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67 Commits

Author SHA1 Message Date
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
77 changed files with 1819 additions and 737 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 **)

2
.gitignore vendored
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@@ -35,3 +35,5 @@ build/
*.dSYM/**
cmake-build*/**
.idea
puml/**
.vscode/settings.json

3
.gitmodules vendored
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@@ -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

17
.vscode/launch.json vendored
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@@ -10,7 +10,7 @@
"-d",
"iris",
"-m",
"KDB",
"TANLd",
"-s",
"271",
"-p",
@@ -25,12 +25,15 @@
"program": "${workspaceFolder}/build/src/Platform/main",
"args": [
"-m",
"SPODELd",
"BoostAODE",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets",
"--stratified",
"-d",
"iris"
"mfeat-morphological",
"--discretize"
// "--hyperparameters",
// "{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "/Users/rmontanana/Code/discretizbench",
},
@@ -45,6 +48,14 @@
],
"cwd": "/Users/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "list",
"program": "${workspaceFolder}/build/src/Platform/list",
"args": [],
"cwd": "/Users/rmontanana/Code/discretizbench",
},
{
"name": "Build & debug active file",
"type": "cppdbg",

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
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@@ -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."
}
]
}

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@@ -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
@@ -30,7 +30,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
option(ENABLE_CLANG_TIDY "Enable to add clang tidy." OFF)
option(ENABLE_TESTING "Unit testing build" OFF)
option(CODE_COVERAGE "Collect coverage from test library" OFF)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
# CMakes modules
# --------------
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
@@ -40,8 +40,7 @@ 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)
@@ -74,7 +73,6 @@ 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)

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@@ -11,23 +11,36 @@ setup: ## Install dependencies for tests and coverage
pip install gcovr; \
fi
dest ?= ../discretizbench
copy: ## Copy binary files to selected folder
@echo "Destination folder: $(dest)"
make build
@echo ">>> Copying files to $(dest)"
@cp build/src/Platform/main $(dest)
@cp build/src/Platform/list $(dest)
@cp build/src/Platform/manage $(dest)
@echo ">>> Done"
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
build: ## Build the main and BayesNetSample
cmake --build build -t main -t BayesNetSample -j 32
cmake --build build -t main -t BayesNetSample -t manage -t list -j 32
clean: ## Clean the debug info
@echo ">>> Cleaning Debug BayesNet ...";
find . -name "*.gcda" -print0 | xargs -0 rm
@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;
cmake --build build -t main -t BayesNetSample -t manage -t list unit_tests -j 32;
@echo ">>> Done";
release: ## Build a Release version of the project
@@ -35,7 +48,7 @@ release: ## Build a Release version of the project
@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;
cmake --build build -t main -t BayesNetSample -t manage -t list -j 32;
@echo ">>> Done";
test: ## Run tests

View File

@@ -2,4 +2,36 @@
Bayesian Network Classifier with libtorch from scratch
## 0. Setup
### libxlswriter
Before compiling BayesNet.
```bash
cd lib/libxlsxwriter
make
sudo make install
```
It has to be installed in /usr/local/lib otherwise CMakeLists.txt has to be modified accordingly
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

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@@ -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 }

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@@ -1 +0,0 @@
null

BIN
diagrams/BayesNet.pdf Executable file

Binary file not shown.

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

1
lib/libxlsxwriter Submodule

Submodule lib/libxlsxwriter added at 44e72c5862

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}")

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@@ -3,13 +3,14 @@
#include <string>
#include <map>
#include <argparse/argparse.hpp>
#include <nlohmann/json.hpp>
#include "ArffFiles.h"
#include "BayesMetrics.h"
#include "CPPFImdlp.h"
#include "Folding.h"
#include "Models.h"
#include "modelRegister.h"
#include <fstream>
using namespace std;
@@ -57,127 +58,173 @@ pair<vector<vector<int>>, vector<int>> extract_indices(vector<int> indices, vect
int main(int argc, char** argv)
{
map<string, bool> datasets = {
{"diabetes", true},
{"ecoli", true},
{"glass", true},
{"iris", true},
{"kdd_JapaneseVowels", false},
{"letter", true},
{"liver-disorders", true},
{"mfeat-factors", true},
};
auto valid_datasets = vector<string>();
transform(datasets.begin(), datasets.end(), back_inserter(valid_datasets),
[](const pair<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) {
if (find(valid_datasets.begin(), valid_datasets.end(), value) != valid_datasets.end()) {
return value;
torch::Tensor weights_ = torch::full({ 10 }, 1.0 / 10, torch::kFloat64);
torch::Tensor y_ = torch::tensor({ 1, 1, 1, 1, 1, 0, 0, 0, 0, 0 }, torch::kInt32);
torch::Tensor ypred = torch::tensor({ 1, 1, 1, 0, 0, 1, 1, 1, 1, 0 }, torch::kInt32);
cout << "Initial weights_: " << endl;
for (int i = 0; i < 10; i++) {
cout << weights_.index({ i }).item<double>() << ", ";
}
throw runtime_error("file must be one of {diabetes, ecoli, glass, iris, kdd_JapaneseVowels, letter, liver-disorders, mfeat-factors}");
cout << "end." << endl;
cout << "y_: " << endl;
for (int i = 0; i < 10; i++) {
cout << y_.index({ i }).item<int>() << ", ";
}
);
program.add_argument("-p", "--path")
.help(" folder where the data files are located, default")
.default_value(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();
if (find(choices.begin(), choices.end(), value) != choices.end()) {
return value;
cout << "end." << endl;
cout << "ypred: " << endl;
for (int i = 0; i < 10; i++) {
cout << ypred.index({ i }).item<int>() << ", ";
}
throw runtime_error("Model must be one of " + platform::Models::instance()->toString());
cout << "end." << endl;
auto mask_wrong = ypred != y_;
auto mask_right = ypred == y_;
auto masked_weights = weights_ * mask_wrong.to(weights_.dtype());
double epsilon_t = masked_weights.sum().item<double>();
cout << "epsilon_t: " << epsilon_t << endl;
double wt = (1 - epsilon_t) / epsilon_t;
cout << "wt: " << wt << endl;
double alpha_t = epsilon_t == 0 ? 1 : 0.5 * log(wt);
cout << "alpha_t: " << alpha_t << endl;
// Step 3.2: Update weights for next classifier
// Step 3.2.1: Update weights of wrong samples
cout << "exp(alpha_t): " << exp(alpha_t) << endl;
cout << "exp(-alpha_t): " << exp(-alpha_t) << endl;
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>();
cout << "totalWeights: " << totalWeights << endl;
cout << "Before normalization: " << endl;
for (int i = 0; i < 10; i++) {
cout << weights_.index({ i }).item<double>() << endl;
}
);
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) {
try {
auto k = stoi(value);
if (k < 2) {
throw runtime_error("Number of folds must be greater than 1");
}
return k;
}
catch (const runtime_error& err) {
throw runtime_error(err.what());
}
catch (...) {
throw runtime_error("Number of folds must be an integer");
}});
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;
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");
complete_file_name = path + file_name + ".arff";
stratified = program.get<bool>("stratified");
tensors = program.get<bool>("tensors");
nFolds = program.get<int>("folds");
seed = program.get<int>("seed");
dump_cpt = program.get<bool>("dumpcpt");
class_last = datasets[file_name];
if (!file_exists(complete_file_name)) {
throw runtime_error("Data File " + path + file_name + ".arff" + " does not exist");
}
}
catch (const exception& err) {
cerr << err.what() << endl;
cerr << program;
exit(1);
weights_ = weights_ / totalWeights;
cout << "After normalization: " << endl;
for (int i = 0; i < 10; i++) {
cout << weights_.index({ i }).item<double>() << endl;
}
// map<string, bool> datasets = {
// {"diabetes", true},
// {"ecoli", true},
// {"glass", true},
// {"iris", true},
// {"kdd_JapaneseVowels", false},
// {"letter", true},
// {"liver-disorders", true},
// {"mfeat-factors", true},
// };
// auto valid_datasets = vector<string>();
// transform(datasets.begin(), datasets.end(), back_inserter(valid_datasets),
// [](const pair<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) {
// if (find(valid_datasets.begin(), valid_datasets.end(), value) != valid_datasets.end()) {
// return value;
// }
// throw runtime_error("file must be one of {diabetes, ecoli, glass, iris, kdd_JapaneseVowels, letter, liver-disorders, mfeat-factors}");
// }
// );
// program.add_argument("-p", "--path")
// .help(" folder where the data files are located, default")
// .default_value(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();
// if (find(choices.begin(), choices.end(), value) != choices.end()) {
// return value;
// }
// throw runtime_error("Model must be one of " + platform::Models::instance()->toString());
// }
// );
// 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) {
// try {
// auto k = stoi(value);
// if (k < 2) {
// throw runtime_error("Number of folds must be greater than 1");
// }
// return k;
// }
// catch (const runtime_error& err) {
// throw runtime_error(err.what());
// }
// catch (...) {
// throw runtime_error("Number of folds must be an integer");
// }});
// 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;
// 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");
// complete_file_name = path + file_name + ".arff";
// stratified = program.get<bool>("stratified");
// tensors = program.get<bool>("tensors");
// nFolds = program.get<int>("folds");
// seed = program.get<int>("seed");
// dump_cpt = program.get<bool>("dumpcpt");
// class_last = datasets[file_name];
// if (!file_exists(complete_file_name)) {
// throw runtime_error("Data File " + path + file_name + ".arff" + " does not exist");
// }
// }
// catch (const exception& err) {
// cerr << err.what() << endl;
// cerr << program;
// exit(1);
// }
/*
* Begin Processing
*/
auto handler = ArffFiles();
handler.load(complete_file_name, class_last);
// Get Dataset X, y
vector<mdlp::samples_t>& X = handler.getX();
mdlp::labels_t& y = handler.getY();
// Get className & Features
auto className = handler.getClassName();
vector<string> features;
auto attributes = handler.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features),
[](const pair<string, 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;
for (auto feature : features) {
states[feature] = vector<int>(maxes[feature]);
}
states[className] = 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;
clf->dump_cpt();
}
auto lines = clf->show();
for (auto line : lines) {
cout << line << endl;
}
cout << "--- Topological Order ---" << endl;
auto order = clf->topological_order();
for (auto name : order) {
cout << name << ", ";
}
cout << "end." << endl;
auto score = clf->score(Xd, y);
cout << "Score: " << score << endl;
// auto handler = ArffFiles();
// handler.load(complete_file_name, class_last);
// // Get Dataset X, y
// vector<mdlp::samples_t>& X = handler.getX();
// mdlp::labels_t& y = handler.getY();
// // Get className & Features
// auto className = handler.getClassName();
// vector<string> features;
// auto attributes = handler.getAttributes();
// transform(attributes.begin(), attributes.end(), back_inserter(features),
// [](const pair<string, 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;
// for (auto feature : features) {
// states[feature] = vector<int>(maxes[feature]);
// }
// states[className] = 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;
// clf->dump_cpt();
// }
// auto lines = clf->show();
// for (auto line : lines) {
// cout << line << endl;
// }
// cout << "--- Topological Order ---" << endl;
// auto order = clf->topological_order();
// for (auto name : order) {
// cout << name << ", ";
// }
// cout << "end." << 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");
@@ -194,11 +241,11 @@ int main(int argc, char** argv)
// Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
// }
// float total_score = 0, total_score_train = 0, score_train, score_test;
// Fold* fold;
// platform::Fold* fold;
// if (stratified)
// fold = new StratifiedKFold(nFolds, y, seed);
// fold = new platform::StratifiedKFold(nFolds, y, seed);
// else
// fold = new KFold(nFolds, y.size(), seed);
// fold = new platform::KFold(nFolds, y.size(), seed);
// for (auto i = 0; i < nFolds; ++i) {
// auto [train, test] = fold->getFold(i);
// cout << "Fold: " << i + 1 << endl;

