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3 Commits

Author SHA1 Message Date
d8764db716 Fix linter warnings 2023-07-29 01:16:19 +02:00
8049df436c Add Models class 2023-07-28 12:11:52 +02:00
b420ad2bc2 Add dotenv and possible multiple seeds 2023-07-28 00:53:16 +02:00
156 changed files with 1850 additions and 9450 deletions

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@@ -13,4 +13,5 @@ HeaderFilterRegex: 'src/*'
AnalyzeTemporaryDtors: false
WarningsAsErrors: ''
FormatStyle: file
FormatStyleOptions: ''
...

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@@ -1,31 +0,0 @@
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 **)

5
.gitignore vendored
View File

@@ -31,10 +31,7 @@
*.exe
*.out
*.app
build/**
build_*/**
build/
*.dSYM/**
cmake-build*/**
.idea
puml/**
.vscode/settings.json

13
.gitmodules vendored
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@@ -1,25 +1,12 @@
[submodule "lib/mdlp"]
path = lib/mdlp
url = https://github.com/rmontanana/mdlp
main = main
update = merge
[submodule "lib/catch2"]
path = lib/catch2
main = v2.x
update = merge
url = https://github.com/catchorg/Catch2.git
[submodule "lib/argparse"]
path = lib/argparse
url = https://github.com/p-ranav/argparse
master = master
update = merge
[submodule "lib/json"]
path = lib/json
url = https://github.com/nlohmann/json.git
master = master
update = merge
[submodule "lib/libxlsxwriter"]
path = lib/libxlsxwriter
url = https://github.com/jmcnamara/libxlsxwriter.git
main = main
update = merge

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

109
.vscode/launch.json vendored
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@@ -5,119 +5,44 @@
"type": "lldb",
"request": "launch",
"name": "sample",
"program": "${workspaceFolder}/build_debug/sample/BayesNetSample",
"program": "${workspaceFolder}/build/sample/BayesNetSample",
"args": [
"-d",
"iris",
"-m",
"TANLd",
"-s",
"271",
"TAN",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets/",
"../../data/",
"--tensors"
],
//"cwd": "${workspaceFolder}/build/sample/",
"cwd": "${workspaceFolder}/build/sample/",
},
{
"type": "lldb",
"request": "launch",
"name": "experimentPy",
"program": "${workspaceFolder}/build_debug/src/Platform/b_main",
"args": [
"-m",
"STree",
"--stratified",
"-d",
"iris",
//"--discretize"
// "--hyperparameters",
// "{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "gridsearch",
"program": "${workspaceFolder}/build_debug/src/Platform/b_grid",
"args": [
"-m",
"KDB",
"--discretize",
"--continue",
"glass",
"--only",
"--compute"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "experimentBayes",
"program": "${workspaceFolder}/build_debug/src/Platform/b_main",
"name": "experiment",
"program": "${workspaceFolder}/build/src/Platform/main",
"args": [
"-m",
"TAN",
"--stratified",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets",
"--discretize",
"--stratified",
"--title",
"Debug test",
"--seeds",
"1",
"-d",
"iris",
"--hyperparameters",
"{\"repeatSparent\": true, \"maxModels\": 12}"
"ionosphere"
],
"cwd": "/home/rmontanana/Code/discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "best",
"program": "${workspaceFolder}/build_debug/src/Platform/b_best",
"args": [
"-m",
"BoostAODE",
"-s",
"accuracy",
"--build",
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "manage",
"program": "${workspaceFolder}/build_debug/src/Platform/b_manage",
"args": [
"-n",
"20"
],
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "list",
"program": "${workspaceFolder}/build_debug/src/Platform/b_list",
"args": [],
//"cwd": "/Users/rmontanana/Code/discretizbench",
"cwd": "${workspaceFolder}/../discretizbench",
},
{
"type": "lldb",
"request": "launch",
"name": "test",
"program": "${workspaceFolder}/build_debug/tests/unit_tests",
"args": [
"-c=\"Metrics Test\"",
// "-s",
],
"cwd": "${workspaceFolder}/build/tests",
"cwd": "${workspaceFolder}/build/src/Platform",
},
{
"name": "Build & debug active file",
"type": "cppdbg",
"request": "launch",
"program": "${workspaceFolder}/build_debug/bayesnet",
"program": "${workspaceFolder}/build/bayesnet",
"args": [],
"stopAtEntry": false,
"cwd": "${workspaceFolder}",

109
.vscode/settings.json vendored Normal file
View File

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

23
.vscode/tasks.json vendored
View File

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

View File

@@ -1,20 +1,16 @@
cmake_minimum_required(VERSION 3.20)
project(BayesNet
VERSION 0.2.0
VERSION 0.1.0
DESCRIPTION "Bayesian Network and basic classifiers Library."
HOMEPAGE_URL "https://github.com/rmontanana/bayesnet"
LANGUAGES CXX
)
if (CODE_COVERAGE AND NOT ENABLE_TESTING)
MESSAGE(FATAL_ERROR "Code coverage requires testing enabled")
endif (CODE_COVERAGE AND NOT ENABLE_TESTING)
find_package(Torch REQUIRED)
if (POLICY CMP0135)
cmake_policy(SET CMP0135 NEW)
cmake_policy(SET CMP0135 NEW)
endif ()
# Global CMake variables
@@ -24,82 +20,57 @@ set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
# Options
# -------
option(ENABLE_CLANG_TIDY "Enable to add clang tidy." OFF)
option(ENABLE_TESTING "Unit testing build" OFF)
option(CODE_COVERAGE "Collect coverage from test library" OFF)
option(MPI_ENABLED "Enable MPI options" ON)
option(ENABLE_TESTING "Unit testing build" ON)
option(CODE_COVERAGE "Collect coverage from test library" ON)
if (MPI_ENABLED)
find_package(MPI REQUIRED)
message("MPI_CXX_LIBRARIES=${MPI_CXX_LIBRARIES}")
message("MPI_CXX_INCLUDE_DIRS=${MPI_CXX_INCLUDE_DIRS}")
endif (MPI_ENABLED)
# Boost Library
set(Boost_USE_STATIC_LIBS OFF)
set(Boost_USE_MULTITHREADED ON)
set(Boost_USE_STATIC_RUNTIME OFF)
find_package(Boost 1.66.0 REQUIRED COMPONENTS python3 numpy3)
if(Boost_FOUND)
message("Boost_INCLUDE_DIRS=${Boost_INCLUDE_DIRS}")
include_directories(${Boost_INCLUDE_DIRS})
endif()
# Python
find_package(Python3 3.11...3.11.9 COMPONENTS Interpreter Development REQUIRED)
message("Python3_LIBRARIES=${Python3_LIBRARIES}")
set(CMAKE_BUILD_TYPE "Debug")
# CMakes modules
# --------------
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
include(AddGitSubmodule)
if (CODE_COVERAGE)
enable_testing()
include(CodeCoverage)
MESSAGE("Code coverage enabled")
set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage -O0 -g")
SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
endif (CODE_COVERAGE)
if (ENABLE_CLANG_TIDY)
include(StaticAnalyzers) # clang-tidy
endif (ENABLE_CLANG_TIDY)
include(StaticAnalyzers) # clang-tidy
include(CodeCoverage)
# External libraries - dependencies of BayesNet
# ---------------------------------------------
# include(FetchContent)
add_git_submodule("lib/mdlp")
add_git_submodule("lib/catch2")
add_git_submodule("lib/argparse")
add_git_submodule("lib/json")
find_library(XLSXWRITER_LIB NAMES libxlsxwriter.dylib libxlsxwriter.so PATHS ${BayesNet_SOURCE_DIR}/lib/libxlsxwriter/lib)
message("XLSXWRITER_LIB=${XLSXWRITER_LIB}")
# Subdirectories
# --------------
add_subdirectory(config)
add_subdirectory(lib/Files)
add_subdirectory(src/BayesNet)
add_subdirectory(src/Platform)
add_subdirectory(src/PyClassifiers)
add_subdirectory(sample)
file(GLOB BayesNet_HEADERS CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.h ${BayesNet_SOURCE_DIR}/BayesNet/*.h)
file(GLOB BayesNet_HEADERS CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.h ${BayesNet_SOURCE_DIR}/BayesNet/*.hpp)
file(GLOB BayesNet_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/BayesNet/*.cc ${BayesNet_SOURCE_DIR}/src/BayesNet/*.cpp)
file(GLOB Platform_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/Platform/*.cc ${BayesNet_SOURCE_DIR}/src/Platform/*.cpp)
# Testing
# -------
if (ENABLE_TESTING)
MESSAGE("Testing enabled")
add_git_submodule("lib/catch2")
enable_testing()
if (CODE_COVERAGE)
#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(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
endif (CODE_COVERAGE)
#find_package(Catch2 3 REQUIRED)
include(CTest)
#include(Catch)
add_subdirectory(tests)
endif (ENABLE_TESTING)

