10,6 @@
[submodule "lib/json"]
path = lib/json
url = https://github.com/nlohmann/json.git
[submodule "lib/libxlsxwriter"]
path = lib/libxlsxwriter
url = https://github.com/jmcnamara/libxlsxwriter.git

18
.vscode/c_cpp_properties.json vendored Normal file
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@@ -0,0 +1,18 @@
{
"configurations": [
{
"name": "Mac",
"includePath": [
"${workspaceFolder}/**"
],
"defines": [],
"macFrameworkPath": [
"/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks"
],
"cStandard": "c17",
"cppStandard": "c++17",
"compileCommands": "${workspaceFolder}/cmake-build-release/compile_commands.json"
}
],
"version": 4
}

59
.vscode/launch.json vendored
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@@ -5,16 +5,16 @@
"type": "lldb",
"request": "launch",
"name": "sample",
"program": "${workspaceFolder}/build/sample/BayesNetSample",
"program": "${workspaceFolder}/build_debug/sample/BayesNetSample",
"args": [
"-d",
"iris",
"-m",
"KDB",
"TANLd",
"-s",
"271",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets/",
"/home/rmontanana/Code/discretizbench/datasets/",
],
//"cwd": "${workspaceFolder}/build/sample/",
},
@@ -22,34 +22,69 @@
"type": "lldb",
"request": "launch",
"name": "experiment",
"program": "${workspaceFolder}/build/src/Platform/main",
"program": "${workspaceFolder}/build_debug/src/Platform/b_main",
"args": [
"-m",
"SPODELd",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets",
"STree",
"--stratified",
"-d",
"iris"
"iris",
//"--discretize"
// "--hyperparameters",
// "{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "/Users/rmontanana/Code/discretizbench",
"cwd": "/home/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "best",
"program": "${workspaceFolder}/build_debug/src/Platform/b_best",
"args": [
"-m",
"BoostAODE",
"-s",
"accuracy",
"--build",
],
"cwd": "/home/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "manage",
"program": "${workspaceFolder}/build/src/Platform/manage",
"program": "${workspaceFolder}/build_debug/src/Platform/b_manage",
"args": [
"-n",
"20"
],
"cwd": "/Users/rmontanana/Code/discretizbench",
"cwd": "/home/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "list",
"program": "${workspaceFolder}/build_debug/src/Platform/b_list",
"args": [],
//"cwd": "/Users/rmontanana/Code/discretizbench",
"cwd": "/home/rmontanana/Code/covbench",
},
{
"type": "lldb",
"request": "launch",
"name": "test",
"program": "${workspaceFolder}/build_debug/tests/unit_tests",
"args": [
"-c=\"Metrics Test\"",
// "-s",
],
"cwd": "${workspaceFolder}/build/tests",
},
{
"name": "Build & debug active file",
"type": "cppdbg",
"request": "launch",
"program": "${workspaceFolder}/build/bayesnet",
"program": "${workspaceFolder}/build_debug/bayesnet",
"args": [],
"stopAtEntry": false,
"cwd": "${workspaceFolder}",

109
.vscode/settings.json vendored
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@@ -1,109 +0,0 @@
{
"files.associations": {
"*.rmd": "markdown",
"*.py": "python",
"vector": "cpp",
"__bit_reference": "cpp",
"__bits": "cpp",
"__config": "cpp",
"__debug": "cpp",
"__errc": "cpp",
"__hash_table": "cpp",
"__locale": "cpp",
"__mutex_base": "cpp",
"__node_handle": "cpp",
"__nullptr": "cpp",
"__split_buffer": "cpp",
"__string": "cpp",
"__threading_support": "cpp",
"__tuple": "cpp",
"array": "cpp",
"atomic": "cpp",
"bitset": "cpp",
"cctype": "cpp",
"chrono": "cpp",
"clocale": "cpp",
"cmath": "cpp",
"compare": "cpp",
"complex": "cpp",
"concepts": "cpp",
"cstdarg": "cpp",
"cstddef": "cpp",
"cstdint": "cpp",
"cstdio": "cpp",
"cstdlib": "cpp",
"cstring": "cpp",
"ctime": "cpp",
"cwchar": "cpp",
"cwctype": "cpp",
"exception": "cpp",
"initializer_list": "cpp",
"ios": "cpp",
"iosfwd": "cpp",
"istream": "cpp",
"limits": "cpp",
"locale": "cpp",
"memory": "cpp",
"mutex": "cpp",
"new": "cpp",
"optional": "cpp",
"ostream": "cpp",
"ratio": "cpp",
"sstream": "cpp",
"stdexcept": "cpp",
"streambuf": "cpp",
"string": "cpp",
"string_view": "cpp",
"system_error": "cpp",
"tuple": "cpp",
"type_traits": "cpp",
"typeinfo": "cpp",
"unordered_map": "cpp",
"variant": "cpp",
"algorithm": "cpp",
"iostream": "cpp",
"iomanip": "cpp",
"numeric": "cpp",
"set": "cpp",
"__tree": "cpp",
"deque": "cpp",
"list": "cpp",
"map": "cpp",
"unordered_set": "cpp",
"any": "cpp",
"condition_variable": "cpp",
"forward_list": "cpp",
"fstream": "cpp",
"stack": "cpp",
"thread": "cpp",
"__memory": "cpp",
"filesystem": "cpp",
"*.toml": "toml",
"utility": "cpp",
"__verbose_abort": "cpp",
"bit": "cpp",
"random": "cpp",
"*.tcc": "cpp",
"functional": "cpp",
"iterator": "cpp",
"memory_resource": "cpp",
"format": "cpp",
"valarray": "cpp",
"regex": "cpp",
"span": "cpp",
"cfenv": "cpp",
"cinttypes": "cpp",
"csetjmp": "cpp",
"future": "cpp",
"queue": "cpp",
"typeindex": "cpp",
"shared_mutex": "cpp",
"*.ipp": "cpp",
"cassert": "cpp",
"charconv": "cpp",
"source_location": "cpp",
"ranges": "cpp"
},
"cmake.configureOnOpen": false,
"C_Cpp.default.configurationProvider": "ms-vscode.cmake-tools"
}

23
.vscode/tasks.json vendored
View File

@@ -32,6 +32,29 @@
],
"group": "build",
"detail": "Task generated by Debugger."
},
{
"type": "cppbuild",
"label": "C/C++: g++ build active file",
"command": "/usr/bin/g++",
"args": [
"-fdiagnostics-color=always",
"-g",
"${file}",
"-o",
"${fileDirname}/${fileBasenameNoExtension}"
],
"options": {
"cwd": "${fileDirname}"
},
"problemMatcher": [
"$gcc"
],
"group": {
"kind": "build",
"isDefault": true
},
"detail": "Task generated by Debugger."
}
]
}

View File

@@ -1,7 +1,7 @@
cmake_minimum_required(VERSION 3.20)
project(BayesNet
VERSION 0.1.0
VERSION 0.2.0
DESCRIPTION "Bayesian Network and basic classifiers Library."
HOMEPAGE_URL "https://github.com/rmontanana/bayesnet"
LANGUAGES CXX
@@ -24,6 +24,7 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
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")
# Options
# -------
@@ -31,17 +32,30 @@ 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)
# Boost Library
set(Boost_USE_STATIC_LIBS OFF)
set(Boost_USE_MULTITHREADED ON)
set(Boost_USE_STATIC_RUNTIME OFF)
find_package(Boost 1.66.0 REQUIRED COMPONENTS python3 numpy3)
if(Boost_FOUND)
message("Boost_INCLUDE_DIRS=${Boost_INCLUDE_DIRS}")
include_directories(${Boost_INCLUDE_DIRS})
endif()
# Python
find_package(Python3 3.11...3.11.9 COMPONENTS Interpreter Development REQUIRED)
message("Python3_LIBRARIES=${Python3_LIBRARIES}")
# CMakes modules
# --------------
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
include(AddGitSubmodule)
if (CODE_COVERAGE)
enable_testing()
include(CodeCoverage)
MESSAGE("Code coverage enabled")
set(CMAKE_C_FLAGS " ${CMAKE_C_FLAGS} -fprofile-arcs -ftest-coverage")
set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
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)
@@ -56,15 +70,21 @@ add_git_submodule("lib/mdlp")
add_git_submodule("lib/argparse")
add_git_submodule("lib/json")
find_library(XLSXWRITER_LIB NAMES libxlsxwriter.dylib libxlsxwriter.so PATHS ${BayesNet_SOURCE_DIR}/lib/libxlsxwriter/lib)
message("XLSXWRITER_LIB=${XLSXWRITER_LIB}")
# Subdirectories
# --------------
add_subdirectory(config)
add_subdirectory(lib/Files)
add_subdirectory(src/BayesNet)
add_subdirectory(src/Platform)
add_subdirectory(src/PyClassifiers)
add_subdirectory(sample)
file(GLOB BayesNet_HEADERS CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.h ${BayesNet_SOURCE_DIR}/BayesNet/*.hpp)
file(GLOB BayesNet_HEADERS CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.h ${BayesNet_SOURCE_DIR}/BayesNet/*.h)
file(GLOB BayesNet_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.cc ${BayesNet_SOURCE_DIR}/src/BayesNet/*.cpp)
file(GLOB Platform_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/Platform/*.cc ${BayesNet_SOURCE_DIR}/src/Platform/*.cpp)
@@ -74,7 +94,6 @@ file(GLOB Platform_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/Platform
if (ENABLE_TESTING)
MESSAGE("Testing enabled")
add_git_submodule("lib/catch2")
include(CTest)
add_subdirectory(tests)
endif (ENABLE_TESTING)

114
Makefile
View File

@@ -1,6 +1,26 @@
SHELL := /bin/bash
.DEFAULT_GOAL := help
.PHONY: coverage setup help build test
.PHONY: coverage setup help build test clean debug release
f_release = build_release
f_debug = build_debug
app_targets = b_best b_list b_main b_manage
test_targets = unit_tests_bayesnet unit_tests_platform
n_procs = -j 16
define ClearTests
@for t in $(test_targets); do \
if [ -f $(f_debug)/tests/$$t ]; then \
echo ">>> Cleaning $$t..." ; \
rm -f $(f_debug)/tests/$$t ; \
fi ; \
done
@nfiles="$(find . -name "*.gcda" -print0)" ; \
if test "${nfiles}" != "" ; then \
find . -name "*.gcda" -print0 | xargs -0 rm 2>/dev/null ;\
fi ;
endef
setup: ## Install dependencies for tests and coverage
@if [ "$(shell uname)" = "Darwin" ]; then \
@@ -11,49 +31,85 @@ setup: ## Install dependencies for tests and coverage
pip install gcovr; \
fi
dest ?= ${HOME}/bin
install: ## Copy binary files to bin folder
@echo "Destination folder: $(dest)"
make buildr
@echo ">>> Copying files to $(dest)"
@cp $(f_release)/src/Platform/b_main $(dest)
@cp $(f_release)/src/Platform/b_list $(dest)
@cp $(f_release)/src/Platform/b_manage $(dest)
@cp $(f_release)/src/Platform/b_best $(dest)
dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
cd build && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o 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
build: ## Build the main and BayesNetSample
cmake --build build -t main -t BayesNetSample -j 32
buildd: ## Build the debug targets
cmake --build $(f_debug) -t $(app_targets) $(n_procs)
clean: ## Clean the debug info
@echo ">>> Cleaning Debug BayesNet ...";
find . -name "*.gcda" -print0 | xargs -0 rm
buildr: ## Build the release targets
cmake --build $(f_release) -t $(app_targets) $(n_procs)
clean: ## Clean the tests info
@echo ">>> Cleaning Debug BayesNet tests...";
$(call ClearTests)
@echo ">>> Done";
clang-uml: ## Create uml class and sequence diagrams
clang-uml -p --add-compile-flag -I /usr/lib/gcc/x86_64-redhat-linux/8/include/
debug: ## Build a debug version of the project
@echo ">>> Building Debug BayesNet...";
@if [ -d ./build ]; then rm -rf ./build; fi
@mkdir build;
cmake -S . -B build -D CMAKE_BUILD_TYPE=Debug -D ENABLE_TESTING=ON -D CODE_COVERAGE=ON; \
cmake --build build -j 32;
@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 ./build ]; then rm -rf ./build; fi
@mkdir build;
cmake -S . -B build -D CMAKE_BUILD_TYPE=Release; \
cmake --build build -t main -t BayesNetSample -j 32;
@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";
test: ## Run tests
@echo "* Running tests...";
find . -name "*.gcda" -print0 | xargs -0 rm
@cd build; \
cmake --build . --target unit_tests ;
@cd build/tests; \
./unit_tests;
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)
@for t in $(test_targets); do \
if [ -f $(f_debug)/tests/$$t ]; then \
cd $(f_debug)/tests ; \
./$$t $(opt) ; \
fi ; \
done
@echo ">>> Done";
opt = ""
testp: ## Run platform tests (opt="-s") to verbose output the tests, (opt="-c='Stratified Fold Test'") to run only that section
@echo ">>> Running Platform tests...";
@$(MAKE) clean
@cmake --build $(f_debug) --target unit_tests_platform $(n_procs)
@if [ -f $(f_debug)/tests/unit_tests_platform ]; then cd $(f_debug)/tests ; ./unit_tests_platform $(opt) ; fi ;
@echo ">>> Done";
opt = ""
testb: ## Run BayesNet tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
@echo ">>> Running BayesNet tests...";
@$(MAKE) clean
@cmake --build $(f_debug) --target unit_tests_bayesnet $(n_procs)
@if [ -f $(f_debug)/tests/unit_tests_bayesnet ]; then cd $(f_debug)/tests ; ./unit_tests_bayesnet $(opt) ; fi ;
@echo ">>> Done";
coverage: ## Run tests and generate coverage report (build/index.html)
@echo "*Building tests...";
find . -name "*.gcda" -print0 | xargs -0 rm
@cd build; \
cmake --build . --target unit_tests ;
@cd build/tests; \
./unit_tests;
gcovr ;
@echo ">>> Building tests with coverage...";
@$(MAKE) test
@cd $(f_debug) ; \
gcovr --config ../gcovr.cfg tests ;
@echo ">>> Done";
help: ## Show help message
@IFS=$$'\n' ; \

View File

@@ -1,5 +1,53 @@
# BayesNet
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
Bayesian Network Classifier with libtorch from scratch
## 0. Setup
Before compiling BayesNet.
### boost library
[Getting Started](<https://www.boost.org/doc/libs/1_83_0/more/getting_started/index.html>)
The best option is install the packages that the Linux distribution have in its repository. If this is the case:
```bash
sudo dnf install boost-devel
```
If this is not possible and the compressed packaged is installed, the following environment variable has to be set:
```bash
export BOOST_ROOT=/path/to/library/
```
### libxlswriter
```bash
cd lib/libxlsxwriter
make
make install DESTDIR=/home/rmontanana/Code PREFIX=
```
Environment variable has to be set:
```bash
export LD_LIBRARY_PATH=/usr/local/lib
```
### Release
```bash
make release
```
### Debug & Tests
```bash
make debug
```
## 1. Introduction

View File

@@ -1,12 +0,0 @@
digraph BayesNet {
label=<BayesNet >
fontsize=30
fontcolor=blue
labelloc=t
layout=circo
class [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ]
class -> sepallength class -> sepalwidth class -> petallength class -> petalwidth petallength [shape=circle]
petallength -> sepallength petalwidth [shape=circle]
sepallength [shape=circle]
sepallength -> sepalwidth sepalwidth [shape=circle]
sepalwidth -> petalwidth }

View File

@@ -1 +0,0 @@
null

BIN
diagrams/BayesNet.pdf Executable file

Binary file not shown.

View File

@@ -4,11 +4,9 @@
#include <map>
#include <iostream>
using namespace std;
ArffFiles::ArffFiles() = default;
vector<string> ArffFiles::getLines() const
std::vector<std::string> ArffFiles::getLines() const
{
return lines;
}
@@ -18,48 +16,48 @@ unsigned long int ArffFiles::getSize() const
return lines.size();
}
vector<pair<string, string>> ArffFiles::getAttributes() const
std::vector<std::pair<std::string, std::string>> ArffFiles::getAttributes() const
{
return attributes;
}
string ArffFiles::getClassName() const
std::string ArffFiles::getClassName() const
{
return className;
}
string ArffFiles::getClassType() const
std::string ArffFiles::getClassType() const
{
return classType;
}
vector<vector<float>>& ArffFiles::getX()
std::vector<std::vector<float>>& ArffFiles::getX()
{
return X;
}
vector<int>& ArffFiles::getY()
std::vector<int>& ArffFiles::getY()
{
return y;
}
void ArffFiles::loadCommon(string fileName)
void ArffFiles::loadCommon(std::string fileName)
{
ifstream file(fileName);
std::ifstream file(fileName);
if (!file.is_open()) {
throw invalid_argument("Unable to open file");
throw std::invalid_argument("Unable to open file");
}
string line;
string keyword;
string attribute;
string type;
string type_w;
std::string line;
std::string keyword;
std::string attribute;
std::string type;
std::string type_w;
while (getline(file, line)) {
if (line.empty() || line[0] == '%' || line == "\r" || line == " ") {
continue;
}
if (line.find("@attribute") != string::npos || line.find("@ATTRIBUTE") != string::npos) {
stringstream ss(line);
if (line.find("@attribute") != std::string::npos || line.find("@ATTRIBUTE") != std::string::npos) {
std::stringstream ss(line);
ss >> keyword >> attribute;
type = "";
while (ss >> type_w)
@@ -74,35 +72,35 @@ void ArffFiles::loadCommon(string fileName)
}
file.close();
if (attributes.empty())
throw invalid_argument("No attributes found");
throw std::invalid_argument("No attributes found");
}
void ArffFiles::load(const string& fileName, bool classLast)
void ArffFiles::load(const std::string& fileName, bool classLast)
{
int labelIndex;
loadCommon(fileName);
if (classLast) {
className = get<0>(attributes.back());
classType = get<1>(attributes.back());
className = std::get<0>(attributes.back());
classType = std::get<1>(attributes.back());
attributes.pop_back();
labelIndex = static_cast<int>(attributes.size());
} else {
className = get<0>(attributes.front());
classType = get<1>(attributes.front());
className = std::get<0>(attributes.front());
classType = std::get<1>(attributes.front());
attributes.erase(attributes.begin());
labelIndex = 0;
}
generateDataset(labelIndex);
}
void ArffFiles::load(const string& fileName, const string& name)
void ArffFiles::load(const std::string& fileName, const std::string& name)
{
int labelIndex;
loadCommon(fileName);
bool found = false;
for (int i = 0; i < attributes.size(); ++i) {
if (attributes[i].first == name) {
className = get<0>(attributes[i]);
classType = get<1>(attributes[i]);
className = std::get<0>(attributes[i]);
classType = std::get<1>(attributes[i]);
attributes.erase(attributes.begin() + i);
labelIndex = i;
found = true;
@@ -110,19 +108,19 @@ void ArffFiles::load(const string& fileName, const string& name)
}
}
if (!found) {
throw invalid_argument("Class name not found");
throw std::invalid_argument("Class name not found");
}
generateDataset(labelIndex);
}
void ArffFiles::generateDataset(int labelIndex)
{
X = vector<vector<float>>(attributes.size(), vector<float>(lines.size()));
auto yy = vector<string>(lines.size(), "");
auto removeLines = vector<int>(); // Lines with missing values
X = std::vector<std::vector<float>>(attributes.size(), std::vector<float>(lines.size()));
auto yy = std::vector<std::string>(lines.size(), "");
auto removeLines = std::vector<int>(); // Lines with missing values
for (size_t i = 0; i < lines.size(); i++) {
stringstream ss(lines[i]);
string value;
std::stringstream ss(lines[i]);
std::string value;
int pos = 0;
int xIndex = 0;
while (getline(ss, value, ',')) {
@@ -146,21 +144,21 @@ void ArffFiles::generateDataset(int labelIndex)
y = factorize(yy);
}
string ArffFiles::trim(const string& source)
std::string ArffFiles::trim(const std::string& source)
{
string s(source);
std::string s(source);
s.erase(0, s.find_first_not_of(" '\n\r\t"));
s.erase(s.find_last_not_of(" '\n\r\t") + 1);
return s;
}
vector<int> ArffFiles::factorize(const vector<string>& labels_t)
std::vector<int> ArffFiles::factorize(const std::vector<std::string>& labels_t)
{
vector<int> yy;
std::vector<int> yy;
yy.reserve(labels_t.size());
map<string, int> labelMap;
std::map<std::string, int> labelMap;
int i = 0;
for (const string& label : labels_t) {
for (const std::string& label : labels_t) {
if (labelMap.find(label) == labelMap.end()) {
labelMap[label] = i++;
}

View File

@@ -4,31 +4,29 @@
#include <string>
#include <vector>
using namespace std;
class ArffFiles {
private:
vector<string> lines;
vector<pair<string, string>> attributes;
string className;
string classType;
vector<vector<float>> X;
vector<int> y;
std::vector<std::string> lines;
std::vector<std::pair<std::string, std::string>> attributes;
std::string className;
std::string classType;
std::vector<std::vector<float>> X;
std::vector<int> y;
void generateDataset(int);
void loadCommon(string);
void loadCommon(std::string);
public:
ArffFiles();
void load(const string&, bool = true);
void load(const string&, const string&);
vector<string> getLines() const;
void load(const std::string&, bool = true);
void load(const std::string&, const std::string&);
std::vector<std::string> getLines() const;
unsigned long int getSize() const;
string getClassName() const;
string getClassType() const;
static string trim(const string&);
vector<vector<float>>& getX();
vector<int>& getY();
vector<pair<string, string>> getAttributes() const;
static vector<int> factorize(const vector<string>& labels_t);
std::string getClassName() const;
std::string getClassType() const;
static std::string trim(const std::string&);
std::vector<std::vector<float>>& getX();
std::vector<int>& getY();
std::vector<std::pair<std::string, std::string>> getAttributes() const;
static std::vector<int> factorize(const std::vector<std::string>& labels_t);
};
#endif

View File

@@ -1,2 +1 @@
add_library(ArffFiles ArffFiles.cc)
#target_link_libraries(BayesNet "${TORCH_LIBRARIES}")

1
lib/libxlsxwriter Submodule

Submodule lib/libxlsxwriter added at 29355a0887

View File

@@ -3,5 +3,6 @@ include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/argparse/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
add_executable(BayesNetSample sample.cc ${BayesNet_SOURCE_DIR}/src/Platform/Folding.cc ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNetSample BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")