View File

@@ -2,12 +2,14 @@
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 = vector<double>(n_models, 1.0);
}
vector<string> AODE::graph(const string& title) const
{

View File

@@ -5,7 +5,7 @@
namespace bayesnet {
class AODE : public Ensemble {
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
AODE();
virtual ~AODE() {};

View File

@@ -4,9 +4,9 @@
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 vector<string>& features_, const string& className_, map<string, 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_;
@@ -19,15 +19,16 @@ 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 = 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);

View File

@@ -8,13 +8,13 @@ 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 vector<string>& features_, const string& className_, map<string, vector<int>>& states_) override;
virtual ~AODELd() = default;
vector<string> graph(const string& name = "AODE") const override;
vector<string> graph(const string& name = "AODELd") const override;
static inline string version() { return "0.0.1"; };
};
}

View File

@@ -1,21 +1,25 @@
#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;
virtual BaseClassifier& fit(vector<vector<int>>& X, vector<int>& y, const vector<string>& features, const string& className, map<string, 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 vector<string>& features, const string& className, map<string, vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const vector<string>& features, const string& className, map<string, vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const vector<string>& features, const string& className, map<string, 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;
status_t virtual getStatus() const = 0;
float virtual score(vector<vector<int>>& X, vector<int>& y) = 0;
float virtual score(torch::Tensor& X, torch::Tensor& y) = 0;
int virtual getNumberOfNodes()const = 0;
@@ -23,9 +27,10 @@ namespace bayesnet {
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"; };
const string inline getVersion() const { return "0.2.0"; };
vector<string> virtual topological_order() = 0;
void virtual dump_cpt()const = 0;
virtual void setHyperparameters(nlohmann::json& hyperparameters) = 0;
};
}
#endif

View File

@@ -21,6 +21,45 @@ namespace bayesnet {
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
}
vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, bool ascending, unsigned k)
{
// 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());
}
}
} 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);
}
return featuresKBest;
}
vector<double> Metrics::getScoresKBest() const
{
return scoresKBest;
}
vector<pair<string, string>> Metrics::doCombinations(const vector<string>& source)
{
vector<pair<string, string>> result;
@@ -32,17 +71,17 @@ namespace bayesnet {
}
return result;
}
torch::Tensor Metrics::conditionalEdge()
torch::Tensor Metrics::conditionalEdge(const torch::Tensor& weights)
{
auto result = vector<double>();
auto source = vector<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 +91,9 @@ 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 +110,32 @@ namespace bayesnet {
return matrix;
}
// To use in Python
vector<float> Metrics::conditionalEdgeWeights()
vector<float> Metrics::conditionalEdgeWeights(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();
torch::Tensor featureCounts = secondFeature.bincount(weights);
unordered_map<int, 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;
@@ -115,9 +156,9 @@ 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

View File

@@ -12,16 +12,20 @@ namespace bayesnet {
vector<string> features;
string className;
int classNumStates = 0;
vector<double> scoresKBest;
vector<int> featuresKBest; // sorted indices of the features
double entropy(const Tensor& feature, const Tensor& weights);
double conditionalEntropy(const Tensor& firstFeature, const Tensor& secondFeature, const Tensor& weights);
vector<pair<string, string>> doCombinations(const vector<string>&);
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>&);
Metrics(const torch::Tensor& samples, const vector<string>& features, const string& className, const int classNumStates);
Metrics(const vector<vector<int>>& vsamples, const vector<int>& labels, const vector<string>& features, const string& className, const int classNumStates);
vector<int> SelectKBestWeighted(const torch::Tensor& weights, bool ascending=false, unsigned k = 0);
vector<double> getScoresKBest() const;
double mutualInformation(const Tensor& firstFeature, const Tensor& secondFeature, const Tensor& weights);
vector<float> conditionalEdgeWeights(vector<float>& weights); // To use in Python
Tensor conditionalEdge(const torch::Tensor& weights);
vector<pair<int, int>> maximumSpanningTree(const vector<string>& features, const Tensor& weights, const int root);
};
}