118
Makefile
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@@ -1,26 +1,6 @@
SHELL := /bin/bash
.DEFAULT_GOAL := help
.PHONY: coverage setup help build test clean debug release
f_release = build_release
f_debug = build_debug
app_targets = b_best b_list b_main b_manage b_grid
test_targets = unit_tests_bayesnet unit_tests_platform
n_procs = -j 16
define ClearTests
@for t in $(test_targets); do \
if [ -f $(f_debug)/tests/$$t ]; then \
echo ">>> Cleaning $$t..." ; \
rm -f $(f_debug)/tests/$$t ; \
fi ; \
done
@nfiles="$(find . -name "*.gcda" -print0)" ; \
if test "${nfiles}" != "" ; then \
find . -name "*.gcda" -print0 | xargs -0 rm 2>/dev/null ;\
fi ;
endef
.PHONY: coverage setup help build test
setup: ## Install dependencies for tests and coverage
@if [ "$(shell uname)" = "Darwin" ]; then \
@@ -31,87 +11,35 @@ setup: ## Install dependencies for tests and coverage
pip install gcovr; \
fi
dest ?= ${HOME}/bin
install: ## Copy binary files to bin folder
@echo "Destination folder: $(dest)"
make buildr
@echo "*******************************************"
@echo ">>> Copying files to $(dest)"
@echo "*******************************************"
@for item in $(app_targets); do \
echo ">>> Copying $$item" ; \
cp $(f_release)/src/Platform/$$item $(dest) ; \
done
dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
@echo ">>> Creating dependency graph diagram of the project...";
$(MAKE) debug
cd $(f_debug) && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png
cd build && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png
buildd: ## Build the debug targets
cmake --build $(f_debug) -t $(app_targets) BayesNetSample $(n_procs)
build: ## Build the project
@echo ">>> Building BayesNet ...";
@if [ -d ./build ]; then rm -rf ./build; fi
@mkdir build;
cmake -S . -B build; \
cd build; \
make; \
buildr: ## Build the release targets
cmake --build $(f_release) -t $(app_targets) BayesNetSample $(n_procs)
clean: ## Clean the tests info
@echo ">>> Cleaning Debug BayesNet tests...";
$(call ClearTests)
@echo ">>> Done";
clang-uml: ## Create uml class and sequence diagrams
clang-uml -p --add-compile-flag -I /usr/lib/gcc/x86_64-redhat-linux/8/include/
debug: ## Build a debug version of the project
@echo ">>> Building Debug BayesNet...";
@if [ -d ./$(f_debug) ]; then rm -rf ./$(f_debug); fi
@mkdir $(f_debug);
@cmake -S . -B $(f_debug) -D CMAKE_BUILD_TYPE=Debug -D ENABLE_TESTING=ON -D CODE_COVERAGE=ON
@echo ">>> Done";
release: ## Build a Release version of the project
@echo ">>> Building Release BayesNet...";
@if [ -d ./$(f_release) ]; then rm -rf ./$(f_release); fi
@mkdir $(f_release);
@cmake -S . -B $(f_release) -D CMAKE_BUILD_TYPE=Release
@echo ">>> Done";
opt = ""
test: ## Run tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
@echo ">>> Running BayesNet & Platform tests...";
@$(MAKE) clean
@cmake --build $(f_debug) -t $(test_targets) $(n_procs)
@for t in $(test_targets); do \
if [ -f $(f_debug)/tests/$$t ]; then \
cd $(f_debug)/tests ; \
./$$t $(opt) ; \
fi ; \
done
@echo ">>> Done";
opt = ""
testp: ## Run platform tests (opt="-s") to verbose output the tests, (opt="-c='Stratified Fold Test'") to run only that section
@echo ">>> Running Platform tests...";
@$(MAKE) clean
@cmake --build $(f_debug) --target unit_tests_platform $(n_procs)
@if [ -f $(f_debug)/tests/unit_tests_platform ]; then cd $(f_debug)/tests ; ./unit_tests_platform $(opt) ; fi ;
@echo ">>> Done";
opt = ""
testb: ## Run BayesNet tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
@echo ">>> Running BayesNet tests...";
@$(MAKE) clean
@cmake --build $(f_debug) --target unit_tests_bayesnet $(n_procs)
@if [ -f $(f_debug)/tests/unit_tests_bayesnet ]; then cd $(f_debug)/tests ; ./unit_tests_bayesnet $(opt) ; fi ;
@echo ">>> Done";
test: ## Run tests
@echo "* Running tests...";
find . -name "*.gcda" -print0 | xargs -0 rm
@cd build; \
cmake --build . --target unit_tests ;
@cd build/tests; \
./unit_tests;
coverage: ## Run tests and generate coverage report (build/index.html)
@echo ">>> Building tests with coverage...";
@$(MAKE) test
@cd $(f_debug) ; \
gcovr --config ../gcovr.cfg tests ;
@echo ">>> Done";
@echo "*Building tests...";
find . -name "*.gcda" -print0 | xargs -0 rm
@cd build; \
cmake --build . --target unit_tests ;
@cd build/tests; \
./unit_tests;
gcovr ;
help: ## Show help message
@IFS=$$'\n' ; \

View File

@@ -1,79 +1,5 @@
# BayesNet
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
Bayesian Network Classifier with libtorch from scratch
## 0. Setup
Before compiling BayesNet.
### MPI
In Linux just install openmpi & openmpi-devel packages. Only cmake can't find openmpi install (like in Oracle Linux) set the following variable:
```bash
export MPI_HOME="/usr/lib64/openmpi"
```
In Mac OS X, install mpich with brew and if cmake doesn't find it, edit mpicxx wrapper to remove the ",-commons,use_dylibs" from final_ldflags
```bash
vi /opt/homebrew/bin/mpicx
```
### boost library
[Getting Started](<https://www.boost.org/doc/libs/1_83_0/more/getting_started/index.html>)
The best option is install the packages that the Linux distribution have in its repository. If this is the case:
```bash
sudo dnf install boost-devel
```
If this is not possible and the compressed packaged is installed, the following environment variable has to be set pointing to the folder where it was unzipped to:
```bash
export BOOST_ROOT=/path/to/library/
```
In some cases, it is needed to build the library, to do so:
```bash
cd /path/to/library
mkdir own
./bootstrap.sh --prefix=/path/to/library/own
./b2 install
export BOOST_ROOT=/path/to/library/own/
```
Don't forget to add the export BOOST_ROOT statement to .bashrc or wherever it is meant to be.
### libxlswriter
```bash
cd lib/libxlsxwriter
make
make install DESTDIR=/home/rmontanana/Code PREFIX=
```
Environment variable has to be set:
```bash
export LD_LIBRARY_PATH=/usr/local/lib
```
### Release
```bash
make release
```
### Debug & Tests
```bash
make debug
```
## 1. Introduction

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@@ -0,0 +1 @@
null

Binary file not shown.

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@@ -1,4 +1,5 @@
filter = src/
exclude-directories = build/lib/
exclude = external/
exclude = tests/
print-summary = yes
sort-percentage = yes