View File

@@ -1,24 +1,23 @@
#include <iostream>
#include <torch/torch.h>
#include <string>
#include <std::string>
#include <map>
#include <argparse/argparse.hpp>
#include "ArffFiles.h"
#include <nlohmann/json.hpp>
#include "ArffFiles.h"v
#include "BayesMetrics.h"
#include "CPPFImdlp.h"
#include "Folding.h"
#include "Models.h"
#include "modelRegister.h"
#include <fstream>
const std::string PATH = "../../data/";
using namespace std;
const string PATH = "../../data/";
pair<vector<mdlp::labels_t>, map<string, int>> discretize(vector<mdlp::samples_t>& X, mdlp::labels_t& y, vector<string> features)
pair<std::vector<mdlp::labels_t>, map<std::string, int>> discretize(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y, std::vector<std::string> features)
{
vector<mdlp::labels_t>Xd;
map<string, int> maxes;
std::vector<mdlp::labels_t>Xd;
map<std::string, int> maxes;
auto fimdlp = mdlp::CPPFImdlp();
for (int i = 0; i < X.size(); i++) {
@@ -30,7 +29,7 @@ pair<vector<mdlp::labels_t>, map<string, int>> discretize(vector<mdlp::samples_t
return { Xd, maxes };
}
bool file_exists(const std::string& name)
bool file_exists(const std::std::std::string& name)
{
if (FILE* file = fopen(name.c_str(), "r")) {
fclose(file);
@@ -39,12 +38,12 @@ bool file_exists(const std::string& name)
return false;
}
}
pair<vector<vector<int>>, vector<int>> extract_indices(vector<int> indices, vector<vector<int>> X, vector<int> y)
pair<std::vector<std::vector<int>>, std::vector<int>> extract_indices(std::vector<int> indices, std::vector<std::vector<int>> X, std::vector<int> y)
{
vector<vector<int>> Xr; // nxm
vector<int> yr;
std::vector<std::vector<int>> Xr; // nxm
std::vector<int> yr;
for (int col = 0; col < X.size(); ++col) {
Xr.push_back(vector<int>());
Xr.push_back(std::vector<int>());
}
for (auto index : indices) {
for (int col = 0; col < X.size(); ++col) {
@@ -57,7 +56,7 @@ pair<vector<vector<int>>, vector<int>> extract_indices(vector<int> indices, vect
int main(int argc, char** argv)
{
map<string, bool> datasets = {
map<std::string, bool> datasets = {
{"diabetes", true},
{"ecoli", true},
{"glass", true},
@@ -67,13 +66,13 @@ int main(int argc, char** argv)
{"liver-disorders", true},
{"mfeat-factors", true},
};
auto valid_datasets = vector<string>();
auto valid_datasets = std::vector<std::string>();
transform(datasets.begin(), datasets.end(), back_inserter(valid_datasets),
[](const pair<string, bool>& pair) { return pair.first; });
[](const pair<std::string, bool>& pair) { return pair.first; });
argparse::ArgumentParser program("BayesNetSample");
program.add_argument("-d", "--dataset")
.help("Dataset file name")
.action([valid_datasets](const std::string& value) {
.action([valid_datasets](const std::std::std::string& value) {
if (find(valid_datasets.begin(), valid_datasets.end(), value) != valid_datasets.end()) {
return value;
}
@@ -82,23 +81,23 @@ int main(int argc, char** argv)
);
program.add_argument("-p", "--path")
.help(" folder where the data files are located, default")
.default_value(string{ PATH }
.default_value(std::string{ PATH }
);
program.add_argument("-m", "--model")
.help("Model to use " + platform::Models::instance()->toString())
.action([](const std::string& value) {
static const vector<string> choices = platform::Models::instance()->getNames();
.help("Model to use " + platform::Models::instance()->tostd::string())
.action([](const std::std::std::string& value) {
static const std::vector<std::string> choices = platform::Models::instance()->getNames();
if (find(choices.begin(), choices.end(), value) != choices.end()) {
return value;
}
throw runtime_error("Model must be one of " + platform::Models::instance()->toString());
throw runtime_error("Model must be one of " + platform::Models::instance()->tostd::string());
}
);
program.add_argument("--discretize").help("Discretize input dataset").default_value(false).implicit_value(true);
program.add_argument("--dumpcpt").help("Dump CPT Tables").default_value(false).implicit_value(true);
program.add_argument("--stratified").help("If Stratified KFold is to be done").default_value(false).implicit_value(true);
program.add_argument("--tensors").help("Use tensors to store samples").default_value(false).implicit_value(true);
program.add_argument("-f", "--folds").help("Number of folds").default_value(5).scan<'i', int>().action([](const string& value) {
program.add_argument("-f", "--folds").help("Number of folds").default_value(5).scan<'i', int>().action([](const std::std::string& value) {
try {
auto k = stoi(value);
if (k < 2) {
@@ -114,13 +113,13 @@ int main(int argc, char** argv)
}});
program.add_argument("-s", "--seed").help("Random seed").default_value(-1).scan<'i', int>();
bool class_last, stratified, tensors, dump_cpt;
string model_name, file_name, path, complete_file_name;
std::string model_name, file_name, path, complete_file_name;
int nFolds, seed;
try {
program.parse_args(argc, argv);
file_name = program.get<string>("dataset");
path = program.get<string>("path");
model_name = program.get<string>("model");
file_name = program.get<std::string>("dataset");
path = program.get<std::string>("path");
model_name = program.get<std::string>("model");
complete_file_name = path + file_name + ".arff";
stratified = program.get<bool>("stratified");
tensors = program.get<bool>("tensors");
@@ -133,7 +132,7 @@ int main(int argc, char** argv)
}
}
catch (const exception& err) {
cerr << err.what() << endl;
cerr << err.what() << std::endl;
cerr << program;
exit(1);
}
@@ -144,93 +143,93 @@ int main(int argc, char** argv)
auto handler = ArffFiles();
handler.load(complete_file_name, class_last);
// Get Dataset X, y
vector<mdlp::samples_t>& X = handler.getX();
std::vector<mdlp::samples_t>& X = handler.getX();
mdlp::labels_t& y = handler.getY();
// Get className & Features
auto className = handler.getClassName();
vector<string> features;
std::vector<std::string> features;
auto attributes = handler.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features),
[](const pair<string, string>& item) { return item.first; });
[](const pair<std::string, std::string>& item) { return item.first; });
// Discretize Dataset
auto [Xd, maxes] = discretize(X, y, features);
maxes[className] = *max_element(y.begin(), y.end()) + 1;
map<string, vector<int>> states;
map<std::string, std::vector<int>> states;
for (auto feature : features) {
states[feature] = vector<int>(maxes[feature]);
states[feature] = std::vector<int>(maxes[feature]);
}
states[className] = vector<int>(maxes[className]);
states[className] = std::vector<int>(maxes[className]);
auto clf = platform::Models::instance()->create(model_name);
clf->fit(Xd, y, features, className, states);
if (dump_cpt) {
cout << "--- CPT Tables ---" << endl;
std::cout << "--- CPT Tables ---" << std::endl;
clf->dump_cpt();
}
auto lines = clf->show();
for (auto line : lines) {
cout << line << endl;
std::cout << line << std::endl;
}
cout << "--- Topological Order ---" << endl;
std::cout << "--- Topological Order ---" << std::endl;
auto order = clf->topological_order();
for (auto name : order) {
cout << name << ", ";
std::cout << name << ", ";
}
cout << "end." << endl;
std::cout << "end." << std::endl;
auto score = clf->score(Xd, y);
cout << "Score: " << score << endl;
// auto graph = clf->graph();
// auto dot_file = model_name + "_" + file_name;
// ofstream file(dot_file + ".dot");
// file << graph;
// file.close();
// cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << endl;
// cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << endl;
// string stratified_string = stratified ? " Stratified" : "";
// cout << nFolds << " Folds" << stratified_string << " Cross validation" << endl;
// cout << "==========================================" << endl;
// torch::Tensor Xt = torch::zeros({ static_cast<int>(Xd.size()), static_cast<int>(Xd[0].size()) }, torch::kInt32);
// torch::Tensor yt = torch::tensor(y, torch::kInt32);
// for (int i = 0; i < features.size(); ++i) {
// Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
// }
// float total_score = 0, total_score_train = 0, score_train, score_test;
// Fold* fold;
// if (stratified)
// fold = new StratifiedKFold(nFolds, y, seed);
// else
// fold = new KFold(nFolds, y.size(), seed);
// for (auto i = 0; i < nFolds; ++i) {
// auto [train, test] = fold->getFold(i);
// cout << "Fold: " << i + 1 << endl;
// if (tensors) {
// auto ttrain = torch::tensor(train, torch::kInt64);
// auto ttest = torch::tensor(test, torch::kInt64);
// torch::Tensor Xtraint = torch::index_select(Xt, 1, ttrain);
// torch::Tensor ytraint = yt.index({ ttrain });
// torch::Tensor Xtestt = torch::index_select(Xt, 1, ttest);
// torch::Tensor ytestt = yt.index({ ttest });
// clf->fit(Xtraint, ytraint, features, className, states);
// auto temp = clf->predict(Xtraint);
// score_train = clf->score(Xtraint, ytraint);
// score_test = clf->score(Xtestt, ytestt);
// } else {
// auto [Xtrain, ytrain] = extract_indices(train, Xd, y);
// auto [Xtest, ytest] = extract_indices(test, Xd, y);
// clf->fit(Xtrain, ytrain, features, className, states);
// score_train = clf->score(Xtrain, ytrain);
// score_test = clf->score(Xtest, ytest);
// }
// if (dump_cpt) {
// cout << "--- CPT Tables ---" << endl;
// clf->dump_cpt();
// }
// total_score_train += score_train;
// total_score += score_test;
// cout << "Score Train: " << score_train << endl;
// cout << "Score Test : " << score_test << endl;
// cout << "-------------------------------------------------------------------------------" << endl;
// }
// cout << "**********************************************************************************" << endl;
// cout << "Average Score Train: " << total_score_train / nFolds << endl;
// cout << "Average Score Test : " << total_score / nFolds << endl;return 0;
std::cout << "Score: " << score << std::endl;
auto graph = clf->graph();
auto dot_file = model_name + "_" + file_name;
ofstream file(dot_file + ".dot");
file << graph;
file.close();
std::cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << std::endl;
std::cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << std::endl;
std::string stratified_std::string = stratified ? " Stratified" : "";
std::cout << nFolds << " Folds" << stratified_std::string << " Cross validation" << std::endl;
std::cout << "==========================================" << std::endl;
torch::Tensor Xt = torch::zeros({ static_cast<int>(Xd.size()), static_cast<int>(Xd[0].size()) }, torch::kInt32);
torch::Tensor yt = torch::tensor(y, torch::kInt32);
for (int i = 0; i < features.size(); ++i) {
Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
}
float total_score = 0, total_score_train = 0, score_train, score_test;
platform::Fold* fold;
if (stratified)
fold = new platform::StratifiedKFold(nFolds, y, seed);
else
fold = new platform::KFold(nFolds, y.size(), seed);
for (auto i = 0; i < nFolds; ++i) {
auto [train, test] = fold->getFold(i);
std::cout << "Fold: " << i + 1 << std::endl;
if (tensors) {
auto ttrain = torch::tensor(train, torch::kInt64);
auto ttest = torch::tensor(test, torch::kInt64);
torch::Tensor Xtraint = torch::index_select(Xt, 1, ttrain);
torch::Tensor ytraint = yt.index({ ttrain });
torch::Tensor Xtestt = torch::index_select(Xt, 1, ttest);
torch::Tensor ytestt = yt.index({ ttest });
clf->fit(Xtraint, ytraint, features, className, states);
auto temp = clf->predict(Xtraint);
score_train = clf->score(Xtraint, ytraint);
score_test = clf->score(Xtestt, ytestt);
} else {
auto [Xtrain, ytrain] = extract_indices(train, Xd, y);
auto [Xtest, ytest] = extract_indices(test, Xd, y);
clf->fit(Xtrain, ytrain, features, className, states);
score_train = clf->score(Xtrain, ytrain);
score_test = clf->score(Xtest, ytest);
}
if (dump_cpt) {
std::cout << "--- CPT Tables ---" << std::endl;
clf->dump_cpt();
}
total_score_train += score_train;
total_score += score_test;
std::cout << "Score Train: " << score_train << std::endl;
std::cout << "Score Test : " << score_test << std::endl;
std::cout << "-------------------------------------------------------------------------------" << std::endl;
}
std::cout << "**********************************************************************************" << std::endl;
std::cout << "Average Score Train: " << total_score_train / nFolds << std::endl;
std::cout << "Average Score Test : " << total_score / nFolds << std::endl;return 0;
}

View File

@@ -2,14 +2,16 @@
namespace bayesnet {
AODE::AODE() : Ensemble() {}
void AODE::buildModel()
void AODE::buildModel(const torch::Tensor& weights)
{
models.clear();
for (int i = 0; i < features.size(); ++i) {
models.push_back(std::make_unique<SPODE>(i));
}
n_models = models.size();
significanceModels = std::vector<double>(n_models, 1.0);
}
vector<string> AODE::graph(const string& title) const
std::vector<std::string> AODE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}

View File

@@ -5,11 +5,11 @@
namespace bayesnet {
class AODE : public Ensemble {
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
AODE();
virtual ~AODE() {};
vector<string> graph(const string& title = "AODE") const override;
std::vector<std::string> graph(const std::string& title = "AODE") const override;
};
}
#endif

View File

@@ -1,17 +1,15 @@
#include "AODELd.h"
#include "Models.h"
namespace bayesnet {
using namespace std;
AODELd::AODELd() : Ensemble(), Proposal(dataset, features, className) {}
AODELd& AODELd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, 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_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
// 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
@@ -19,21 +17,22 @@ namespace bayesnet {
return *this;
}
void AODELd::buildModel()
void AODELd::buildModel(const torch::Tensor& weights)
{
models.clear();
for (int i = 0; i < features.size(); ++i) {
models.push_back(std::make_unique<SPODELd>(i));
}
n_models = models.size();
significanceModels = std::vector<double>(n_models, 1.0);
}
void AODELd::trainModel()
void AODELd::trainModel(const torch::Tensor& weights)
{
for (const auto& model : models) {
model->fit(Xf, y, features, className, states);
}
}
vector<string> AODELd::graph(const string& name) const
std::vector<std::string> AODELd::graph(const std::string& name) const
{
return Ensemble::graph(name);
}

View File

@@ -5,17 +5,16 @@
#include "SPODELd.h"
namespace bayesnet {
using namespace std;
class AODELd : public Ensemble, public Proposal {
protected:
void trainModel() override;
void buildModel() override;
void trainModel(const torch::Tensor& weights) override;
void buildModel(const torch::Tensor& weights) override;
public:
AODELd();
AODELd& fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_) override;
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_) override;
virtual ~AODELd() = default;
vector<string> graph(const string& name = "AODE") const override;
static inline string version() { return "0.0.1"; };
std::vector<std::string> graph(const std::string& name = "AODELd") const override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !AODELD_H

View File

@@ -1,31 +1,35 @@
#ifndef BASE_H
#define BASE_H
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <vector>
namespace bayesnet {
using namespace std;
enum status_t { NORMAL, WARNING, ERROR };
class BaseClassifier {
protected:
virtual void trainModel() = 0;
virtual void trainModel(const torch::Tensor& weights) = 0;
public:
// X is nxm vector, y is nx1 vector
virtual BaseClassifier& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
// 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, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
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;
torch::Tensor virtual predict(torch::Tensor& X) = 0;
vector<int> virtual predict(vector<vector<int>>& X) = 0;
float virtual score(vector<vector<int>>& X, vector<int>& y) = 0;
std::vector<int> virtual predict(std::vector<std::vector<int >>& X) = 0;
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 getNumberOfStates() const = 0;
vector<string> virtual show() const = 0;
vector<string> virtual graph(const string& title = "") const = 0;
const string inline getVersion() const { return "0.1.0"; };
vector<string> virtual topological_order() = 0;
std::vector<std::string> virtual show() const = 0;
std::vector<std::string> virtual graph(const std::string& title = "") const = 0;
virtual std::string getVersion() = 0;
std::vector<std::string> virtual topological_order() = 0;
void virtual dump_cpt()const = 0;
virtual void setHyperparameters(nlohmann::json& hyperparameters) = 0;
};
}
#endif

View File

@@ -1,16 +1,16 @@
#include "BayesMetrics.h"
#include "Mst.h"
namespace bayesnet {
//samples is nxm tensor used to fit the model
Metrics::Metrics(const torch::Tensor& samples, const vector<string>& features, const string& className, const int classNumStates)
//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)
, classNumStates(classNumStates)
{
}
//samples is nxm vector used to fit the model
Metrics::Metrics(const vector<vector<int>>& vsamples, const vector<int>& labels, const vector<string>& features, const string& className, const int classNumStates)
//samples is nxm 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)
, className(className)
, classNumStates(classNumStates)
@@ -21,28 +21,57 @@ namespace bayesnet {
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
}
vector<pair<string, string>> Metrics::doCombinations(const vector<string>& source)
std::vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, bool ascending, unsigned k)
{
vector<pair<string, string>> result;
for (int i = 0; i < source.size(); ++i) {
string temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
// Return the K Best features
auto n = samples.size(0) - 1;
if (k == 0) {
k = n;
}
// compute scores
scoresKBest.clear();
featuresKBest.clear();
auto label = samples.index({ -1, "..." });
for (int i = 0; i < n; ++i) {
scoresKBest.push_back(mutualInformation(label, samples.index({ i, "..." }), weights));
featuresKBest.push_back(i);
}
// sort & reduce scores and features
if (ascending) {
sort(featuresKBest.begin(), featuresKBest.end(), [&](int i, int j)
{ return scoresKBest[i] < scoresKBest[j]; });
sort(scoresKBest.begin(), scoresKBest.end(), std::less<double>());
if (k < n) {
for (int i = 0; i < n - k; ++i) {
featuresKBest.erase(featuresKBest.begin());
scoresKBest.erase(scoresKBest.begin());
}
}
return result;
} else {
sort(featuresKBest.begin(), featuresKBest.end(), [&](int i, int j)
{ return scoresKBest[i] > scoresKBest[j]; });
sort(scoresKBest.begin(), scoresKBest.end(), std::greater<double>());
featuresKBest.resize(k);
scoresKBest.resize(k);
}
torch::Tensor Metrics::conditionalEdge()
return featuresKBest;
}
std::vector<double> Metrics::getScoresKBest() const
{
auto result = vector<double>();
auto source = vector<string>(features);
return scoresKBest;
}
torch::Tensor Metrics::conditionalEdge(const torch::Tensor& weights)
{
auto result = std::vector<double>();
auto source = std::vector<std::string>(features);
source.push_back(className);
auto combinations = doCombinations(source);
// Compute class prior
auto margin = torch::zeros({ classNumStates });
auto margin = torch::zeros({ classNumStates }, torch::kFloat);
for (int value = 0; value < classNumStates; ++value) {
auto mask = samples.index({ -1, "..." }) == value;
margin[value] = mask.sum().item<float>() / samples.size(1);
margin[value] = mask.sum().item<double>() / samples.size(1);
}
for (auto [first, second] : combinations) {
int index_first = find(features.begin(), features.end(), first) - features.begin();
@@ -52,8 +81,9 @@ namespace bayesnet {
auto mask = samples.index({ -1, "..." }) == value;
auto first_dataset = samples.index({ index_first, mask });
auto second_dataset = samples.index({ index_second, mask });
auto mi = mutualInformation(first_dataset, second_dataset);
auto pb = margin[value].item<float>();
auto weights_dataset = weights.index({ mask });
auto mi = mutualInformation(first_dataset, second_dataset, weights_dataset);
auto pb = margin[value].item<double>();
accumulated += pb * mi;
}
result.push_back(accumulated);
@@ -70,31 +100,32 @@ namespace bayesnet {
return matrix;
}
// To use in Python
vector<float> Metrics::conditionalEdgeWeights()
std::vector<float> Metrics::conditionalEdgeWeights(std::vector<float>& weights_)
{
auto matrix = conditionalEdge();
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;
}
double Metrics::entropy(const torch::Tensor& feature)
double Metrics::entropy(const torch::Tensor& feature, const torch::Tensor& weights)
{
torch::Tensor counts = feature.bincount();
int totalWeight = counts.sum().item<int>();
torch::Tensor counts = feature.bincount(weights);
double totalWeight = counts.sum().item<double>();
torch::Tensor probs = counts.to(torch::kFloat) / totalWeight;
torch::Tensor logProbs = torch::log(probs);
torch::Tensor entropy = -probs * logProbs;
return entropy.nansum().item<double>();
}
// H(Y|X) = sum_{x in X} p(x) H(Y|X=x)
double Metrics::conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature)
double Metrics::conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights)
{
int numSamples = firstFeature.sizes()[0];
torch::Tensor featureCounts = secondFeature.bincount();
unordered_map<int, unordered_map<int, double>> jointCounts;
torch::Tensor featureCounts = secondFeature.bincount(weights);
std::unordered_map<int, std::unordered_map<int, double>> jointCounts;
double totalWeight = 0;
for (auto i = 0; i < numSamples; i++) {
jointCounts[secondFeature[i].item<int>()][firstFeature[i].item<int>()] += 1;
totalWeight += 1;
jointCounts[secondFeature[i].item<int>()][firstFeature[i].item<int>()] += weights[i].item<double>();
totalWeight += weights[i].item<float>();
}
if (totalWeight == 0)
return 0;
@@ -115,16 +146,16 @@ namespace bayesnet {
return entropyValue;
}
// I(X;Y) = H(Y) - H(Y|X)
double Metrics::mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature)
double Metrics::mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights)
{
return entropy(firstFeature) - conditionalEntropy(firstFeature, secondFeature);
return entropy(firstFeature, weights) - conditionalEntropy(firstFeature, secondFeature, weights);
}
/*
Compute the maximum spanning tree considering the weights as distances
and the indices of the weights as nodes of this square matrix using
Kruskal algorithm
*/
vector<pair<int, int>> Metrics::maximumSpanningTree(const vector<string>& features, const Tensor& weights, const int root)
std::vector<std::pair<int, int>> Metrics::maximumSpanningTree(const std::vector<std::string>& features, const torch::Tensor& weights, const int root)
{
auto mst = MST(features, weights, root);
return mst.maximumSpanningTree();

View File

@@ -4,25 +4,46 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
using namespace torch;
class Metrics {
private:
Tensor samples; // nxm tensor used to fit the model
vector<string> features;
string className;
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);
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) {
T temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
}
}
return result;
}
template <class T>
T pop_first(std::vector<T>& v)
{
T temp = v[0];
v.erase(v.begin());
return temp;
}
public:
Metrics() = default;
Metrics(const Tensor&, const vector<string>&, const string&, const int);
Metrics(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&, const int);
double entropy(const Tensor&);
double conditionalEntropy(const Tensor&, const Tensor&);
double mutualInformation(const Tensor&, const Tensor&);
vector<float> conditionalEdgeWeights(); // To use in Python
Tensor conditionalEdge();
vector<pair<string, string>> doCombinations(const vector<string>&);
vector<pair<int, int>> maximumSpanningTree(const vector<string>& features, const Tensor& weights, const int root);
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);
};
}
#endif

196
src/BayesNet/BoostAODE.cc Normal file
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@@ -0,0 +1,196 @@
#include <set>
#include <functional>
#include <limits.h>
#include "BoostAODE.h"
#include "Colors.h"
#include "Folding.h"
#include "Paths.h"
#include "CFS.h"
#include "FCBF.h"
#include "IWSS.h"
namespace bayesnet {
BoostAODE::BoostAODE() : Ensemble() {}
void BoostAODE::buildModel(const torch::Tensor& weights)
{
// Models shall be built in trainModel
models.clear();
n_models = 0;
// Prepare the validation dataset
auto y_ = dataset.index({ -1, "..." });
if (convergence) {
// Prepare train & validation sets from train data
auto fold = platform::StratifiedKFold(5, y_, 271);
dataset_ = torch::clone(dataset);
// save input dataset
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();
metrics = Metrics(dataset, features, className, n_classes);
// Build dataset with train data
buildDataset(y_train);
} else {
// Use all data to train
X_train = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." });
y_train = y_;
}
}
void BoostAODE::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid
const std::vector<std::string> validKeys = { "repeatSparent", "maxModels", "ascending", "convergence", "threshold", "select_features" };
checkHyperparameters(validKeys, hyperparameters);
if (hyperparameters.contains("repeatSparent")) {
repeatSparent = hyperparameters["repeatSparent"];
}
if (hyperparameters.contains("maxModels")) {
maxModels = hyperparameters["maxModels"];
}
if (hyperparameters.contains("ascending")) {
ascending = hyperparameters["ascending"];
}
if (hyperparameters.contains("convergence")) {
convergence = hyperparameters["convergence"];
}
if (hyperparameters.contains("threshold")) {
threshold = hyperparameters["threshold"];
}
if (hyperparameters.contains("select_features")) {
auto selectedAlgorithm = hyperparameters["select_features"];
std::vector<std::string> algos = { "IWSS", "FCBF", "CFS" };
selectFeatures = true;
algorithm = selectedAlgorithm;
if (std::find(algos.begin(), algos.end(), selectedAlgorithm) == algos.end()) {
throw std::invalid_argument("Invalid selectFeatures value [IWSS, FCBF, CFS]");
}
}
}
std::unordered_set<int> BoostAODE::initializeModels()
{
std::unordered_set<int> featuresUsed;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
int maxFeatures = 0;
if (algorithm == "CFS") {
featureSelector = new CFS(dataset, features, className, maxFeatures, states.at(className).size(), weights_);
} else if (algorithm == "IWSS") {
if (threshold < 0 || threshold >0.5) {
throw std::invalid_argument("Invalid threshold value for IWSS [0, 0.5]");
}
featureSelector = new IWSS(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
} else if (algorithm == "FCBF") {
if (threshold < 1e-7 || threshold > 1) {
throw std::invalid_argument("Invalid threshold value [1e-7, 1]");
}
featureSelector = new FCBF(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
}
featureSelector->fit();
auto cfsFeatures = featureSelector->getFeatures();
for (const int& feature : cfsFeatures) {
// std::cout << "Feature: [" << feature << "] " << feature << " " << features.at(feature) << std::endl;
featuresUsed.insert(feature);
std::unique_ptr<Classifier> model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_);
models.push_back(std::move(model));
significanceModels.push_back(1.0);
n_models++;
}
delete featureSelector;
return featuresUsed;
}
void BoostAODE::trainModel(const torch::Tensor& weights)
{
std::unordered_set<int> featuresUsed;
int tolerance = 5; // number of times the accuracy can be lower than the threshold
if (selectFeatures) {
featuresUsed = initializeModels();
tolerance = 0; // Remove tolerance if features are selected
}
if (maxModels == 0)
maxModels = .1 * n > 10 ? .1 * n : n;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
bool exitCondition = false;
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double delta = 1.0;
double threshold = 1e-4;
int count = 0; // number of times the accuracy is lower than the threshold
fitted = true; // to enable predict
// Step 0: Set the finish condition
// if not repeatSparent a finish condition is run out of features
// n_models == maxModels
// epsilon sub t > 0.5 => inverse the weights policy
// validation error is not decreasing
while (!exitCondition) {
// Step 1: Build ranking with mutual information
auto featureSelection = metrics.SelectKBestWeighted(weights_, ascending, n); // Get all the features sorted
std::unique_ptr<Classifier> model;
auto feature = featureSelection[0];
if (!repeatSparent || featuresUsed.size() < featureSelection.size()) {
bool used = true;
for (const auto& feat : featureSelection) {
if (std::find(featuresUsed.begin(), featuresUsed.end(), feat) != featuresUsed.end()) {
continue;
}
used = false;
feature = feat;
break;
}
if (used) {
exitCondition = true;
continue;
}
}
featuresUsed.insert(feature);
model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_);
auto ypred = model->predict(X_train);
// Step 3.1: Compute the classifier amout of say
auto mask_wrong = ypred != y_train;
auto mask_right = ypred == y_train;
auto masked_weights = weights_ * mask_wrong.to(weights_.dtype());
double epsilon_t = masked_weights.sum().item<double>();
double wt = (1 - epsilon_t) / epsilon_t;
double 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;
// Step 3.4: Store classifier and its accuracy to weigh its future vote
models.push_back(std::move(model));
significanceModels.push_back(alpha_t);
n_models++;
if (convergence) {
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 {
delta = accuracy - priorAccuracy;
}
if (delta < threshold) {
count++;
}
}
exitCondition = n_models >= maxModels && repeatSparent || epsilon_t > 0.5 || count > tolerance;
}
if (featuresUsed.size() != features.size()) {
status = WARNING;
}
}
std::vector<std::string> BoostAODE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}
}

32
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@@ -0,0 +1,32 @@
#ifndef BOOSTAODE_H
#define BOOSTAODE_H
#include "Ensemble.h"
#include <map>
#include "SPODE.h"
#include "FeatureSelect.h"
namespace bayesnet {
class BoostAODE : public Ensemble {
public:
BoostAODE();
virtual ~BoostAODE() {};
std::vector<std::string> graph(const std::string& title = "BoostAODE") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override;
protected:
void buildModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights) override;
private:
torch::Tensor dataset_;
torch::Tensor X_train, y_train, X_test, y_test;
std::unordered_set<int> initializeModels();
// Hyperparameters
bool repeatSparent = false; // if true, a feature can be selected more than once
int maxModels = 0;
bool ascending = false; //Process KBest features ascending or descending order
bool convergence = false; //if true, stop when the model does not improve
bool selectFeatures = false; // if true, use feature selection
std::string algorithm = ""; // Selected feature selection algorithm
FeatureSelect* featureSelector = nullptr;
double threshold = -1;
};
}
#endif

72
src/BayesNet/CFS.cc Normal file
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@@ -0,0 +1,72 @@
#include "CFS.h"
#include <limits>
#include "bayesnetUtils.h"
namespace bayesnet {
void CFS::fit()
{
initialize();
computeSuLabels();
auto featureOrder = argsort(suLabels); // sort descending order
auto continueCondition = true;
auto feature = featureOrder[0];
selectedFeatures.push_back(feature);
selectedScores.push_back(suLabels[feature]);
selectedFeatures.erase(selectedFeatures.begin());
while (continueCondition) {
double merit = std::numeric_limits<double>::lowest();
int bestFeature = -1;
for (auto feature : featureOrder) {
selectedFeatures.push_back(feature);
// Compute merit with selectedFeatures
auto meritNew = computeMeritCFS();
if (meritNew > merit) {
merit = meritNew;
bestFeature = feature;
}
selectedFeatures.pop_back();
}
if (bestFeature == -1) {
// meritNew has to be nan due to constant features
break;
}
selectedFeatures.push_back(bestFeature);
selectedScores.push_back(merit);
featureOrder.erase(remove(featureOrder.begin(), featureOrder.end(), bestFeature), featureOrder.end());
continueCondition = computeContinueCondition(featureOrder);
}
fitted = true;
}
bool CFS::computeContinueCondition(const std::vector<int>& featureOrder)
{
if (selectedFeatures.size() == maxFeatures || featureOrder.size() == 0) {
return false;
}
if (selectedScores.size() >= 5) {
/*
"To prevent the best first search from exploring the entire
feature subset search space, a stopping criterion is imposed.
The search will terminate if five consecutive fully expanded
subsets show no improvement over the current best subset."
as stated in Mark A.Hall Thesis
*/
double item_ant = std::numeric_limits<double>::lowest();
int num = 0;
std::vector<double> lastFive(selectedScores.end() - 5, selectedScores.end());
for (auto item : lastFive) {
if (item_ant == std::numeric_limits<double>::lowest()) {
item_ant = item;
}
if (item > item_ant) {
break;
} else {
num++;
item_ant = item;
}
}
if (num == 5) {
return false;
}
}
return true;
}
}

20
src/BayesNet/CFS.h Normal file
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@@ -0,0 +1,20 @@
#ifndef CFS_H
#define CFS_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
namespace bayesnet {
class CFS : public FeatureSelect {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
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) :
FeatureSelect(samples, features, className, maxFeatures, classNumStates, weights)
{
}
virtual ~CFS() {};
void fit() override;
private:
bool computeContinueCondition(const std::vector<int>& featureOrder);
};
}
#endif

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@@ -1,7 +1,12 @@
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/src/PyClassifiers)
include_directories(${Python3_INCLUDE_DIRS})
add_library(BayesNet bayesnetUtils.cc Network.cc Node.cc BayesMetrics.cc Classifier.cc
KDB.cc TAN.cc SPODE.cc Ensemble.cc AODE.cc TANLd.cc KDBLd.cc SPODELd.cc AODELd.cc Mst.cc Proposal.cc ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNet mdlp ArffFiles "${TORCH_LIBRARIES}")
KDB.cc TAN.cc SPODE.cc Ensemble.cc AODE.cc TANLd.cc KDBLd.cc SPODELd.cc AODELd.cc BoostAODE.cc
Mst.cc Proposal.cc CFS.cc FCBF.cc IWSS.cc FeatureSelect.cc ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNet mdlp "${TORCH_LIBRARIES}")