148
src/BayesNet/BoostAODE.cc Normal file
View File

@@ -0,0 +1,148 @@
#include "BoostAODE.h"
#include <set>
#include "BayesMetrics.h"
#include "Colors.h"
#include "Folding.h"
#include <limits.h>
namespace bayesnet {
BoostAODE::BoostAODE() : Ensemble() {}
void BoostAODE::buildModel(const torch::Tensor& weights)
{
// Models shall be built in trainModel
}
void BoostAODE::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid
const vector<string> validKeys = { "repeatSparent", "maxModels", "ascending", "convergence" };
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"];
}
}
void BoostAODE::validationInit()
{
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::trainModel(const torch::Tensor& weights)
{
models.clear();
n_models = 0;
if (maxModels == 0)
maxModels = .1 * n > 10 ? .1 * n : n;
validationInit();
Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
bool exitCondition = false;
unordered_set<int> featuresUsed;
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double delta = 1.0;
double threshold = 1e-4;
int tolerance = 5; // number of times the accuracy can be lower than the threshold
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
// epsiolon 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
unique_ptr<Classifier> model;
auto feature = featureSelection[0];
if (!repeatSparent || featuresUsed.size() < featureSelection.size()) {
bool found = false;
for (auto feat : featureSelection) {
if (find(featuresUsed.begin(), featuresUsed.end(), feat) != featuresUsed.end()) {
continue;
}
found = true;
feature = feat;
break;
}
if (!found) {
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;
}
}
vector<string> BoostAODE::graph(const string& title) const
{
return Ensemble::graph(title);
}
}

25
src/BayesNet/BoostAODE.h Normal file
View File

@@ -0,0 +1,25 @@
#ifndef BOOSTAODE_H
#define BOOSTAODE_H
#include "Ensemble.h"
#include "SPODE.h"
namespace bayesnet {
class BoostAODE : public Ensemble {
public:
BoostAODE();
virtual ~BoostAODE() {};
vector<string> graph(const 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;
void validationInit();
bool repeatSparent = false;
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
};
}
#endif

View File

@@ -1,7 +1,9 @@
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)
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 ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNet mdlp "${TORCH_LIBRARIES}")

View File

@@ -5,7 +5,7 @@ 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 vector<string>& features, const string& className, map<string, vector<int>>& states, const torch::Tensor& weights)
{
this->features = features;
this->className = className;
@@ -13,15 +13,14 @@ 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)
{
try {
@@ -35,19 +34,20 @@ namespace bayesnet {
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 vector<string>& features, const string& className, map<string, 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(vector<vector<int>>& X, vector<int>& y, const vector<string>& features, const string& className, map<string, vector<int>>& states)
{
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, kInt32);
for (int i = 0; i < X.size(); ++i) {
@@ -55,17 +55,27 @@ namespace bayesnet {
}
auto ytmp = torch::tensor(y, 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 vector<string>& features, const string& className, map<string, 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 vector<string>& features, const string& className, map<string, 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 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 invalid_argument("Classifier: X " + to_string(n) + " and features " + 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");
@@ -145,4 +155,18 @@ namespace bayesnet {
{
model.dump_cpt();
}
void Classifier::checkHyperparameters(const vector<string>& validKeys, nlohmann::json& hyperparameters)
{
for (const auto& item : hyperparameters.items()) {
if (find(validKeys.begin(), validKeys.end(), item.key()) == validKeys.end()) {
throw invalid_argument("Hyperparameter " + item.key() + " is not valid");
}
}
}
void Classifier::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid, default is no hyperparameters
const vector<string> validKeys = { };
checkHyperparameters(validKeys, hyperparameters);
}
}

View File

@@ -10,37 +10,42 @@ 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 vector<string>& features, const string& className, map<string, 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;
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 vector<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(vector<vector<int>>& X, vector<int>& y, const vector<string>& features, const string& className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& features, const string& className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const vector<string>& features, const string& className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const vector<string>& features, const string& className, map<string, 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;
status_t getStatus() const override { return status; }
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;
void dump_cpt() const override;
void setHyperparameters(nlohmann::json& hyperparameters) override;
};
}
#endif

View File

@@ -3,9 +3,9 @@
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) {
@@ -17,10 +17,14 @@ namespace bayesnet {
{
auto y_pred_ = y_pred.accessor<int, 2>();
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
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);
@@ -34,7 +38,6 @@ namespace bayesnet {
throw 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;
for (auto i = 0; i < n_models; ++i) {

View File

@@ -14,7 +14,8 @@ namespace bayesnet {
protected:
unsigned n_models;
vector<unique_ptr<Classifier>> models;
void trainModel() override;
vector<double> significanceModels;
void trainModel(const torch::Tensor& weights) override;
vector<int> voting(Tensor& y_pred);
public:
Ensemble();

View File

@@ -4,7 +4,19 @@ 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 vector<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),
@@ -29,13 +41,13 @@ namespace bayesnet {
// where C is the class.
addNodes();
const Tensor& y = dataset.index({ -1, "..." });
vector <float> mi;
vector<double> mi;
for (auto i = 0; i < features.size(); i++) {
Tensor firstFeature = dataset.index({ i, "..." });
mi.push_back(metrics.mutualInformation(firstFeature, y));
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;
// 4. Let the DAG network being constructed, BN, begin with a single

View File

@@ -1,5 +1,6 @@
#ifndef KDB_H
#define KDB_H
#include <torch/torch.h>
#include "Classifier.h"
#include "bayesnetUtils.h"
namespace bayesnet {
@@ -11,10 +12,11 @@ namespace bayesnet {
float theta;
void add_m_edges(int idx, vector<int>& S, Tensor& weights);
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() {};
void setHyperparameters(nlohmann::json& hyperparameters) override;
vector<string> graph(const string& name = "KDB") const override;
};
}

View File

@@ -3,9 +3,9 @@
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 vector<string>& features_, const string& className_, map<string, 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_;

View File

@@ -10,7 +10,7 @@ namespace bayesnet {
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;
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& features, const 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"; };

View File

@@ -3,9 +3,8 @@
#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(vector<string>()), className(""), classNumStates(0), fitted(false), laplaceSmoothing(0) {}
Network::Network(float maxT) : features(vector<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)
{
@@ -104,8 +103,11 @@ namespace bayesnet {
{
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 vector<string>& featureNames, const string& className, const map<string, vector<int>>& states, const torch::Tensor& weights)
{
if (weights.size(0) != n_samples) {
throw invalid_argument("Weights (" + to_string(weights.size(0)) + ") must have the same number of elements as samples (" + 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) + ")");
}
@@ -130,34 +132,35 @@ namespace bayesnet {
void Network::setStates(const map<string, 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 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 vector<string>& featureNames, const string& className, const map<string, 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);
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 vector<string>& featureNames, const string& className, const map<string, 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 vector<vector<int>>& input_data, const vector<int>& labels, const vector<float>& weights_, const vector<string>& featureNames, const string& className, const map<string, 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 map<string, vector<int>>& states, const torch::Tensor& weights)
{
setStates(states);
int maxThreadsRunning = static_cast<int>(std::thread::hardware_concurrency() * maxThreads);
if (maxThreadsRunning < 1) {
maxThreadsRunning = 1;
}
laplaceSmoothing = 1.0 / samples.size(1); // To use in CPT computation
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();
for (auto& node : nodes) {
threads.emplace_back([this, &node, &weights]() {
node.second->computeCPT(samples, features, laplaceSmoothing, weights);
});
++activeThreads;
}
for (auto& thread : threads) {
thread.join();
@@ -343,7 +321,7 @@ 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
@@ -395,7 +373,6 @@ namespace bayesnet {
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) {
@@ -431,6 +408,7 @@ namespace bayesnet {
{
for (auto& node : nodes) {
cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << endl;
cout << node.second->getCPT() << endl;
}
}
}

View File

@@ -13,21 +13,21 @@ namespace bayesnet {
int classNumStates;
vector<string> features; // Including classname
string className;
int laplaceSmoothing = 1;
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 completeFit(const map<string, vector<int>>& states, const torch::Tensor& weights);
void checkFitData(int n_features, int n_samples, int n_samples_y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states, const torch::Tensor& weights);
void setStates(const map<string, 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&);
@@ -39,9 +39,9 @@ namespace bayesnet {
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>>&);
void fit(const vector<vector<int>>& input_data, const vector<int>& labels, const vector<float>& weights, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states);
void fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states);
void fit(const torch::Tensor& samples, const torch::Tensor& weights, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states);
vector<int> predict(const vector<vector<int>>&); // Return mx1 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);
@@ -53,7 +53,7 @@ namespace bayesnet {
vector<string> graph(const string& title) const; // Returns a vector of strings representing the graph in graphviz format
void initialize();
void dump_cpt() const;
inline string version() { return "0.1.0"; }
inline string version() { return "0.2.0"; }
};
}
#endif