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@@ -1,162 +0,0 @@
{
"balance-scale": {
"C": 10000.0,
"gamma": 0.1,
"kernel": "rbf",
"max_iter": 10000
},
"balloons": {
"C": 7,
"gamma": 0.1,
"kernel": "rbf",
"max_iter": 10000
},
"breast-cancer-wisc-diag": {
"C": 0.2,
"max_iter": 10000
},
"breast-cancer-wisc-prog": {
"C": 0.2,
"max_iter": 10000
},
"breast-cancer-wisc": {},
"breast-cancer": {},
"cardiotocography-10clases": {},
"cardiotocography-3clases": {},
"conn-bench-sonar-mines-rocks": {},
"cylinder-bands": {},
"dermatology": {
"C": 55,
"max_iter": 10000
},
"echocardiogram": {
"C": 7,
"gamma": 0.1,
"kernel": "poly",
"max_features": "auto",
"max_iter": 10000
},
"fertility": {
"C": 0.05,
"max_features": "auto",
"max_iter": 10000
},
"haberman-survival": {},
"heart-hungarian": {
"C": 0.05,
"max_iter": 10000
},
"hepatitis": {
"C": 7,
"gamma": 0.1,
"kernel": "rbf",
"max_iter": 10000
},
"ilpd-indian-liver": {},
"ionosphere": {
"C": 7,
"gamma": 0.1,
"kernel": "rbf",
"max_iter": 10000
},
"iris": {},
"led-display": {},
"libras": {
"C": 0.08,
"max_iter": 10000
},
"low-res-spect": {
"C": 0.05,
"max_iter": 10000
},
"lymphography": {
"C": 0.05,
"max_iter": 10000
},
"mammographic": {},
"molec-biol-promoter": {
"C": 0.05,
"gamma": 0.1,
"kernel": "poly",
"max_iter": 10000
},
"musk-1": {
"C": 0.05,
"gamma": 0.1,
"kernel": "poly",
"max_iter": 10000
},
"oocytes_merluccius_nucleus_4d": {
"C": 8.25,
"gamma": 0.1,
"kernel": "poly"
},
"oocytes_merluccius_states_2f": {},
"oocytes_trisopterus_nucleus_2f": {},
"oocytes_trisopterus_states_5b": {
"C": 0.11,
"max_iter": 10000
},
"parkinsons": {},
"pima": {},
"pittsburg-bridges-MATERIAL": {
"C": 7,
"gamma": 0.1,
"kernel": "rbf",
"max_iter": 10000
},
"pittsburg-bridges-REL-L": {},
"pittsburg-bridges-SPAN": {
"C": 0.05,
"max_iter": 10000
},
"pittsburg-bridges-T-OR-D": {},
"planning": {
"C": 7,
"gamma": 10.0,
"kernel": "rbf",
"max_iter": 10000
},
"post-operative": {
"C": 55,
"degree": 5,
"gamma": 0.1,
"kernel": "poly",
"max_iter": 10000
},
"seeds": {
"C": 10000.0,
"max_iter": 10000
},
"statlog-australian-credit": {
"C": 0.05,
"max_features": "auto",
"max_iter": 10000
},
"statlog-german-credit": {},
"statlog-heart": {},
"statlog-image": {
"C": 7,
"max_iter": 10000
},
"statlog-vehicle": {},
"synthetic-control": {
"C": 0.55,
"max_iter": 10000
},
"tic-tac-toe": {
"C": 0.2,
"gamma": 0.1,
"kernel": "poly",
"max_iter": 10000
},
"vertebral-column-2clases": {},
"wine": {
"C": 0.55,
"max_iter": 10000
},
"zoo": {
"C": 0.1,
"max_iter": 10000
}
}

View File

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

View File

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

View File

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

View File

@@ -1,10 +1,7 @@
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/PyClassifiers)
include_directories(${Python3_INCLUDE_DIRS})
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}" PyWrap)
target_link_libraries(BayesNetSample BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")

View File

@@ -1,23 +1,24 @@
#include <iostream>
#include <torch/torch.h>
#include <string>
#include <thread>
#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>
const std::string PATH = "../../data/";
pair<std::vector<mdlp::labels_t>, map<std::string, int>> discretize(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y, std::vector<std::string> features)
using namespace std;
const string PATH = "../../data/";
pair<vector<mdlp::labels_t>, map<string, int>> discretize(vector<mdlp::samples_t>& X, mdlp::labels_t& y, vector<string> features)
{
std::vector<mdlp::labels_t>Xd;
map<std::string, int> maxes;
vector<mdlp::labels_t>Xd;
map<string, int> maxes;
auto fimdlp = mdlp::CPPFImdlp();
for (int i = 0; i < X.size(); i++) {
@@ -38,12 +39,12 @@ bool file_exists(const std::string& name)
return false;
}
}
pair<std::vector<std::vector<int>>, std::vector<int>> extract_indices(std::vector<int> indices, std::vector<std::vector<int>> X, std::vector<int> y)
pair<vector<vector<int>>, vector<int>> extract_indices(vector<int> indices, vector<vector<int>> X, vector<int> y)
{
std::vector<std::vector<int>> Xr; // nxm
std::vector<int> yr;
vector<vector<int>> Xr;
vector<int> yr;
for (int col = 0; col < X.size(); ++col) {
Xr.push_back(std::vector<int>());
Xr.push_back(vector<int>());
}
for (auto index : indices) {
for (int col = 0; col < X.size(); ++col) {
@@ -56,7 +57,7 @@ pair<std::vector<std::vector<int>>, std::vector<int>> extract_indices(std::vecto
int main(int argc, char** argv)
{
map<std::string, bool> datasets = {
map<string, bool> datasets = {
{"diabetes", true},
{"ecoli", true},
{"glass", true},
@@ -66,9 +67,10 @@ int main(int argc, char** argv)
{"liver-disorders", true},
{"mfeat-factors", true},
};
auto valid_datasets = std::vector<std::string>();
transform(datasets.begin(), datasets.end(), back_inserter(valid_datasets),
[](const pair<std::string, bool>& pair) { return pair.first; });
auto valid_datasets = vector<string>();
for (auto dataset : datasets) {
valid_datasets.push_back(dataset.first);
}
argparse::ArgumentParser program("BayesNetSample");
program.add_argument("-d", "--dataset")
.help("Dataset file name")
@@ -81,23 +83,22 @@ int main(int argc, char** argv)
);
program.add_argument("-p", "--path")
.help(" folder where the data files are located, default")
.default_value(std::string{ PATH }
.default_value(string{ PATH }
);
program.add_argument("-m", "--model")
.help("Model to use " + platform::Models::instance()->tostring())
.help("Model to use " + platform::Models::toString())
.action([](const std::string& value) {
static const std::vector<std::string> choices = platform::Models::instance()->getNames();
static const vector<string> choices = platform::Models::getNames();
if (find(choices.begin(), choices.end(), value) != choices.end()) {
return value;
}
throw runtime_error("Model must be one of " + platform::Models::instance()->tostring());
throw runtime_error("Model must be one of " + platform::Models::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 std::string& value) {
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) {
@@ -112,27 +113,26 @@ int main(int argc, char** argv)
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;
std::string model_name, file_name, path, complete_file_name;
bool class_last, stratified, tensors;
string model_name, file_name, path, complete_file_name;
int nFolds, seed;
try {
program.parse_args(argc, argv);
file_name = program.get<std::string>("dataset");
path = program.get<std::string>("path");
model_name = program.get<std::string>("model");
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() << std::endl;
cerr << err.what() << endl;
cerr << program;
exit(1);
}
@@ -143,64 +143,55 @@ int main(int argc, char** argv)
auto handler = ArffFiles();
handler.load(complete_file_name, class_last);
// Get Dataset X, y
std::vector<mdlp::samples_t>& X = handler.getX();
vector<mdlp::samples_t>& X = handler.getX();
mdlp::labels_t& y = handler.getY();
// Get className & Features
auto className = handler.getClassName();
std::vector<std::string> features;
auto attributes = handler.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features),
[](const pair<std::string, std::string>& item) { return item.first; });
vector<string> features;
for (auto feature : handler.getAttributes()) {
features.push_back(feature.first);
}
// Discretize Dataset
auto [Xd, maxes] = discretize(X, y, features);
maxes[className] = *max_element(y.begin(), y.end()) + 1;
map<std::string, std::vector<int>> states;
map<string, vector<int>> states;
for (auto feature : features) {
states[feature] = std::vector<int>(maxes[feature]);
states[feature] = vector<int>(maxes[feature]);
}
states[className] = std::vector<int>(maxes[className]);
auto clf = platform::Models::instance()->create(model_name);
states[className] = vector<int>(maxes[className]);
bayesnet::BaseClassifier* clf = platform::Models::get(model_name);
clf->fit(Xd, y, features, className, states);
if (dump_cpt) {
std::cout << "--- CPT Tables ---" << std::endl;
clf->dump_cpt();
}
auto lines = clf->show();
for (auto line : lines) {
std::cout << line << std::endl;
}
std::cout << "--- Topological Order ---" << std::endl;
auto order = clf->topological_order();
for (auto name : order) {
std::cout << name << ", ";
}
std::cout << "end." << std::endl;
auto score = clf->score(Xd, y);
std::cout << "Score: " << score << std::endl;
auto lines = clf->show();
auto graph = clf->graph();
for (auto line : lines) {
cout << line << endl;
}
cout << "Score: " << score << endl;
auto dot_file = model_name + "_" + file_name;
ofstream file(dot_file + ".dot");
file << graph;
file.close();
std::cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << std::endl;
std::cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << std::endl;
std::string stratified_string = stratified ? " Stratified" : "";
std::cout << nFolds << " Folds" << stratified_string << " Cross validation" << std::endl;
std::cout << "==========================================" << std::endl;
cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << endl;
cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << endl;
string stratified_string = stratified ? " Stratified" : "";
cout << nFolds << " Folds" << stratified_string << " Cross validation" << endl;
cout << "==========================================" << endl;
torch::Tensor Xt = torch::zeros({ static_cast<int>(Xd.size()), static_cast<int>(Xd[0].size()) }, torch::kInt32);
torch::Tensor yt = torch::tensor(y, torch::kInt32);
for (int i = 0; i < features.size(); ++i) {
Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
}
float total_score = 0, total_score_train = 0, score_train, score_test;
platform::Fold* fold;
Fold* fold;
if (stratified)
fold = new platform::StratifiedKFold(nFolds, y, seed);
fold = new StratifiedKFold(nFolds, y, seed);
else
fold = new platform::KFold(nFolds, y.size(), seed);
fold = new KFold(nFolds, y.size(), seed);
for (auto i = 0; i < nFolds; ++i) {
auto [train, test] = fold->getFold(i);
std::cout << "Fold: " << i + 1 << std::endl;
cout << "Fold: " << i + 1 << endl;
if (tensors) {
auto ttrain = torch::tensor(train, torch::kInt64);
auto ttest = torch::tensor(test, torch::kInt64);
@@ -209,7 +200,6 @@ int main(int argc, char** argv)
torch::Tensor Xtestt = torch::index_select(Xt, 1, ttest);
torch::Tensor ytestt = yt.index({ ttest });
clf->fit(Xtraint, ytraint, features, className, states);
auto temp = clf->predict(Xtraint);
score_train = clf->score(Xtraint, ytraint);
score_test = clf->score(Xtestt, ytestt);
} else {
@@ -219,17 +209,14 @@ int main(int argc, char** argv)
score_train = clf->score(Xtrain, ytrain);
score_test = clf->score(Xtest, ytest);
}
if (dump_cpt) {
std::cout << "--- CPT Tables ---" << std::endl;
clf->dump_cpt();
}
total_score_train += score_train;
total_score += score_test;
std::cout << "Score Train: " << score_train << std::endl;
std::cout << "Score Test : " << score_test << std::endl;
std::cout << "-------------------------------------------------------------------------------" << std::endl;
cout << "Score Train: " << score_train << endl;
cout << "Score Test : " << score_test << endl;
cout << "-------------------------------------------------------------------------------" << endl;
}
std::cout << "**********************************************************************************" << std::endl;
std::cout << "Average Score Train: " << total_score_train / nFolds << std::endl;
std::cout << "Average Score Test : " << total_score / nFolds << std::endl;return 0;
cout << "**********************************************************************************" << endl;
cout << "Average Score Train: " << total_score_train / nFolds << endl;
cout << "Average Score Test : " << total_score / nFolds << endl;
return 0;
}