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@@ -2,10 +2,8 @@
#include "bayesnetUtils.h"
namespace bayesnet {
using namespace torch;
Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false) {}
Classifier& Classifier::build(vector<string>& features, string className, map<string, vector<int>>& states)
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)
{
this->features = features;
this->className = className;
@@ -13,16 +11,15 @@ namespace bayesnet {
m = dataset.size(1);
n = dataset.size(0) - 1;
checkFitParameters();
auto n_classes = states[className].size();
auto n_classes = states.at(className).size();
metrics = Metrics(dataset, features, className, n_classes);
model.initialize();
buildModel();
trainModel();
buildModel(weights);
trainModel(weights);
fitted = true;
return *this;
}
void Classifier::buildDataset(Tensor& ytmp)
void Classifier::buildDataset(torch::Tensor& ytmp)
{
try {
auto yresized = torch::transpose(ytmp.view({ ytmp.size(0), 1 }), 0, 1);
@@ -30,89 +27,100 @@ namespace bayesnet {
}
catch (const std::exception& e) {
std::cerr << e.what() << '\n';
cout << "X dimensions: " << dataset.sizes() << "\n";
cout << "y dimensions: " << ytmp.sizes() << "\n";
std::cout << "X dimensions: " << dataset.sizes() << "\n";
std::cout << "y dimensions: " << ytmp.sizes() << "\n";
exit(1);
}
}
void Classifier::trainModel()
void Classifier::trainModel(const torch::Tensor& weights)
{
model.fit(dataset, features, className, states);
model.fit(dataset, weights, features, className, states);
}
// 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, vector<string>& features, string className, map<string, 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)
{
dataset = X;
buildDataset(y);
return build(features, className, states);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, 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)
{
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, kInt32);
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, torch::kInt32);
for (int i = 0; i < X.size(); ++i) {
dataset.index_put_({ i, "..." }, torch::tensor(X[i], kInt32));
dataset.index_put_({ i, "..." }, torch::tensor(X[i], torch::kInt32));
}
auto ytmp = torch::tensor(y, kInt32);
auto ytmp = torch::tensor(y, torch::kInt32);
buildDataset(ytmp);
return build(features, className, states);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
}
Classifier& Classifier::fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, 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)
{
this->dataset = dataset;
return build(features, className, states);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, 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)
{
this->dataset = dataset;
return build(features, className, states, weights);
}
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 invalid_argument("X " + to_string(n) + " and features " + to_string(features.size()) + " must have the same number of features");
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 (states.find(className) == states.end()) {
throw invalid_argument("className not found in states");
throw std::invalid_argument("className not found in states");
}
for (auto feature : features) {
if (states.find(feature) == states.end()) {
throw invalid_argument("feature [" + feature + "] not found in states");
throw std::invalid_argument("feature [" + feature + "] not found in states");
}
}
}
Tensor Classifier::predict(Tensor& X)
torch::Tensor Classifier::predict(torch::Tensor& X)
{
if (!fitted) {
throw logic_error("Classifier has not been fitted");
throw std::logic_error("Classifier has not been fitted");
}
return model.predict(X);
}
vector<int> Classifier::predict(vector<vector<int>>& X)
std::vector<int> Classifier::predict(std::vector<std::vector<int>>& X)
{
if (!fitted) {
throw logic_error("Classifier has not been fitted");
throw std::logic_error("Classifier has not been fitted");
}
auto m_ = X[0].size();
auto n_ = X.size();
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
std::vector<std::vector<int>> Xd(n_, std::vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = vector<int>(X[i].begin(), X[i].end());
Xd[i] = std::vector<int>(X[i].begin(), X[i].end());
}
auto yp = model.predict(Xd);
return yp;
}
float Classifier::score(Tensor& X, Tensor& y)
float Classifier::score(torch::Tensor& X, torch::Tensor& y)
{
if (!fitted) {
throw logic_error("Classifier has not been fitted");
throw std::logic_error("Classifier has not been fitted");
}
Tensor y_pred = predict(X);
torch::Tensor y_pred = predict(X);
return (y_pred == y).sum().item<float>() / y.size(0);
}
float Classifier::score(vector<vector<int>>& X, vector<int>& y)
float Classifier::score(std::vector<std::vector<int>>& X, std::vector<int>& y)
{
if (!fitted) {
throw logic_error("Classifier has not been fitted");
throw std::logic_error("Classifier has not been fitted");
}
return model.score(X, y);
}
vector<string> Classifier::show() const
std::vector<std::string> Classifier::show() const
{
return model.show();
}
@@ -127,7 +135,7 @@ namespace bayesnet {
int Classifier::getNumberOfNodes() const
{
// Features does not include class
return fitted ? model.getFeatures().size() + 1 : 0;
return fitted ? model.getFeatures().size() : 0;
}
int Classifier::getNumberOfEdges() const
{
@@ -137,7 +145,7 @@ namespace bayesnet {
{
return fitted ? model.getStates() : 0;
}
vector<string> Classifier::topological_order()
std::vector<std::string> Classifier::topological_order()
{
return model.topological_sort();
}
@@ -145,4 +153,18 @@ namespace bayesnet {
{
model.dump_cpt();
}
void Classifier::checkHyperparameters(const std::vector<std::string>& validKeys, nlohmann::json& hyperparameters)
{
for (const auto& item : hyperparameters.items()) {
if (find(validKeys.begin(), validKeys.end(), item.key()) == validKeys.end()) {
throw std::invalid_argument("Hyperparameter " + item.key() + " is not valid");
}
}
}
void Classifier::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid, default is no hyperparameters
const std::vector<std::string> validKeys = { };
checkHyperparameters(validKeys, hyperparameters);
}
}

View File

@@ -4,43 +4,47 @@
#include "BaseClassifier.h"
#include "Network.h"
#include "BayesMetrics.h"
using namespace std;
using namespace torch;
namespace bayesnet {
class Classifier : public BaseClassifier {
private:
void buildDataset(torch::Tensor& y);
Classifier& build(vector<string>& features, string className, map<string, vector<int>>& states);
Classifier& build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
protected:
bool fitted;
Network model;
int m, n; // m: number of samples, n: number of features
Tensor dataset; // (n+1)xm tensor
Network model;
Metrics metrics;
vector<string> features;
string className;
map<string, vector<int>> states;
std::vector<std::string> features;
std::string className;
std::map<std::string, std::vector<int>> states;
torch::Tensor dataset; // (n+1)xm tensor
status_t status = NORMAL;
void checkFitParameters();
virtual void buildModel() = 0;
void trainModel() override;
virtual void buildModel(const torch::Tensor& weights) = 0;
void trainModel(const torch::Tensor& weights) override;
void checkHyperparameters(const std::vector<std::string>& validKeys, nlohmann::json& hyperparameters);
void buildDataset(torch::Tensor& y);
public:
Classifier(Network model);
virtual ~Classifier() = default;
Classifier& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) 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) 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;
void addNodes();
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
Tensor predict(Tensor& X) override;
vector<int> predict(vector<vector<int>>& X) override;
float score(Tensor& X, Tensor& y) override;
float score(vector<vector<int>>& X, vector<int>& y) override;
vector<string> show() const override;
vector<string> topological_order() override;
torch::Tensor predict(torch::Tensor& X) override;
status_t getStatus() const override { return status; }
std::string getVersion() override { return "0.2.0"; };
std::vector<int> predict(std::vector<std::vector<int>>& 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::vector<std::string> show() const override;
std::vector<std::string> topological_order() override;
void dump_cpt() const override;
void setHyperparameters(nlohmann::json& hyperparameters) override;
};
}
#endif

View File

@@ -1,26 +1,29 @@
#include "Ensemble.h"
namespace bayesnet {
using namespace torch;
Ensemble::Ensemble() : Classifier(Network()) {}
Ensemble::Ensemble() : Classifier(Network()), n_models(0) {}
void Ensemble::trainModel()
void Ensemble::trainModel(const torch::Tensor& weights)
{
n_models = models.size();
for (auto i = 0; i < n_models; ++i) {
// fit with vectors
// fit with std::vectors
models[i]->fit(dataset, features, className, states);
}
}
vector<int> Ensemble::voting(Tensor& y_pred)
std::vector<int> Ensemble::voting(torch::Tensor& y_pred)
{
auto y_pred_ = y_pred.accessor<int, 2>();
vector<int> y_pred_final;
std::vector<int> y_pred_final;
int numClasses = states.at(className).size();
// y_pred is m x n_models with the prediction of every model for each sample
for (int i = 0; i < y_pred.size(0); ++i) {
vector<float> votes(y_pred.size(1), 0);
for (int j = 0; j < y_pred.size(1); ++j) {
votes[y_pred_[i][j]] += 1;
// votes store in each index (value of class) the significance added by each model
// i.e. votes[0] contains how much value has the value 0 of class. That value is generated by the models predictions
std::vector<double> votes(numClasses, 0.0);
for (int j = 0; j < n_models; ++j) {
votes[y_pred_[i][j]] += significanceModels.at(j);
}
// argsort in descending order
auto indices = argsort(votes);
@@ -28,19 +31,18 @@ namespace bayesnet {
}
return y_pred_final;
}
Tensor Ensemble::predict(Tensor& X)
torch::Tensor Ensemble::predict(torch::Tensor& X)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
throw std::logic_error("Ensemble has not been fitted");
}
Tensor y_pred = torch::zeros({ X.size(1), n_models }, kInt32);
//Create a threadpool
auto threads{ vector<thread>() };
mutex mtx;
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(thread([&, i]() {
threads.push_back(std::thread([&, i]() {
auto ypredict = models[i]->predict(X);
lock_guard<mutex> lock(mtx);
std::lock_guard<std::mutex> lock(mtx);
y_pred.index_put_({ "...", i }, ypredict);
}));
}
@@ -49,27 +51,27 @@ namespace bayesnet {
}
return torch::tensor(voting(y_pred));
}
vector<int> Ensemble::predict(vector<vector<int>>& X)
std::vector<int> Ensemble::predict(std::vector<std::vector<int>>& X)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
throw std::logic_error("Ensemble has not been fitted");
}
long m_ = X[0].size();
long n_ = X.size();
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
std::vector<std::vector<int>> Xd(n_, std::vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = vector<int>(X[i].begin(), X[i].end());
Xd[i] = std::vector<int>(X[i].begin(), X[i].end());
}
Tensor y_pred = torch::zeros({ m_, n_models }, kInt32);
torch::Tensor y_pred = torch::zeros({ m_, n_models }, torch::kInt32);
for (auto i = 0; i < n_models; ++i) {
y_pred.index_put_({ "...", i }, torch::tensor(models[i]->predict(Xd), kInt32));
y_pred.index_put_({ "...", i }, torch::tensor(models[i]->predict(Xd), torch::kInt32));
}
return voting(y_pred);
}
float Ensemble::score(Tensor& X, Tensor& y)
float Ensemble::score(torch::Tensor& X, torch::Tensor& y)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
throw std::logic_error("Ensemble has not been fitted");
}
auto y_pred = predict(X);
int correct = 0;
@@ -80,10 +82,10 @@ namespace bayesnet {
}
return (double)correct / y_pred.size(0);
}
float Ensemble::score(vector<vector<int>>& X, vector<int>& y)
float Ensemble::score(std::vector<std::vector<int>>& X, std::vector<int>& y)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
throw std::logic_error("Ensemble has not been fitted");
}
auto y_pred = predict(X);
int correct = 0;
@@ -94,20 +96,20 @@ namespace bayesnet {
}
return (double)correct / y_pred.size();
}
vector<string> Ensemble::show() const
std::vector<std::string> Ensemble::show() const
{
auto result = vector<string>();
auto result = std::vector<std::string>();
for (auto i = 0; i < n_models; ++i) {
auto res = models[i]->show();
result.insert(result.end(), res.begin(), res.end());
}
return result;
}
vector<string> Ensemble::graph(const string& title) const
std::vector<std::string> Ensemble::graph(const std::string& title) const
{
auto result = vector<string>();
auto result = std::vector<std::string>();
for (auto i = 0; i < n_models; ++i) {
auto res = models[i]->graph(title + "_" + to_string(i));
auto res = models[i]->graph(title + "_" + std::to_string(i));
result.insert(result.end(), res.begin(), res.end());
}
return result;

View File

@@ -4,33 +4,32 @@
#include "Classifier.h"
#include "BayesMetrics.h"
#include "bayesnetUtils.h"
using namespace std;
using namespace torch;
namespace bayesnet {
class Ensemble : public Classifier {
private:
Ensemble& build(vector<string>& features, string className, map<string, vector<int>>& states);
Ensemble& build(std::vector<std::string>& features, std::string className, std::map<std::string, std::vector<int>>& states);
protected:
unsigned n_models;
vector<unique_ptr<Classifier>> models;
void trainModel() override;
vector<int> voting(Tensor& y_pred);
std::vector<std::unique_ptr<Classifier>> models;
std::vector<double> significanceModels;
void trainModel(const torch::Tensor& weights) override;
std::vector<int> voting(torch::Tensor& y_pred);
public:
Ensemble();
virtual ~Ensemble() = default;
Tensor predict(Tensor& X) override;
vector<int> predict(vector<vector<int>>& X) override;
float score(Tensor& X, Tensor& y) override;
float score(vector<vector<int>>& X, vector<int>& y) override;
torch::Tensor predict(torch::Tensor& X) override;
std::vector<int> predict(std::vector<std::vector<int>>& X) override;
float score(torch::Tensor& X, torch::Tensor& y) override;
float score(std::vector<std::vector<int>>& X, std::vector<int>& y) override;
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
vector<string> show() const override;
vector<string> graph(const string& title) const override;
vector<string> topological_order() override
std::vector<std::string> show() const override;
std::vector<std::string> graph(const std::string& title) const override;
std::vector<std::string> topological_order() override
{
return vector<string>();
return std::vector<std::string>();
}
void dump_cpt() const override
{

44
src/BayesNet/FCBF.cc Normal file
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@@ -0,0 +1,44 @@
#include "bayesnetUtils.h"
#include "FCBF.h"
namespace bayesnet {
FCBF::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) :
FeatureSelect(samples, features, className, maxFeatures, classNumStates, weights), threshold(threshold)
{
if (threshold < 1e-7) {
throw std::invalid_argument("Threshold cannot be less than 1e-7");
}
}
void FCBF::fit()
{
initialize();
computeSuLabels();
auto featureOrder = argsort(suLabels); // sort descending order
auto featureOrderCopy = featureOrder;
for (const auto& feature : featureOrder) {
// Don't self compare
featureOrderCopy.erase(featureOrderCopy.begin());
if (suLabels.at(feature) == 0.0) {
// The feature has been removed from the list
continue;
}
if (suLabels.at(feature) < threshold) {
break;
}
// Remove redundant features
for (const auto& featureCopy : featureOrderCopy) {
double value = computeSuFeatures(feature, featureCopy);
if (value >= suLabels.at(featureCopy)) {
// Remove feature from list
suLabels[featureCopy] = 0.0;
}
}
selectedFeatures.push_back(feature);
selectedScores.push_back(suLabels[feature]);
if (selectedFeatures.size() == maxFeatures) {
break;
}
}
fitted = true;
}
}

17
src/BayesNet/FCBF.h Normal file
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@@ -0,0 +1,17 @@
#ifndef FCBF_H
#define FCBF_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
namespace bayesnet {
class FCBF : public FeatureSelect {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
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);
virtual ~FCBF() {};
void fit() override;
private:
double threshold = -1;
};
}
#endif

View File

@@ -0,0 +1,79 @@
#include "FeatureSelect.h"
#include <limits>
#include "bayesnetUtils.h"
namespace bayesnet {
FeatureSelect::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) :
Metrics(samples, features, className, classNumStates), maxFeatures(maxFeatures == 0 ? samples.size(0) - 1 : maxFeatures), weights(weights)
{
}
void FeatureSelect::initialize()
{
selectedFeatures.clear();
selectedScores.clear();
}
double FeatureSelect::symmetricalUncertainty(int a, int b)
{
/*
Compute symmetrical uncertainty. Normalize* information gain (mutual
information) with the entropies of the features in order to compensate
the bias due to high cardinality features. *Range [0, 1]
(https://www.sciencedirect.com/science/article/pii/S0020025519303603)
*/
auto x = samples.index({ a, "..." });
auto y = samples.index({ b, "..." });
auto mu = mutualInformation(x, y, weights);
auto hx = entropy(x, weights);
auto hy = entropy(y, weights);
return 2.0 * mu / (hx + hy);
}
void FeatureSelect::computeSuLabels()
{
// Compute Simmetrical Uncertainty between features and labels
// https://en.wikipedia.org/wiki/Symmetric_uncertainty
for (int i = 0; i < features.size(); ++i) {
suLabels.push_back(symmetricalUncertainty(i, -1));
}
}
double FeatureSelect::computeSuFeatures(const int firstFeature, const int secondFeature)
{
// Compute Simmetrical Uncertainty between features
// https://en.wikipedia.org/wiki/Symmetric_uncertainty
try {
return suFeatures.at({ firstFeature, secondFeature });
}
catch (const std::out_of_range& e) {
double result = symmetricalUncertainty(firstFeature, secondFeature);
suFeatures[{firstFeature, secondFeature}] = result;
return result;
}
}
double FeatureSelect::computeMeritCFS()
{
double result;
double rcf = 0;
for (auto feature : selectedFeatures) {
rcf += suLabels[feature];
}
double rff = 0;
int n = selectedFeatures.size();
for (const auto& item : doCombinations(selectedFeatures)) {
rff += computeSuFeatures(item.first, item.second);
}
return rcf / sqrt(n + (n * n - n) * rff);
}
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;
}
}

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@@ -0,0 +1,30 @@
#ifndef FEATURE_SELECT_H
#define FEATURE_SELECT_H
#include <torch/torch.h>
#include <vector>
#include "BayesMetrics.h"
namespace bayesnet {
class FeatureSelect : public Metrics {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
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);
virtual ~FeatureSelect() {};
virtual void fit() = 0;
std::vector<int> getFeatures() const;
std::vector<double> getScores() const;
protected:
void initialize();
void computeSuLabels();
double computeSuFeatures(const int a, const int b);
double symmetricalUncertainty(int a, int b);
double computeMeritCFS();
const torch::Tensor& weights;
int maxFeatures;
std::vector<int> selectedFeatures;
std::vector<double> selectedScores;
std::vector<double> suLabels;
std::map<std::pair<int, int>, double> suFeatures;
bool fitted = false;
};
}
#endif

47
src/BayesNet/IWSS.cc Normal file
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@@ -0,0 +1,47 @@
#include "IWSS.h"
#include <limits>
#include "bayesnetUtils.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)
{
if (threshold < 0 || threshold > .5) {
throw std::invalid_argument("Threshold has to be in [0, 0.5]");
}
}
void IWSS::fit()
{
initialize();
computeSuLabels();
auto featureOrder = argsort(suLabels); // sort descending order
auto featureOrderCopy = featureOrder;
// Add first and second features to result
// First with its own score
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);
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;
if (meritNew > merit || delta < threshold) {
if (meritNew > merit) {
merit = meritNew;
}
selectedScores.push_back(meritNew);
} else {
selectedFeatures.pop_back();
break;
}
if (selectedFeatures.size() == maxFeatures) {
break;
}
}
fitted = true;
}
}

17
src/BayesNet/IWSS.h Normal file
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@@ -0,0 +1,17 @@
#ifndef IWSS_H
#define IWSS_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
namespace bayesnet {
class IWSS : public FeatureSelect {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
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);
virtual ~IWSS() {};
void fit() override;
private:
double threshold = -1;
};
}
#endif

View File

@@ -1,10 +1,20 @@
#include "KDB.h"
namespace bayesnet {
using namespace torch;
KDB::KDB(int k, float theta) : Classifier(Network()), k(k), theta(theta) {}
void KDB::buildModel()
void KDB::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid
const std::vector<std::string> validKeys = { "k", "theta" };
checkHyperparameters(validKeys, hyperparameters);
if (hyperparameters.contains("k")) {
k = hyperparameters["k"];
}
if (hyperparameters.contains("theta")) {
theta = hyperparameters["theta"];
}
}
void KDB::buildModel(const torch::Tensor& weights)
{
/*
1. For each feature Xi, compute mutual information, I(X;C),
@@ -28,16 +38,16 @@ namespace bayesnet {
// 1. For each feature Xi, compute mutual information, I(X;C),
// where C is the class.
addNodes();
const Tensor& y = dataset.index({ -1, "..." });
vector <float> mi;
const torch::Tensor& y = dataset.index({ -1, "..." });
std::vector<double> mi;
for (auto i = 0; i < features.size(); i++) {
Tensor firstFeature = dataset.index({ i, "..." });
mi.push_back(metrics.mutualInformation(firstFeature, y));
torch::Tensor firstFeature = dataset.index({ i, "..." });
mi.push_back(metrics.mutualInformation(firstFeature, y, weights));
}
// 2. Compute class conditional mutual information I(Xi;XjIC), f or each
auto conditionalEdgeWeights = metrics.conditionalEdge();
auto conditionalEdgeWeights = metrics.conditionalEdge(weights);
// 3. Let the used variable list, S, be empty.
vector<int> S;
std::vector<int> S;
// 4. Let the DAG network being constructed, BN, begin with a single
// class node, C.
// 5. Repeat until S includes all domain features
@@ -55,9 +65,9 @@ namespace bayesnet {
S.push_back(idx);
}
}
void KDB::add_m_edges(int idx, vector<int>& S, Tensor& weights)
void KDB::add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights)
{
auto n_edges = min(k, static_cast<int>(S.size()));
auto n_edges = std::min(k, static_cast<int>(S.size()));
auto cond_w = clone(weights);
bool exit_cond = k == 0;
int num = 0;
@@ -69,7 +79,7 @@ namespace bayesnet {
model.addEdge(features[max_minfo], features[idx]);
num++;
}
catch (const invalid_argument& e) {
catch (const std::invalid_argument& e) {
// Loops are not allowed
}
}
@@ -79,11 +89,11 @@ namespace bayesnet {
exit_cond = num == n_edges || candidates.size(0) == 0;
}
}
vector<string> KDB::graph(const string& title) const
std::vector<std::string> KDB::graph(const std::string& title) const
{
string header{ title };
std::string header{ title };
if (title == "KDB") {
header += " (k=" + to_string(k) + ", theta=" + to_string(theta) + ")";
header += " (k=" + std::to_string(k) + ", theta=" + std::to_string(theta) + ")";
}
return model.graph(header);
}

View File

@@ -1,21 +1,21 @@
#ifndef KDB_H
#define KDB_H
#include <torch/torch.h>
#include "Classifier.h"
#include "bayesnetUtils.h"
namespace bayesnet {
using namespace std;
using namespace torch;
class KDB : public Classifier {
private:
int k;
float theta;
void add_m_edges(int idx, vector<int>& S, Tensor& weights);
void add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights);
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() {};
vector<string> graph(const string& name = "KDB") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override;
std::vector<std::string> graph(const std::string& name = "KDB") const override;
};
}
#endif

View File

@@ -1,16 +1,15 @@
#include "KDBLd.h"
namespace bayesnet {
using namespace std;
KDBLd::KDBLd(int k) : KDB(k), Proposal(dataset, features, className) {}
KDBLd& KDBLd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
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_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
// 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 KDB structure, KDB::fit initializes the base Bayesian network
@@ -18,12 +17,12 @@ namespace bayesnet {
states = localDiscretizationProposal(states, model);
return *this;
}
Tensor KDBLd::predict(Tensor& X)
torch::Tensor KDBLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return KDB::predict(Xt);
}
vector<string> KDBLd::graph(const string& name) const
std::vector<std::string> KDBLd::graph(const std::string& name) const
{
return KDB::graph(name);
}

View File

@@ -4,16 +4,15 @@
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class KDBLd : public KDB, public Proposal {
private:
public:
explicit KDBLd(int k);
virtual ~KDBLd() = default;
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "KDB") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
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) override;
std::vector<std::string> graph(const std::string& name = "KDB") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !KDBLD_H

View File

@@ -1,13 +1,13 @@
#include "Mst.h"
#include <vector>
#include <list>
/*
Based on the code from https://www.softwaretestinghelp.com/minimum-spanning-tree-tutorial/
*/
namespace bayesnet {
using namespace std;
Graph::Graph(int V) : V(V), parent(vector<int>(V))
Graph::Graph(int V) : V(V), parent(std::vector<int>(V))
{
for (int i = 0; i < V; i++)
parent[i] = i;
@@ -34,36 +34,45 @@ namespace bayesnet {
void Graph::kruskal_algorithm()
{
// sort the edges ordered on decreasing weight
sort(G.begin(), G.end(), [](const auto& left, const auto& right) {return left.first > right.first;});
stable_sort(G.begin(), G.end(), [](const auto& left, const auto& right) {return left.first > right.first;});
for (int i = 0; i < G.size(); i++) {
int uSt, vEd;
uSt = find_set(G[i].second.first);
vEd = find_set(G[i].second.second);
if (uSt != vEd) {
T.push_back(G[i]); // add to mst vector
T.push_back(G[i]); // add to mst std::vector
union_set(uSt, vEd);
}
}
}
void Graph::display_mst()
{
cout << "Edge :" << " Weight" << endl;
std::cout << "Edge :" << " Weight" << std::endl;
for (int i = 0; i < T.size(); i++) {
cout << T[i].second.first << " - " << T[i].second.second << " : "
std::cout << T[i].second.first << " - " << T[i].second.second << " : "
<< T[i].first;
cout << endl;
std::cout << std::endl;
}
}
vector<pair<int, int>> reorder(vector<pair<float, pair<int, int>>> T, int root_original)
void insertElement(std::list<int>& variables, int variable)
{
auto result = vector<pair<int, int>>();
auto visited = vector<int>();
auto nextVariables = unordered_set<int>();
nextVariables.emplace(root_original);
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)
{
// 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
auto result = std::vector<std::pair<int, int>>();
auto visited = std::vector<int>();
auto nextVariables = std::list<int>();
nextVariables.push_front(root_original);
while (nextVariables.size() > 0) {
int root = *nextVariables.begin();
nextVariables.erase(nextVariables.begin());
int root = nextVariables.front();
nextVariables.pop_front();
for (int i = 0; i < T.size(); ++i) {
auto [weight, edge] = T[i];
auto [from, to] = edge;
@@ -71,10 +80,10 @@ namespace bayesnet {
visited.insert(visited.begin(), i);
if (from == root) {
result.push_back({ from, to });
nextVariables.emplace(to);
insertElement(nextVariables, to);
} else {
result.push_back({ to, from });
nextVariables.emplace(from);
insertElement(nextVariables, from);
}
}
}
@@ -94,12 +103,11 @@ namespace bayesnet {
return result;
}
MST::MST(const vector<string>& features, const Tensor& weights, const int root) : features(features), weights(weights), root(root) {}
vector<pair<int, int>> MST::maximumSpanningTree()
MST::MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root) : features(features), weights(weights), root(root) {}
std::vector<std::pair<int, int>> MST::maximumSpanningTree()
{
auto num_features = features.size();
Graph g(num_features);
// Make a complete graph
for (int i = 0; i < num_features - 1; ++i) {
for (int j = i + 1; j < num_features; ++j) {

View File

@@ -4,24 +4,22 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
using namespace torch;
class MST {
private:
Tensor weights;
vector<string> features;
torch::Tensor weights;
std::vector<std::string> features;
int root = 0;
public:
MST() = default;
MST(const vector<string>& features, const Tensor& weights, const int root);
vector<pair<int, int>> maximumSpanningTree();
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
vector <pair<float, pair<int, int>>> G; // vector for graph
vector <pair<float, pair<int, int>>> T; // vector for mst
vector<int> parent;
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);
@@ -29,7 +27,7 @@ namespace bayesnet {
void union_set(int u, int v);
void kruskal_algorithm();
void display_mst();
vector <pair<float, pair<int, int>>> get_mst() { return T; }
std::vector <std::pair<float, std::pair<int, int>>> get_mst() { return T; }
};
}
#endif