View File

@@ -84,7 +84,7 @@ namespace bayesnet {
}
return result;
}
void Node::computeCPT(const torch::Tensor& dataset, const vector<string>& features, const int laplaceSmoothing)
void Node::computeCPT(const torch::Tensor& dataset, const vector<string>& features, const double laplaceSmoothing, const torch::Tensor& weights)
{
dimensions.clear();
// Get dimensions of the CPT
@@ -100,7 +100,7 @@ namespace bayesnet {
}
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());
@@ -111,17 +111,17 @@ namespace bayesnet {
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)
{
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(), 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)

View File

@@ -26,7 +26,7 @@ namespace bayesnet {
vector<Node*>& getParents();
vector<Node*>& getChildren();
torch::Tensor& getCPT();
void computeCPT(const torch::Tensor&, const vector<string>&, const int);
void computeCPT(const torch::Tensor& dataset, const vector<string>& features, const double laplaceSmoothing, const torch::Tensor& weights);
int getNumStates() const;
void setNumStates(int);
unsigned minFill();

View File

@@ -9,6 +9,15 @@ namespace bayesnet {
delete value;
}
}
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<string, vector<int>> Proposal::localDiscretizationProposal(const map<string, vector<int>>& oldStates, Network& model)
{
// order of local discretization is important. no good 0, 1, 2...
@@ -44,15 +53,6 @@ namespace bayesnet {
auto xvf_ptr = Xf.index({ index }).data_ptr<float>();
auto xvf = 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
@@ -65,7 +65,8 @@ namespace bayesnet {
//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;
}

View File

@@ -13,6 +13,7 @@ namespace bayesnet {
Proposal(torch::Tensor& pDataset, vector<string>& features_, 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);

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();

View File

@@ -7,7 +7,7 @@ namespace bayesnet {
private:
int root;
protected:
void buildModel() override;
void buildModel(const torch::Tensor& weights) override;
public:
explicit SPODE(int root);
virtual ~SPODE() {};

View File

@@ -3,9 +3,9 @@
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 vector<string>& features_, const string& className_, map<string, 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_;
@@ -18,12 +18,13 @@ 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 vector<string>& features_, const string& className_, map<string, 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

View File

@@ -9,8 +9,8 @@ namespace bayesnet {
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;
SPODELd& fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& features, const string& className, map<string, vector<int>>& states) override;
SPODELd& fit(torch::Tensor& dataset, const vector<string>& features, const 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"; };

View File

@@ -5,7 +5,7 @@ namespace bayesnet {
TAN::TAN() : Classifier(Network()) {}
void TAN::buildModel()
void TAN::buildModel(const torch::Tensor& weights)
{
// 0. Add all nodes to the model
addNodes();
@@ -15,15 +15,15 @@ namespace bayesnet {
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);
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];

View File

@@ -3,11 +3,10 @@
#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() {};

View File

@@ -3,9 +3,9 @@
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 vector<string>& features_, const string& className_, map<string, 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_;

View File

@@ -10,7 +10,7 @@ namespace bayesnet {
public:
TANLd();
virtual ~TANLd() = default;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& features, const 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"; };

View File

@@ -4,7 +4,7 @@ namespace bayesnet {
using namespace std;
using namespace torch;
// Return the indices in descending order
vector<int> argsort(vector<float>& nums)
vector<int> argsort(vector<double>& nums)
{
int n = nums.size();
vector<int> indices(n);

View File

@@ -5,7 +5,7 @@
namespace bayesnet {
using namespace std;
using namespace torch;
vector<int> argsort(vector<float>& nums);
vector<int> argsort(vector<double>& nums);
vector<vector<int>> tensorToVector(Tensor& tensor);
}
#endif //BAYESNET_UTILS_H

View File

@@ -4,7 +4,13 @@ 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)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc Models.cc ReportConsole.cc ReportBase.cc)
add_executable(manage manage.cc Results.cc ReportConsole.cc ReportExcel.cc ReportBase.cc Datasets.cc platformUtils.cc)
add_executable(list list.cc platformUtils Datasets.cc)
target_link_libraries(main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(manage "${TORCH_LIBRARIES}")
if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux")
target_link_libraries(manage "${TORCH_LIBRARIES}" libxlsxwriter.so ArffFiles mdlp stdc++fs)
else()
target_link_libraries(manage "${TORCH_LIBRARIES}" libxlsxwriter.so ArffFiles mdlp)
endif()
target_link_libraries(list ArffFiles mdlp "${TORCH_LIBRARIES}")

View File

@@ -1,6 +1,7 @@
#include "Datasets.h"
#include "platformUtils.h"
#include "ArffFiles.h"
#include <fstream>
namespace platform {
void Datasets::load()
{
@@ -24,75 +25,110 @@ namespace platform {
transform(datasets.begin(), datasets.end(), back_inserter(result), [](const auto& d) { return d.first; });
return result;
}
vector<string> Datasets::getFeatures(string name)
vector<string> Datasets::getFeatures(const 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.");
}
}
map<string, vector<int>> Datasets::getStates(string name)
map<string, vector<int>> Datasets::getStates(const 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.");
}
}
string Datasets::getClassName(string name)
void Datasets::loadDataset(const string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getClassName();
if (datasets.at(name)->isLoaded()) {
return;
} else {
datasets.at(name)->load();
}
}
string Datasets::getClassName(const string& name) const
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getClassName();
} else {
throw invalid_argument("Dataset not loaded.");
}
}
int Datasets::getNSamples(string name)
int Datasets::getNSamples(const string& name) const
{
if (datasets[name]->isLoaded()) {
return datasets[name]->getNSamples();
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getNSamples();
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<float>>&, vector<int>&> Datasets::getVectors(string name)
int Datasets::getNClasses(const 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 *max_element(yv.begin(), yv.end()) + 1;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
vector<int> Datasets::getClassesCounts(const string& name) const
{
if (datasets.at(name)->isLoaded()) {
auto [Xv, yv] = datasets.at(name)->getVectors();
vector<int> counts(*max_element(yv.begin(), yv.end()) + 1);
for (auto y : yv) {
counts[y]++;
}
return counts;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<float>>&, vector<int>&> Datasets::getVectors(const string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getVectors();
}
pair<vector<vector<int>>&, vector<int>&> Datasets::getVectorsDiscretized(string name)
pair<vector<vector<int>>&, vector<int>&> Datasets::getVectorsDiscretized(const 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 string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getTensors();
}
bool Datasets::isDataset(const string& name)
bool Datasets::isDataset(const 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()
string Dataset::getName() const
{
return name;
}
string Dataset::getClassName()
string Dataset::getClassName() const
{
return className;
}
vector<string> Dataset::getFeatures()
vector<string> Dataset::getFeatures() const
{
if (loaded) {
return features;
@@ -100,7 +136,7 @@ namespace platform {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNFeatures()
int Dataset::getNFeatures() const
{
if (loaded) {
return n_features;
@@ -108,7 +144,7 @@ namespace platform {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNSamples()
int Dataset::getNSamples() const
{
if (loaded) {
return n_samples;
@@ -116,7 +152,7 @@ namespace platform {
throw invalid_argument("Dataset not loaded.");
}
}
map<string, vector<int>> Dataset::getStates()
map<string, vector<int>> Dataset::getStates() const
{
if (loaded) {
return states;
@@ -177,10 +213,11 @@ namespace platform {
{
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);
auto item = states.at(features[i]);
iota(begin(item), end(item), 0);
}
states[className] = vector<int>(*max_element(yv.begin(), yv.end()) + 1);
iota(begin(states[className]), end(states[className]), 0);
iota(begin(states.at(className)), end(states.at(className)), 0);
}
void Dataset::load_arff()
{