View File

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

View File

@@ -5,11 +5,10 @@
namespace bayesnet {
class AODE : public Ensemble {
protected:
void buildModel(const torch::Tensor& weights) override;
void train() override;
public:
AODE();
virtual ~AODE() {};
std::vector<std::string> graph(const std::string& title = "AODE") const override;
vector<string> graph(string title = "AODE") override;
};
}
#endif

View File

@@ -1,39 +0,0 @@
#include "AODELd.h"
namespace bayesnet {
AODELd::AODELd() : Ensemble(), Proposal(dataset, features, className) {}
AODELd& AODELd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal TAN structure, TAN::fit initializes the base Bayesian network
Ensemble::fit(dataset, features, className, states);
return *this;
}
void AODELd::buildModel(const torch::Tensor& weights)
{
models.clear();
for (int i = 0; i < features.size(); ++i) {
models.push_back(std::make_unique<SPODELd>(i));
}
n_models = models.size();
significanceModels = std::vector<double>(n_models, 1.0);
}
void AODELd::trainModel(const torch::Tensor& weights)
{
for (const auto& model : models) {
model->fit(Xf, y, features, className, states);
}
}
std::vector<std::string> AODELd::graph(const std::string& name) const
{
return Ensemble::graph(name);
}
}

View File

@@ -1,20 +0,0 @@
#ifndef AODELD_H
#define AODELD_H
#include "Ensemble.h"
#include "Proposal.h"
#include "SPODELd.h"
namespace bayesnet {
class AODELd : public Ensemble, public Proposal {
protected:
void trainModel(const torch::Tensor& weights) override;
void buildModel(const torch::Tensor& weights) override;
public:
AODELd();
AODELd& fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_) override;
virtual ~AODELd() = default;
std::vector<std::string> graph(const std::string& name = "AODELd") const override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !AODELD_H

View File

@@ -1,37 +1,23 @@
#ifndef BASE_H
#define BASE_H
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <vector>
namespace bayesnet {
enum status_t { NORMAL, WARNING, ERROR };
using namespace std;
class BaseClassifier {
public:
// X is nxm std::vector, y is nx1 std::vector
virtual BaseClassifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
// X is nxm tensor, y is nx1 tensor
virtual BaseClassifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights) = 0;
virtual ~BaseClassifier() = default;
torch::Tensor virtual predict(torch::Tensor& X) = 0;
std::vector<int> virtual predict(std::vector<std::vector<int >>& X) = 0;
status_t virtual getStatus() const = 0;
float virtual score(std::vector<std::vector<int>>& X, std::vector<int>& y) = 0;
virtual BaseClassifier& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
vector<int> virtual predict(vector<vector<int>>& X) = 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;
int virtual getNumberOfEdges()const = 0;
int virtual getNumberOfStates() const = 0;
std::vector<std::string> virtual show() const = 0;
std::vector<std::string> virtual graph(const std::string& title = "") const = 0;
virtual std::string getVersion() = 0;
std::vector<std::string> virtual topological_order() = 0;
void virtual dump_cpt()const = 0;
virtual void setHyperparameters(const nlohmann::json& hyperparameters) = 0;
std::vector<std::string>& getValidHyperparameters() { return validHyperparameters; }
protected:
virtual void trainModel(const torch::Tensor& weights) = 0;
std::vector<std::string> validHyperparameters;
int virtual getNumberOfNodes() = 0;
int virtual getNumberOfEdges() = 0;
int virtual getNumberOfStates() = 0;
vector<string> virtual show() = 0;
vector<string> virtual graph(string title = "") = 0;
virtual ~BaseClassifier() = default;
const string inline getVersion() const { return "0.1.0"; };
};
}
#endif

View File

@@ -1,89 +1,57 @@
#include "BayesMetrics.h"
#include "Mst.h"
namespace bayesnet {
//samples is n+1xm tensor used to fit the model
Metrics::Metrics(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int classNumStates)
Metrics::Metrics(torch::Tensor& samples, vector<string>& features, string& className, int classNumStates)
: samples(samples)
, features(features)
, className(className)
, classNumStates(classNumStates)
{
}
//samples is nxm std::vector used to fit the model
Metrics::Metrics(const std::vector<std::vector<int>>& vsamples, const std::vector<int>& labels, const std::vector<std::string>& features, const std::string& className, const int classNumStates)
Metrics::Metrics(const vector<vector<int>>& vsamples, const vector<int>& labels, const vector<string>& features, const string& className, const int classNumStates)
: features(features)
, className(className)
, classNumStates(classNumStates)
, samples(torch::zeros({ static_cast<int>(vsamples[0].size()), static_cast<int>(vsamples.size() + 1) }, torch::kInt32))
{
for (int i = 0; i < vsamples.size(); ++i) {
samples.index_put_({ i, "..." }, torch::tensor(vsamples[i], torch::kInt32));
samples.index_put_({ "...", i }, torch::tensor(vsamples[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
samples.index_put_({ "...", -1 }, torch::tensor(labels, torch::kInt32));
}
std::vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, bool ascending, unsigned k)
vector<pair<string, string>> Metrics::doCombinations(const vector<string>& source)
{
// 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());
}
vector<pair<string, string>> result;
for (int i = 0; i < source.size(); ++i) {
string temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
}
} 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;
return result;
}
std::vector<double> Metrics::getScoresKBest() const
torch::Tensor Metrics::conditionalEdge()
{
return scoresKBest;
}
torch::Tensor Metrics::conditionalEdge(const torch::Tensor& weights)
{
auto result = std::vector<double>();
auto source = std::vector<std::string>(features);
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 }, torch::kFloat);
auto margin = torch::zeros({ classNumStates });
for (int value = 0; value < classNumStates; ++value) {
auto mask = samples.index({ -1, "..." }) == value;
margin[value] = mask.sum().item<double>() / samples.size(1);
auto mask = samples.index({ "...", -1 }) == value;
margin[value] = mask.sum().item<float>() / samples.sizes()[0];
}
for (auto [first, second] : combinations) {
int index_first = find(features.begin(), features.end(), first) - features.begin();
int index_second = find(features.begin(), features.end(), second) - features.begin();
double accumulated = 0;
for (int value = 0; value < classNumStates; ++value) {
auto mask = samples.index({ -1, "..." }) == value;
auto first_dataset = samples.index({ index_first, mask });
auto second_dataset = samples.index({ index_second, mask });
auto weights_dataset = weights.index({ mask });
auto mi = mutualInformation(first_dataset, second_dataset, weights_dataset);
auto pb = margin[value].item<double>();
auto mask = samples.index({ "...", -1 }) == value;
auto first_dataset = samples.index({ mask, index_first });
auto second_dataset = samples.index({ mask, index_second });
auto mi = mutualInformation(first_dataset, second_dataset);
auto pb = margin[value].item<float>();
accumulated += pb * mi;
}
result.push_back(accumulated);
@@ -99,33 +67,32 @@ namespace bayesnet {
}
return matrix;
}
// To use in Python
std::vector<float> Metrics::conditionalEdgeWeights(std::vector<float>& weights_)
// To Interface with Python
vector<float> Metrics::conditionalEdgeWeights()
{
const torch::Tensor weights = torch::tensor(weights_);
auto matrix = conditionalEdge(weights);
auto matrix = conditionalEdge();
std::vector<float> v(matrix.data_ptr<float>(), matrix.data_ptr<float>() + matrix.numel());
return v;
}
double Metrics::entropy(const torch::Tensor& feature, const torch::Tensor& weights)
double Metrics::entropy(torch::Tensor& feature)
{
torch::Tensor counts = feature.bincount(weights);
double totalWeight = counts.sum().item<double>();
torch::Tensor counts = feature.bincount();
int totalWeight = counts.sum().item<int>();
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, const torch::Tensor& weights)
double Metrics::conditionalEntropy(torch::Tensor& firstFeature, torch::Tensor& secondFeature)
{
int numSamples = firstFeature.sizes()[0];
torch::Tensor featureCounts = secondFeature.bincount(weights);
std::unordered_map<int, std::unordered_map<int, double>> jointCounts;
torch::Tensor featureCounts = secondFeature.bincount();
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>()] += weights[i].item<double>();
totalWeight += weights[i].item<float>();
jointCounts[secondFeature[i].item<int>()][firstFeature[i].item<int>()] += 1;
totalWeight += 1;
}
if (totalWeight == 0)
return 0;
@@ -146,16 +113,16 @@ namespace bayesnet {
return entropyValue;
}
// I(X;Y) = H(Y) - H(Y|X)
double Metrics::mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights)
double Metrics::mutualInformation(torch::Tensor& firstFeature, torch::Tensor& secondFeature)
{
return entropy(firstFeature, weights) - conditionalEntropy(firstFeature, secondFeature, weights);
return entropy(firstFeature) - conditionalEntropy(firstFeature, secondFeature);
}
/*
Compute the maximum spanning tree considering the weights as distances
and the indices of the weights as nodes of this square matrix using
Kruskal algorithm
*/
std::vector<std::pair<int, int>> Metrics::maximumSpanningTree(const std::vector<std::string>& features, const torch::Tensor& weights, const int root)
vector<pair<int, int>> Metrics::maximumSpanningTree(vector<string> features, Tensor& weights, int root)
{
auto mst = MST(features, weights, root);
return mst.maximumSpanningTree();