View File

@@ -3,19 +3,18 @@
#include "Network.h"
#include "bayesnetUtils.h"
namespace bayesnet {
Network::Network() : features(vector<string>()), className(""), classNumStates(0), fitted(false) {}
Network::Network(float maxT) : features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network(float maxT, int smoothing) : laplaceSmoothing(smoothing), features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
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)
{
for (const auto& pair : other.nodes) {
nodes[pair.first] = std::make_unique<Node>(*pair.second);
for (const auto& node : other.nodes) {
nodes[node.first] = std::make_unique<Node>(*node.second);
}
}
void Network::initialize()
{
features = vector<string>();
features = std::vector<std::string>();
className = "";
classNumStates = 0;
fitted = false;
@@ -30,10 +29,10 @@ namespace bayesnet {
{
return samples;
}
void Network::addNode(const string& name)
void Network::addNode(const std::string& name)
{
if (name == "") {
throw invalid_argument("Node name cannot be empty");
throw std::invalid_argument("Node name cannot be empty");
}
if (nodes.find(name) != nodes.end()) {
return;
@@ -43,7 +42,7 @@ namespace bayesnet {
}
nodes[name] = std::make_unique<Node>(name);
}
vector<string> Network::getFeatures() const
std::vector<std::string> Network::getFeatures() const
{
return features;
}
@@ -59,11 +58,11 @@ namespace bayesnet {
}
return result;
}
string Network::getClassName() const
std::string Network::getClassName() const
{
return className;
}
bool Network::isCyclic(const string& nodeId, unordered_set<string>& visited, unordered_set<string>& recStack)
bool Network::isCyclic(const std::string& nodeId, std::unordered_set<std::string>& visited, std::unordered_set<std::string>& recStack)
{
if (visited.find(nodeId) == visited.end()) // if node hasn't been visited yet
{
@@ -79,85 +78,89 @@ namespace bayesnet {
recStack.erase(nodeId); // remove node from recursion stack before function ends
return false;
}
void Network::addEdge(const string& parent, const string& child)
void Network::addEdge(const std::string& parent, const std::string& child)
{
if (nodes.find(parent) == nodes.end()) {
throw invalid_argument("Parent node " + parent + " does not exist");
throw std::invalid_argument("Parent node " + parent + " does not exist");
}
if (nodes.find(child) == nodes.end()) {
throw invalid_argument("Child node " + child + " does not exist");
throw std::invalid_argument("Child node " + child + " does not exist");
}
// Temporarily add edge to check for cycles
nodes[parent]->addChild(nodes[child].get());
nodes[child]->addParent(nodes[parent].get());
unordered_set<string> visited;
unordered_set<string> recStack;
std::unordered_set<std::string> visited;
std::unordered_set<std::string> recStack;
if (isCyclic(nodes[child]->getName(), visited, recStack)) // if adding this edge forms a cycle
{
// remove problematic edge
nodes[parent]->removeChild(nodes[child].get());
nodes[child]->removeParent(nodes[parent].get());
throw invalid_argument("Adding this edge forms a cycle in the graph.");
throw std::invalid_argument("Adding this edge forms a cycle in the graph.");
}
}
map<string, std::unique_ptr<Node>>& Network::getNodes()
std::map<std::string, std::unique_ptr<Node>>& Network::getNodes()
{
return nodes;
}
void Network::checkFitData(int n_samples, int n_features, int n_samples_y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states)
void Network::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)
{
if (weights.size(0) != n_samples) {
throw std::invalid_argument("Weights (" + std::to_string(weights.size(0)) + ") must have the same number of elements as samples (" + std::to_string(n_samples) + ") in Network::fit");
}
if (n_samples != n_samples_y) {
throw invalid_argument("X and y must have the same number of samples in Network::fit (" + to_string(n_samples) + " != " + to_string(n_samples_y) + ")");
throw std::invalid_argument("X and y must have the same number of samples in Network::fit (" + std::to_string(n_samples) + " != " + std::to_string(n_samples_y) + ")");
}
if (n_features != featureNames.size()) {
throw invalid_argument("X and features must have the same number of features in Network::fit (" + to_string(n_features) + " != " + to_string(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 (n_features != features.size() - 1) {
throw invalid_argument("X and local features must have the same number of features in Network::fit (" + to_string(n_features) + " != " + to_string(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 invalid_argument("className not found in Network::features");
throw std::invalid_argument("className not found in Network::features");
}
for (auto& feature : featureNames) {
if (find(features.begin(), features.end(), feature) == features.end()) {
throw invalid_argument("Feature " + feature + " not found in Network::features");
throw std::invalid_argument("Feature " + feature + " not found in Network::features");
}
if (states.find(feature) == states.end()) {
throw invalid_argument("Feature " + feature + " not found in states");
throw std::invalid_argument("Feature " + feature + " not found in states");
}
}
}
void Network::setStates(const map<string, vector<int>>& states)
void Network::setStates(const std::map<std::string, std::vector<int>>& states)
{
// Set states to every Node in the network
for (int i = 0; i < features.size(); ++i) {
nodes[features[i]]->setNumStates(states.at(features[i]).size());
}
classNumStates = nodes[className]->getNumStates();
for_each(features.begin(), features.end(), [this, &states](const std::string& feature) {
nodes.at(feature)->setNumStates(states.at(feature).size());
});
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 vector<string>& featureNames, const string& className, const map<string, 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)
{
checkFitData(X.size(1), X.size(0), y.size(0), featureNames, className, states);
checkFitData(X.size(1), X.size(0), y.size(0), featureNames, className, states, weights);
this->className = className;
Tensor ytmp = torch::transpose(y.view({ y.size(0), 1 }), 0, 1);
torch::Tensor ytmp = torch::transpose(y.view({ y.size(0), 1 }), 0, 1);
samples = torch::cat({ X , ytmp }, 0);
for (int i = 0; i < featureNames.size(); ++i) {
auto row_feature = X.index({ i, "..." });
}
completeFit(states);
completeFit(states, weights);
}
void Network::fit(const torch::Tensor& samples, const vector<string>& featureNames, const string& className, const map<string, 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)
{
checkFitData(samples.size(1), samples.size(0) - 1, samples.size(1), featureNames, className, states);
checkFitData(samples.size(1), samples.size(0) - 1, samples.size(1), featureNames, className, states, weights);
this->className = className;
this->samples = samples;
completeFit(states);
completeFit(states, weights);
}
// input_data comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const vector<vector<int>>& input_data, const vector<int>& labels, const vector<string>& featureNames, const string& className, const map<string, 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)
{
checkFitData(input_data[0].size(), input_data.size(), labels.size(), featureNames, className, states);
const torch::Tensor weights = torch::tensor(weights_, torch::kFloat64);
checkFitData(input_data[0].size(), input_data.size(), labels.size(), featureNames, className, states, weights);
this->className = className;
// Build tensor of samples (nxm) (n+1 because of the class)
samples = torch::zeros({ static_cast<int>(input_data.size() + 1), static_cast<int>(input_data[0].size()) }, torch::kInt32);
@@ -165,42 +168,17 @@ namespace bayesnet {
samples.index_put_({ i, "..." }, torch::tensor(input_data[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
completeFit(states);
completeFit(states, weights);
}
void Network::completeFit(const map<string, vector<int>>& states)
void Network::completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
{
setStates(states);
int maxThreadsRunning = static_cast<int>(std::thread::hardware_concurrency() * maxThreads);
if (maxThreadsRunning < 1) {
maxThreadsRunning = 1;
}
vector<thread> threads;
mutex mtx;
condition_variable cv;
int activeThreads = 0;
int nextNodeIndex = 0;
while (nextNodeIndex < nodes.size()) {
unique_lock<mutex> lock(mtx);
cv.wait(lock, [&activeThreads, &maxThreadsRunning]() { return activeThreads < maxThreadsRunning; });
threads.emplace_back([this, &nextNodeIndex, &mtx, &cv, &activeThreads]() {
while (true) {
unique_lock<mutex> lock(mtx);
if (nextNodeIndex >= nodes.size()) {
break; // No more work remaining
}
auto& pair = *std::next(nodes.begin(), nextNodeIndex);
++nextNodeIndex;
lock.unlock();
pair.second->computeCPT(samples, features, laplaceSmoothing);
lock.lock();
nodes[pair.first] = std::move(pair.second);
lock.unlock();
}
lock_guard<mutex> lock(mtx);
--activeThreads;
cv.notify_one();
laplaceSmoothing = 1.0 / samples.size(1); // To use in CPT computation
std::vector<std::thread> threads;
for (auto& node : nodes) {
threads.emplace_back([this, &node, &weights]() {
node.second->computeCPT(samples, features, laplaceSmoothing, weights);
});
++activeThreads;
}
for (auto& thread : threads) {
thread.join();
@@ -210,12 +188,12 @@ namespace bayesnet {
torch::Tensor Network::predict_tensor(const torch::Tensor& samples, const bool proba)
{
if (!fitted) {
throw logic_error("You must call fit() before calling predict()");
throw std::logic_error("You must call fit() before calling predict()");
}
torch::Tensor result;
result = torch::zeros({ samples.size(1), classNumStates }, torch::kFloat64);
for (int i = 0; i < samples.size(1); ++i) {
const Tensor sample = samples.index({ "...", i });
const torch::Tensor sample = samples.index({ "...", i });
auto psample = predict_sample(sample);
auto temp = torch::tensor(psample, torch::kFloat64);
// result.index_put_({ i, "..." }, torch::tensor(predict_sample(sample), torch::kFloat64));
@@ -223,36 +201,35 @@ namespace bayesnet {
}
if (proba)
return result;
else
return result.argmax(1);
}
// Return mxn tensor of probabilities
Tensor Network::predict_proba(const Tensor& samples)
torch::Tensor Network::predict_proba(const torch::Tensor& samples)
{
return predict_tensor(samples, true);
}
// Return mxn tensor of probabilities
Tensor Network::predict(const Tensor& samples)
torch::Tensor Network::predict(const torch::Tensor& samples)
{
return predict_tensor(samples, false);
}
// Return mx1 vector of predictions
// tsamples is nxm vector of samples
vector<int> Network::predict(const vector<vector<int>>& tsamples)
// Return mx1 std::vector of predictions
// tsamples is nxm std::vector of samples
std::vector<int> Network::predict(const std::vector<std::vector<int>>& tsamples)
{
if (!fitted) {
throw logic_error("You must call fit() before calling predict()");
throw std::logic_error("You must call fit() before calling predict()");
}
vector<int> predictions;
vector<int> sample;
std::vector<int> predictions;
std::vector<int> sample;
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]);
}
vector<double> classProbabilities = predict_sample(sample);
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);
@@ -260,14 +237,14 @@ namespace bayesnet {
}
return predictions;
}
// Return mxn vector of probabilities
vector<vector<double>> Network::predict_proba(const vector<vector<int>>& tsamples)
// Return mxn std::vector of probabilities
std::vector<std::vector<double>> Network::predict_proba(const std::vector<std::vector<int>>& tsamples)
{
if (!fitted) {
throw logic_error("You must call fit() before calling predict_proba()");
throw std::logic_error("You must call fit() before calling predict_proba()");
}
vector<vector<double>> predictions;
vector<int> sample;
std::vector<std::vector<double>> predictions;
std::vector<int> sample;
for (int row = 0; row < tsamples[0].size(); ++row) {
sample.clear();
for (int col = 0; col < tsamples.size(); ++col) {
@@ -277,9 +254,9 @@ namespace bayesnet {
}
return predictions;
}
double Network::score(const vector<vector<int>>& tsamples, const vector<int>& labels)
double Network::score(const std::vector<std::vector<int>>& tsamples, const std::vector<int>& labels)
{
vector<int> y_pred = predict(tsamples);
std::vector<int> y_pred = predict(tsamples);
int correct = 0;
for (int i = 0; i < y_pred.size(); ++i) {
if (y_pred[i] == labels[i]) {
@@ -288,35 +265,35 @@ namespace bayesnet {
}
return (double)correct / y_pred.size();
}
// Return 1xn vector of probabilities
vector<double> Network::predict_sample(const vector<int>& sample)
// 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 invalid_argument("Sample size (" + to_string(sample.size()) +
") does not match the number of features (" + to_string(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) + ")");
}
map<string, int> evidence;
std::map<std::string, int> evidence;
for (int i = 0; i < sample.size(); ++i) {
evidence[features[i]] = sample[i];
}
return exactInference(evidence);
}
// Return 1xn vector of probabilities
vector<double> Network::predict_sample(const Tensor& sample)
// 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 invalid_argument("Sample size (" + to_string(sample.size(0)) +
") does not match the number of features (" + to_string(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) + ")");
}
map<string, int> evidence;
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(map<string, int>& completeEvidence)
double Network::computeFactor(std::map<std::string, int>& completeEvidence)
{
double result = 1.0;
for (auto& node : getNodes()) {
@@ -324,17 +301,17 @@ namespace bayesnet {
}
return result;
}
vector<double> Network::exactInference(map<string, int>& evidence)
std::vector<double> Network::exactInference(std::map<std::string, int>& evidence)
{
vector<double> result(classNumStates, 0.0);
vector<thread> threads;
mutex mtx;
std::vector<double> result(classNumStates, 0.0);
std::vector<std::thread> threads;
std::mutex mtx;
for (int i = 0; i < classNumStates; ++i) {
threads.emplace_back([this, &result, &evidence, i, &mtx]() {
auto completeEvidence = map<string, int>(evidence);
auto completeEvidence = std::map<std::string, int>(evidence);
completeEvidence[getClassName()] = i;
double factor = computeFactor(completeEvidence);
lock_guard<mutex> lock(mtx);
std::lock_guard<std::mutex> lock(mtx);
result[i] = factor;
});
}
@@ -343,15 +320,15 @@ namespace bayesnet {
}
// Normalize result
double sum = accumulate(result.begin(), result.end(), 0.0);
transform(result.begin(), result.end(), result.begin(), [sum](double& value) { return value / sum; });
transform(result.begin(), result.end(), result.begin(), [sum](const double& value) { return value / sum; });
return result;
}
vector<string> Network::show() const
std::vector<std::string> Network::show() const
{
vector<string> result;
std::vector<std::string> result;
// Draw the network
for (auto& node : nodes) {
string line = node.first + " -> ";
std::string line = node.first + " -> ";
for (auto child : node.second->getChildren()) {
line += child->getName() + ", ";
}
@@ -359,12 +336,12 @@ namespace bayesnet {
}
return result;
}
vector<string> Network::graph(const string& title) const
std::vector<std::string> Network::graph(const std::string& title) const
{
auto output = vector<string>();
auto output = std::vector<std::string>();
auto prefix = "digraph BayesNet {\nlabel=<BayesNet ";
auto suffix = ">\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n";
string header = prefix + title + suffix;
std::string header = prefix + title + suffix;
output.push_back(header);
for (auto& node : nodes) {
auto result = node.second->graph(className);
@@ -373,9 +350,9 @@ namespace bayesnet {
output.push_back("}\n");
return output;
}
vector<pair<string, string>> Network::getEdges() const
std::vector<std::pair<std::string, std::string>> Network::getEdges() const
{
auto edges = vector<pair<string, string>>();
auto edges = std::vector<std::pair<std::string, std::string>>();
for (const auto& node : nodes) {
auto head = node.first;
for (const auto& child : node.second->getChildren()) {
@@ -389,13 +366,12 @@ namespace bayesnet {
{
return getEdges().size();
}
vector<string> Network::topological_sort()
std::vector<std::string> Network::topological_sort()
{
/* Check if al the fathers of every node are before the node */
auto result = features;
result.erase(remove(result.begin(), result.end(), className), result.end());
bool ending{ false };
int idx = 0;
while (!ending) {
ending = true;
for (auto feature : features) {
@@ -417,10 +393,10 @@ namespace bayesnet {
ending = false;
}
} else {
throw logic_error("Error in topological sort because of node " + feature + " is not in result");
throw std::logic_error("Error in topological sort because of node " + feature + " is not in result");
}
} else {
throw logic_error("Error in topological sort because of node father " + fatherName + " is not in result");
throw std::logic_error("Error in topological sort because of node father " + fatherName + " is not in result");
}
}
}
@@ -430,7 +406,8 @@ namespace bayesnet {
void Network::dump_cpt() const
{
for (auto& node : nodes) {
cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << endl;
std::cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << std::endl;
std::cout << node.second->getCPT() << std::endl;
}
}
}

View File

@@ -7,53 +7,56 @@
namespace bayesnet {
class Network {
private:
map<string, unique_ptr<Node>> nodes;
std::map<std::string, std::unique_ptr<Node>> nodes;
bool fitted;
float maxThreads = 0.95;
int classNumStates;
vector<string> features; // Including classname
string className;
int laplaceSmoothing = 1;
std::vector<std::string> features; // Including classname
std::string className;
double laplaceSmoothing;
torch::Tensor samples; // nxm tensor used to fit the model
bool isCyclic(const std::string&, std::unordered_set<std::string>&, std::unordered_set<std::string>&);
vector<double> predict_sample(const vector<int>&);
vector<double> predict_sample(const torch::Tensor&);
vector<double> exactInference(map<string, int>&);
double computeFactor(map<string, int>&);
void completeFit(const map<string, vector<int>>&);
void checkFitData(int n_features, int n_samples, int n_samples_y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>&);
void setStates(const map<string, vector<int>>&);
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 setStates(const std::map<std::string, std::vector<int>>&);
public:
Network();
explicit Network(float, int);
explicit Network(float);
explicit Network(Network&);
~Network() = default;
torch::Tensor& getSamples();
float getmaxThreads();
void addNode(const string&);
void addEdge(const string&, const string&);
map<string, std::unique_ptr<Node>>& getNodes();
vector<string> getFeatures() const;
void addNode(const std::string&);
void addEdge(const std::string&, const std::string&);
std::map<std::string, std::unique_ptr<Node>>& getNodes();
std::vector<std::string> getFeatures() const;
int getStates() const;
vector<pair<string, string>> getEdges() const;
std::vector<std::pair<std::string, std::string>> getEdges() const;
int getNumEdges() const;
int getClassNumStates() const;
string getClassName() const;
void fit(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&, const map<string, vector<int>>&);
void fit(const torch::Tensor&, const torch::Tensor&, const vector<string>&, const string&, const map<string, vector<int>>&);
void fit(const torch::Tensor&, const vector<string>&, const string&, const map<string, vector<int>>&);
vector<int> predict(const vector<vector<int>>&); // Return mx1 vector of predictions
std::string getClassName() const;
/*
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);
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);
vector<vector<double>> predict_proba(const vector<vector<int>>&); // Return mxn vector of probabilities
std::vector<std::vector<double>> predict_proba(const std::vector<std::vector<int>>&); // Return mxn std::vector of probabilities
torch::Tensor predict_proba(const torch::Tensor&); // Return mxn tensor of probabilities
double score(const vector<vector<int>>&, const vector<int>&);
vector<string> topological_sort();
vector<string> show() const;
vector<string> graph(const string& title) const; // Returns a vector of strings representing the graph in graphviz format
double score(const std::vector<std::vector<int>>&, const std::vector<int>&);
std::vector<std::string> topological_sort();
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;
inline string version() { return "0.1.0"; }
inline std::string version() { return "0.2.0"; }
};
}
#endif

View File

@@ -3,7 +3,7 @@
namespace bayesnet {
Node::Node(const std::string& name)
: name(name), numStates(0), cpTable(torch::Tensor()), parents(vector<Node*>()), children(vector<Node*>())
: name(name), numStates(0), cpTable(torch::Tensor()), parents(std::vector<Node*>()), children(std::vector<Node*>())
{
}
void Node::clear()
@@ -14,7 +14,7 @@ namespace bayesnet {
dimensions.clear();
numStates = 0;
}
string Node::getName() const
std::string Node::getName() const
{
return name;
}
@@ -34,11 +34,11 @@ namespace bayesnet {
{
children.push_back(child);
}
vector<Node*>& Node::getParents()
std::vector<Node*>& Node::getParents()
{
return parents;
}
vector<Node*>& Node::getChildren()
std::vector<Node*>& Node::getChildren()
{
return children;
}
@@ -63,28 +63,28 @@ namespace bayesnet {
*/
unsigned Node::minFill()
{
unordered_set<string> neighbors;
std::unordered_set<std::string> neighbors;
for (auto child : children) {
neighbors.emplace(child->getName());
}
for (auto parent : parents) {
neighbors.emplace(parent->getName());
}
auto source = vector<string>(neighbors.begin(), neighbors.end());
auto source = std::vector<std::string>(neighbors.begin(), neighbors.end());
return combinations(source).size();
}
vector<pair<string, string>> Node::combinations(const vector<string>& source)
std::vector<std::pair<std::string, std::string>> Node::combinations(const std::vector<std::string>& source)
{
vector<pair<string, string>> result;
std::vector<std::pair<std::string, std::string>> result;
for (int i = 0; i < source.size(); ++i) {
string temp = source[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 vector<string>& features, const int laplaceSmoothing)
void Node::computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double laplaceSmoothing, const torch::Tensor& weights)
{
dimensions.clear();
// Get dimensions of the CPT
@@ -96,37 +96,37 @@ namespace bayesnet {
// Fill table with counts
auto pos = find(features.begin(), features.end(), name);
if (pos == features.end()) {
throw logic_error("Feature " + name + " not found in dataset");
throw std::logic_error("Feature " + name + " not found in dataset");
}
int name_index = pos - features.begin();
for (int n_sample = 0; n_sample < dataset.size(1); ++n_sample) {
torch::List<c10::optional<torch::Tensor>> coordinates;
c10::List<c10::optional<at::Tensor>> coordinates;
coordinates.push_back(dataset.index({ name_index, n_sample }));
for (auto parent : parents) {
pos = find(features.begin(), features.end(), parent->getName());
if (pos == features.end()) {
throw logic_error("Feature parent " + parent->getName() + " not found in dataset");
throw std::logic_error("Feature parent " + parent->getName() + " not found in dataset");
}
int parent_index = pos - features.begin();
coordinates.push_back(dataset.index({ parent_index, n_sample }));
}
// Increment the count of the corresponding coordinate
cpTable.index_put_({ coordinates }, cpTable.index({ coordinates }) + 1);
cpTable.index_put_({ coordinates }, cpTable.index({ coordinates }) + weights.index({ n_sample }).item<double>());
}
// Normalize the counts
cpTable = cpTable / cpTable.sum(0);
}
float Node::getFactorValue(map<string, int>& evidence)
float Node::getFactorValue(std::map<std::string, int>& evidence)
{
torch::List<c10::optional<torch::Tensor>> coordinates;
c10::List<c10::optional<at::Tensor>> coordinates;
// following predetermined order of indices in the cpTable (see Node.h)
coordinates.push_back(torch::tensor(evidence[name]));
transform(parents.begin(), parents.end(), back_inserter(coordinates), [&evidence](const auto& parent) { return torch::tensor(evidence[parent->getName()]); });
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<float>();
}
vector<string> Node::graph(const string& className)
std::vector<std::string> Node::graph(const std::string& className)
{
auto output = vector<string>();
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(); });

View File

@@ -5,33 +5,32 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
class Node {
private:
string name;
vector<Node*> parents;
vector<Node*> children;
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, ...
vector<int64_t> dimensions; // dimensions of the cpTable
std::vector<int64_t> dimensions; // dimensions of the cpTable
std::vector<std::pair<std::string, std::string>> combinations(const std::vector<std::string>&);
public:
vector<pair<string, string>> combinations(const vector<string>&);
explicit Node(const string&);
explicit Node(const std::string&);
void clear();
void addParent(Node*);
void addChild(Node*);
void removeParent(Node*);
void removeChild(Node*);
string getName() const;
vector<Node*>& getParents();
vector<Node*>& getChildren();
std::string getName() const;
std::vector<Node*>& getParents();
std::vector<Node*>& getChildren();
torch::Tensor& getCPT();
void computeCPT(const torch::Tensor&, const vector<string>&, const int);
void computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double laplaceSmoothing, const torch::Tensor& weights);
int getNumStates() const;
void setNumStates(int);
unsigned minFill();
vector<string> graph(const string& clasName); // Returns a vector of strings representing the graph in graphviz format
float getFactorValue(map<string, int>&);
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>&);
};
}
#endif

View File

@@ -2,21 +2,30 @@
#include "ArffFiles.h"
namespace bayesnet {
Proposal::Proposal(torch::Tensor& dataset_, vector<string>& features_, string& className_) : pDataset(dataset_), pFeatures(features_), pClassName(className_) {}
Proposal::Proposal(torch::Tensor& dataset_, std::vector<std::string>& features_, std::string& className_) : pDataset(dataset_), pFeatures(features_), pClassName(className_) {}
Proposal::~Proposal()
{
for (auto& [key, value] : discretizers) {
delete value;
}
}
map<string, vector<int>> Proposal::localDiscretizationProposal(const map<string, vector<int>>& oldStates, Network& model)
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");
}
}
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<string, vector<int>> states = oldStates;
vector<int> indicesToReDiscretize;
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();
@@ -24,16 +33,16 @@ namespace bayesnet {
upgrade = true;
int index = find(pFeatures.begin(), pFeatures.end(), feature) - pFeatures.begin();
indicesToReDiscretize.push_back(index); // We need to re-discretize this feature
vector<string> parents;
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
vector<int> indices;
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)
vector<string> yJoinParents(Xf.size(1));
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>());
@@ -42,55 +51,47 @@ namespace bayesnet {
auto arff = ArffFiles();
auto yxv = arff.factorize(yJoinParents);
auto xvf_ptr = Xf.index({ index }).data_ptr<float>();
auto xvf = vector<mdlp::precision_t>(xvf_ptr, xvf_ptr + Xf.size(1));
auto xvf = std::vector<mdlp::precision_t>(xvf_ptr, xvf_ptr + Xf.size(1));
discretizers[feature]->fit(xvf, yxv);
//
//
//
// auto tmp = discretizers[feature]->transform(xvf);
// Xv[index] = tmp;
// auto xStates = vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
// iota(xStates.begin(), xStates.end(), 0);
// //Update new states of the feature/node
// states[feature] = xStates;
}
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 = vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
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 = vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
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;
}
model.fit(pDataset, pFeatures, pClassName, states);
const torch::Tensor weights = torch::full({ pDataset.size(1) }, 1.0 / pDataset.size(1), torch::kDouble);
model.fit(pDataset, weights, pFeatures, pClassName, states);
}
return states;
}
map<string, vector<int>> Proposal::fit_local_discretization(const torch::Tensor& y)
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<string, vector<int>> states;
pDataset = torch::zeros({ n + 1, m }, kInt32);
auto yv = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.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)
for (auto i = 0; i < pFeatures.size(); ++i) {
auto* discretizer = new mdlp::CPPFImdlp();
auto Xt_ptr = Xf.index({ i }).data_ptr<float>();
auto Xt = vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
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 = vector<int>(discretizer->getCutPoints().size() + 1);
auto xStates = std::vector<int>(discretizer->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
states[pFeatures[i]] = xStates;
discretizers[pFeatures[i]] = discretizer;
}
int n_classes = torch::max(y).item<int>() + 1;
auto yStates = vector<int>(n_classes);
auto yStates = std::vector<int>(n_classes);
iota(yStates.begin(), yStates.end(), 0);
states[pClassName] = yStates;
pDataset.index_put_({ n, "..." }, y);
@@ -100,7 +101,7 @@ namespace bayesnet {
{
auto Xtd = torch::zeros_like(X, torch::kInt32);
for (int i = 0; i < X.size(0); ++i) {
auto Xt = vector<float>(X[i].data_ptr<float>(), X[i].data_ptr<float>() + X.size(1));
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));
}

View File

@@ -10,19 +10,20 @@
namespace bayesnet {
class Proposal {
public:
Proposal(torch::Tensor& pDataset, vector<string>& features_, string& className_);
Proposal(torch::Tensor& pDataset, std::vector<std::string>& features_, std::string& className_);
virtual ~Proposal();
protected:
void checkInput(const torch::Tensor& X, const torch::Tensor& y);
torch::Tensor prepareX(torch::Tensor& X);
map<string, vector<int>> localDiscretizationProposal(const map<string, vector<int>>& states, Network& model);
map<string, vector<int>> fit_local_discretization(const torch::Tensor& y);
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);
torch::Tensor Xf; // X continuous nxm tensor
torch::Tensor y; // y discrete nx1 tensor
map<string, mdlp::CPPFImdlp*> discretizers;
map<std::string, mdlp::CPPFImdlp*> discretizers;
private:
torch::Tensor& pDataset; // (n+1)xm tensor
vector<string>& pFeatures;
string& pClassName;
std::vector<std::string>& pFeatures;
std::string& pClassName;
};
}

View File

@@ -4,7 +4,7 @@ namespace bayesnet {
SPODE::SPODE(int root) : Classifier(Network()), root(root) {}
void SPODE::buildModel()
void SPODE::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
addNodes();
@@ -17,7 +17,7 @@ namespace bayesnet {
}
}
}
vector<string> SPODE::graph(const string& name) const
std::vector<std::string> SPODE::graph(const std::string& name) const
{
return model.graph(name);
}

View File

@@ -7,11 +7,11 @@ namespace bayesnet {
private:
int root;
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
explicit SPODE(int root);
virtual ~SPODE() {};
vector<string> graph(const string& name = "SPODE") const override;
std::vector<std::string> graph(const std::string& name = "SPODE") const override;
};
}
#endif

View File

@@ -1,16 +1,15 @@
#include "SPODELd.h"
namespace bayesnet {
using namespace std;
SPODELd::SPODELd(int root) : SPODE(root), Proposal(dataset, features, className) {}
SPODELd& SPODELd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
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_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
// 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 SPODE structure, SPODE::fit initializes the base Bayesian network
@@ -18,15 +17,16 @@ namespace bayesnet {
states = localDiscretizationProposal(states, model);
return *this;
}
SPODELd& SPODELd::fit(torch::Tensor& dataset, vector<string>& features_, string className_, map<string, vector<int>>& states_)
SPODELd& SPODELd::fit(torch::Tensor& dataset, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
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();
cout << "Xf " << Xf.sizes() << " dtype: " << Xf.dtype() << endl;
y = dataset.index({ -1, "..." }).clone();
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
// 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 SPODE structure, SPODE::fit initializes the base Bayesian network
@@ -35,12 +35,12 @@ namespace bayesnet {
return *this;
}
Tensor SPODELd::predict(Tensor& X)
torch::Tensor SPODELd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return SPODE::predict(Xt);
}
vector<string> SPODELd::graph(const string& name) const
std::vector<std::string> SPODELd::graph(const std::string& name) const
{
return SPODE::graph(name);
}

View File

@@ -4,16 +4,15 @@
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class SPODELd : public SPODE, public Proposal {
public:
explicit SPODELd(int root);
virtual ~SPODELd() = default;
SPODELd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
SPODELd& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "SPODE") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
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) override;
SPODELd& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states) override;
std::vector<std::string> graph(const std::string& name = "SPODE") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !SPODELD_H