View File

@@ -29,15 +29,15 @@ namespace platform {
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();
string getName() const;
string getClassName() const;
vector<string> getFeatures() const;
map<string, vector<int>> getStates() const;
pair<vector<vector<float>>&, vector<int>&> getVectors();
pair<vector<vector<int>>&, vector<int>&> getVectorsDiscretized();
pair<torch::Tensor&, torch::Tensor&> getTensors();
int getNFeatures();
int getNSamples();
int getNFeatures() const;
int getNSamples() const;
void load();
const bool inline isLoaded() const { return loaded; };
};
@@ -51,14 +51,17 @@ namespace platform {
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);
vector<string> getFeatures(const string& name) const;
int getNSamples(const string& name) const;
string getClassName(const string& name) const;
int getNClasses(const string& name);
vector<int> getClassesCounts(const string& name) const;
map<string, vector<int>> getStates(const string& name) const;
pair<vector<vector<float>>&, vector<int>&> getVectors(const string& name);
pair<vector<vector<int>>&, vector<int>&> getVectorsDiscretized(const string& name);
pair<torch::Tensor&, torch::Tensor&> getTensors(const string& name);
bool isDataset(const string& name) const;
void loadDataset(const string& name) const;
};
};

View File

@@ -1,8 +1,8 @@
#include "Experiment.h"
#include "Datasets.h"
#include "Models.h"
#include "Report.h"
#include "ReportConsole.h"
#include <fstream>
namespace platform {
using json = nlohmann::json;
string get_date()
@@ -25,6 +25,7 @@ namespace platform {
oss << std::put_time(timeinfo, "%H:%M:%S");
return oss.str();
}
Experiment::Experiment() : hyperparameters(json::parse("{}")) {}
string Experiment::get_file_name()
{
string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
@@ -90,7 +91,7 @@ namespace platform {
void Experiment::report()
{
json data = build_json();
Report report(data);
ReportConsole report(data);
report.show();
}
@@ -110,6 +111,26 @@ namespace platform {
}
}
string getColor(bayesnet::status_t status)
{
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 string& color, const string& phase)
{
string prefix = phase == "a" ? "" : "\b\b\b\b";
cout << prefix << color << fold << Colors::RESET() << "(" << color << phase << Colors::RESET() << ")" << flush;
}
void Experiment::cross_validation(const string& path, const string& fileName)
{
auto datasets = platform::Datasets(path, discretized, platform::ARFF);
@@ -124,6 +145,8 @@ namespace platform {
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 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);
@@ -144,6 +167,10 @@ 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);
@@ -152,24 +179,31 @@ 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;
showProgress(nfold + 1, getColor(clf->getStatus()), "a");
// Train model
clf->fit(X_train, y_train, features, className, states);
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
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;
cout << "\b\b\b, " << flush;
// Store results and times in 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++;
clf.reset();
}
cout << "end. " << flush;
delete fold;
@@ -177,6 +211,7 @@ namespace platform {
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

@@ -29,7 +29,8 @@ namespace platform {
};
class Result {
private:
string dataset, hyperparameters, model_version;
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 };
@@ -37,7 +38,7 @@ namespace platform {
public:
Result() = default;
Result& setDataset(const string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const string& hyperparameters) { this->hyperparameters = hyperparameters; 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; }
@@ -59,7 +60,7 @@ namespace platform {
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 json& getHyperparameters() const { return hyperparameters; }
const int getSamples() const { return samples; }
const int getFeatures() const { return features; }
const int getClasses() const { return classes; }
@@ -85,11 +86,12 @@ namespace platform {
bool discretized{ false }, stratified{ false };
vector<Result> results;
vector<int> randomSeeds;
json hyperparameters = "{}";
int nfolds{ 0 };
float duration{ 0 };
json build_json();
public:
Experiment() = default;
Experiment();
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; }
@@ -103,6 +105,7 @@ namespace platform {
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; }
Experiment& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
string get_file_name();
void save(const string& path);
void cross_validation(const string& path, const string& fileName);

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@@ -1,6 +1,7 @@
#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;
@@ -93,3 +94,4 @@ pair<vector<int>, vector<int>> StratifiedKFold::getFold(int nFold)
}
return { train_indices, test_indices };
}
}

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@@ -4,7 +4,7 @@
#include <vector>
#include <random>
using namespace std;
namespace platform {
class Fold {
protected:
int k;
@@ -34,4 +34,5 @@ public:
StratifiedKFold(int k, torch::Tensor& y, int seed = -1);
pair<vector<int>, vector<int>> getFold(int nFold) override;
};
}
#endif

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@@ -26,7 +26,7 @@ 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;
}

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@@ -10,6 +10,7 @@
#include "KDBLd.h"
#include "SPODELd.h"
#include "AODELd.h"
#include "BoostAODE.h"
namespace platform {
class Models {
private:

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@@ -1,10 +1,12 @@
#ifndef PATHS_H
#define PATHS_H
#include <string>
namespace platform {
class Paths {
public:
static std::string datasets() { return "datasets/"; }
static std::string results() { return "results/"; }
static std::string excel() { return "excel/"; }
};
}
#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

107
src/Platform/ReportBase.cc Normal file
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@@ -0,0 +1,107 @@
#include <sstream>
#include <locale>
#include "Datasets.h"
#include "ReportBase.h"
#include "BestResult.h"
namespace platform {
ReportBase::ReportBase(json data_, bool compare) : data(data_), compare(compare), margin(0.1)
{
stringstream oss;
oss << "Better than ZeroR + " << 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()}
};
}
string ReportBase::fromVector(const string& key)
{
stringstream oss;
string sep = "";
oss << "[";
for (auto& item : data[key]) {
oss << sep << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
string ReportBase::fVector(const string& title, const json& data, const int width, const int precision)
{
stringstream oss;
string sep = "";
oss << title << "[";
for (const auto& item : data) {
oss << sep << fixed << setw(width) << setprecision(precision) << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
void ReportBase::show()
{
header();
body();
}
string ReportBase::compareResult(const string& dataset, double result)
{
string status = " ";
if (compare) {
double best = bestResult(dataset, data["model"].get<string>());
if (result == best) {
status = Symbols::equal_best;
} else if (result > best) {
status = Symbols::better_best;
}
} else {
if (data["score_name"].get<string>() == "accuracy") {
auto dt = Datasets(Paths::datasets(), false);
dt.loadDataset(dataset);
auto numClasses = dt.getNClasses(dataset);
if (numClasses == 2) {
vector<int> distribution = dt.getClassesCounts(dataset);
double nSamples = dt.getNSamples(dataset);
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 string& dataset, const string& model)
{
double value = 0.0;
if (bestResults.size() == 0) {
// try to load the best results
string score = data["score_name"];
replace(score.begin(), score.end(), '_', '-');
string fileName = "best_results_" + score + "_" + model + ".json";
ifstream resultData(Paths::results() + "/" + fileName);
if (resultData.is_open()) {
bestResults = json::parse(resultData);
}
}
try {
value = bestResults.at(dataset).at(0);
}
catch (exception) {
value = 1.0;
}
return value;
}
}

44
src/Platform/ReportBase.h Normal file
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@@ -0,0 +1,44 @@
#ifndef REPORTBASE_H
#define REPORTBASE_H
#include <string>
#include <iostream>
#include "Paths.h"
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
using namespace std;
class Symbols {
public:
inline static const string check_mark{ "\u2714" };
inline static const string exclamation{ "\u2757" };
inline static const string black_star{ "\u2605" };
inline static const string cross{ "\u2717" };
inline static const string upward_arrow{ "\u27B6" };
inline static const string down_arrow{ "\u27B4" };
inline static const string equal_best{ check_mark };
inline static const string better_best{ black_star };
};
class ReportBase {
public:
explicit ReportBase(json data_, bool compare);
virtual ~ReportBase() = default;
void show();
protected:
json data;
string fromVector(const string& key);
string fVector(const string& title, const json& data, const int width, const int precision);
virtual void header() = 0;
virtual void body() = 0;
virtual void showSummary() = 0;
string compareResult(const string& dataset, double result);
map<string, int> summary;
double margin;
map<string, string> meaning;
private:
double bestResult(const string& dataset, const string& model);
bool compare;
json bestResults;
};
};
#endif