View File

@@ -4,46 +4,25 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
using namespace torch;
class Metrics {
private:
int classNumStates = 0;
std::vector<double> scoresKBest;
std::vector<int> featuresKBest; // sorted indices of the features
double conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
protected:
torch::Tensor samples; // n+1xm torch::Tensor used to fit the model where samples[-1] is the y std::vector
std::string className;
double entropy(const torch::Tensor& feature, const torch::Tensor& weights);
std::vector<std::string> features;
template <class T>
std::vector<std::pair<T, T>> doCombinations(const std::vector<T>& source)
{
std::vector<std::pair<T, T>> result;
for (int i = 0; i < source.size(); ++i) {
T temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
}
}
return result;
}
template <class T>
T pop_first(std::vector<T>& v)
{
T temp = v[0];
v.erase(v.begin());
return temp;
}
Tensor samples;
vector<string> features;
string className;
int classNumStates;
public:
Metrics() = default;
Metrics(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
Metrics(const std::vector<std::vector<int>>& vsamples, const std::vector<int>& labels, const std::vector<std::string>& features, const std::string& className, const int classNumStates);
std::vector<int> SelectKBestWeighted(const torch::Tensor& weights, bool ascending = false, unsigned k = 0);
std::vector<double> getScoresKBest() const;
double mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature, const torch::Tensor& weights);
std::vector<float> conditionalEdgeWeights(std::vector<float>& weights); // To use in Python
torch::Tensor conditionalEdge(const torch::Tensor& weights);
std::vector<std::pair<int, int>> maximumSpanningTree(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
Metrics(Tensor&, vector<string>&, string&, int);
Metrics(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&, const int);
double entropy(Tensor&);
double conditionalEntropy(Tensor&, Tensor&);
double mutualInformation(Tensor&, Tensor&);
vector<float> conditionalEdgeWeights();
Tensor conditionalEdge();
vector<pair<string, string>> doCombinations(const vector<string>&);
vector<pair<int, int>> maximumSpanningTree(vector<string> features, Tensor& weights, int root);
};
}
#endif

View File

@@ -1,209 +0,0 @@
#include <set>
#include <functional>
#include <limits.h>
#include "BoostAODE.h"
#include "Colors.h"
#include "Folding.h"
#include "Paths.h"
#include "CFS.h"
#include "FCBF.h"
#include "IWSS.h"
namespace bayesnet {
BoostAODE::BoostAODE() : Ensemble()
{
validHyperparameters = { "repeatSparent", "maxModels", "ascending", "convergence", "threshold", "select_features", "tolerance" };
}
void BoostAODE::buildModel(const torch::Tensor& weights)
{
// Models shall be built in trainModel
models.clear();
n_models = 0;
// Prepare the validation dataset
auto y_ = dataset.index({ -1, "..." });
if (convergence) {
// Prepare train & validation sets from train data
auto fold = platform::StratifiedKFold(5, y_, 271);
dataset_ = torch::clone(dataset);
// save input dataset
auto [train, test] = fold.getFold(0);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
// Get train and validation sets
X_train = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), train_t });
y_train = dataset.index({ -1, train_t });
X_test = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), test_t });
y_test = dataset.index({ -1, test_t });
dataset = X_train;
m = X_train.size(1);
auto n_classes = states.at(className).size();
metrics = Metrics(dataset, features, className, n_classes);
// Build dataset with train data
buildDataset(y_train);
} else {
// Use all data to train
X_train = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." });
y_train = y_;
}
}
void BoostAODE::setHyperparameters(const nlohmann::json& hyperparameters_)
{
auto hyperparameters = hyperparameters_;
if (hyperparameters.contains("repeatSparent")) {
repeatSparent = hyperparameters["repeatSparent"];
hyperparameters.erase("repeatSparent");
}
if (hyperparameters.contains("maxModels")) {
maxModels = hyperparameters["maxModels"];
hyperparameters.erase("maxModels");
}
if (hyperparameters.contains("ascending")) {
ascending = hyperparameters["ascending"];
hyperparameters.erase("ascending");
}
if (hyperparameters.contains("convergence")) {
convergence = hyperparameters["convergence"];
hyperparameters.erase("convergence");
}
if (hyperparameters.contains("threshold")) {
threshold = hyperparameters["threshold"];
hyperparameters.erase("threshold");
}
if (hyperparameters.contains("tolerance")) {
tolerance = hyperparameters["tolerance"];
hyperparameters.erase("tolerance");
}
if (hyperparameters.contains("select_features")) {
auto selectedAlgorithm = hyperparameters["select_features"];
std::vector<std::string> algos = { "IWSS", "FCBF", "CFS" };
selectFeatures = true;
algorithm = selectedAlgorithm;
if (std::find(algos.begin(), algos.end(), selectedAlgorithm) == algos.end()) {
throw std::invalid_argument("Invalid selectFeatures value [IWSS, FCBF, CFS]");
}
hyperparameters.erase("select_features");
}
if (!hyperparameters.empty()) {
throw std::invalid_argument("Invalid hyperparameters" + hyperparameters.dump());
}
}
std::unordered_set<int> BoostAODE::initializeModels()
{
std::unordered_set<int> featuresUsed;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
int maxFeatures = 0;
if (algorithm == "CFS") {
featureSelector = new CFS(dataset, features, className, maxFeatures, states.at(className).size(), weights_);
} else if (algorithm == "IWSS") {
if (threshold < 0 || threshold >0.5) {
throw std::invalid_argument("Invalid threshold value for IWSS [0, 0.5]");
}
featureSelector = new IWSS(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
} else if (algorithm == "FCBF") {
if (threshold < 1e-7 || threshold > 1) {
throw std::invalid_argument("Invalid threshold value [1e-7, 1]");
}
featureSelector = new FCBF(dataset, features, className, maxFeatures, states.at(className).size(), weights_, threshold);
}
featureSelector->fit();
auto cfsFeatures = featureSelector->getFeatures();
for (const int& feature : cfsFeatures) {
// std::cout << "Feature: [" << feature << "] " << feature << " " << features.at(feature) << std::endl;
featuresUsed.insert(feature);
std::unique_ptr<Classifier> model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_);
models.push_back(std::move(model));
significanceModels.push_back(1.0);
n_models++;
}
delete featureSelector;
return featuresUsed;
}
void BoostAODE::trainModel(const torch::Tensor& weights)
{
std::unordered_set<int> featuresUsed;
if (selectFeatures) {
featuresUsed = initializeModels();
}
if (maxModels == 0)
maxModels = .1 * n > 10 ? .1 * n : n;
torch::Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
bool exitCondition = false;
// Variables to control the accuracy finish condition
double priorAccuracy = 0.0;
double delta = 1.0;
double threshold = 1e-4;
int count = 0; // number of times the accuracy is lower than the threshold
fitted = true; // to enable predict
// Step 0: Set the finish condition
// if not repeatSparent a finish condition is run out of features
// n_models == maxModels
// epsilon sub t > 0.5 => inverse the weights policy
// validation error is not decreasing
while (!exitCondition) {
// Step 1: Build ranking with mutual information
auto featureSelection = metrics.SelectKBestWeighted(weights_, ascending, n); // Get all the features sorted
std::unique_ptr<Classifier> model;
auto feature = featureSelection[0];
if (!repeatSparent || featuresUsed.size() < featureSelection.size()) {
bool used = true;
for (const auto& feat : featureSelection) {
if (std::find(featuresUsed.begin(), featuresUsed.end(), feat) != featuresUsed.end()) {
continue;
}
used = false;
feature = feat;
break;
}
if (used) {
exitCondition = true;
continue;
}
}
featuresUsed.insert(feature);
model = std::make_unique<SPODE>(feature);
model->fit(dataset, features, className, states, weights_);
auto ypred = model->predict(X_train);
// Step 3.1: Compute the classifier amout of say
auto mask_wrong = ypred != y_train;
auto mask_right = ypred == y_train;
auto masked_weights = weights_ * mask_wrong.to(weights_.dtype());
double epsilon_t = masked_weights.sum().item<double>();
double wt = (1 - epsilon_t) / epsilon_t;
double alpha_t = epsilon_t == 0 ? 1 : 0.5 * log(wt);
// Step 3.2: Update weights for next classifier
// Step 3.2.1: Update weights of wrong samples
weights_ += mask_wrong.to(weights_.dtype()) * exp(alpha_t) * weights_;
// Step 3.2.2: Update weights of right samples
weights_ += mask_right.to(weights_.dtype()) * exp(-alpha_t) * weights_;
// Step 3.3: Normalise the weights
double totalWeights = torch::sum(weights_).item<double>();
weights_ = weights_ / totalWeights;
// Step 3.4: Store classifier and its accuracy to weigh its future vote
models.push_back(std::move(model));
significanceModels.push_back(alpha_t);
n_models++;
if (convergence) {
auto y_val_predict = predict(X_test);
double accuracy = (y_val_predict == y_test).sum().item<double>() / (double)y_test.size(0);
if (priorAccuracy == 0) {
priorAccuracy = accuracy;
} else {
delta = accuracy - priorAccuracy;
}
if (delta < threshold) {
count++;
}
}
exitCondition = n_models >= maxModels && repeatSparent || epsilon_t > 0.5 || count > tolerance;
}
if (featuresUsed.size() != features.size()) {
status = WARNING;
}
}
std::vector<std::string> BoostAODE::graph(const std::string& title) const
{
return Ensemble::graph(title);
}
}