View File

@@ -1,29 +1,27 @@
#include "TAN.h"
namespace bayesnet {
using namespace torch;
TAN::TAN() : Classifier(Network()) {}
void TAN::buildModel()
void TAN::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
addNodes();
// 1. Compute mutual information between each feature and the class and set the root node
// as the highest mutual information with the class
auto mi = vector <pair<int, float >>();
Tensor class_dataset = dataset.index({ -1, "..." });
auto mi = std::vector <std::pair<int, float >>();
torch::Tensor class_dataset = dataset.index({ -1, "..." });
for (int i = 0; i < static_cast<int>(features.size()); ++i) {
Tensor feature_dataset = dataset.index({ i, "..." });
auto mi_value = metrics.mutualInformation(class_dataset, feature_dataset);
torch::Tensor feature_dataset = dataset.index({ i, "..." });
auto mi_value = metrics.mutualInformation(class_dataset, feature_dataset, weights);
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;
// 2. Compute mutual information between each feature and the class
auto weights = metrics.conditionalEdge();
auto weights_matrix = metrics.conditionalEdge(weights);
// 3. Compute the maximum spanning tree
auto mst = metrics.maximumSpanningTree(features, weights, root);
auto mst = metrics.maximumSpanningTree(features, weights_matrix, root);
// 4. Add edges from the maximum spanning tree to the model
for (auto i = 0; i < mst.size(); ++i) {
auto [from, to] = mst[i];
@@ -34,7 +32,7 @@ namespace bayesnet {
model.addEdge(className, feature);
}
}
vector<string> TAN::graph(const string& title) const
std::vector<std::string> TAN::graph(const std::string& title) const
{
return model.graph(title);
}

View File

@@ -2,16 +2,14 @@
#define TAN_H
#include "Classifier.h"
namespace bayesnet {
using namespace std;
using namespace torch;
class TAN : public Classifier {
private:
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
TAN();
virtual ~TAN() {};
vector<string> graph(const string& name = "TAN") const override;
std::vector<std::string> graph(const std::string& name = "TAN") const override;
};
}
#endif

View File

@@ -1,16 +1,15 @@
#include "TANLd.h"
namespace bayesnet {
using namespace std;
TANLd::TANLd() : TAN(), Proposal(dataset, features, className) {}
TANLd& TANLd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
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_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
// 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
@@ -19,12 +18,12 @@ namespace bayesnet {
return *this;
}
Tensor TANLd::predict(Tensor& X)
torch::Tensor TANLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return TAN::predict(Xt);
}
vector<string> TANLd::graph(const string& name) const
std::vector<std::string> TANLd::graph(const std::string& name) const
{
return TAN::graph(name);
}

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@@ -4,16 +4,15 @@
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class TANLd : public TAN, public Proposal {
private:
public:
TANLd();
virtual ~TANLd() = default;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "TAN") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
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) override;
std::vector<std::string> graph(const std::string& name = "TAN") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !TANLD_H

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@@ -1,25 +1,23 @@
#include "bayesnetUtils.h"
namespace bayesnet {
using namespace std;
using namespace torch;
// Return the indices in descending order
vector<int> argsort(vector<float>& nums)
std::vector<int> argsort(std::vector<double>& nums)
{
int n = nums.size();
vector<int> indices(n);
std::vector<int> indices(n);
iota(indices.begin(), indices.end(), 0);
sort(indices.begin(), indices.end(), [&nums](int i, int j) {return nums[i] > nums[j];});
return indices;
}
vector<vector<int>> tensorToVector(Tensor& tensor)
std::vector<std::vector<int>> tensorToVector(torch::Tensor& tensor)
{
// convert mxn tensor to nxm vector
vector<vector<int>> result;
// convert mxn tensor to nxm std::vector
std::vector<std::vector<int>> result;
// Iterate over cols
for (int i = 0; i < tensor.size(1); ++i) {
auto col_tensor = tensor.index({ "...", i });
auto col = vector<int>(col_tensor.data_ptr<int>(), col_tensor.data_ptr<int>() + tensor.size(0));
auto col = std::vector<int>(col_tensor.data_ptr<int>(), col_tensor.data_ptr<int>() + tensor.size(0));
result.push_back(col);
}
return result;

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@@ -3,9 +3,7 @@
#include <torch/torch.h>
#include <vector>
namespace bayesnet {
using namespace std;
using namespace torch;
vector<int> argsort(vector<float>& nums);
vector<vector<int>> tensorToVector(Tensor& tensor);
std::vector<int> argsort(std::vector<double>& nums);
std::vector<std::vector<int>> tensorToVector(torch::Tensor& tensor);
}
#endif //BAYESNET_UTILS_H

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@@ -1,10 +0,0 @@
#ifndef BESTRESULT_H
#define BESTRESULT_H
#include <string>
class BestResult {
public:
static std::string title() { return "STree_default (linear-ovo)"; }
static double score() { return 22.109799; }
static std::string scoreName() { return "accuracy"; }
};
#endif

343
src/Platform/BestResults.cc Normal file
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@@ -0,0 +1,343 @@
#include <filesystem>
#include <set>
#include <fstream>
#include <iostream>
#include <sstream>
#include <algorithm>
#include "BestResults.h"
#include "Result.h"
#include "Colors.h"
#include "Statistics.h"
#include "BestResultsExcel.h"
#include "CLocale.h"
namespace fs = std::filesystem;
// function ftime_to_std::string, Code taken from
// https://stackoverflow.com/a/58237530/1389271
template <typename TP>
std::string ftime_to_string(TP tp)
{
auto sctp = std::chrono::time_point_cast<std::chrono::system_clock::duration>(tp - TP::clock::now()
+ std::chrono::system_clock::now());
auto tt = std::chrono::system_clock::to_time_t(sctp);
std::tm* gmt = std::gmtime(&tt);
std::stringstream buffer;
buffer << std::put_time(gmt, "%Y-%m-%d %H:%M");
return buffer.str();
}
namespace platform {
std::string BestResults::build()
{
auto files = loadResultFiles();
if (files.size() == 0) {
std::cerr << Colors::MAGENTA() << "No result files were found!" << Colors::RESET() << std::endl;
exit(1);
}
json bests;
for (const auto& file : files) {
auto result = Result(path, file);
auto data = result.load();
for (auto const& item : data.at("results")) {
bool update = false;
// Check if results file contains only one dataset
auto datasetName = item.at("dataset").get<std::string>();
if (bests.contains(datasetName)) {
if (item.at("score").get<double>() > bests[datasetName].at(0).get<double>()) {
update = true;
}
} else {
update = true;
}
if (update) {
bests[datasetName] = { item.at("score").get<double>(), item.at("hyperparameters"), file };
}
}
}
std::string bestFileName = path + bestResultFile();
if (FILE* fileTest = fopen(bestFileName.c_str(), "r")) {
fclose(fileTest);
std::cout << Colors::MAGENTA() << "File " << bestFileName << " already exists and it shall be overwritten." << Colors::RESET() << std::endl;
}
std::ofstream file(bestFileName);
file << bests;
file.close();
return bestFileName;
}
std::string BestResults::bestResultFile()
{
return "best_results_" + score + "_" + model + ".json";
}
std::pair<std::string, std::string> getModelScore(std::string name)
{
// results_accuracy_BoostAODE_MacBookpro16_2023-09-06_12:27:00_1.json
int i = 0;
auto pos = name.find("_");
auto pos2 = name.find("_", pos + 1);
std::string score = name.substr(pos + 1, pos2 - pos - 1);
pos = name.find("_", pos2 + 1);
std::string model = name.substr(pos2 + 1, pos - pos2 - 1);
return { model, score };
}
std::vector<std::string> BestResults::loadResultFiles()
{
std::vector<std::string> files;
using std::filesystem::directory_iterator;
std::string fileModel, fileScore;
for (const auto& file : directory_iterator(path)) {
auto fileName = file.path().filename().string();
if (fileName.find(".json") != std::string::npos && fileName.find("results_") == 0) {
tie(fileModel, fileScore) = getModelScore(fileName);
if (score == fileScore && (model == fileModel || model == "any")) {
files.push_back(fileName);
}
}
}
return files;
}
json BestResults::loadFile(const std::string& fileName)
{
std::ifstream resultData(fileName);
if (resultData.is_open()) {
json data = json::parse(resultData);
return data;
}
throw std::invalid_argument("Unable to open result file. [" + fileName + "]");
}
std::vector<std::string> BestResults::getModels()
{
std::set<std::string> models;
std::vector<std::string> result;
auto files = loadResultFiles();
if (files.size() == 0) {
std::cerr << Colors::MAGENTA() << "No result files were found!" << Colors::RESET() << std::endl;
exit(1);
}
std::string fileModel, fileScore;
for (const auto& file : files) {
// extract the model from the file name
tie(fileModel, fileScore) = getModelScore(file);
// add the model to the std::vector of models
models.insert(fileModel);
}
result = std::vector<std::string>(models.begin(), models.end());
return result;
}
std::vector<std::string> BestResults::getDatasets(json table)
{
std::vector<std::string> datasets;
for (const auto& dataset : table.items()) {
datasets.push_back(dataset.key());
}
return datasets;
}
void BestResults::buildAll()
{
auto models = getModels();
for (const auto& model : models) {
std::cout << "Building best results for model: " << model << std::endl;
this->model = model;
build();
}
model = "any";
}
void BestResults::listFile()
{
std::string bestFileName = path + bestResultFile();
if (FILE* fileTest = fopen(bestFileName.c_str(), "r")) {
fclose(fileTest);
} else {
std::cerr << Colors::MAGENTA() << "File " << bestFileName << " doesn't exist." << Colors::RESET() << std::endl;
exit(1);
}
auto temp = ConfigLocale();
auto date = ftime_to_string(std::filesystem::last_write_time(bestFileName));
auto data = loadFile(bestFileName);
auto datasets = getDatasets(data);
int maxDatasetName = (*max_element(datasets.begin(), datasets.end(), [](const std::string& a, const std::string& b) { return a.size() < b.size(); })).size();
int maxFileName = 0;
int maxHyper = 15;
for (auto const& item : data.items()) {
maxHyper = std::max(maxHyper, (int)item.value().at(1).dump().size());
maxFileName = std::max(maxFileName, (int)item.value().at(2).get<std::string>().size());
}
std::stringstream oss;
oss << Colors::GREEN() << "Best results for " << model << " as of " << date << std::endl;
std::cout << oss.str();
std::cout << std::string(oss.str().size() - 8, '-') << std::endl;
std::cout << Colors::GREEN() << " # " << std::setw(maxDatasetName + 1) << std::left << "Dataset" << "Score " << std::setw(maxFileName) << "File" << " Hyperparameters" << std::endl;
std::cout << "=== " << std::string(maxDatasetName, '=') << " =========== " << std::string(maxFileName, '=') << " " << std::string(maxHyper, '=') << std::endl;
auto i = 0;
bool odd = true;
double total = 0;
for (auto const& item : data.items()) {
auto color = odd ? Colors::BLUE() : Colors::CYAN();
double value = item.value().at(0).get<double>();
std::cout << color << std::setw(3) << std::fixed << std::right << i++ << " ";
std::cout << std::setw(maxDatasetName) << std::left << item.key() << " ";
std::cout << std::setw(11) << std::setprecision(9) << std::fixed << value << " ";
std::cout << std::setw(maxFileName) << item.value().at(2).get<std::string>() << " ";
std::cout << item.value().at(1) << " ";
std::cout << std::endl;
total += value;
odd = !odd;
}
std::cout << Colors::GREEN() << "=== " << std::string(maxDatasetName, '=') << " ===========" << std::endl;
std::cout << std::setw(5 + maxDatasetName) << "Total.................. " << std::setw(11) << std::setprecision(8) << std::fixed << total << std::endl;
}
json BestResults::buildTableResults(std::vector<std::string> models)
{
json table;
auto maxDate = std::filesystem::file_time_type::max();
for (const auto& model : models) {
this->model = model;
std::string bestFileName = path + bestResultFile();
if (FILE* fileTest = fopen(bestFileName.c_str(), "r")) {
fclose(fileTest);
} else {
std::cerr << Colors::MAGENTA() << "File " << bestFileName << " doesn't exist." << Colors::RESET() << std::endl;
exit(1);
}
auto dateWrite = std::filesystem::last_write_time(bestFileName);
if (dateWrite < maxDate) {
maxDate = dateWrite;
}
auto data = loadFile(bestFileName);
table[model] = data;
}
table["dateTable"] = ftime_to_string(maxDate);
return table;
}
void BestResults::printTableResults(std::vector<std::string> models, json table)
{
std::stringstream oss;
oss << Colors::GREEN() << "Best results for " << score << " as of " << table.at("dateTable").get<std::string>() << std::endl;
std::cout << oss.str();
std::cout << std::string(oss.str().size() - 8, '-') << std::endl;
std::cout << Colors::GREEN() << " # " << std::setw(maxDatasetName + 1) << std::left << std::string("Dataset");
for (const auto& model : models) {
std::cout << std::setw(maxModelName) << std::left << model << " ";
}
std::cout << std::endl;
std::cout << "=== " << std::string(maxDatasetName, '=') << " ";
for (const auto& model : models) {
std::cout << std::string(maxModelName, '=') << " ";
}
std::cout << std::endl;
auto i = 0;
bool odd = true;
std::map<std::string, double> totals;
int nDatasets = table.begin().value().size();
for (const auto& model : models) {
totals[model] = 0.0;
}
auto datasets = getDatasets(table.begin().value());
for (auto const& dataset : datasets) {
auto color = odd ? Colors::BLUE() : Colors::CYAN();
std::cout << color << std::setw(3) << std::fixed << std::right << i++ << " ";
std::cout << std::setw(maxDatasetName) << std::left << dataset << " ";
double maxValue = 0;
// Find out the max value for this dataset
for (const auto& model : models) {
double value = table[model].at(dataset).at(0).get<double>();
if (value > maxValue) {
maxValue = value;
}
}
// Print the row with red colors on max values
for (const auto& model : models) {
std::string efectiveColor = color;
double value = table[model].at(dataset).at(0).get<double>();
if (value == maxValue) {
efectiveColor = Colors::RED();
}
totals[model] += value;
std::cout << efectiveColor << std::setw(maxModelName) << std::setprecision(maxModelName - 2) << std::fixed << value << " ";
}
std::cout << std::endl;
odd = !odd;
}
std::cout << Colors::GREEN() << "=== " << std::string(maxDatasetName, '=') << " ";
for (const auto& model : models) {
std::cout << std::string(maxModelName, '=') << " ";
}
std::cout << std::endl;
std::cout << Colors::GREEN() << std::setw(5 + maxDatasetName) << " Totals...................";
double max = 0.0;
for (const auto& total : totals) {
if (total.second > max) {
max = total.second;
}
}
for (const auto& model : models) {
std::string efectiveColor = Colors::GREEN();
if (totals[model] == max) {
efectiveColor = Colors::RED();
}
std::cout << efectiveColor << std::right << std::setw(maxModelName) << std::setprecision(maxModelName - 4) << std::fixed << totals[model] << " ";
}
std::cout << std::endl;
}
void BestResults::reportSingle(bool excel)
{
listFile();
if (excel) {
auto models = getModels();
// Build the table of results
json table = buildTableResults(models);
std::vector<std::string> datasets = getDatasets(table.begin().value());
BestResultsExcel excel(score, datasets);
excel.reportSingle(model, path + bestResultFile());
messageExcelFile(excel.getFileName());
}
}
void BestResults::reportAll(bool excel)
{
auto models = getModels();
// Build the table of results
json table = buildTableResults(models);
std::vector<std::string> datasets = getDatasets(table.begin().value());
maxModelName = (*max_element(models.begin(), models.end(), [](const std::string& a, const std::string& b) { return a.size() < b.size(); })).size();
maxModelName = std::max(12, maxModelName);
maxDatasetName = (*max_element(datasets.begin(), datasets.end(), [](const std::string& a, const std::string& b) { return a.size() < b.size(); })).size();
maxDatasetName = std::max(25, maxDatasetName);
// Print the table of results
printTableResults(models, table);
// Compute the Friedman test
std::map<std::string, std::map<std::string, float>> ranksModels;
if (friedman) {
Statistics stats(models, datasets, table, significance);
auto result = stats.friedmanTest();
stats.postHocHolmTest(result);
ranksModels = stats.getRanks();
}
if (excel) {
BestResultsExcel excel(score, datasets);
excel.reportAll(models, table, ranksModels, friedman, significance);
if (friedman) {
int idx = -1;
double min = 2000;
// Find out the control model
auto totals = std::vector<double>(models.size(), 0.0);
for (const auto& dataset : datasets) {
for (int i = 0; i < models.size(); ++i) {
totals[i] += ranksModels[dataset][models[i]];
}
}
for (int i = 0; i < models.size(); ++i) {
if (totals[i] < min) {
min = totals[i];
idx = i;
}
}
model = models.at(idx);
excel.reportSingle(model, path + bestResultFile());
}
messageExcelFile(excel.getFileName());
}
}
void BestResults::messageExcelFile(const std::string& fileName)
{
std::cout << Colors::YELLOW() << "** Excel file generated: " << fileName << Colors::RESET() << std::endl;
}
}

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@@ -0,0 +1,36 @@
#ifndef BESTRESULTS_H
#define BESTRESULTS_H
#include <string>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
class BestResults {
public:
explicit BestResults(const std::string& path, const std::string& score, const std::string& model, bool friedman, double significance = 0.05)
: path(path), score(score), model(model), friedman(friedman), significance(significance)
{
}
std::string build();
void reportSingle(bool excel);
void reportAll(bool excel);
void buildAll();
private:
std::vector<std::string> getModels();
std::vector<std::string> getDatasets(json table);
std::vector<std::string> loadResultFiles();
void messageExcelFile(const std::string& fileName);
json buildTableResults(std::vector<std::string> models);
void printTableResults(std::vector<std::string> models, json table);
std::string bestResultFile();
json loadFile(const std::string& fileName);
void listFile();
std::string path;
std::string score;
std::string model;
bool friedman;
double significance;
int maxModelName = 0;
int maxDatasetName = 0;
};
}
#endif //BESTRESULTS_H

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@@ -0,0 +1,300 @@
#include <sstream>
#include "BestResultsExcel.h"
#include "Paths.h"
#include <map>
#include <nlohmann/json.hpp>
#include "Statistics.h"
#include "ReportExcel.h"
namespace platform {
json loadResultData(const std::string& fileName)
{
json data;
std::ifstream resultData(fileName);
if (resultData.is_open()) {
data = json::parse(resultData);
} else {
throw std::invalid_argument("Unable to open result file. [" + fileName + "]");
}
return data;
}
std::string getColumnName(int colNum)
{
std::string columnName = "";
if (colNum == 0)
return "A";
while (colNum > 0) {
int modulo = colNum % 26;
columnName = char(65 + modulo) + columnName;
colNum = (int)((colNum - modulo) / 26);
}
return columnName;
}
BestResultsExcel::BestResultsExcel(const std::string& score, const std::vector<std::string>& datasets) : score(score), datasets(datasets)
{
workbook = workbook_new((Paths::excel() + fileName).c_str());
setProperties("Best Results");
int maxDatasetName = (*max_element(datasets.begin(), datasets.end(), [](const std::string& a, const std::string& b) { return a.size() < b.size(); })).size();
datasetNameSize = std::max(datasetNameSize, maxDatasetName);
createFormats();
}
void BestResultsExcel::reportAll(const std::vector<std::string>& models, const json& table, const std::map<std::string, std::map<std::string, float>>& ranks, bool friedman, double significance)
{
this->table = table;
this->models = models;
ranksModels = ranks;
this->friedman = friedman;
this->significance = significance;
worksheet = workbook_add_worksheet(workbook, "Best Results");
int maxModelName = (*std::max_element(models.begin(), models.end(), [](const std::string& a, const std::string& b) { return a.size() < b.size(); })).size();
modelNameSize = std::max(modelNameSize, maxModelName);
formatColumns();
build();
}
void BestResultsExcel::reportSingle(const std::string& model, const std::string& fileName)
{
worksheet = workbook_add_worksheet(workbook, "Report");
if (FILE* fileTest = fopen(fileName.c_str(), "r")) {
fclose(fileTest);
} else {
std::cerr << "File " << fileName << " doesn't exist." << std::endl;
exit(1);
}
json data = loadResultData(fileName);
std::string title = "Best results for " + model;
worksheet_merge_range(worksheet, 0, 0, 0, 4, title.c_str(), styles["headerFirst"]);
// Body header
row = 3;
int col = 1;
writeString(row, 0, "", "bodyHeader");
writeString(row, 1, "Dataset", "bodyHeader");
writeString(row, 2, "Score", "bodyHeader");
writeString(row, 3, "File", "bodyHeader");
writeString(row, 4, "Hyperparameters", "bodyHeader");
auto i = 0;
std::string hyperparameters;
int hypSize = 22;
std::map<std::string, std::string> files; // map of files imported and their tabs
for (auto const& item : data.items()) {
row++;
writeInt(row, 0, i++, "ints");
writeString(row, 1, item.key().c_str(), "text");
writeDouble(row, 2, item.value().at(0).get<double>(), "result");
auto fileName = item.value().at(2).get<std::string>();
std::string hyperlink = "";
try {
hyperlink = files.at(fileName);
}
catch (const std::out_of_range& oor) {
auto tabName = "table_" + std::to_string(i);
auto worksheetNew = workbook_add_worksheet(workbook, tabName.c_str());
json data = loadResultData(Paths::results() + fileName);
auto report = ReportExcel(data, false, workbook, worksheetNew);
report.show();
hyperlink = "#table_" + std::to_string(i);
files[fileName] = hyperlink;
}
hyperlink += "!H" + std::to_string(i + 6);
std::string fileNameText = "=HYPERLINK(\"" + hyperlink + "\",\"" + fileName + "\")";
worksheet_write_formula(worksheet, row, 3, fileNameText.c_str(), efectiveStyle("text"));
hyperparameters = item.value().at(1).dump();
if (hyperparameters.size() > hypSize) {
hypSize = hyperparameters.size();
}
writeString(row, 4, hyperparameters, "text");
}
row++;
// Set Totals
writeString(row, 1, "Total", "bodyHeader");
std::stringstream oss;
auto colName = getColumnName(2);
oss << "=sum(" << colName << "5:" << colName << row << ")";
worksheet_write_formula(worksheet, row, 2, oss.str().c_str(), styles["bodyHeader_odd"]);
// Set format
worksheet_freeze_panes(worksheet, 4, 2);
std::vector<int> columns_sizes = { 5, datasetNameSize, modelNameSize, 66, hypSize + 1 };
for (int i = 0; i < columns_sizes.size(); ++i) {
worksheet_set_column(worksheet, i, i, columns_sizes.at(i), NULL);
}
}
BestResultsExcel::~BestResultsExcel()
{
workbook_close(workbook);
}
void BestResultsExcel::formatColumns()
{
worksheet_freeze_panes(worksheet, 4, 2);
std::vector<int> columns_sizes = { 5, datasetNameSize };
for (int i = 0; i < models.size(); ++i) {
columns_sizes.push_back(modelNameSize);
}
for (int i = 0; i < columns_sizes.size(); ++i) {
worksheet_set_column(worksheet, i, i, columns_sizes.at(i), NULL);
}
}
void BestResultsExcel::addConditionalFormat(std::string formula)
{
// Add conditional format for max/min values in scores/ranks sheets
lxw_format* custom_format = workbook_add_format(workbook);
format_set_bg_color(custom_format, 0xFFC7CE);
format_set_font_color(custom_format, 0x9C0006);
// Create a conditional format object. A static object would also work.
lxw_conditional_format* conditional_format = (lxw_conditional_format*)calloc(1, sizeof(lxw_conditional_format));
conditional_format->type = LXW_CONDITIONAL_TYPE_FORMULA;
std::string col = getColumnName(models.size() + 1);
std::stringstream oss;
oss << "=C5=" << formula << "($C5:$" << col << "5)";
auto formulaValue = oss.str();
conditional_format->value_string = formulaValue.c_str();
conditional_format->format = custom_format;
worksheet_conditional_format_range(worksheet, 4, 2, datasets.size() + 3, models.size() + 1, conditional_format);
}
void BestResultsExcel::build()
{
// Create Sheet with scores
header(false);
body(false);
// Add conditional format for max values
addConditionalFormat("max");
footer(false);
if (friedman) {
// Create Sheet with ranks
worksheet = workbook_add_worksheet(workbook, "Ranks");
formatColumns();
header(true);
body(true);
addConditionalFormat("min");
footer(true);
// Create Sheet with Friedman Test
doFriedman();
}
}
std::string BestResultsExcel::getFileName()
{
return Paths::excel() + fileName;
}
void BestResultsExcel::header(bool ranks)
{
row = 0;
std::string message = ranks ? "Ranks for score " + score : "Best results for " + score;
worksheet_merge_range(worksheet, 0, 0, 0, 1 + models.size(), message.c_str(), styles["headerFirst"]);
// Body header
row = 3;
int col = 1;
writeString(row, 0, "", "bodyHeader");
writeString(row, 1, "Dataset", "bodyHeader");
for (const auto& model : models) {
writeString(row, ++col, model.c_str(), "bodyHeader");
}
}
void BestResultsExcel::body(bool ranks)
{
row = 4;
int i = 0;
json origin = table.begin().value();
for (auto const& item : origin.items()) {
writeInt(row, 0, i++, "ints");
writeString(row, 1, item.key().c_str(), "text");
int col = 1;
for (const auto& model : models) {
double value = ranks ? ranksModels[item.key()][model] : table[model].at(item.key()).at(0).get<double>();
writeDouble(row, ++col, value, "result");
}
++row;
}
}
void BestResultsExcel::footer(bool ranks)
{
// Set Totals
writeString(row, 1, "Total", "bodyHeader");
int col = 1;
for (const auto& model : models) {
std::stringstream oss;
auto colName = getColumnName(col + 1);
oss << "=SUM(" << colName << "5:" << colName << row << ")";
worksheet_write_formula(worksheet, row, ++col, oss.str().c_str(), styles["bodyHeader_odd"]);
}
if (ranks) {
row++;
writeString(row, 1, "Average ranks", "bodyHeader");
int col = 1;
for (const auto& model : models) {
auto colName = getColumnName(col + 1);
std::stringstream oss;
oss << "=SUM(" << colName << "5:" << colName << row - 1 << ")/" << datasets.size();
worksheet_write_formula(worksheet, row, ++col, oss.str().c_str(), styles["bodyHeader_odd"]);
}
}
}
void BestResultsExcel::doFriedman()
{
worksheet = workbook_add_worksheet(workbook, "Friedman");
std::vector<int> columns_sizes = { 5, datasetNameSize };
for (int i = 0; i < models.size(); ++i) {
columns_sizes.push_back(modelNameSize);
}
for (int i = 0; i < columns_sizes.size(); ++i) {
worksheet_set_column(worksheet, i, i, columns_sizes.at(i), NULL);
}
worksheet_merge_range(worksheet, 0, 0, 0, 1 + models.size(), "Friedman Test", styles["headerFirst"]);
row = 2;
Statistics stats(models, datasets, table, significance, false);
auto result = stats.friedmanTest();
stats.postHocHolmTest(result);
auto friedmanResult = stats.getFriedmanResult();
auto holmResult = stats.getHolmResult();
worksheet_merge_range(worksheet, row, 0, row, 1 + models.size(), "Null hypothesis: H0 'There is no significant differences between all the classifiers.'", styles["headerSmall"]);
row += 2;
writeString(row, 1, "Friedman Q", "bodyHeader");
writeDouble(row, 2, friedmanResult.statistic, "bodyHeader");
row++;
writeString(row, 1, "Critical χ2 value", "bodyHeader");
writeDouble(row, 2, friedmanResult.criticalValue, "bodyHeader");
row++;
writeString(row, 1, "p-value", "bodyHeader");
writeDouble(row, 2, friedmanResult.pvalue, "bodyHeader");
writeString(row, 3, friedmanResult.reject ? "<" : ">", "bodyHeader");
writeDouble(row, 4, significance, "bodyHeader");
writeString(row, 5, friedmanResult.reject ? "Reject H0" : "Accept H0", "bodyHeader");
row += 3;
worksheet_merge_range(worksheet, row, 0, row, 1 + models.size(), "Holm Test", styles["headerFirst"]);
row += 2;
worksheet_merge_range(worksheet, row, 0, row, 1 + models.size(), "Null hypothesis: H0 'There is no significant differences between the control model and the other models.'", styles["headerSmall"]);
row += 2;
std::string controlModel = "Control Model: " + holmResult.model;
worksheet_merge_range(worksheet, row, 1, row, 7, controlModel.c_str(), styles["bodyHeader_odd"]);
row++;
writeString(row, 1, "Model", "bodyHeader");
writeString(row, 2, "p-value", "bodyHeader");
writeString(row, 3, "Rank", "bodyHeader");
writeString(row, 4, "Win", "bodyHeader");
writeString(row, 5, "Tie", "bodyHeader");
writeString(row, 6, "Loss", "bodyHeader");
writeString(row, 7, "Reject H0", "bodyHeader");
row++;
bool first = true;
for (const auto& item : holmResult.holmLines) {
writeString(row, 1, item.model, "text");
if (first) {
// Control model info
first = false;
writeString(row, 2, "", "text");
writeDouble(row, 3, item.rank, "result");
writeString(row, 4, "", "text");
writeString(row, 5, "", "text");
writeString(row, 6, "", "text");
writeString(row, 7, "", "textCentered");
} else {
// Rest of the models info
writeDouble(row, 2, item.pvalue, "result");
writeDouble(row, 3, item.rank, "result");
writeInt(row, 4, item.wtl.win, "ints");
writeInt(row, 5, item.wtl.tie, "ints");
writeInt(row, 6, item.wtl.loss, "ints");
writeString(row, 7, item.reject ? "Yes" : "No", "textCentered");
}
row++;
}
}
}