View File

@@ -0,0 +1,109 @@
#include <sstream>
#include <locale>
#include "ReportConsole.h"
#include "BestResult.h"
namespace platform {
struct separated : numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
string do_grouping() const { return "\03"; }
};
string ReportConsole::headerLine(const string& text, int utf = 0)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + string(n + utf, ' ') + "*\n";
}
void ReportConsole::header()
{
locale mylocale(cout.getloc(), new separated);
locale::global(mylocale);
cout.imbue(mylocale);
stringstream oss;
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"));
oss << "Execution took " << setprecision(2) << fixed << data["duration"].get<float>() << " seconds, " << data["duration"].get<float>() / 3600 << " hours, on " << data["platform"].get<string>();
cout << headerLine(oss.str());
cout << headerLine("Score is " + data["score_name"].get<string>());
cout << string(MAXL, '*') << endl;
cout << endl;
}
void ReportConsole::body()
{
cout << Colors::GREEN() << " # Dataset Sampl. Feat. Cls Nodes Edges States Score Time Hyperparameters" << endl;
cout << "=== ========================= ====== ===== === ========= ========= ========= =============== =================== ====================" << 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();
cout << color;
cout << setw(3) << index++ << " ";
cout << setw(25) << 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(9) << setprecision(2) << fixed << r["nodes"].get<float>() << " ";
cout << setw(9) << setprecision(2) << fixed << r["leaves"].get<float>() << " ";
cout << setw(9) << 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>();
const string status = compareResult(r["dataset"].get<string>(), r["score"].get<double>());
cout << status;
cout << setw(12) << 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 || selectedIndex != -1) {
cout << string(MAXL, '*') << endl;
cout << headerLine(fVector("Train scores: ", lastResult["scores_train"], 14, 12));
cout << headerLine(fVector("Test scores: ", lastResult["scores_test"], 14, 12));
cout << headerLine(fVector("Train times: ", lastResult["times_train"], 10, 3));
cout << headerLine(fVector("Test times: ", lastResult["times_test"], 10, 3));
cout << string(MAXL, '*') << endl;
} else {
footer(totalScore);
}
}
void ReportConsole::showSummary()
{
for (const auto& item : summary) {
stringstream oss;
oss << setw(3) << left << item.first;
oss << setw(3) << right << item.second << " ";
oss << left << meaning.at(item.first);
cout << headerLine(oss.str(), 2);
}
}
void ReportConsole::footer(double totalScore)
{
cout << Colors::MAGENTA() << string(MAXL, '*') << endl;
showSummary();
auto score = data["score_name"].get<string>();
if (score == BestResult::scoreName()) {
stringstream oss;
oss << score << " compared to " << BestResult::title() << " .: " << totalScore / BestResult::score();
cout << headerLine(oss.str());
}
cout << string(MAXL, '*') << endl << Colors::RESET();
}
}

View File

@@ -0,0 +1,24 @@
#ifndef REPORTCONSOLE_H
#define REPORTCONSOLE_H
#include <string>
#include <iostream>
#include "ReportBase.h"
#include "Colors.h"
namespace platform {
using namespace std;
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;
string headerLine(const string& text, int utf);
void header() override;
void body() override;
void footer(double totalScore);
void showSummary();
};
};
#endif

330
src/Platform/ReportExcel.cc Normal file
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@@ -0,0 +1,330 @@
#include <sstream>
#include <locale>
#include "ReportExcel.h"
#include "BestResult.h"
namespace platform {
struct separated : numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
string do_grouping() const { return "\03"; }
};
ReportExcel::ReportExcel(json data_, bool compare, lxw_workbook* workbook) : ReportBase(data_, compare), row(0), workbook(workbook)
{
normalSize = 14; //font size for report body
colorTitle = 0xB1A0C7;
colorOdd = 0xDCE6F1;
colorEven = 0xFDE9D9;
createFile();
}
lxw_workbook* ReportExcel::getWorkbook()
{
return workbook;
}
lxw_format* ReportExcel::efectiveStyle(const string& style)
{
lxw_format* efectiveStyle;
if (style == "") {
efectiveStyle = NULL;
} else {
string suffix = row % 2 ? "_odd" : "_even";
efectiveStyle = styles.at(style + suffix);
}
return efectiveStyle;
}
void ReportExcel::writeString(int row, int col, const string& text, const string& style)
{
worksheet_write_string(worksheet, row, col, text.c_str(), efectiveStyle(style));
}
void ReportExcel::writeInt(int row, int col, const int number, const string& style)
{
worksheet_write_number(worksheet, row, col, number, efectiveStyle(style));
}
void ReportExcel::writeDouble(int row, int col, const double number, const string& style)
{
worksheet_write_number(worksheet, row, col, number, efectiveStyle(style));
}
void ReportExcel::formatColumns()
{
worksheet_freeze_panes(worksheet, 6, 1);
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::addColor(lxw_format* style, bool odd)
{
uint32_t efectiveColor = odd ? colorEven : colorOdd;
format_set_bg_color(style, lxw_color_t(efectiveColor));
}
void ReportExcel::createStyle(const 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 ReportExcel::createFormats()
{
auto styleNames = { "text", "textCentered", "bodyHeader", "result", "time", "ints", "floats" };
lxw_format* style;
for (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;
}
void ReportExcel::setProperties()
{
char line[data["title"].get<string>().size() + 1];
strcpy(line, data["title"].get<string>().c_str());
lxw_doc_properties properties = {
.title = line,
.subject = "Machine learning results",
.author = "Ricardo Montañana Gómez",
.manager = "Dr. J. A. Gámez, Dr. J. M. Puerta",
.company = "UCLM",
.comments = "Created with libxlsxwriter and c++",
};
workbook_set_properties(workbook, &properties);
}
void ReportExcel::createFile()
{
if (workbook == NULL) {
workbook = workbook_new((Paths::excel() + fileName).c_str());
}
const string name = data["model"].get<string>();
string suffix = "";
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 = to_string(++num);
} else {
worksheet = workbook_add_worksheet(workbook, efectiveName.c_str());
break;
}
if (num > 100) {
throw invalid_argument("Couldn't create sheet " + efectiveName);
}
}
cout << "Adding sheet " << efectiveName << " to " << Paths::excel() + fileName << endl;
setProperties();
createFormats();
formatColumns();
}
void ReportExcel::closeFile()
{
workbook_close(workbook);
}
void ReportExcel::header()
{
locale mylocale(cout.getloc(), new separated);
locale::global(mylocale);
cout.imbue(mylocale);
stringstream oss;
string message = data["model"].get<string>() + " ver. " + data["version"].get<string>() + " " +
data["language"].get<string>() + " ver. " + data["language_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>();
worksheet_merge_range(worksheet, 0, 0, 0, 12, message.c_str(), styles["headerFirst"]);
worksheet_merge_range(worksheet, 1, 0, 1, 12, data["title"].get<string>().c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 0, 3, 0, ("Score is " + data["score_name"].get<string>()).c_str(), styles["headerRest"]);
worksheet_merge_range(worksheet, 2, 1, 3, 3, "Execution time", styles["headerRest"]);
oss << setprecision(2) << 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 << setprecision(2) << 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<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 = vector<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;
string hyperparameters;
for (const auto& r : data["results"]) {
writeString(row, col, r["dataset"].get<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 string status = compareResult(r["dataset"].get<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");
try {
hyperparameters = r["hyperparameters"].get<string>();
}
catch (const exception& err) {
stringstream oss;
oss << r["hyperparameters"];
hyperparameters = oss.str();
}
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 string& group : { "scores_train", "scores_test", "times_train", "times_test" }) {
row++;
col = 1;
writeString(row, col, group, "text");
for (double item : lastResult[group]) {
string style = group.find("scores") != 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<string>();
if (score == BestResult::scoreName()) {
worksheet_merge_range(worksheet, row, 1, row, 5, (score + " compared to " + BestResult::title() + " .:").c_str(), efectiveStyle("text"));
writeDouble(row, 6, totalScore / BestResult::score(), "result");
}
}
}

View File

@@ -0,0 +1,42 @@
#ifndef REPORTEXCEL_H
#define REPORTEXCEL_H
#include<map>
#include "xlsxwriter.h"
#include "ReportBase.h"
#include "Colors.h"
namespace platform {
using namespace std;
const int MAXLL = 128;
class ReportExcel : public ReportBase {
public:
explicit ReportExcel(json data_, bool compare, lxw_workbook* workbook);
lxw_workbook* getWorkbook();
private:
void writeString(int row, int col, const string& text, const string& style = "");
void writeInt(int row, int col, const int number, const string& style = "");
void writeDouble(int row, int col, const double number, const string& style = "");
void formatColumns();
void createFormats();
void setProperties();
void createFile();
void closeFile();
void showSummary();
lxw_workbook* workbook;
lxw_worksheet* worksheet;
map<string, lxw_format*> styles;
int row;
int normalSize; //font size for report body
uint32_t colorTitle;
uint32_t colorOdd;
uint32_t colorEven;
const string fileName = "some_results.xlsx";
void header() override;
void body() override;
void footer(double totalScore, int row);
void createStyle(const string& name, lxw_format* style, bool odd);
void addColor(lxw_format* style, bool odd);
lxw_format* efectiveStyle(const string& name);
};
};
#endif // !REPORTEXCEL_H