View File

@@ -1,33 +0,0 @@
#ifndef BOOSTAODE_H
#define BOOSTAODE_H
#include "Ensemble.h"
#include <map>
#include "SPODE.h"
#include "FeatureSelect.h"
namespace bayesnet {
class BoostAODE : public Ensemble {
public:
BoostAODE();
virtual ~BoostAODE() = default;
std::vector<std::string> graph(const std::string& title = "BoostAODE") const override;
void setHyperparameters(const nlohmann::json& hyperparameters) override;
protected:
void buildModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights) override;
private:
torch::Tensor dataset_;
torch::Tensor X_train, y_train, X_test, y_test;
std::unordered_set<int> initializeModels();
// Hyperparameters
bool repeatSparent = false; // if true, a feature can be selected more than once
int maxModels = 0;
int tolerance = 0;
bool ascending = false; //Process KBest features ascending or descending order
bool convergence = false; //if true, stop when the model does not improve
bool selectFeatures = false; // if true, use feature selection
std::string algorithm = ""; // Selected feature selection algorithm
FeatureSelect* featureSelector = nullptr;
double threshold = -1;
};
}
#endif

View File

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

View File

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

View File

@@ -1,12 +1,2 @@
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/src/PyClassifiers)
include_directories(${Python3_INCLUDE_DIRS})
add_library(BayesNet bayesnetUtils.cc Network.cc Node.cc BayesMetrics.cc Classifier.cc
KDB.cc TAN.cc SPODE.cc Ensemble.cc AODE.cc TANLd.cc KDBLd.cc SPODELd.cc AODELd.cc BoostAODE.cc
Mst.cc Proposal.cc CFS.cc FCBF.cc IWSS.cc FeatureSelect.cc ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNet mdlp "${TORCH_LIBRARIES}")
add_library(BayesNet bayesnetUtils.cc Network.cc Node.cc BayesMetrics.cc Classifier.cc KDB.cc TAN.cc SPODE.cc Ensemble.cc AODE.cc Mst.cc)
target_link_libraries(BayesNet "${TORCH_LIBRARIES}")

View File

@@ -2,159 +2,146 @@
#include "bayesnetUtils.h"
namespace bayesnet {
Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false) {}
Classifier& Classifier::build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
using namespace torch;
Classifier::Classifier(const 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)
{
dataset = torch::cat({ X, y.view({y.size(0), 1}) }, 1);
this->features = features;
this->className = className;
this->states = states;
m = dataset.size(1);
n = dataset.size(0) - 1;
checkFitParameters();
auto n_classes = states.at(className).size();
auto n_classes = states[className].size();
metrics = Metrics(dataset, features, className, n_classes);
model.initialize();
buildModel(weights);
trainModel(weights);
train();
if (Xv == vector<vector<int>>()) {
// fit with tensors
model.fit(X, y, features, className);
} else {
// fit with vectors
model.fit(Xv, yv, features, className);
}
fitted = true;
return *this;
}
void Classifier::buildDataset(torch::Tensor& ytmp)
Classifier& Classifier::fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states)
{
try {
auto yresized = torch::transpose(ytmp.view({ ytmp.size(0), 1 }), 0, 1);
dataset = torch::cat({ dataset, yresized }, 0);
}
catch (const std::exception& e) {
std::cerr << e.what() << '\n';
std::cout << "X dimensions: " << dataset.sizes() << "\n";
std::cout << "y dimensions: " << ytmp.sizes() << "\n";
exit(1);
}
this->X = torch::transpose(X, 0, 1);
this->y = y;
Xv = vector<vector<int>>();
yv = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
return build(features, className, states);
}
void Classifier::trainModel(const torch::Tensor& weights)
Classifier& Classifier::fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& 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, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
{
dataset = X;
buildDataset(y);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
{
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, torch::kInt32);
this->X = torch::zeros({ static_cast<int>(X[0].size()), static_cast<int>(X.size()) }, kInt32);
Xv = X;
for (int i = 0; i < X.size(); ++i) {
dataset.index_put_({ i, "..." }, torch::tensor(X[i], torch::kInt32));
this->X.index_put_({ "...", i }, torch::tensor(X[i], kInt32));
}
auto ytmp = torch::tensor(y, torch::kInt32);
buildDataset(ytmp);
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
}
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states)
{
this->dataset = dataset;
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
return build(features, className, states, weights);
}
Classifier& Classifier::fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
{
this->dataset = dataset;
return build(features, className, states, weights);
this->y = torch::tensor(y, kInt32);
yv = y;
return build(features, className, states);
}
void Classifier::checkFitParameters()
{
if (torch::is_floating_point(dataset)) {
throw std::invalid_argument("dataset (X, y) must be of type Integer");
auto sizes = X.sizes();
m = sizes[0];
n = sizes[1];
if (m != y.size(0)) {
throw invalid_argument("X and y must have the same number of samples");
}
if (n != features.size()) {
throw std::invalid_argument("Classifier: X " + std::to_string(n) + " and features " + std::to_string(features.size()) + " must have the same number of features");
throw invalid_argument("X and features must have the same number of features");
}
if (states.find(className) == states.end()) {
throw std::invalid_argument("className not found in states");
throw invalid_argument("className not found in states");
}
for (auto feature : features) {
if (states.find(feature) == states.end()) {
throw std::invalid_argument("feature [" + feature + "] not found in states");
throw invalid_argument("feature [" + feature + "] not found in states");
}
}
}
torch::Tensor Classifier::predict(torch::Tensor& X)
Tensor Classifier::predict(Tensor& X)
{
if (!fitted) {
throw std::logic_error("Classifier has not been fitted");
throw logic_error("Classifier has not been fitted");
}
return model.predict(X);
auto m_ = X.size(0);
auto n_ = X.size(1);
//auto Xt = torch::transpose(X, 0, 1);
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
auto temp = X.index({ "...", i });
Xd[i] = vector<int>(temp.data_ptr<int>(), temp.data_ptr<int>() + temp.numel());
}
auto yp = model.predict(Xd);
auto ypred = torch::tensor(yp, torch::kInt32);
return ypred;
}
std::vector<int> Classifier::predict(std::vector<std::vector<int>>& X)
vector<int> Classifier::predict(vector<vector<int>>& X)
{
if (!fitted) {
throw std::logic_error("Classifier has not been fitted");
throw logic_error("Classifier has not been fitted");
}
auto m_ = X[0].size();
auto n_ = X.size();
std::vector<std::vector<int>> Xd(n_, std::vector<int>(m_, 0));
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = std::vector<int>(X[i].begin(), X[i].end());
Xd[i] = vector<int>(X[i].begin(), X[i].end());
}
auto yp = model.predict(Xd);
return yp;
}
float Classifier::score(torch::Tensor& X, torch::Tensor& y)
float Classifier::score(Tensor& X, Tensor& y)
{
if (!fitted) {
throw std::logic_error("Classifier has not been fitted");
throw logic_error("Classifier has not been fitted");
}
torch::Tensor y_pred = predict(X);
auto Xt = torch::transpose(X, 0, 1);
Tensor y_pred = predict(Xt);
return (y_pred == y).sum().item<float>() / y.size(0);
}
float Classifier::score(std::vector<std::vector<int>>& X, std::vector<int>& y)
float Classifier::score(vector<vector<int>>& X, vector<int>& y)
{
if (!fitted) {
throw std::logic_error("Classifier has not been fitted");
throw logic_error("Classifier has not been fitted");
}
return model.score(X, y);
auto m_ = X[0].size();
auto n_ = X.size();
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = vector<int>(X[i].begin(), X[i].end());
}
return model.score(Xd, y);
}
std::vector<std::string> Classifier::show() const
vector<string> Classifier::show()
{
return model.show();
}
void Classifier::addNodes()
{
// Add all nodes to the network
for (const auto& feature : features) {
model.addNode(feature);
for (auto feature : features) {
model.addNode(feature, states[feature].size());
}
model.addNode(className);
model.addNode(className, states[className].size());
}
int Classifier::getNumberOfNodes() const
int Classifier::getNumberOfNodes()
{
// Features does not include class
return fitted ? model.getFeatures().size() : 0;
return fitted ? model.getFeatures().size() + 1 : 0;
}
int Classifier::getNumberOfEdges() const
int Classifier::getNumberOfEdges()
{
return fitted ? model.getNumEdges() : 0;
return fitted ? model.getEdges().size() : 0;
}
int Classifier::getNumberOfStates() const
int Classifier::getNumberOfStates()
{
return fitted ? model.getStates() : 0;
}
std::vector<std::string> Classifier::topological_order()
{
return model.topological_sort();
}
void Classifier::dump_cpt() const
{
model.dump_cpt();
}
void Classifier::setHyperparameters(const nlohmann::json& hyperparameters)
{
//For classifiers that don't have hyperparameters
}
}