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#ifndef BESTRESULTS_EXCEL_H
#define BESTRESULTS_EXCEL_H
#include "ExcelFile.h"
#include <vector>
#include <map>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
class BestResultsExcel : ExcelFile {
public:
BestResultsExcel(const std::string& score, const std::vector<std::string>& datasets);
~BestResultsExcel();
void reportAll(const std::vector<std::string>& models, const json& table, const std::map<std::string, std::map<std::string, float>>& ranks, bool friedman, double significance);
void reportSingle(const std::string& model, const std::string& fileName);
std::string getFileName();
private:
void build();
void header(bool ranks);
void body(bool ranks);
void footer(bool ranks);
void formatColumns();
void doFriedman();
void addConditionalFormat(std::string formula);
const std::string fileName = "BestResults.xlsx";
std::string score;
std::vector<std::string> models;
std::vector<std::string> datasets;
json table;
std::map<std::string, std::map<std::string, float>> ranksModels;
bool friedman;
double significance;
int modelNameSize = 12; // Min size of the column
int datasetNameSize = 25; // Min size of the column
};
}
#endif //BESTRESULTS_EXCEL_H

28
src/Platform/BestScore.h Normal file
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#ifndef BESTSCORE_H
#define BESTSCORE_H
#include <string>
#include <map>
#include <utility>
#include "DotEnv.h"
namespace platform {
class BestScore {
public:
static std::pair<std::string, double> getScore(const std::string& metric)
{
static std::map<std::pair<std::string, std::string>, std::pair<std::string, double>> data = {
{{"discretiz", "accuracy"}, {"STree_default (linear-ovo)", 22.109799}},
{{"odte", "accuracy"}, {"STree_default (linear-ovo)", 22.109799}},
};
auto env = platform::DotEnv();
std::string experiment = env.get("experiment");
try {
return data[{experiment, metric}];
}
catch (...) {
return { "", 0.0 };
}
}
};
}
#endif

22
src/Platform/CLocale.h Normal file
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#ifndef LOCALE_H
#define LOCALE_H
#include <locale>
#include <iostream>
#include <string>
namespace platform {
struct separation : std::numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
std::string do_grouping() const { return "\03"; }
};
class ConfigLocale {
public:
explicit ConfigLocale()
{
std::locale mylocale(std::cout.getloc(), new separation);
std::locale::global(mylocale);
std::cout.imbue(mylocale);
}
};
}
#endif

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@@ -1,10 +1,19 @@
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/src/PyClassifiers)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/argparse/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc Models.cc Report.cc)
add_executable(manage manage.cc Results.cc Report.cc)
target_link_libraries(main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(manage "${TORCH_LIBRARIES}")
include_directories(${BayesNet_SOURCE_DIR}/lib/libxlsxwriter/include)
include_directories(${Python3_INCLUDE_DIRS})
add_executable(b_main b_main.cc Folding.cc Experiment.cc Datasets.cc Dataset.cc Models.cc ReportConsole.cc ReportBase.cc)
add_executable(b_manage b_manage.cc Results.cc ManageResults.cc CommandParser.cc Result.cc ReportConsole.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
add_executable(b_list b_list.cc Datasets.cc Dataset.cc)
add_executable(b_best b_best.cc BestResults.cc Result.cc Statistics.cc BestResultsExcel.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
target_link_libraries(b_main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}" PyWrap)
target_link_libraries(b_manage "${TORCH_LIBRARIES}" "${XLSXWRITER_LIB}" ArffFiles mdlp)
target_link_libraries(b_best Boost::boost "${XLSXWRITER_LIB}" "${TORCH_LIBRARIES}" ArffFiles mdlp)
target_link_libraries(b_list ArffFiles mdlp "${TORCH_LIBRARIES}")

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#include "CommandParser.h"
#include <iostream>
#include <sstream>
#include <algorithm>
#include "Colors.h"
#include "Utils.h"
namespace platform {
void CommandParser::messageError(const std::string& message)
{
std::cout << Colors::RED() << message << Colors::RESET() << std::endl;
}
std::pair<char, int> CommandParser::parse(const std::string& color, const std::vector<std::tuple<std::string, char, bool>>& options, const char defaultCommand, const int maxIndex)
{
bool finished = false;
while (!finished) {
std::stringstream oss;
std::string line;
oss << color << "Choose option (";
bool first = true;
for (auto& option : options) {
if (first) {
first = false;
} else {
oss << ", ";
}
oss << std::get<char>(option) << "=" << std::get<std::string>(option);
}
oss << "): ";
std::cout << oss.str();
getline(std::cin, line);
std::cout << Colors::RESET();
line = trim(line);
if (line.size() == 0)
continue;
if (all_of(line.begin(), line.end(), ::isdigit)) {
command = defaultCommand;
index = stoi(line);
if (index > maxIndex || index < 0) {
messageError("Index out of range");
continue;
}
finished = true;
break;
}
bool found = false;
for (auto& option : options) {
if (line[0] == std::get<char>(option)) {
found = true;
// it's a match
line.erase(line.begin());
line = trim(line);
if (std::get<bool>(option)) {
// The option requires a value
if (line.size() == 0) {
messageError("Option " + std::get<std::string>(option) + " requires a value");
break;
}
try {
index = stoi(line);
if (index > maxIndex || index < 0) {
messageError("Index out of range");
break;
}
}
catch (const std::invalid_argument& ia) {
messageError("Invalid value: " + line);
break;
}
} else {
if (line.size() > 0) {
messageError("option " + std::get<std::string>(option) + " doesn't accept values");
break;
}
}
command = std::get<char>(option);
finished = true;
break;
}
}
if (!found) {
messageError("I don't know " + line);
}
}
return { command, index };
}
} /* namespace platform */

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#ifndef COMMAND_PARSER_H
#define COMMAND_PARSER_H
#include <string>
#include <vector>
#include <tuple>
namespace platform {
class CommandParser {
public:
CommandParser() = default;
std::pair<char, int> parse(const std::string& color, const std::vector<std::tuple<std::string, char, bool>>& options, const char defaultCommand, const int maxIndex);
char getCommand() const { return command; };
int getIndex() const { return index; };
private:
void messageError(const std::string& message);
char command;
int index;
};
} /* namespace platform */
#endif /* COMMAND_PARSER_H */

215
src/Platform/Dataset.cc Normal file
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#include "Dataset.h"
#include "ArffFiles.h"
#include <fstream>
namespace platform {
Dataset::Dataset(const Dataset& dataset) : path(dataset.path), name(dataset.name), className(dataset.className), n_samples(dataset.n_samples), n_features(dataset.n_features), features(dataset.features), states(dataset.states), loaded(dataset.loaded), discretize(dataset.discretize), X(dataset.X), y(dataset.y), Xv(dataset.Xv), Xd(dataset.Xd), yv(dataset.yv), fileType(dataset.fileType)
{
}
std::string Dataset::getName() const
{
return name;
}
std::string Dataset::getClassName() const
{
return className;
}
std::vector<std::string> Dataset::getFeatures() const
{
if (loaded) {
return features;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNFeatures() const
{
if (loaded) {
return n_features;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNSamples() const
{
if (loaded) {
return n_samples;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
std::map<std::string, std::vector<int>> Dataset::getStates() const
{
if (loaded) {
return states;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<std::vector<std::vector<float>>&, std::vector<int>&> Dataset::getVectors()
{
if (loaded) {
return { Xv, yv };
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<std::vector<std::vector<int>>&, std::vector<int>&> Dataset::getVectorsDiscretized()
{
if (loaded) {
return { Xd, yv };
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<torch::Tensor&, torch::Tensor&> Dataset::getTensors()
{
if (loaded) {
buildTensors();
return { X, y };
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
void Dataset::load_csv()
{
ifstream file(path + "/" + name + ".csv");
if (file.is_open()) {
std::string line;
getline(file, line);
std::vector<std::string> tokens = split(line, ',');
features = std::vector<std::string>(tokens.begin(), tokens.end() - 1);
if (className == "-1") {
className = tokens.back();
}
for (auto i = 0; i < features.size(); ++i) {
Xv.push_back(std::vector<float>());
}
while (getline(file, line)) {
tokens = split(line, ',');
for (auto i = 0; i < features.size(); ++i) {
Xv[i].push_back(stof(tokens[i]));
}
yv.push_back(stoi(tokens.back()));
}
file.close();
} else {
throw std::invalid_argument("Unable to open dataset file.");
}
}
void Dataset::computeStates()
{
for (int i = 0; i < features.size(); ++i) {
states[features[i]] = std::vector<int>(*max_element(Xd[i].begin(), Xd[i].end()) + 1);
auto item = states.at(features[i]);
iota(begin(item), end(item), 0);
}
states[className] = std::vector<int>(*max_element(yv.begin(), yv.end()) + 1);
iota(begin(states.at(className)), end(states.at(className)), 0);
}
void Dataset::load_arff()
{
auto arff = ArffFiles();
arff.load(path + "/" + name + ".arff", className);
// Get Dataset X, y
Xv = arff.getX();
yv = arff.getY();
// Get className & Features
className = arff.getClassName();
auto attributes = arff.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features), [](const auto& attribute) { return attribute.first; });
}
std::vector<std::string> tokenize(std::string line)
{
std::vector<std::string> tokens;
for (auto i = 0; i < line.size(); ++i) {
if (line[i] == ' ' || line[i] == '\t' || line[i] == '\n') {
std::string token = line.substr(0, i);
tokens.push_back(token);
line.erase(line.begin(), line.begin() + i + 1);
i = 0;
while (line[i] == ' ' || line[i] == '\t' || line[i] == '\n')
line.erase(line.begin(), line.begin() + i + 1);
}
}
if (line.size() > 0) {
tokens.push_back(line);
}
return tokens;
}
void Dataset::load_rdata()
{
ifstream file(path + "/" + name + "_R.dat");
if (file.is_open()) {
std::string line;
getline(file, line);
line = ArffFiles::trim(line);
std::vector<std::string> tokens = tokenize(line);
transform(tokens.begin(), tokens.end() - 1, back_inserter(features), [](const auto& attribute) { return ArffFiles::trim(attribute); });
if (className == "-1") {
className = ArffFiles::trim(tokens.back());
}
for (auto i = 0; i < features.size(); ++i) {
Xv.push_back(std::vector<float>());
}
while (getline(file, line)) {
tokens = tokenize(line);
// We have to skip the first token, which is the instance number.
for (auto i = 1; i < features.size() + 1; ++i) {
const float value = stof(tokens[i]);
Xv[i - 1].push_back(value);
}
yv.push_back(stoi(tokens.back()));
}
file.close();
} else {
throw std::invalid_argument("Unable to open dataset file.");
}
}
void Dataset::load()
{
if (loaded) {
return;
}
if (fileType == CSV) {
load_csv();
} else if (fileType == ARFF) {
load_arff();
} else if (fileType == RDATA) {
load_rdata();
}
if (discretize) {
Xd = discretizeDataset(Xv, yv);
computeStates();
}
n_samples = Xv[0].size();
n_features = Xv.size();
loaded = true;
}
void Dataset::buildTensors()
{
if (discretize) {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kInt32);
} else {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kFloat32);
}
for (int i = 0; i < features.size(); ++i) {
if (discretize) {
X.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
} else {
X.index_put_({ i, "..." }, torch::tensor(Xv[i], torch::kFloat32));
}
}
y = torch::tensor(yv, torch::kInt32);
}
std::vector<mdlp::labels_t> Dataset::discretizeDataset(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y)
{
std::vector<mdlp::labels_t> Xd;
auto fimdlp = mdlp::CPPFImdlp();
for (int i = 0; i < X.size(); i++) {
fimdlp.fit(X[i], y);
mdlp::labels_t& xd = fimdlp.transform(X[i]);
Xd.push_back(xd);
}
return Xd;
}
}

78
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#ifndef DATASET_H
#define DATASET_H
#include <torch/torch.h>
#include <map>
#include <vector>
#include <string>
#include "CPPFImdlp.h"
#include "Utils.h"
namespace platform {
enum fileType_t { CSV, ARFF, RDATA };
class SourceData {
public:
SourceData(std::string source)
{
if (source == "Surcov") {
path = "datasets/";
fileType = CSV;
} else if (source == "Arff") {
path = "datasets/";
fileType = ARFF;
} else if (source == "Tanveer") {
path = "data/";
fileType = RDATA;
} else {
throw std::invalid_argument("Unknown source.");
}
}
std::string getPath()
{
return path;
}
fileType_t getFileType()
{
return fileType;
}
private:
std::string path;
fileType_t fileType;
};
class Dataset {
private:
std::string path;
std::string name;
fileType_t fileType;
std::string className;
int n_samples{ 0 }, n_features{ 0 };
std::vector<std::string> features;
std::map<std::string, std::vector<int>> states;
bool loaded;
bool discretize;
torch::Tensor X, y;
std::vector<std::vector<float>> Xv;
std::vector<std::vector<int>> Xd;
std::vector<int> yv;
void buildTensors();
void load_csv();
void load_arff();
void load_rdata();
void computeStates();
std::vector<mdlp::labels_t> discretizeDataset(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y);
public:
Dataset(const std::string& path, const std::string& name, const std::string& className, bool discretize, fileType_t fileType) : path(path), name(name), className(className), discretize(discretize), loaded(false), fileType(fileType) {};
explicit Dataset(const Dataset&);
std::string getName() const;
std::string getClassName() const;
std::vector<string> getFeatures() const;
std::map<std::string, std::vector<int>> getStates() const;
std::pair<vector<std::vector<float>>&, std::vector<int>&> getVectors();
std::pair<vector<std::vector<int>>&, std::vector<int>&> getVectorsDiscretized();
std::pair<torch::Tensor&, torch::Tensor&> getTensors();
int getNFeatures() const;
int getNSamples() const;
void load();
const bool inline isLoaded() const { return loaded; };
};
};
#endif

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@@ -1,231 +1,129 @@
#include "Datasets.h"
#include "platformUtils.h"
#include "ArffFiles.h"
#include <fstream>
namespace platform {
void Datasets::load()
{
ifstream catalog(path + "/all.txt");
auto sd = SourceData(sfileType);
fileType = sd.getFileType();
path = sd.getPath();
ifstream catalog(path + "all.txt");
if (catalog.is_open()) {
string line;
std::string line;
while (getline(catalog, line)) {
vector<string> tokens = split(line, ',');
string name = tokens[0];
string className = tokens[1];
if (line.empty() || line[0] == '#') {
continue;
}
std::vector<std::string> tokens = split(line, ',');
std::string name = tokens[0];
std::string className;
if (tokens.size() == 1) {
className = "-1";
} else {
className = tokens[1];
}
datasets[name] = make_unique<Dataset>(path, name, className, discretize, fileType);
}
catalog.close();
} else {
throw invalid_argument("Unable to open catalog file. [" + path + "/all.txt" + "]");
throw std::invalid_argument("Unable to open catalog file. [" + path + "all.txt" + "]");
}
}
vector<string> Datasets::getNames()
std::vector<std::string> Datasets::getNames()
{
vector<string> result;
std::vector<std::string> result;
transform(datasets.begin(), datasets.end(), back_inserter(result), [](const auto& d) { return d.first; });
return result;
}
vector<string> Datasets::getFeatures(string name)
std::vector<std::string> Datasets::getFeatures(const std::string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getFeatures();
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getFeatures();
} else {
throw invalid_argument("Dataset not loaded.");
throw std::invalid_argument("Dataset not loaded.");
}
}
map<string, vector<int>> Datasets::getStates(string name)
map<std::string, std::vector<int>> Datasets::getStates(const std::string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getStates();
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getStates();
} else {
throw invalid_argument("Dataset not loaded.");
throw std::invalid_argument("Dataset not loaded.");
}
}
string Datasets::getClassName(string name)
void Datasets::loadDataset(const std::string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getClassName();
if (datasets.at(name)->isLoaded()) {
return;
} else {
throw invalid_argument("Dataset not loaded.");
datasets.at(name)->load();
}
}
int Datasets::getNSamples(string name)
std::string Datasets::getClassName(const std::string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getNSamples();
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getClassName();
} else {
throw invalid_argument("Dataset not loaded.");
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<float>>&, vector<int>&> Datasets::getVectors(string name)
int Datasets::getNSamples(const std::string& name) const
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getNSamples();
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
int Datasets::getNClasses(const std::string& name)
{
if (datasets.at(name)->isLoaded()) {
auto className = datasets.at(name)->getClassName();
if (discretize) {
auto states = getStates(name);
return states.at(className).size();
}
auto [Xv, yv] = getVectors(name);
return *std::max_element(yv.begin(), yv.end()) + 1;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
std::vector<int> Datasets::getClassesCounts(const std::string& name) const
{
if (datasets.at(name)->isLoaded()) {
auto [Xv, yv] = datasets.at(name)->getVectors();
std::vector<int> counts(*std::max_element(yv.begin(), yv.end()) + 1);
for (auto y : yv) {
counts[y]++;
}
return counts;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<std::vector<std::vector<float>>&, std::vector<int>&> Datasets::getVectors(const std::string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getVectors();
}
pair<vector<vector<int>>&, vector<int>&> Datasets::getVectorsDiscretized(string name)
pair<std::vector<std::vector<int>>&, std::vector<int>&> Datasets::getVectorsDiscretized(const std::string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getVectorsDiscretized();
}
pair<torch::Tensor&, torch::Tensor&> Datasets::getTensors(string name)
pair<torch::Tensor&, torch::Tensor&> Datasets::getTensors(const std::string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getTensors();
}
bool Datasets::isDataset(const string& name)
bool Datasets::isDataset(const std::string& name) const
{
return datasets.find(name) != datasets.end();
}
Dataset::Dataset(const Dataset& dataset) : path(dataset.path), name(dataset.name), className(dataset.className), n_samples(dataset.n_samples), n_features(dataset.n_features), features(dataset.features), states(dataset.states), loaded(dataset.loaded), discretize(dataset.discretize), X(dataset.X), y(dataset.y), Xv(dataset.Xv), Xd(dataset.Xd), yv(dataset.yv), fileType(dataset.fileType)
{
}
string Dataset::getName()
{
return name;
}
string Dataset::getClassName()
{
return className;
}
vector<string> Dataset::getFeatures()
{
if (loaded) {
return features;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNFeatures()
{
if (loaded) {
return n_features;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNSamples()
{
if (loaded) {
return n_samples;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
map<string, vector<int>> Dataset::getStates()
{
if (loaded) {
return states;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<float>>&, vector<int>&> Dataset::getVectors()
{
if (loaded) {
return { Xv, yv };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<int>>&, vector<int>&> Dataset::getVectorsDiscretized()
{
if (loaded) {
return { Xd, yv };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<torch::Tensor&, torch::Tensor&> Dataset::getTensors()
{
if (loaded) {
buildTensors();
return { X, y };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
void Dataset::load_csv()
{
ifstream file(path + "/" + name + ".csv");
if (file.is_open()) {
string line;
getline(file, line);
vector<string> tokens = split(line, ',');
features = vector<string>(tokens.begin(), tokens.end() - 1);
className = tokens.back();
for (auto i = 0; i < features.size(); ++i) {
Xv.push_back(vector<float>());
}
while (getline(file, line)) {
tokens = split(line, ',');
for (auto i = 0; i < features.size(); ++i) {
Xv[i].push_back(stof(tokens[i]));
}
yv.push_back(stoi(tokens.back()));
}
file.close();
} else {
throw invalid_argument("Unable to open dataset file.");
}
}
void Dataset::computeStates()
{
for (int i = 0; i < features.size(); ++i) {
states[features[i]] = vector<int>(*max_element(Xd[i].begin(), Xd[i].end()) + 1);
iota(begin(states[features[i]]), end(states[features[i]]), 0);
}
states[className] = vector<int>(*max_element(yv.begin(), yv.end()) + 1);
iota(begin(states[className]), end(states[className]), 0);
}
void Dataset::load_arff()
{
auto arff = ArffFiles();
arff.load(path + "/" + name + ".arff", className);
// Get Dataset X, y
Xv = arff.getX();
yv = arff.getY();
// Get className & Features
className = arff.getClassName();
auto attributes = arff.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features), [](const auto& attribute) { return attribute.first; });
}
void Dataset::load()
{
if (loaded) {
return;
}
if (fileType == CSV) {
load_csv();
} else if (fileType == ARFF) {
load_arff();
}
if (discretize) {
Xd = discretizeDataset(Xv, yv);
computeStates();
}
n_samples = Xv[0].size();
n_features = Xv.size();
loaded = true;
}
void Dataset::buildTensors()
{
if (discretize) {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kInt32);
} else {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kFloat32);
}
for (int i = 0; i < features.size(); ++i) {
if (discretize) {
X.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
} else {
X.index_put_({ i, "..." }, torch::tensor(Xv[i], torch::kFloat32));
}
}
y = torch::tensor(yv, torch::kInt32);
}
}

View File

@@ -1,64 +1,29 @@
#ifndef DATASETS_H
#define DATASETS_H
#include <torch/torch.h>
#include <map>
#include <vector>
#include <string>
#include "Dataset.h"
namespace platform {
using namespace std;
enum fileType_t { CSV, ARFF };
class Dataset {
private:
string path;
string name;
fileType_t fileType;
string className;
int n_samples{ 0 }, n_features{ 0 };
vector<string> features;
map<string, vector<int>> states;
bool loaded;
bool discretize;
torch::Tensor X, y;
vector<vector<float>> Xv;
vector<vector<int>> Xd;
vector<int> yv;
void buildTensors();
void load_csv();
void load_arff();
void computeStates();
public:
Dataset(const string& path, const string& name, const string& className, bool discretize, fileType_t fileType) : path(path), name(name), className(className), discretize(discretize), loaded(false), fileType(fileType) {};
explicit Dataset(const Dataset&);
string getName();
string getClassName();
vector<string> getFeatures();
map<string, vector<int>> getStates();
pair<vector<vector<float>>&, vector<int>&> getVectors();
pair<vector<vector<int>>&, vector<int>&> getVectorsDiscretized();
pair<torch::Tensor&, torch::Tensor&> getTensors();
int getNFeatures();
int getNSamples();
void load();
const bool inline isLoaded() const { return loaded; };
};
class Datasets {
private:
string path;
std::string path;
fileType_t fileType;
map<string, unique_ptr<Dataset>> datasets;
std::string sfileType;
std::map<std::string, std::unique_ptr<Dataset>> datasets;
bool discretize;
void load(); // Loads the list of datasets
public:
explicit Datasets(const string& path, bool discretize = false, fileType_t fileType = ARFF) : path(path), discretize(discretize), fileType(fileType) { load(); };
vector<string> getNames();
vector<string> getFeatures(string name);
int getNSamples(string name);
string getClassName(string name);
map<string, vector<int>> getStates(string name);
pair<vector<vector<float>>&, vector<int>&> getVectors(string name);
pair<vector<vector<int>>&, vector<int>&> getVectorsDiscretized(string name);
pair<torch::Tensor&, torch::Tensor&> getTensors(string name);
bool isDataset(const string& name);
explicit Datasets(bool discretize, std::string sfileType) : discretize(discretize), sfileType(sfileType) { load(); };
std::vector<string> getNames();
std::vector<string> getFeatures(const std::string& name) const;
int getNSamples(const std::string& name) const;
std::string getClassName(const std::string& name) const;
int getNClasses(const std::string& name);
std::vector<int> getClassesCounts(const std::string& name) const;
std::map<std::string, std::vector<int>> getStates(const std::string& name) const;
std::pair<std::vector<std::vector<float>>&, std::vector<int>&> getVectors(const std::string& name);
std::pair<std::vector<std::vector<int>>&, std::vector<int>&> getVectorsDiscretized(const std::string& name);
std::pair<torch::Tensor&, torch::Tensor&> getTensors(const std::string& name);
bool isDataset(const std::string& name) const;
void loadDataset(const std::string& name) const;
};
};

View File

@@ -4,22 +4,15 @@
#include <map>
#include <fstream>
#include <sstream>
#include "platformUtils.h"
#include <algorithm>
#include <iostream>
#include "Utils.h"
//#include "Dataset.h"
namespace platform {
class DotEnv {
private:
std::map<std::string, std::string> env;
std::string trim(const std::string& str)
{
std::string result = str;
result.erase(result.begin(), std::find_if(result.begin(), result.end(), [](int ch) {
return !std::isspace(ch);
}));
result.erase(std::find_if(result.rbegin(), result.rend(), [](int ch) {
return !std::isspace(ch);
}).base(), result.end());
return result;
}
public:
DotEnv()
{
@@ -43,7 +36,7 @@ namespace platform {
}
std::string get(const std::string& key)
{
return env[key];
return env.at(key);
}
std::vector<int> getSeeds()
{