View File

@@ -1,7 +1,8 @@
#include <filesystem>
#include "platformUtils.h"
#include "Results.h"
#include "Report.h"
#include "ReportConsole.h"
#include "ReportExcel.h"
#include "BestResult.h"
#include "Colors.h"
namespace platform {
@@ -22,6 +23,7 @@ namespace platform {
title = data["title"];
duration = data["duration"];
model = data["model"];
complete = data["results"].size() > 1;
}
json Result::load() const
{
@@ -40,7 +42,7 @@ namespace platform {
if (filename.find(".json") != string::npos && filename.find("results_") == 0) {
auto result = Result(path, filename);
bool addResult = true;
if (model != "any" && result.getModel() != model || scoreName != "any" && scoreName != result.getScoreName())
if (model != "any" && result.getModel() != model || scoreName != "any" && scoreName != result.getScoreName() || complete && !result.isComplete() || partial && result.isComplete())
addResult = false;
if (addResult)
files.push_back(result);
@@ -54,6 +56,8 @@ namespace platform {
oss << setw(12) << left << model << " ";
oss << setw(11) << left << scoreName << " ";
oss << right << setw(11) << setprecision(7) << fixed << score << " ";
auto completeString = isComplete() ? "C" : "P";
oss << setw(1) << " " << completeString << " ";
oss << setw(9) << setprecision(3) << fixed << duration << " ";
oss << setw(50) << left << title << " ";
return oss.str();
@@ -62,9 +66,15 @@ namespace platform {
{
cout << Colors::GREEN() << "Results found: " << files.size() << endl;
cout << "-------------------" << endl;
if (complete) {
cout << Colors::MAGENTA() << "Only listing complete results" << endl;
}
if (partial) {
cout << Colors::MAGENTA() << "Only listing partial results" << endl;
}
auto i = 0;
cout << " # Date Model Score Name Score Duration Title" << endl;
cout << "=== ========== ============ =========== =========== ========= =============================================================" << endl;
cout << Colors::GREEN() << " # Date Model Score Name Score C/P Duration Title" << endl;
cout << "=== ========== ============ =========== =========== === ========= =============================================================" << endl;
bool odd = true;
for (const auto& result : files) {
auto color = odd ? Colors::BLUE() : Colors::CYAN();
@@ -94,21 +104,51 @@ namespace platform {
cout << "Invalid index" << endl;
return -1;
}
void Results::report(const int index) const
void Results::report(const int index, const bool excelReport)
{
cout << Colors::YELLOW() << "Reporting " << files.at(index).getFilename() << endl;
auto data = files.at(index).load();
Report report(data);
report.show();
if (excelReport) {
ReportExcel reporter(data, compare, workbook);
reporter.show();
openExcel = true;
workbook = reporter.getWorkbook();
} else {
ReportConsole reporter(data, compare);
reporter.show();
}
}
void Results::showIndex(const int index, const int idx) const
{
auto data = files.at(index).load();
if (idx < 0 or idx >= static_cast<int>(data["results"].size())) {
cout << "Invalid index" << endl;
return;
}
cout << Colors::YELLOW() << "Showing " << files.at(index).getFilename() << endl;
ReportConsole reporter(data, compare, idx);
reporter.show();
}
void Results::menu()
{
char option;
int index;
bool finished = false;
string filename, line, options = "qldhsr";
string color, context;
string filename, line, options = "qldhsre";
while (!finished) {
cout << Colors::RESET() << "Choose option (quit='q', list='l', delete='d', hide='h', sort='s', report='r'): ";
if (indexList) {
color = Colors::GREEN();
context = " (quit='q', list='l', delete='d', hide='h', sort='s', report='r', excel='e'): ";
options = "qldhsre";
} else {
color = Colors::MAGENTA();
context = " (quit='q', list='l'): ";
options = "ql";
}
cout << Colors::RESET() << color;
cout << "Choose option " << context;
getline(cin, line);
if (line.size() == 0)
continue;
@@ -119,12 +159,23 @@ namespace platform {
}
option = line[0];
} else {
index = stoi(line);
if (all_of(line.begin(), line.end(), ::isdigit)) {
int idx = stoi(line);
if (indexList) {
// The value is about the files list
index = idx;
if (index >= 0 && index < files.size()) {
report(index);
} else {
cout << "Invalid option" << endl;
report(index, false);
indexList = false;
continue;
}
} else {
// The value is about the result showed on screen
showIndex(index, idx);
continue;
}
}
cout << "Invalid option" << endl;
continue;
}
switch (option) {
@@ -133,6 +184,7 @@ namespace platform {
break;
case 'l':
show();
indexList = true;
break;
case 'd':
index = getIndex("delete");
@@ -144,6 +196,7 @@ namespace platform {
files.erase(files.begin() + index);
cout << "File: " + filename + " deleted!" << endl;
show();
indexList = true;
break;
case 'h':
index = getIndex("hide");
@@ -155,16 +208,26 @@ namespace platform {
files.erase(files.begin() + index);
show();
menu();
indexList = true;
break;
case 's':
sortList();
indexList = true;
show();
break;
case 'r':
index = getIndex("report");
if (index == -1)
break;
report(index);
indexList = false;
report(index, false);
break;
case 'e':
index = getIndex("excel");
if (index == -1)
break;
indexList = true;
report(index, true);
break;
default:
cout << "Invalid option" << endl;
@@ -231,8 +294,12 @@ namespace platform {
cout << "No results found!" << endl;
exit(0);
}
sortDate();
show();
menu();
if (openExcel) {
workbook_close(workbook);
}
cout << "Done!" << endl;
}

View File

@@ -1,5 +1,6 @@
#ifndef RESULTS_H
#define RESULTS_H
#include "xlsxwriter.h"
#include <map>
#include <vector>
#include <string>
@@ -20,6 +21,7 @@ namespace platform {
double getDuration() const { return duration; };
string getModel() const { return model; };
string getScoreName() const { return scoreName; };
bool isComplete() const { return complete; };
private:
string path;
string filename;
@@ -29,20 +31,32 @@ namespace platform {
double duration;
string model;
string scoreName;
bool complete;
};
class Results {
public:
Results(const string& path, const int max, const string& model, const string& score) : path(path), max(max), model(model), scoreName(score) { load(); };
Results(const string& path, const int max, const string& model, const string& score, bool complete, bool partial, bool compare) :
path(path), max(max), model(model), scoreName(score), complete(complete), partial(partial), compare(compare)
{
load();
};
void manage();
private:
string path;
int max;
string model;
string scoreName;
bool complete;
bool partial;
bool indexList = true;
bool openExcel = false;
bool compare;
lxw_workbook* workbook = NULL;
vector<Result> files;
void load(); // Loads the list of results
void show() const;
void report(const int index) const;
void report(const int index, const bool excelReport);
void showIndex(const int index, const int idx) const;
int getIndex(const string& intent) const;
void menu();
void sortList();