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@@ -4,46 +4,42 @@
#include "BaseClassifier.h"
#include "Network.h"
#include "BayesMetrics.h"
using namespace std;
using namespace torch;
namespace bayesnet {
class Classifier : public BaseClassifier {
private:
Classifier& build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
protected:
bool fitted;
int m, n; // m: number of samples, n: number of features
Classifier& build(vector<string>& features, string className, map<string, vector<int>>& states);
protected:
Network model;
int m, n; // m: number of samples, n: number of features
Tensor X;
vector<vector<int>> Xv;
Tensor y;
vector<int> yv;
Tensor dataset;
Metrics metrics;
std::vector<std::string> features;
std::string className;
std::map<std::string, std::vector<int>> states;
torch::Tensor dataset; // (n+1)xm tensor
status_t status = NORMAL;
vector<string> features;
string className;
map<string, vector<int>> states;
void checkFitParameters();
virtual void buildModel(const torch::Tensor& weights) = 0;
void trainModel(const torch::Tensor& weights) override;
void buildDataset(torch::Tensor& y);
virtual void train() = 0;
public:
Classifier(Network model);
Classifier(const Network& model);
virtual ~Classifier() = default;
Classifier& fit(std::vector<std::vector<int>>& X, std::vector<int>& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights) override;
Classifier& fit(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;
void addNodes();
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
torch::Tensor predict(torch::Tensor& X) override;
status_t getStatus() const override { return status; }
std::string getVersion() override { return "0.2.0"; };
std::vector<int> predict(std::vector<std::vector<int>>& X) override;
float score(torch::Tensor& X, torch::Tensor& y) override;
float score(std::vector<std::vector<int>>& X, std::vector<int>& y) override;
std::vector<std::string> show() const override;
std::vector<std::string> topological_order() override;
void dump_cpt() const override;
void setHyperparameters(const nlohmann::json& hyperparameters) override; //For classifiers that don't have hyperparameters
int getNumberOfNodes() override;
int getNumberOfEdges() override;
int getNumberOfStates() override;
Tensor predict(Tensor& X);
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() override;
};
}
#endif

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@@ -1,77 +1,92 @@
#include "Ensemble.h"
namespace bayesnet {
using namespace torch;
Ensemble::Ensemble() : Classifier(Network()), n_models(0) {}
void Ensemble::trainModel(const torch::Tensor& weights)
Ensemble::Ensemble() : m(0), n(0), n_models(0), metrics(Metrics()), fitted(false) {}
Ensemble& Ensemble::build(vector<string>& features, string className, map<string, vector<int>>& states)
{
dataset = cat({ X, y.view({y.size(0), 1}) }, 1);
this->features = features;
this->className = className;
this->states = states;
auto n_classes = states[className].size();
metrics = Metrics(dataset, features, className, n_classes);
// Build models
train();
// Train models
n_models = models.size();
for (auto i = 0; i < n_models; ++i) {
// fit with std::vectors
models[i]->fit(dataset, features, className, states);
models[i]->fit(Xv, yv, features, className, states);
}
fitted = true;
return *this;
}
std::vector<int> Ensemble::voting(torch::Tensor& y_pred)
Ensemble& Ensemble::fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states)
{
this->X = X;
this->y = y;
Xv = vector<vector<int>>();
yv = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
return build(features, className, states);
}
Ensemble& Ensemble::fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states)
{
this->X = torch::zeros({ static_cast<int>(X[0].size()), static_cast<int>(X.size()) }, kInt32);
Xv = X;
for (int i = 0; i < X.size(); ++i) {
this->X.index_put_({ "...", i }, torch::tensor(X[i], kInt32));
}
this->y = torch::tensor(y, kInt32);
yv = y;
return build(features, className, states);
}
Tensor Ensemble::predict(Tensor& X)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
}
Tensor y_pred = torch::zeros({ X.size(0), n_models }, kInt32);
for (auto i = 0; i < n_models; ++i) {
y_pred.index_put_({ "...", i }, models[i]->predict(X));
}
return torch::tensor(voting(y_pred));
}
vector<int> Ensemble::voting(Tensor& y_pred)
{
auto y_pred_ = y_pred.accessor<int, 2>();
std::vector<int> y_pred_final;
int numClasses = states.at(className).size();
// y_pred is m x n_models with the prediction of every model for each sample
vector<int> y_pred_final;
for (int i = 0; i < y_pred.size(0); ++i) {
// votes store in each index (value of class) the significance added by each model
// i.e. votes[0] contains how much value has the value 0 of class. That value is generated by the models predictions
std::vector<double> votes(numClasses, 0.0);
for (int j = 0; j < n_models; ++j) {
votes[y_pred_[i][j]] += significanceModels.at(j);
vector<float> votes(states[className].size(), 0);
for (int j = 0; j < y_pred.size(1); ++j) {
votes[y_pred_[i][j]] += 1;
}
// argsort in descending order
auto indices = argsort(votes);
y_pred_final.push_back(indices[0]);
}
return y_pred_final;
}
torch::Tensor Ensemble::predict(torch::Tensor& X)
vector<int> Ensemble::predict(vector<vector<int>>& X)
{
if (!fitted) {
throw std::logic_error("Ensemble has not been fitted");
}
torch::Tensor y_pred = torch::zeros({ X.size(1), n_models }, torch::kInt32);
auto threads{ std::vector<std::thread>() };
std::mutex mtx;
for (auto i = 0; i < n_models; ++i) {
threads.push_back(std::thread([&, i]() {
auto ypredict = models[i]->predict(X);
std::lock_guard<std::mutex> lock(mtx);
y_pred.index_put_({ "...", i }, ypredict);
}));
}
for (auto& thread : threads) {
thread.join();
}
return torch::tensor(voting(y_pred));
}
std::vector<int> Ensemble::predict(std::vector<std::vector<int>>& X)
{
if (!fitted) {
throw std::logic_error("Ensemble has not been fitted");
throw logic_error("Ensemble has not been fitted");
}
long m_ = X[0].size();
long n_ = X.size();
std::vector<std::vector<int>> Xd(n_, std::vector<int>(m_, 0));
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = std::vector<int>(X[i].begin(), X[i].end());
Xd[i] = vector<int>(X[i].begin(), X[i].end());
}
torch::Tensor y_pred = torch::zeros({ m_, n_models }, torch::kInt32);
Tensor y_pred = torch::zeros({ m_, n_models }, kInt32);
for (auto i = 0; i < n_models; ++i) {
y_pred.index_put_({ "...", i }, torch::tensor(models[i]->predict(Xd), torch::kInt32));
y_pred.index_put_({ "...", i }, torch::tensor(models[i]->predict(Xd), kInt32));
}
return voting(y_pred);
}
float Ensemble::score(torch::Tensor& X, torch::Tensor& y)
float Ensemble::score(Tensor& X, Tensor& y)
{
if (!fitted) {
throw std::logic_error("Ensemble has not been fitted");
throw logic_error("Ensemble has not been fitted");
}
auto y_pred = predict(X);
int correct = 0;
@@ -82,10 +97,10 @@ namespace bayesnet {
}
return (double)correct / y_pred.size(0);
}
float Ensemble::score(std::vector<std::vector<int>>& X, std::vector<int>& y)
float Ensemble::score(vector<vector<int>>& X, vector<int>& y)
{
if (!fitted) {
throw std::logic_error("Ensemble has not been fitted");
throw logic_error("Ensemble has not been fitted");
}
auto y_pred = predict(X);
int correct = 0;
@@ -95,26 +110,27 @@ namespace bayesnet {
}
}
return (double)correct / y_pred.size();
}
std::vector<std::string> Ensemble::show() const
vector<string> Ensemble::show()
{
auto result = std::vector<std::string>();
auto result = vector<string>();
for (auto i = 0; i < n_models; ++i) {
auto res = models[i]->show();
result.insert(result.end(), res.begin(), res.end());
}
return result;
}
std::vector<std::string> Ensemble::graph(const std::string& title) const
vector<string> Ensemble::graph(string title)
{
auto result = std::vector<std::string>();
auto result = vector<string>();
for (auto i = 0; i < n_models; ++i) {
auto res = models[i]->graph(title + "_" + std::to_string(i));
auto res = models[i]->graph(title + "_" + to_string(i));
result.insert(result.end(), res.begin(), res.end());
}
return result;
}
int Ensemble::getNumberOfNodes() const
int Ensemble::getNumberOfNodes()
{
int nodes = 0;
for (auto i = 0; i < n_models; ++i) {
@@ -122,7 +138,7 @@ namespace bayesnet {
}
return nodes;
}
int Ensemble::getNumberOfEdges() const
int Ensemble::getNumberOfEdges()
{
int edges = 0;
for (auto i = 0; i < n_models; ++i) {
@@ -130,7 +146,7 @@ namespace bayesnet {
}
return edges;
}
int Ensemble::getNumberOfStates() const
int Ensemble::getNumberOfStates()
{
int nstates = 0;
for (auto i = 0; i < n_models; ++i) {