168
src/Platform/ExcelFile.cc Normal file
View File

@@ -0,0 +1,168 @@
#include "ExcelFile.h"
namespace platform {
ExcelFile::ExcelFile()
{
setDefault();
}
ExcelFile::ExcelFile(lxw_workbook* workbook) : workbook(workbook)
{
setDefault();
}
ExcelFile::ExcelFile(lxw_workbook* workbook, lxw_worksheet* worksheet) : workbook(workbook), worksheet(worksheet)
{
setDefault();
}
void ExcelFile::setDefault()
{
normalSize = 14; //font size for report body
row = 0;
colorTitle = 0xB1A0C7;
colorOdd = 0xDCE6F1;
colorEven = 0xFDE9D9;
}
lxw_workbook* ExcelFile::getWorkbook()
{
return workbook;
}
void ExcelFile::setProperties(std::string title)
{
char line[title.size() + 1];
strcpy(line, title.c_str());
lxw_doc_properties properties = {
.title = line,
.subject = (char*)"Machine learning results",
.author = (char*)"Ricardo Montañana Gómez",
.manager = (char*)"Dr. J. A. Gámez, Dr. J. M. Puerta",
.company = (char*)"UCLM",
.comments = (char*)"Created with libxlsxwriter and c++",
};
workbook_set_properties(workbook, &properties);
}
lxw_format* ExcelFile::efectiveStyle(const std::string& style)
{
lxw_format* efectiveStyle = NULL;
if (style != "") {
std::string suffix = row % 2 ? "_odd" : "_even";
try {
efectiveStyle = styles.at(style + suffix);
}
catch (const std::out_of_range& oor) {
try {
efectiveStyle = styles.at(style);
}
catch (const std::out_of_range& oor) {
throw std::invalid_argument("Style " + style + " not found");
}
}
}
return efectiveStyle;
}
void ExcelFile::writeString(int row, int col, const std::string& text, const std::string& style)
{
worksheet_write_string(worksheet, row, col, text.c_str(), efectiveStyle(style));
}
void ExcelFile::writeInt(int row, int col, const int number, const std::string& style)
{
worksheet_write_number(worksheet, row, col, number, efectiveStyle(style));
}
void ExcelFile::writeDouble(int row, int col, const double number, const std::string& style)
{
worksheet_write_number(worksheet, row, col, number, efectiveStyle(style));
}
void ExcelFile::addColor(lxw_format* style, bool odd)
{
uint32_t efectiveColor = odd ? colorEven : colorOdd;
format_set_bg_color(style, lxw_color_t(efectiveColor));
}
void ExcelFile::createStyle(const std::string& name, lxw_format* style, bool odd)
{
addColor(style, odd);
if (name == "textCentered") {
format_set_align(style, LXW_ALIGN_CENTER);
format_set_font_size(style, normalSize);
format_set_border(style, LXW_BORDER_THIN);
} else if (name == "text") {
format_set_font_size(style, normalSize);
format_set_border(style, LXW_BORDER_THIN);
} else if (name == "bodyHeader") {
format_set_bold(style);
format_set_font_size(style, normalSize);
format_set_align(style, LXW_ALIGN_CENTER);
format_set_align(style, LXW_ALIGN_VERTICAL_CENTER);
format_set_border(style, LXW_BORDER_THIN);
format_set_bg_color(style, lxw_color_t(colorTitle));
} else if (name == "result") {
format_set_font_size(style, normalSize);
format_set_border(style, LXW_BORDER_THIN);
format_set_num_format(style, "0.0000000");
} else if (name == "time") {
format_set_font_size(style, normalSize);
format_set_border(style, LXW_BORDER_THIN);
format_set_num_format(style, "#,##0.000000");
} else if (name == "ints") {
format_set_font_size(style, normalSize);
format_set_num_format(style, "###,##0");
format_set_border(style, LXW_BORDER_THIN);
} else if (name == "floats") {
format_set_border(style, LXW_BORDER_THIN);
format_set_font_size(style, normalSize);
format_set_num_format(style, "#,##0.00");
}
}
void ExcelFile::createFormats()
{
auto styleNames = { "text", "textCentered", "bodyHeader", "result", "time", "ints", "floats" };
lxw_format* style;
for (std::string name : styleNames) {
lxw_format* style = workbook_add_format(workbook);
style = workbook_add_format(workbook);
createStyle(name, style, true);
styles[name + "_odd"] = style;
style = workbook_add_format(workbook);
createStyle(name, style, false);
styles[name + "_even"] = style;
}
// Header 1st line
lxw_format* headerFirst = workbook_add_format(workbook);
format_set_bold(headerFirst);
format_set_font_size(headerFirst, 18);
format_set_align(headerFirst, LXW_ALIGN_CENTER);
format_set_align(headerFirst, LXW_ALIGN_VERTICAL_CENTER);
format_set_border(headerFirst, LXW_BORDER_THIN);
format_set_bg_color(headerFirst, lxw_color_t(colorTitle));
// Header rest
lxw_format* headerRest = workbook_add_format(workbook);
format_set_bold(headerRest);
format_set_align(headerRest, LXW_ALIGN_CENTER);
format_set_font_size(headerRest, 16);
format_set_align(headerRest, LXW_ALIGN_VERTICAL_CENTER);
format_set_border(headerRest, LXW_BORDER_THIN);
format_set_bg_color(headerRest, lxw_color_t(colorOdd));
// Header small
lxw_format* headerSmall = workbook_add_format(workbook);
format_set_bold(headerSmall);
format_set_align(headerSmall, LXW_ALIGN_LEFT);
format_set_font_size(headerSmall, 12);
format_set_border(headerSmall, LXW_BORDER_THIN);
format_set_align(headerSmall, LXW_ALIGN_VERTICAL_CENTER);
format_set_bg_color(headerSmall, lxw_color_t(colorOdd));
// Summary style
lxw_format* summaryStyle = workbook_add_format(workbook);
format_set_bold(summaryStyle);
format_set_font_size(summaryStyle, 16);
format_set_border(summaryStyle, LXW_BORDER_THIN);
format_set_align(summaryStyle, LXW_ALIGN_VERTICAL_CENTER);
styles["headerFirst"] = headerFirst;
styles["headerRest"] = headerRest;
styles["headerSmall"] = headerSmall;
styles["summaryStyle"] = summaryStyle;
}
}

43
src/Platform/ExcelFile.h Normal file
View File

@@ -0,0 +1,43 @@
#ifndef EXCELFILE_H
#define EXCELFILE_H
#include <locale>
#include <string>
#include <map>
#include "xlsxwriter.h"
namespace platform {
struct separated : std::numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
std::string do_grouping() const { return "\03"; }
};
class ExcelFile {
public:
ExcelFile();
ExcelFile(lxw_workbook* workbook);
ExcelFile(lxw_workbook* workbook, lxw_worksheet* worksheet);
lxw_workbook* getWorkbook();
protected:
void setProperties(std::string title);
void writeString(int row, int col, const std::string& text, const std::string& style = "");
void writeInt(int row, int col, const int number, const std::string& style = "");
void writeDouble(int row, int col, const double number, const std::string& style = "");
void createFormats();
void createStyle(const std::string& name, lxw_format* style, bool odd);
void addColor(lxw_format* style, bool odd);
lxw_format* efectiveStyle(const std::string& name);
lxw_workbook* workbook;
lxw_worksheet* worksheet;
std::map<std::string, lxw_format*> styles;
int row;
int normalSize; //font size for report body
uint32_t colorTitle;
uint32_t colorOdd;
uint32_t colorEven;
private:
void setDefault();
};
}
#endif // !EXCELFILE_H

View File

@@ -1,11 +1,12 @@
#include <fstream>
#include "Experiment.h"
#include "Datasets.h"
#include "Models.h"
#include "Report.h"
#include "ReportConsole.h"
#include "Paths.h"
namespace platform {
using json = nlohmann::json;
string get_date()
std::string get_date()
{
time_t rawtime;
tm* timeinfo;
@@ -15,7 +16,7 @@ namespace platform {
oss << std::put_time(timeinfo, "%Y-%m-%d");
return oss.str();
}
string get_time()
std::string get_time()
{
time_t rawtime;
tm* timeinfo;
@@ -25,9 +26,10 @@ namespace platform {
oss << std::put_time(timeinfo, "%H:%M:%S");
return oss.str();
}
string Experiment::get_file_name()
Experiment::Experiment() : hyperparameters(json::parse("{}")) {}
std::string Experiment::get_file_name()
{
string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
std::string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
return result;
}
@@ -79,7 +81,7 @@ namespace platform {
}
return result;
}
void Experiment::save(const string& path)
void Experiment::save(const std::string& path)
{
json data = build_json();
ofstream file(path + "/" + get_file_name());
@@ -90,40 +92,64 @@ namespace platform {
void Experiment::report()
{
json data = build_json();
Report report(data);
ReportConsole report(data);
report.show();
}
void Experiment::show()
{
json data = build_json();
cout << data.dump(4) << endl;
std::cout << data.dump(4) << std::endl;
}
void Experiment::go(vector<string> filesToProcess, const string& path)
void Experiment::go(std::vector<std::string> filesToProcess, bool quiet)
{
cout << "*** Starting experiment: " << title << " ***" << endl;
std::cout << "*** Starting experiment: " << title << " ***" << std::endl;
for (auto fileName : filesToProcess) {
cout << "- " << setw(20) << left << fileName << " " << right << flush;
cross_validation(path, fileName);
cout << endl;
std::cout << "- " << setw(20) << left << fileName << " " << right << flush;
cross_validation(fileName, quiet);
std::cout << std::endl;
}
}
void Experiment::cross_validation(const string& path, const string& fileName)
std::string getColor(bayesnet::status_t status)
{
auto datasets = platform::Datasets(path, discretized, platform::ARFF);
switch (status) {
case bayesnet::NORMAL:
return Colors::GREEN();
case bayesnet::WARNING:
return Colors::YELLOW();
case bayesnet::ERROR:
return Colors::RED();
default:
return Colors::RESET();
}
}
void showProgress(int fold, const std::string& color, const std::string& phase)
{
std::string prefix = phase == "a" ? "" : "\b\b\b\b";
std::cout << prefix << color << fold << Colors::RESET() << "(" << color << phase << Colors::RESET() << ")" << flush;
}
void Experiment::cross_validation(const std::string& fileName, bool quiet)
{
auto datasets = platform::Datasets(discretized, Paths::datasets());
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
auto features = datasets.getFeatures(fileName);
auto samples = datasets.getNSamples(fileName);
auto className = datasets.getClassName(fileName);
cout << " (" << setw(5) << samples << "," << setw(3) << features.size() << ") " << flush;
if (!quiet) {
std::cout << " (" << setw(5) << samples << "," << setw(3) << features.size() << ") " << flush;
}
// Prepare Result
auto result = Result();
auto [values, counts] = at::_unique(y);
result.setSamples(X.size(1)).setFeatures(X.size(0)).setClasses(values.size(0));
result.setHyperparameters(hyperparameters);
// Initialize results std::vectors
int nResults = nfolds * static_cast<int>(randomSeeds.size());
auto accuracy_test = torch::zeros({ nResults }, torch::kFloat64);
auto accuracy_train = torch::zeros({ nResults }, torch::kFloat64);
@@ -135,7 +161,8 @@ namespace platform {
Timer train_timer, test_timer;
int item = 0;
for (auto seed : randomSeeds) {
cout << "(" << seed << ") doing Fold: " << flush;
if (!quiet)
std::cout << "(" << seed << ") doing Fold: " << flush;
Fold* fold;
if (stratified)
fold = new StratifiedKFold(nfolds, y, seed);
@@ -144,6 +171,10 @@ namespace platform {
for (int nfold = 0; nfold < nfolds; nfold++) {
auto clf = Models::instance()->create(model);
setModelVersion(clf->getVersion());
if (hyperparameters.size() != 0) {
clf->setHyperparameters(hyperparameters);
}
// Split train - test dataset
train_timer.start();
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
@@ -152,31 +183,43 @@ namespace platform {
auto y_train = y.index({ train_t });
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
cout << nfold + 1 << ", " << flush;
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "a");
// Train model
clf->fit(X_train, y_train, features, className, states);
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "b");
nodes[item] = clf->getNumberOfNodes();
edges[item] = clf->getNumberOfEdges();
num_states[item] = clf->getNumberOfStates();
train_time[item] = train_timer.getDuration();
// Score train
auto accuracy_train_value = clf->score(X_train, y_train);
// Test model
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "c");
test_timer.start();
auto accuracy_test_value = clf->score(X_test, y_test);
test_time[item] = test_timer.getDuration();
accuracy_train[item] = accuracy_train_value;
accuracy_test[item] = accuracy_test_value;
// Store results and times in vector
if (!quiet)
std::cout << "\b\b\b, " << flush;
// Store results and times in std::vector
result.addScoreTrain(accuracy_train_value);
result.addScoreTest(accuracy_test_value);
result.addTimeTrain(train_time[item].item<double>());
result.addTimeTest(test_time[item].item<double>());
item++;
}
cout << "end. " << flush;
if (!quiet)
std::cout << "end. " << flush;
delete fold;
}
result.setScoreTest(torch::mean(accuracy_test).item<double>()).setScoreTrain(torch::mean(accuracy_train).item<double>());
result.setScoreTestStd(torch::std(accuracy_test).item<double>()).setScoreTrainStd(torch::std(accuracy_train).item<double>());
result.setTrainTime(torch::mean(train_time).item<double>()).setTestTime(torch::mean(test_time).item<double>());
result.setTestTimeStd(torch::std(test_time).item<double>()).setTrainTimeStd(torch::std(train_time).item<double>());
result.setNodes(torch::mean(nodes).item<double>()).setLeaves(torch::mean(edges).item<double>()).setDepth(torch::mean(num_states).item<double>());
result.setDataset(fileName);
addResult(result);

View File

@@ -10,34 +10,34 @@
#include "KDB.h"
#include "AODE.h"
using namespace std;
namespace platform {
using json = nlohmann::json;
class Timer {
private:
chrono::high_resolution_clock::time_point begin;
std::chrono::high_resolution_clock::time_point begin;
public:
Timer() = default;
~Timer() = default;
void start() { begin = chrono::high_resolution_clock::now(); }
void start() { begin = std::chrono::high_resolution_clock::now(); }
double getDuration()
{
chrono::high_resolution_clock::time_point end = chrono::high_resolution_clock::now();
chrono::duration<double> time_span = chrono::duration_cast<chrono::duration<double>>(end - begin);
std::chrono::high_resolution_clock::time_point end = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> time_span = std::chrono::duration_cast<std::chrono::duration<double >> (end - begin);
return time_span.count();
}
};
class Result {
private:
string dataset, hyperparameters, model_version;
std::string dataset, model_version;
json hyperparameters;
int samples{ 0 }, features{ 0 }, classes{ 0 };
double score_train{ 0 }, score_test{ 0 }, score_train_std{ 0 }, score_test_std{ 0 }, train_time{ 0 }, train_time_std{ 0 }, test_time{ 0 }, test_time_std{ 0 };
float nodes{ 0 }, leaves{ 0 }, depth{ 0 };
vector<double> scores_train, scores_test, times_train, times_test;
std::vector<double> scores_train, scores_test, times_train, times_test;
public:
Result() = default;
Result& setDataset(const string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const string& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setDataset(const std::string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setSamples(int samples) { this->samples = samples; return *this; }
Result& setFeatures(int features) { this->features = features; return *this; }
Result& setClasses(int classes) { this->classes = classes; return *this; }
@@ -58,8 +58,8 @@ namespace platform {
Result& addTimeTest(double time) { times_test.push_back(time); return *this; }
const float get_score_train() const { return score_train; }
float get_score_test() { return score_test; }
const string& getDataset() const { return dataset; }
const string& getHyperparameters() const { return hyperparameters; }
const std::string& getDataset() const { return dataset; }
const json& getHyperparameters() const { return hyperparameters; }
const int getSamples() const { return samples; }
const int getFeatures() const { return features; }
const int getClasses() const { return classes; }
@@ -74,39 +74,41 @@ namespace platform {
const float getNodes() const { return nodes; }
const float getLeaves() const { return leaves; }
const float getDepth() const { return depth; }
const vector<double>& getScoresTrain() const { return scores_train; }
const vector<double>& getScoresTest() const { return scores_test; }
const vector<double>& getTimesTrain() const { return times_train; }
const vector<double>& getTimesTest() const { return times_test; }
const std::vector<double>& getScoresTrain() const { return scores_train; }
const std::vector<double>& getScoresTest() const { return scores_test; }
const std::vector<double>& getTimesTrain() const { return times_train; }
const std::vector<double>& getTimesTest() const { return times_test; }
};
class Experiment {
private:
string title, model, platform, score_name, model_version, language_version, language;
std::string title, model, platform, score_name, model_version, language_version, language;
bool discretized{ false }, stratified{ false };
vector<Result> results;
vector<int> randomSeeds;
std::vector<Result> results;
std::vector<int> randomSeeds;
json hyperparameters = "{}";
int nfolds{ 0 };
float duration{ 0 };
json build_json();
public:
Experiment() = default;
Experiment& setTitle(const string& title) { this->title = title; return *this; }
Experiment& setModel(const string& model) { this->model = model; return *this; }
Experiment& setPlatform(const string& platform) { this->platform = platform; return *this; }
Experiment& setScoreName(const string& score_name) { this->score_name = score_name; return *this; }
Experiment& setModelVersion(const string& model_version) { this->model_version = model_version; return *this; }
Experiment& setLanguage(const string& language) { this->language = language; return *this; }
Experiment& setLanguageVersion(const string& language_version) { this->language_version = language_version; return *this; }
Experiment();
Experiment& setTitle(const std::string& title) { this->title = title; return *this; }
Experiment& setModel(const std::string& model) { this->model = model; return *this; }
Experiment& setPlatform(const std::string& platform) { this->platform = platform; return *this; }
Experiment& setScoreName(const std::string& score_name) { this->score_name = score_name; return *this; }
Experiment& setModelVersion(const std::string& model_version) { this->model_version = model_version; return *this; }
Experiment& setLanguage(const std::string& language) { this->language = language; return *this; }
Experiment& setLanguageVersion(const std::string& language_version) { this->language_version = language_version; return *this; }
Experiment& setDiscretized(bool discretized) { this->discretized = discretized; return *this; }
Experiment& setStratified(bool stratified) { this->stratified = stratified; return *this; }
Experiment& setNFolds(int nfolds) { this->nfolds = nfolds; return *this; }
Experiment& addResult(Result result) { results.push_back(result); return *this; }
Experiment& addRandomSeed(int randomSeed) { randomSeeds.push_back(randomSeed); return *this; }
Experiment& setDuration(float duration) { this->duration = duration; return *this; }
string get_file_name();
void save(const string& path);
void cross_validation(const string& path, const string& fileName);
void go(vector<string> filesToProcess, const string& path);
Experiment& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
std::string get_file_name();
void save(const std::string& path);
void cross_validation(const std::string& fileName, bool quiet);
void go(std::vector<std::string> filesToProcess, bool quiet);
void show();
void report();
};

View File

@@ -1,25 +1,26 @@
#include "Folding.h"
#include <algorithm>
#include <map>
namespace platform {
Fold::Fold(int k, int n, int seed) : k(k), n(n), seed(seed)
{
random_device rd;
random_seed = default_random_engine(seed == -1 ? rd() : seed);
srand(seed == -1 ? time(0) : seed);
std::random_device rd;
random_seed = std::default_random_engine(seed == -1 ? rd() : seed);
std::srand(seed == -1 ? time(0) : seed);
}
KFold::KFold(int k, int n, int seed) : Fold(k, n, seed), indices(vector<int>(n))
KFold::KFold(int k, int n, int seed) : Fold(k, n, seed), indices(std::vector<int>(n))
{
iota(begin(indices), end(indices), 0); // fill with 0, 1, ..., n - 1
std::iota(begin(indices), end(indices), 0); // fill with 0, 1, ..., n - 1
shuffle(indices.begin(), indices.end(), random_seed);
}
pair<vector<int>, vector<int>> KFold::getFold(int nFold)
std::pair<std::vector<int>, std::vector<int>> KFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw out_of_range("nFold (" + to_string(nFold) + ") must be less than k (" + to_string(k) + ")");
throw std::out_of_range("nFold (" + std::to_string(nFold) + ") must be less than k (" + std::to_string(k) + ")");
}
int nTest = n / k;
auto train = vector<int>();
auto test = vector<int>();
auto train = std::vector<int>();
auto test = std::vector<int>();
for (int i = 0; i < n; i++) {
if (i >= nTest * nFold && i < nTest * (nFold + 1)) {
test.push_back(indices[i]);
@@ -32,10 +33,10 @@ pair<vector<int>, vector<int>> KFold::getFold(int nFold)
StratifiedKFold::StratifiedKFold(int k, torch::Tensor& y, int seed) : Fold(k, y.numel(), seed)
{
n = y.numel();
this->y = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + n);
this->y = std::vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + n);
build();
}
StratifiedKFold::StratifiedKFold(int k, const vector<int>& y, int seed)
StratifiedKFold::StratifiedKFold(int k, const std::vector<int>& y, int seed)
: Fold(k, y.size(), seed)
{
this->y = y;
@@ -44,11 +45,12 @@ StratifiedKFold::StratifiedKFold(int k, const vector<int>& y, int seed)
}
void StratifiedKFold::build()
{
stratified_indices = vector<vector<int>>(k);
stratified_indices = std::vector<std::vector<int>>(k);
int fold_size = n / k;
// Compute class counts and indices
auto class_indices = map<int, vector<int>>();
vector<int> class_counts(*max_element(y.begin(), y.end()) + 1, 0);
auto class_indices = std::map<int, std::vector<int>>();
std::vector<int> class_counts(*max_element(y.begin(), y.end()) + 1, 0);
for (auto i = 0; i < n; ++i) {
class_counts[y[i]]++;
class_indices[y[i]].push_back(i);
@@ -59,20 +61,26 @@ void StratifiedKFold::build()
}
// Assign indices to folds
for (auto label = 0; label < class_counts.size(); ++label) {
auto num_samples_to_take = class_counts[label] / k;
if (num_samples_to_take == 0)
auto num_samples_to_take = class_counts.at(label) / k;
if (num_samples_to_take == 0) {
std::cerr << "Warning! The number of samples in class " << label << " (" << class_counts.at(label)
<< ") is less than the number of folds (" << k << ")." << std::endl;
faulty = true;
continue;
}
auto remainder_samples_to_take = class_counts[label] % k;
for (auto fold = 0; fold < k; ++fold) {
auto it = next(class_indices[label].begin(), num_samples_to_take);
move(class_indices[label].begin(), it, back_inserter(stratified_indices[fold])); // ##
class_indices[label].erase(class_indices[label].begin(), it);
}
auto chosen = std::vector<bool>(k, false);
while (remainder_samples_to_take > 0) {
int fold = (rand() % static_cast<int>(k));
if (stratified_indices[fold].size() == fold_size + 1) {
if (chosen.at(fold)) {
continue;
}
chosen[fold] = true;
auto it = next(class_indices[label].begin(), 1);
stratified_indices[fold].push_back(*class_indices[label].begin());
class_indices[label].erase(class_indices[label].begin(), it);
@@ -80,16 +88,17 @@ void StratifiedKFold::build()
}
}
}
pair<vector<int>, vector<int>> StratifiedKFold::getFold(int nFold)
std::pair<std::vector<int>, std::vector<int>> StratifiedKFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw out_of_range("nFold (" + to_string(nFold) + ") must be less than k (" + to_string(k) + ")");
throw std::out_of_range("nFold (" + std::to_string(nFold) + ") must be less than k (" + std::to_string(k) + ")");
}
vector<int> test_indices = stratified_indices[nFold];
vector<int> train_indices;
std::vector<int> test_indices = stratified_indices[nFold];
std::vector<int> train_indices;
for (int i = 0; i < k; ++i) {
if (i == nFold) continue;
train_indices.insert(train_indices.end(), stratified_indices[i].begin(), stratified_indices[i].end());
}
return { train_indices, test_indices };
}
}

View File

@@ -3,35 +3,37 @@
#include <torch/torch.h>
#include <vector>
#include <random>
using namespace std;
namespace platform {
class Fold {
protected:
int k;
int n;
int seed;
default_random_engine random_seed;
std::default_random_engine random_seed;
public:
Fold(int k, int n, int seed = -1);
virtual pair<vector<int>, vector<int>> getFold(int nFold) = 0;
virtual std::pair<std::vector<int>, std::vector<int>> getFold(int nFold) = 0;
virtual ~Fold() = default;
int getNumberOfFolds() { return k; }
};
class KFold : public Fold {
private:
vector<int> indices;
std::vector<int> indices;
public:
KFold(int k, int n, int seed = -1);
pair<vector<int>, vector<int>> getFold(int nFold) override;
std::pair<std::vector<int>, std::vector<int>> getFold(int nFold) override;
};
class StratifiedKFold : public Fold {
private:
vector<int> y;
vector<vector<int>> stratified_indices;
std::vector<int> y;
std::vector<std::vector<int>> stratified_indices;
void build();
bool faulty = false; // Only true if the number of samples of any class is less than the number of folds.
public:
StratifiedKFold(int k, const vector<int>& y, int seed = -1);
StratifiedKFold(int k, const std::vector<int>& y, int seed = -1);
StratifiedKFold(int k, torch::Tensor& y, int seed = -1);
pair<vector<int>, vector<int>> getFold(int nFold) override;
std::pair<std::vector<int>, std::vector<int>> getFold(int nFold) override;
bool isFaulty() { return faulty; }
};
}
#endif

View File

@@ -0,0 +1,213 @@
#include "ManageResults.h"
#include "CommandParser.h"
#include <filesystem>
#include <tuple>
#include "Colors.h"
#include "CLocale.h"
#include "Paths.h"
#include "ReportConsole.h"
#include "ReportExcel.h"
namespace platform {
ManageResults::ManageResults(int numFiles, const std::string& model, const std::string& score, bool complete, bool partial, bool compare) :
numFiles{ numFiles }, complete{ complete }, partial{ partial }, compare{ compare }, results(Results(Paths::results(), model, score, complete, partial))
{
indexList = true;
openExcel = false;
workbook = NULL;
if (numFiles == 0) {
this->numFiles = results.size();
}
}
void ManageResults::doMenu()
{
if (results.empty()) {
std::cout << Colors::MAGENTA() << "No results found!" << Colors::RESET() << std::endl;
return;
}
results.sortDate();
list();
menu();
if (openExcel) {
workbook_close(workbook);
}
std::cout << Colors::RESET() << "Done!" << std::endl;
}
void ManageResults::list()
{
auto temp = ConfigLocale();
std::string suffix = numFiles != results.size() ? " of " + std::to_string(results.size()) : "";
std::stringstream oss;
oss << "Results on screen: " << numFiles << suffix;
std::cout << Colors::GREEN() << oss.str() << std::endl;
std::cout << std::string(oss.str().size(), '-') << std::endl;
if (complete) {
std::cout << Colors::MAGENTA() << "Only listing complete results" << std::endl;
}
if (partial) {
std::cout << Colors::MAGENTA() << "Only listing partial results" << std::endl;
}
auto i = 0;
int maxModel = results.maxModelSize();
std::cout << Colors::GREEN() << " # Date " << std::setw(maxModel) << std::left << "Model" << " Score Name Score C/P Duration Title" << std::endl;
std::cout << "=== ========== " << std::string(maxModel, '=') << " =========== =========== === ========= =============================================================" << std::endl;
bool odd = true;
for (auto& result : results) {
auto color = odd ? Colors::BLUE() : Colors::CYAN();
std::cout << color << std::setw(3) << std::fixed << std::right << i++ << " ";
std::cout << result.to_string(maxModel) << std::endl;
if (i == numFiles) {
break;
}
odd = !odd;
}
}
bool ManageResults::confirmAction(const std::string& intent, const std::string& fileName) const
{
std::string color;
if (intent == "delete") {
color = Colors::RED();
} else {
color = Colors::YELLOW();
}
std::string line;
bool finished = false;
while (!finished) {
std::cout << color << "Really want to " << intent << " " << fileName << "? (y/n): ";
getline(std::cin, line);
finished = line.size() == 1 && (tolower(line[0]) == 'y' || tolower(line[0] == 'n'));
}
if (tolower(line[0]) == 'y') {
return true;
}
std::cout << "Not done!" << std::endl;
return false;
}
void ManageResults::report(const int index, const bool excelReport)
{
std::cout << Colors::YELLOW() << "Reporting " << results.at(index).getFilename() << std::endl;
auto data = results.at(index).load();
if (excelReport) {
ReportExcel reporter(data, compare, workbook);
reporter.show();
openExcel = true;
workbook = reporter.getWorkbook();
std::cout << "Adding sheet to " << Paths::excel() + Paths::excelResults() << std::endl;
} else {
ReportConsole reporter(data, compare);
reporter.show();
}
}
void ManageResults::showIndex(const int index, const int idx)
{
// Show a dataset result inside a report
auto data = results.at(index).load();
std::cout << Colors::YELLOW() << "Showing " << results.at(index).getFilename() << std::endl;
ReportConsole reporter(data, compare, idx);
reporter.show();
}
void ManageResults::sortList()
{
std::cout << Colors::YELLOW() << "Choose sorting field (date='d', score='s', duration='u', model='m'): ";
std::string line;
char option;
getline(std::cin, line);
if (line.size() == 0)
return;
if (line.size() > 1) {
std::cout << "Invalid option" << std::endl;
return;
}
option = line[0];
switch (option) {
case 'd':
results.sortDate();
break;
case 's':
results.sortScore();
break;
case 'u':
results.sortDuration();
break;
case 'm':
results.sortModel();
break;
default:
std::cout << "Invalid option" << std::endl;
}
}
void ManageResults::menu()
{
char option;
int index, subIndex;
bool finished = false;
std::string filename;
// tuple<Option, digit, requires value>
std::vector<std::tuple<std::string, char, bool>> mainOptions = {
{"quit", 'q', false},
{"list", 'l', false},
{"delete", 'd', true},
{"hide", 'h', true},
{"sort", 's', false},
{"report", 'r', true},
{"excel", 'e', true}
};
std::vector<std::tuple<std::string, char, bool>> listOptions = {
{"report", 'r', true},
{"list", 'l', false},
{"quit", 'q', false}
};
auto parser = CommandParser();
while (!finished) {
if (indexList) {
std::tie(option, index) = parser.parse(Colors::GREEN(), mainOptions, 'r', numFiles - 1);
} else {
std::tie(option, subIndex) = parser.parse(Colors::MAGENTA(), listOptions, 'r', results.at(index).load()["results"].size() - 1);
}
switch (option) {
case 'q':
finished = true;
break;
case 'l':
list();
indexList = true;
break;
case 'd':
filename = results.at(index).getFilename();
if (!confirmAction("delete", filename))
break;
std::cout << "Deleting " << filename << std::endl;
results.deleteResult(index);
std::cout << "File: " + filename + " deleted!" << std::endl;
list();
break;
case 'h':
filename = results.at(index).getFilename();
if (!confirmAction("hide", filename))
break;
filename = results.at(index).getFilename();
std::cout << "Hiding " << filename << std::endl;
results.hideResult(index, Paths::hiddenResults());
std::cout << "File: " + filename + " hidden! (moved to " << Paths::hiddenResults() << ")" << std::endl;
list();
break;
case 's':
sortList();
list();
break;
case 'r':
if (indexList) {
report(index, false);
indexList = false;
} else {
showIndex(index, subIndex);
}
break;
case 'e':
report(index, true);
break;
}
}
}
} /* namespace platform */