57
src/Platform/list.cc Normal file
View File

@@ -0,0 +1,57 @@
#include <iostream>
#include <locale>
#include "Paths.h"
#include "Colors.h"
#include "Datasets.h"
using namespace std;
const int BALANCE_LENGTH = 75;
struct separated : numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
string do_grouping() const { return "\03"; }
};
void outputBalance(const string& balance)
{
auto temp = string(balance);
while (temp.size() > BALANCE_LENGTH - 1) {
auto part = temp.substr(0, BALANCE_LENGTH);
cout << part << endl;
cout << setw(48) << " ";
temp = temp.substr(BALANCE_LENGTH);
}
cout << temp << endl;
}
int main(int argc, char** argv)
{
auto data = platform::Datasets(platform::Paths().datasets(), false);
locale mylocale(cout.getloc(), new separated);
locale::global(mylocale);
cout.imbue(mylocale);
cout << Colors::GREEN() << "Dataset Sampl. Feat. Cls. Balance" << endl;
string balanceBars = string(BALANCE_LENGTH, '=');
cout << "============================== ====== ===== === " << balanceBars << endl;
bool odd = true;
for (const auto& dataset : data.getNames()) {
auto color = odd ? Colors::CYAN() : Colors::BLUE();
cout << color << setw(30) << left << dataset << " ";
data.loadDataset(dataset);
auto nSamples = data.getNSamples(dataset);
cout << setw(6) << right << nSamples << " ";
cout << setw(5) << right << data.getFeatures(dataset).size() << " ";
cout << setw(3) << right << data.getNClasses(dataset) << " ";
stringstream oss;
string sep = "";
for (auto number : data.getClassesCounts(dataset)) {
oss << sep << setprecision(2) << fixed << (float)number / nSamples * 100.0 << "% (" << number << ")";
sep = " / ";
}
outputBalance(oss.str());
odd = !odd;
}
cout << Colors::RESET() << endl;
return 0;
}

View File

@@ -1,5 +1,6 @@
#include <iostream>
#include <argparse/argparse.hpp>
#include <nlohmann/json.hpp>
#include "platformUtils.h"
#include "Experiment.h"
#include "Datasets.h"
@@ -10,12 +11,14 @@
using namespace std;
using json = nlohmann::json;
argparse::ArgumentParser manageArguments(int argc, char** argv)
{
auto env = platform::DotEnv();
argparse::ArgumentParser program("main");
program.add_argument("-d", "--dataset").default_value("").help("Dataset file name");
program.add_argument("--hyperparameters").default_value("{}").help("Hyperparamters passed to the model in Experiment");
program.add_argument("-p", "--path")
.help("folder where the data files are located, default")
.default_value(string{ platform::Paths::datasets() });
@@ -31,6 +34,7 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
);
program.add_argument("--title").default_value("").help("Experiment title");
program.add_argument("--discretize").help("Discretize input dataset").default_value((bool)stoi(env.get("discretize"))).implicit_value(true);
program.add_argument("--save").help("Save result (always save if no dataset is supplied)").default_value(false).implicit_value(true);
program.add_argument("--stratified").help("If Stratified KFold is to be done").default_value((bool)stoi(env.get("stratified"))).implicit_value(true);
program.add_argument("-f", "--folds").help("Number of folds").default_value(stoi(env.get("n_folds"))).scan<'i', int>().action([](const string& value) {
try {
@@ -59,6 +63,8 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
auto seeds = program.get<vector<int>>("seeds");
auto complete_file_name = path + file_name + ".arff";
auto title = program.get<string>("title");
auto hyperparameters = program.get<string>("hyperparameters");
auto saveResults = program.get<bool>("save");
if (title == "" && file_name == "") {
throw runtime_error("title is mandatory if dataset is not provided");
}
@@ -74,7 +80,6 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
int main(int argc, char** argv)
{
auto program = manageArguments(argc, argv);
bool saveResults = false;
auto file_name = program.get<string>("dataset");
auto path = program.get<string>("path");
auto model_name = program.get<string>("model");
@@ -82,9 +87,11 @@ int main(int argc, char** argv)
auto stratified = program.get<bool>("stratified");
auto n_folds = program.get<int>("folds");
auto seeds = program.get<vector<int>>("seeds");
auto hyperparameters = program.get<string>("hyperparameters");
vector<string> filesToTest;
auto datasets = platform::Datasets(path, true, platform::ARFF);
auto title = program.get<string>("title");
auto saveResults = program.get<bool>("save");
if (file_name != "") {
if (!datasets.isDataset(file_name)) {
cerr << "Dataset " << file_name << " not found" << endl;
@@ -95,7 +102,7 @@ int main(int argc, char** argv)
}
filesToTest.push_back(file_name);
} else {
filesToTest = platform::Datasets(path, true, platform::ARFF).getNames();
filesToTest = datasets.getNames();
saveResults = true;
}
/*
@@ -103,9 +110,10 @@ int main(int argc, char** argv)
*/
auto env = platform::DotEnv();
auto experiment = platform::Experiment();
experiment.setTitle(title).setLanguage("cpp").setLanguageVersion("1.0.0");
experiment.setTitle(title).setLanguage("cpp").setLanguageVersion("14.0.3");
experiment.setDiscretized(discretize_dataset).setModel(model_name).setPlatform(env.get("platform"));
experiment.setStratified(stratified).setNFolds(n_folds).setScoreName("accuracy");
experiment.setHyperparameters(json::parse(hyperparameters));
for (auto seed : seeds) {
experiment.addRandomSeed(seed);
}
@@ -113,9 +121,9 @@ int main(int argc, char** argv)
timer.start();
experiment.go(filesToTest, path);
experiment.setDuration(timer.getDuration());
if (saveResults)
if (saveResults) {
experiment.save(platform::Paths::results());
else
}
experiment.report();
cout << "Done!" << endl;
return 0;

View File

@@ -12,6 +12,9 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
program.add_argument("-n", "--number").default_value(0).help("Number of results to show (0 = all)").scan<'i', int>();
program.add_argument("-m", "--model").default_value("any").help("Filter results of the selected model)");
program.add_argument("-s", "--score").default_value("any").help("Filter results of the score name supplied");
program.add_argument("--complete").help("Show only results with all datasets").default_value(false).implicit_value(true);
program.add_argument("--partial").help("Show only partial results").default_value(false).implicit_value(true);
program.add_argument("--compare").help("Compare with best results").default_value(false).implicit_value(true);
try {
program.parse_args(argc, argv);
auto number = program.get<int>("number");
@@ -20,6 +23,9 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
}
auto model = program.get<string>("model");
auto score = program.get<string>("score");
auto complete = program.get<bool>("complete");
auto partial = program.get<bool>("partial");
auto compare = program.get<bool>("compare");
}
catch (const exception& err) {
cerr << err.what() << endl;
@@ -35,7 +41,12 @@ int main(int argc, char** argv)
auto number = program.get<int>("number");
auto model = program.get<string>("model");
auto score = program.get<string>("score");
auto results = platform::Results(platform::Paths::results(), number, model, score);
auto complete = program.get<bool>("complete");
auto partial = program.get<bool>("partial");
auto compare = program.get<bool>("compare");
if (complete)
partial = false;
auto results = platform::Results(platform::Paths::results(), number, model, score, complete, partial, compare);
results.manage();
return 0;
}

View File

@@ -16,4 +16,6 @@ static platform::Registrar registrarA("AODE",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::AODE();});
static platform::Registrar registrarALD("AODELd",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::AODELd();});
static platform::Registrar registrarBA("BoostAODE",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::BoostAODE();});
#endif

View File

@@ -69,11 +69,12 @@ tuple<Tensor, Tensor, vector<string>, string, map<string, vector<int>>> loadData
Xd = torch::zeros({ static_cast<int>(Xr[0].size()), static_cast<int>(Xr.size()) }, torch::kInt32);
for (int i = 0; i < features.size(); ++i) {
states[features[i]] = vector<int>(*max_element(Xr[i].begin(), Xr[i].end()) + 1);
iota(begin(states[features[i]]), end(states[features[i]]), 0);
auto item = states.at(features[i]);
iota(begin(item), end(item), 0);
Xd.index_put_({ "...", i }, torch::tensor(Xr[i], torch::kInt32));
}
states[className] = vector<int>(*max_element(y.begin(), y.end()) + 1);
iota(begin(states[className]), end(states[className]), 0);
iota(begin(states.at(className)), end(states.at(className)), 0);
} else {
Xd = torch::zeros({ static_cast<int>(X[0].size()), static_cast<int>(X.size()) }, torch::kFloat32);
for (int i = 0; i < features.size(); ++i) {

View File

@@ -4,6 +4,7 @@ if(ENABLE_TESTING)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
set(TEST_SOURCES BayesModels.cc BayesNetwork.cc ${BayesNet_SOURCE_DIR}/src/Platform/platformUtils.cc ${BayesNet_SOURCES})
add_executable(${TEST_MAIN} ${TEST_SOURCES})
target_link_libraries(${TEST_MAIN} PUBLIC "${TORCH_LIBRARIES}" ArffFiles mdlp Catch2::Catch2WithMain)