View File

@@ -0,0 +1,31 @@
#ifndef MANAGE_RESULTS_H
#define MANAGE_RESULTS_H
#include "Results.h"
#include "xlsxwriter.h"
namespace platform {
class ManageResults {
public:
ManageResults(int numFiles, const std::string& model, const std::string& score, bool complete, bool partial, bool compare);
~ManageResults() = default;
void doMenu();
private:
void list();
bool confirmAction(const std::string& intent, const std::string& fileName) const;
void report(const int index, const bool excelReport);
void showIndex(const int index, const int idx);
void sortList();
void menu();
int numFiles;
bool indexList;
bool openExcel;
bool complete;
bool partial;
bool compare;
Results results;
lxw_workbook* workbook;
};
}
#endif /* MANAGE_RESULTS_H */

View File

@@ -1,6 +1,5 @@
#include "Models.h"
namespace platform {
using namespace std;
// Idea from: https://www.codeproject.com/Articles/567242/AplusC-2b-2bplusObjectplusFactory
Models* Models::factory = nullptr;;
Models* Models::instance()
@@ -10,13 +9,13 @@ namespace platform {
factory = new Models();
return factory;
}
void Models::registerFactoryFunction(const string& name,
void Models::registerFactoryFunction(const std::string& name,
function<bayesnet::BaseClassifier* (void)> classFactoryFunction)
{
// register the class factory function
functionRegistry[name] = classFactoryFunction;
}
shared_ptr<bayesnet::BaseClassifier> Models::create(const string& name)
shared_ptr<bayesnet::BaseClassifier> Models::create(const std::string& name)
{
bayesnet::BaseClassifier* instance = nullptr;
@@ -26,27 +25,26 @@ namespace platform {
instance = it->second();
// wrap instance in a shared ptr and return
if (instance != nullptr)
return shared_ptr<bayesnet::BaseClassifier>(instance);
return unique_ptr<bayesnet::BaseClassifier>(instance);
else
return nullptr;
}
vector<string> Models::getNames()
std::vector<std::string> Models::getNames()
{
vector<string> names;
std::vector<std::string> names;
transform(functionRegistry.begin(), functionRegistry.end(), back_inserter(names),
[](const pair<string, function<bayesnet::BaseClassifier* (void)>>& pair) { return pair.first; });
[](const pair<std::string, function<bayesnet::BaseClassifier* (void)>>& pair) { return pair.first; });
return names;
}
string Models::toString()
std::string Models::tostring()
{
string result = "";
std::string result = "";
for (const auto& pair : functionRegistry) {
result += pair.first + ", ";
}
return "{" + result.substr(0, result.size() - 2) + "}";
}
Registrar::Registrar(const string& name, function<bayesnet::BaseClassifier* (void)> classFactoryFunction)
Registrar::Registrar(const std::string& name, function<bayesnet::BaseClassifier* (void)> classFactoryFunction)
{
// register the class factory function
Models::instance()->registerFactoryFunction(name, classFactoryFunction);

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@@ -10,10 +10,15 @@
#include "KDBLd.h"
#include "SPODELd.h"
#include "AODELd.h"
#include "BoostAODE.h"
#include "STree.h"
#include "ODTE.h"
#include "SVC.h"
#include "RandomForest.h"
namespace platform {
class Models {
private:
map<string, function<bayesnet::BaseClassifier* (void)>> functionRegistry;
map<std::string, function<bayesnet::BaseClassifier* (void)>> functionRegistry;
static Models* factory; //singleton
Models() {};
public:
@@ -21,16 +26,16 @@ namespace platform {
void operator=(const Models&) = delete;
// Idea from: https://www.codeproject.com/Articles/567242/AplusC-2b-2bplusObjectplusFactory
static Models* instance();
shared_ptr<bayesnet::BaseClassifier> create(const string& name);
void registerFactoryFunction(const string& name,
shared_ptr<bayesnet::BaseClassifier> create(const std::string& name);
void registerFactoryFunction(const std::string& name,
function<bayesnet::BaseClassifier* (void)> classFactoryFunction);
vector<string> getNames();
string toString();
std::vector<string> getNames();
std::string tostring();
};
class Registrar {
public:
Registrar(const string& className, function<bayesnet::BaseClassifier* (void)> classFactoryFunction);
Registrar(const std::string& className, function<bayesnet::BaseClassifier* (void)> classFactoryFunction);
};
}
#endif

View File

@@ -1,10 +1,20 @@
#ifndef PATHS_H
#define PATHS_H
#include <string>
#include "DotEnv.h"
namespace platform {
class Paths {
public:
static std::string datasets() { return "datasets/"; }
static std::string results() { return "results/"; }
static std::string hiddenResults() { return "hidden_results/"; }
static std::string excel() { return "excel/"; }
static std::string cfs() { return "cfs/"; }
static std::string datasets()
{
auto env = platform::DotEnv();
return env.get("source_data");
}
static std::string excelResults() { return "some_results.xlsx"; }
};
}
#endif

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@@ -1,93 +0,0 @@
#include "Report.h"
#include "BestResult.h"
namespace platform {
string headerLine(const string& text)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + string(n, ' ') + "*\n";
}
string Report::fromVector(const string& key)
{
string result = "";
for (auto& item : data[key]) {
result += to_string(item) + ", ";
}
return "[" + result.substr(0, result.size() - 2) + "]";
}
string fVector(const json& data)
{
string result = "";
for (const auto& item : data) {
result += to_string(item) + ", ";
}
return "[" + result.substr(0, result.size() - 2) + "]";
}
void Report::show()
{
header();
body();
footer();
}
void Report::header()
{
cout << Colors::MAGENTA() << string(MAXL, '*') << endl;
cout << headerLine("Report " + data["model"].get<string>() + " ver. " + data["version"].get<string>() + " with " + to_string(data["folds"].get<int>()) + " Folds cross validation and " + to_string(data["seeds"].size()) + " random seeds. " + data["date"].get<string>() + " " + data["time"].get<string>());
cout << headerLine(data["title"].get<string>());
cout << headerLine("Random seeds: " + fromVector("seeds") + " Stratified: " + (data["stratified"].get<bool>() ? "True" : "False"));
cout << headerLine("Execution took " + to_string(data["duration"].get<float>()) + " seconds, " + to_string(data["duration"].get<float>() / 3600) + " hours, on " + data["platform"].get<string>());
cout << headerLine("Score is " + data["score_name"].get<string>());
cout << string(MAXL, '*') << endl;
cout << endl;
}
void Report::body()
{
cout << Colors::GREEN() << "Dataset Sampl. Feat. Cls Nodes Edges States Score Time Hyperparameters" << endl;
cout << "============================== ====== ===== === ======= ======= ======= =============== ================== ===============" << endl;
json lastResult;
totalScore = 0;
bool odd = true;
for (const auto& r : data["results"]) {
auto color = odd ? Colors::CYAN() : Colors::BLUE();
cout << color << setw(30) << left << r["dataset"].get<string>() << " ";
cout << setw(6) << right << r["samples"].get<int>() << " ";
cout << setw(5) << right << r["features"].get<int>() << " ";
cout << setw(3) << right << r["classes"].get<int>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["nodes"].get<float>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["leaves"].get<float>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["depth"].get<float>() << " ";
cout << setw(8) << right << setprecision(6) << fixed << r["score"].get<double>() << "±" << setw(6) << setprecision(4) << fixed << r["score_std"].get<double>() << " ";
cout << setw(11) << right << setprecision(6) << fixed << r["time"].get<double>() << "±" << setw(6) << setprecision(4) << fixed << r["time_std"].get<double>() << " ";
try {
cout << r["hyperparameters"].get<string>();
}
catch (const exception& err) {
cout << r["hyperparameters"];
}
cout << endl;
lastResult = r;
totalScore += r["score"].get<double>();
odd = !odd;
}
if (data["results"].size() == 1) {
cout << string(MAXL, '*') << endl;
cout << headerLine("Train scores: " + fVector(lastResult["scores_train"]));
cout << headerLine("Test scores: " + fVector(lastResult["scores_test"]));
cout << headerLine("Train times: " + fVector(lastResult["times_train"]));
cout << headerLine("Test times: " + fVector(lastResult["times_test"]));
cout << string(MAXL, '*') << endl;
}
}
void Report::footer()
{
cout << Colors::MAGENTA() << string(MAXL, '*') << endl;
auto score = data["score_name"].get<string>();
if (score == BestResult::scoreName()) {
cout << headerLine(score + " compared to " + BestResult::title() + " .: " + to_string(totalScore / BestResult::score()));
}
cout << string(MAXL, '*') << endl << Colors::RESET();
}
}

View File

@@ -1,26 +0,0 @@
#ifndef REPORT_H
#define REPORT_H
#include <string>
#include <iostream>
#include <nlohmann/json.hpp>
#include "Colors.h"
using json = nlohmann::json;
const int MAXL = 121;
namespace platform {
using namespace std;
class Report {
public:
explicit Report(json data_) { data = data_; };
virtual ~Report() = default;
void show();
private:
void header();
void body();
void footer();
string fromVector(const string& key);
json data;
double totalScore; // Total score of all results in a report
};
};
#endif

113
src/Platform/ReportBase.cc Normal file
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@@ -0,0 +1,113 @@
#include <sstream>
#include <locale>
#include "Datasets.h"
#include "ReportBase.h"
#include "DotEnv.h"
namespace platform {
ReportBase::ReportBase(json data_, bool compare) : data(data_), compare(compare), margin(0.1)
{
std::stringstream oss;
oss << "Better than ZeroR + " << std::setprecision(1) << fixed << margin * 100 << "%";
meaning = {
{Symbols::equal_best, "Equal to best"},
{Symbols::better_best, "Better than best"},
{Symbols::cross, "Less than or equal to ZeroR"},
{Symbols::upward_arrow, oss.str()}
};
}
std::string ReportBase::fromVector(const std::string& key)
{
std::stringstream oss;
std::string sep = "";
oss << "[";
for (auto& item : data[key]) {
oss << sep << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
std::string ReportBase::fVector(const std::string& title, const json& data, const int width, const int precision)
{
std::stringstream oss;
std::string sep = "";
oss << title << "[";
for (const auto& item : data) {
oss << sep << fixed << setw(width) << std::setprecision(precision) << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
void ReportBase::show()
{
header();
body();
}
std::string ReportBase::compareResult(const std::string& dataset, double result)
{
std::string status = " ";
if (compare) {
double best = bestResult(dataset, data["model"].get<std::string>());
if (result == best) {
status = Symbols::equal_best;
} else if (result > best) {
status = Symbols::better_best;
}
} else {
if (data["score_name"].get<std::string>() == "accuracy") {
auto dt = Datasets(false, Paths::datasets());
dt.loadDataset(dataset);
auto numClasses = dt.getNClasses(dataset);
if (numClasses == 2) {
std::vector<int> distribution = dt.getClassesCounts(dataset);
double nSamples = dt.getNSamples(dataset);
std::vector<int>::iterator maxValue = max_element(distribution.begin(), distribution.end());
double mark = *maxValue / nSamples * (1 + margin);
if (mark > 1) {
mark = 0.9995;
}
status = result < mark ? Symbols::cross : result > mark ? Symbols::upward_arrow : "=";
}
}
}
if (status != " ") {
auto item = summary.find(status);
if (item != summary.end()) {
summary[status]++;
} else {
summary[status] = 1;
}
}
return status;
}
double ReportBase::bestResult(const std::string& dataset, const std::string& model)
{
double value = 0.0;
if (bestResults.size() == 0) {
// try to load the best results
std::string score = data["score_name"];
replace(score.begin(), score.end(), '_', '-');
std::string fileName = "best_results_" + score + "_" + model + ".json";
ifstream resultData(Paths::results() + "/" + fileName);
if (resultData.is_open()) {
bestResults = json::parse(resultData);
} else {
existBestFile = false;
}
}
try {
value = bestResults.at(dataset).at(0);
}
catch (exception) {
value = 1.0;
}
return value;
}
bool ReportBase::getExistBestFile()
{
return existBestFile;
}
}

36
src/Platform/ReportBase.h Normal file
View File

@@ -0,0 +1,36 @@
#ifndef REPORTBASE_H
#define REPORTBASE_H
#include <string>
#include <iostream>
#include "Paths.h"
#include "Symbols.h"
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
class ReportBase {
public:
explicit ReportBase(json data_, bool compare);
virtual ~ReportBase() = default;
void show();
protected:
json data;
std::string fromVector(const std::string& key);
std::string fVector(const std::string& title, const json& data, const int width, const int precision);
bool getExistBestFile();
virtual void header() = 0;
virtual void body() = 0;
virtual void showSummary() = 0;
std::string compareResult(const std::string& dataset, double result);
std::map<std::string, int> summary;
double margin;
std::map<std::string, std::string> meaning;
bool compare;
private:
double bestResult(const std::string& dataset, const std::string& model);
json bestResults;
bool existBestFile = true;
};
};
#endif

View File

@@ -0,0 +1,114 @@
#include <iostream>
#include <sstream>
#include <locale>
#include "ReportConsole.h"
#include "BestScore.h"
#include "CLocale.h"
namespace platform {
std::string ReportConsole::headerLine(const std::string& text, int utf = 0)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + std::string(n + utf, ' ') + "*\n";
}
void ReportConsole::header()
{
std::stringstream oss;
std::cout << Colors::MAGENTA() << std::string(MAXL, '*') << std::endl;
std::cout << headerLine(
"Report " + data["model"].get<std::string>() + " ver. " + data["version"].get<std::string>()
+ " with " + std::to_string(data["folds"].get<int>()) + " Folds cross validation and " + std::to_string(data["seeds"].size())
+ " random seeds. " + data["date"].get<std::string>() + " " + data["time"].get<std::string>()
);
std::cout << headerLine(data["title"].get<std::string>());
std::cout << headerLine("Random seeds: " + fromVector("seeds") + " Stratified: " + (data["stratified"].get<bool>() ? "True" : "False"));
oss << "Execution took " << std::setprecision(2) << std::fixed << data["duration"].get<float>()
<< " seconds, " << data["duration"].get<float>() / 3600 << " hours, on " << data["platform"].get<std::string>();
std::cout << headerLine(oss.str());
std::cout << headerLine("Score is " + data["score_name"].get<std::string>());
std::cout << std::string(MAXL, '*') << std::endl;
std::cout << std::endl;
}
void ReportConsole::body()
{
auto tmp = ConfigLocale();
int maxHyper = 15;
int maxDataset = 7;
for (const auto& r : data["results"]) {
maxHyper = std::max(maxHyper, (int)r["hyperparameters"].dump().size());
maxDataset = std::max(maxDataset, (int)r["dataset"].get<std::string>().size());
}
std::cout << Colors::GREEN() << " # " << std::setw(maxDataset) << std::left << "Dataset" << " Sampl. Feat. Cls Nodes Edges States Score Time Hyperparameters" << std::endl;
std::cout << "=== " << std::string(maxDataset, '=') << " ====== ===== === ========= ========= ========= =============== =================== " << std::string(maxHyper, '=') << std::endl;
json lastResult;
double totalScore = 0.0;
bool odd = true;
int index = 0;
for (const auto& r : data["results"]) {
if (selectedIndex != -1 && index != selectedIndex) {
index++;
continue;
}
auto color = odd ? Colors::CYAN() : Colors::BLUE();
std::cout << color;
std::cout << std::setw(3) << std::right << index++ << " ";
std::cout << std::setw(maxDataset) << std::left << r["dataset"].get<std::string>() << " ";
std::cout << std::setw(6) << std::right << r["samples"].get<int>() << " ";
std::cout << std::setw(5) << std::right << r["features"].get<int>() << " ";
std::cout << std::setw(3) << std::right << r["classes"].get<int>() << " ";
std::cout << std::setw(9) << std::setprecision(2) << std::fixed << r["nodes"].get<float>() << " ";
std::cout << std::setw(9) << std::setprecision(2) << std::fixed << r["leaves"].get<float>() << " ";
std::cout << std::setw(9) << std::setprecision(2) << std::fixed << r["depth"].get<float>() << " ";
std::cout << std::setw(8) << std::right << std::setprecision(6) << std::fixed << r["score"].get<double>() << "±" << std::setw(6) << std::setprecision(4) << std::fixed << r["score_std"].get<double>();
const std::string status = compareResult(r["dataset"].get<std::string>(), r["score"].get<double>());
std::cout << status;
std::cout << std::setw(12) << std::right << std::setprecision(6) << std::fixed << r["time"].get<double>() << "±" << std::setw(6) << std::setprecision(4) << std::fixed << r["time_std"].get<double>() << " ";
std::cout << r["hyperparameters"].dump();
std::cout << std::endl;
std::cout << std::flush;
lastResult = r;
totalScore += r["score"].get<double>();
odd = !odd;
}
if (data["results"].size() == 1 || selectedIndex != -1) {
std::cout << std::string(MAXL, '*') << std::endl;
std::cout << headerLine(fVector("Train scores: ", lastResult["scores_train"], 14, 12));
std::cout << headerLine(fVector("Test scores: ", lastResult["scores_test"], 14, 12));
std::cout << headerLine(fVector("Train times: ", lastResult["times_train"], 10, 3));
std::cout << headerLine(fVector("Test times: ", lastResult["times_test"], 10, 3));
std::cout << std::string(MAXL, '*') << std::endl;
} else {
footer(totalScore);
}
}
void ReportConsole::showSummary()
{
for (const auto& item : summary) {
std::stringstream oss;
oss << std::setw(3) << std::left << item.first;
oss << std::setw(3) << std::right << item.second << " ";
oss << std::left << meaning.at(item.first);
std::cout << headerLine(oss.str(), 2);
}
}
void ReportConsole::footer(double totalScore)
{
std::cout << Colors::MAGENTA() << std::string(MAXL, '*') << std::endl;
showSummary();
auto score = data["score_name"].get<std::string>();
auto best = BestScore::getScore(score);
if (best.first != "") {
std::stringstream oss;
oss << score << " compared to " << best.first << " .: " << totalScore / best.second;
std::cout << headerLine(oss.str());
}
if (!getExistBestFile() && compare) {
std::cout << headerLine("*** Best Results File not found. Couldn't compare any result!");
}
std::cout << std::string(MAXL, '*') << std::endl << Colors::RESET();
}
}

View File

@@ -0,0 +1,22 @@
#ifndef REPORTCONSOLE_H
#define REPORTCONSOLE_H
#include <string>
#include "ReportBase.h"
#include "Colors.h"
namespace platform {
const int MAXL = 133;
class ReportConsole : public ReportBase {
public:
explicit ReportConsole(json data_, bool compare = false, int index = -1) : ReportBase(data_, compare), selectedIndex(index) {};
virtual ~ReportConsole() = default;
private:
int selectedIndex;
std::string headerLine(const std::string& text, int utf);
void header() override;
void body() override;
void footer(double totalScore);
void showSummary() override;
};
};
#endif

180
src/Platform/ReportExcel.cc Normal file
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@@ -0,0 +1,180 @@
#include <sstream>
#include <locale>
#include "ReportExcel.h"
#include "BestScore.h"
namespace platform {
ReportExcel::ReportExcel(json data_, bool compare, lxw_workbook* workbook, lxw_worksheet* worksheet) : ReportBase(data_, compare), ExcelFile(workbook, worksheet)
{
createFile();
}
void ReportExcel::formatColumns()
{
worksheet_freeze_panes(worksheet, 6, 1);
std::vector<int> columns_sizes = { 22, 10, 9, 7, 12, 12, 12, 12, 12, 3, 15, 12, 23 };
for (int i = 0; i < columns_sizes.size(); ++i) {
worksheet_set_column(worksheet, i, i, columns_sizes.at(i), NULL);
}
}
void ReportExcel::createWorksheet()
{
const std::string name = data["model"].get<std::string>();
std::string suffix = "";
std::string efectiveName;
int num = 1;
// Create a sheet with the name of the model
while (true) {
efectiveName = name + suffix;
if (workbook_get_worksheet_by_name(workbook, efectiveName.c_str())) {
suffix = std::to_string(++num);
} else {
worksheet = workbook_add_worksheet(workbook, efectiveName.c_str());
break;
}
if (num > 100) {
throw std::invalid_argument("Couldn't create sheet " + efectiveName);
}
}
}
void ReportExcel::createFile()
{
if (workbook == NULL) {
workbook = workbook_new((Paths::excel() + Paths::excelResults()).c_str());
}
if (worksheet == NULL) {
createWorksheet();
}
setProperties(data["title"].get<std::string>());
createFormats();
formatColumns();
}
void ReportExcel::closeFile()
{
workbook_close(workbook);
}
void ReportExcel::header()
{
std::locale mylocale(std::cout.getloc(), new separated);
std::locale::global(mylocale);
std::cout.imbue(mylocale);
std::stringstream oss;
std::string message = data["model"].get<std::string>() + " ver. " + data["version"].get<std::string>() + " " +
data["language"].get<std::string>() + " ver. " + data["language_version"].get<std::string>() +
" with " + std::to_string(data["folds"].get<int>()) + " Folds cross validation and " + std::to_string(data["seeds"].size()) +
" random seeds. " + data["date"].get<std::string>() + " " + data["time"].get<std::string>();
worksheet_merge_range(worksheet, 0, 0, 0, 12, message.c_str(), styles["headerFirst"]);
worksheet_merge_range(worksheet, 1, 0, 1, 12, data["title"].get<std::string>().c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 0, 3, 0, ("Score is " + data["score_name"].get<std::string>()).c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 1, 3, 3, "Execution time", styles["headerRest"]);
oss << std::setprecision(2) << std::fixed << data["duration"].get<float>() << " s";
worksheet_merge_range(worksheet, 2, 4, 2, 5, oss.str().c_str(), styles["headerRest"]);
oss.str("");
oss.clear();
oss << std::setprecision(2) << std::fixed << data["duration"].get<float>() / 3600 << " h";
worksheet_merge_range(worksheet, 3, 4, 3, 5, oss.str().c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 6, 3, 7, "Platform", styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 8, 3, 9, data["platform"].get<std::string>().c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 10, 2, 12, ("Random seeds: " + fromVector("seeds")).c_str(), styles["headerSmall"]);
oss.str("");
oss.clear();
oss << "Stratified: " << (data["stratified"].get<bool>() ? "True" : "False");
worksheet_merge_range(worksheet, 3, 10, 3, 11, oss.str().c_str(), styles["headerSmall"]);
oss.str("");
oss.clear();
oss << "Discretized: " << (data["discretized"].get<bool>() ? "True" : "False");
worksheet_write_string(worksheet, 3, 12, oss.str().c_str(), styles["headerSmall"]);
}
void ReportExcel::body()
{
auto head = std::vector<std::string>(
{ "Dataset", "Samples", "Features", "Classes", "Nodes", "Edges", "States", "Score", "Score Std.", "St.", "Time",
"Time Std.", "Hyperparameters" });
int col = 0;
for (const auto& item : head) {
writeString(5, col++, item, "bodyHeader");
}
row = 6;
col = 0;
int hypSize = 22;
json lastResult;
double totalScore = 0.0;
std::string hyperparameters;
for (const auto& r : data["results"]) {
writeString(row, col, r["dataset"].get<std::string>(), "text");
writeInt(row, col + 1, r["samples"].get<int>(), "ints");
writeInt(row, col + 2, r["features"].get<int>(), "ints");
writeInt(row, col + 3, r["classes"].get<int>(), "ints");
writeDouble(row, col + 4, r["nodes"].get<float>(), "floats");
writeDouble(row, col + 5, r["leaves"].get<float>(), "floats");
writeDouble(row, col + 6, r["depth"].get<double>(), "floats");
writeDouble(row, col + 7, r["score"].get<double>(), "result");
writeDouble(row, col + 8, r["score_std"].get<double>(), "result");
const std::string status = compareResult(r["dataset"].get<std::string>(), r["score"].get<double>());
writeString(row, col + 9, status, "textCentered");
writeDouble(row, col + 10, r["time"].get<double>(), "time");
writeDouble(row, col + 11, r["time_std"].get<double>(), "time");
hyperparameters = r["hyperparameters"].dump();
if (hyperparameters.size() > hypSize) {
hypSize = hyperparameters.size();
}
writeString(row, col + 12, hyperparameters, "text");
lastResult = r;
totalScore += r["score"].get<double>();
row++;
}
// Set the right column width of hyperparameters with the maximum length
worksheet_set_column(worksheet, 12, 12, hypSize + 5, NULL);
// Show totals if only one dataset is present in the result
if (data["results"].size() == 1) {
for (const std::string& group : { "scores_train", "scores_test", "times_train", "times_test" }) {
row++;
col = 1;
writeString(row, col, group, "text");
for (double item : lastResult[group]) {
std::string style = group.find("scores") != std::string::npos ? "result" : "time";
writeDouble(row, ++col, item, style);
}
}
// Set with of columns to show those totals completely
worksheet_set_column(worksheet, 1, 1, 12, NULL);
for (int i = 2; i < 7; ++i) {
// doesn't work with from col to col, so...
worksheet_set_column(worksheet, i, i, 15, NULL);
}
} else {
footer(totalScore, row);
}
}
void ReportExcel::showSummary()
{
for (const auto& item : summary) {
worksheet_write_string(worksheet, row + 2, 1, item.first.c_str(), styles["summaryStyle"]);
worksheet_write_number(worksheet, row + 2, 2, item.second, styles["summaryStyle"]);
worksheet_merge_range(worksheet, row + 2, 3, row + 2, 5, meaning.at(item.first).c_str(), styles["summaryStyle"]);
row += 1;
}
}
void ReportExcel::footer(double totalScore, int row)
{
showSummary();
row += 4 + summary.size();
auto score = data["score_name"].get<std::string>();
auto best = BestScore::getScore(score);
if (best.first != "") {
worksheet_merge_range(worksheet, row, 1, row, 5, (score + " compared to " + best.first + " .:").c_str(), efectiveStyle("text"));
writeDouble(row, 6, totalScore / best.second, "result");
}
if (!getExistBestFile() && compare) {
worksheet_write_string(worksheet, row + 1, 0, "*** Best Results File not found. Couldn't compare any result!", styles["summaryStyle"]);
}
}
}

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#ifndef REPORTEXCEL_H
#define REPORTEXCEL_H
#include<map>
#include "xlsxwriter.h"
#include "ReportBase.h"
#include "ExcelFile.h"
#include "Colors.h"
namespace platform {
class ReportExcel : public ReportBase, public ExcelFile {
public:
explicit ReportExcel(json data_, bool compare, lxw_workbook* workbook, lxw_worksheet* worksheet = NULL);
private:
void formatColumns();
void createFile();
void createWorksheet();
void closeFile();
void header() override;
void body() override;
void showSummary() override;
void footer(double totalScore, int row);
};
};
#endif // !REPORTEXCEL_H

58
src/Platform/Result.cc Normal file
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@@ -0,0 +1,58 @@
#include "Result.h"
#include "BestScore.h"
#include <filesystem>
#include <fstream>
#include <sstream>
#include "Colors.h"
#include "DotEnv.h"
#include "CLocale.h"
namespace platform {
Result::Result(const std::string& path, const std::string& filename)
: path(path)
, filename(filename)
{
auto data = load();
date = data["date"];
score = 0;
for (const auto& result : data["results"]) {
score += result["score"].get<double>();
}
scoreName = data["score_name"];
auto best = BestScore::getScore(scoreName);
if (best.first != "") {
score /= best.second;
}
title = data["title"];
duration = data["duration"];
model = data["model"];
complete = data["results"].size() > 1;
}
json Result::load() const
{
std::ifstream resultData(path + "/" + filename);
if (resultData.is_open()) {
json data = json::parse(resultData);
return data;
}
throw std::invalid_argument("Unable to open result file. [" + path + "/" + filename + "]");
}
std::string Result::to_string(int maxModel) const
{
auto tmp = ConfigLocale();
std::stringstream oss;
double durationShow = duration > 3600 ? duration / 3600 : duration > 60 ? duration / 60 : duration;
std::string durationUnit = duration > 3600 ? "h" : duration > 60 ? "m" : "s";
oss << date << " ";
oss << std::setw(maxModel) << std::left << model << " ";
oss << std::setw(11) << std::left << scoreName << " ";
oss << std::right << std::setw(11) << std::setprecision(7) << std::fixed << score << " ";
auto completeString = isComplete() ? "C" : "P";
oss << std::setw(1) << " " << completeString << " ";
oss << std::setw(7) << std::setprecision(2) << std::fixed << durationShow << " " << durationUnit << " ";
oss << std::setw(50) << std::left << title << " ";
return oss.str();
}
}

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