View File

@@ -4,36 +4,43 @@
#include "Classifier.h"
#include "BayesMetrics.h"
#include "bayesnetUtils.h"
using namespace std;
using namespace torch;
namespace bayesnet {
class Ensemble : public Classifier {
class Ensemble : public BaseClassifier {
private:
Ensemble& build(std::vector<std::string>& features, std::string className, std::map<std::string, std::vector<int>>& states);
bool fitted;
long n_models;
Ensemble& build(vector<string>& features, string className, map<string, vector<int>>& states);
protected:
unsigned n_models;
std::vector<std::unique_ptr<Classifier>> models;
std::vector<double> significanceModels;
void trainModel(const torch::Tensor& weights) override;
std::vector<int> voting(torch::Tensor& y_pred);
vector<unique_ptr<Classifier>> models;
int m, n; // m: number of samples, n: number of features
Tensor X;
vector<vector<int>> Xv;
Tensor y;
vector<int> yv;
Tensor dataset;
Metrics metrics;
vector<string> features;
string className;
map<string, vector<int>> states;
void virtual train() = 0;
vector<int> voting(Tensor& y_pred);
public:
Ensemble();
virtual ~Ensemble() = default;
torch::Tensor predict(torch::Tensor& X) override;
std::vector<int> predict(std::vector<std::vector<int>>& X) override;
float score(torch::Tensor& X, torch::Tensor& y) override;
float score(std::vector<std::vector<int>>& X, std::vector<int>& y) override;
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
std::vector<std::string> show() const override;
std::vector<std::string> graph(const std::string& title) const override;
std::vector<std::string> topological_order() override
{
return std::vector<std::string>();
}
void dump_cpt() const override
{
}
Ensemble& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Ensemble& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Tensor predict(Tensor& X);
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;
int getNumberOfNodes() override;
int getNumberOfEdges() override;
int getNumberOfStates() override;
vector<string> show() override;
vector<string> graph(string title) override;
};
}
#endif

View File

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

View File

@@ -1,17 +0,0 @@
#ifndef FCBF_H
#define FCBF_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
namespace bayesnet {
class FCBF : public FeatureSelect {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
FCBF(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights, const double threshold);
virtual ~FCBF() {};
void fit() override;
private:
double threshold = -1;
};
}
#endif

View File

@@ -1,79 +0,0 @@
#include "FeatureSelect.h"
#include <limits>
#include "bayesnetUtils.h"
namespace bayesnet {
FeatureSelect::FeatureSelect(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights) :
Metrics(samples, features, className, classNumStates), maxFeatures(maxFeatures == 0 ? samples.size(0) - 1 : maxFeatures), weights(weights)
{
}
void FeatureSelect::initialize()
{
selectedFeatures.clear();
selectedScores.clear();
}
double FeatureSelect::symmetricalUncertainty(int a, int b)
{
/*
Compute symmetrical uncertainty. Normalize* information gain (mutual
information) with the entropies of the features in order to compensate
the bias due to high cardinality features. *Range [0, 1]
(https://www.sciencedirect.com/science/article/pii/S0020025519303603)
*/
auto x = samples.index({ a, "..." });
auto y = samples.index({ b, "..." });
auto mu = mutualInformation(x, y, weights);
auto hx = entropy(x, weights);
auto hy = entropy(y, weights);
return 2.0 * mu / (hx + hy);
}
void FeatureSelect::computeSuLabels()
{
// Compute Simmetrical Uncertainty between features and labels
// https://en.wikipedia.org/wiki/Symmetric_uncertainty
for (int i = 0; i < features.size(); ++i) {
suLabels.push_back(symmetricalUncertainty(i, -1));
}
}
double FeatureSelect::computeSuFeatures(const int firstFeature, const int secondFeature)
{
// Compute Simmetrical Uncertainty between features
// https://en.wikipedia.org/wiki/Symmetric_uncertainty
try {
return suFeatures.at({ firstFeature, secondFeature });
}
catch (const std::out_of_range& e) {
double result = symmetricalUncertainty(firstFeature, secondFeature);
suFeatures[{firstFeature, secondFeature}] = result;
return result;
}
}
double FeatureSelect::computeMeritCFS()
{
double result;
double rcf = 0;
for (auto feature : selectedFeatures) {
rcf += suLabels[feature];
}
double rff = 0;
int n = selectedFeatures.size();
for (const auto& item : doCombinations(selectedFeatures)) {
rff += computeSuFeatures(item.first, item.second);
}
return rcf / sqrt(n + (n * n - n) * rff);
}
std::vector<int> FeatureSelect::getFeatures() const
{
if (!fitted) {
throw std::runtime_error("FeatureSelect not fitted");
}
return selectedFeatures;
}
std::vector<double> FeatureSelect::getScores() const
{
if (!fitted) {
throw std::runtime_error("FeatureSelect not fitted");
}
return selectedScores;
}
}

View File

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

View File

@@ -1,47 +0,0 @@
#include "IWSS.h"
#include <limits>
#include "bayesnetUtils.h"
namespace bayesnet {
IWSS::IWSS(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights, const double threshold) :
FeatureSelect(samples, features, className, maxFeatures, classNumStates, weights), threshold(threshold)
{
if (threshold < 0 || threshold > .5) {
throw std::invalid_argument("Threshold has to be in [0, 0.5]");
}
}
void IWSS::fit()
{
initialize();
computeSuLabels();
auto featureOrder = argsort(suLabels); // sort descending order
auto featureOrderCopy = featureOrder;
// Add first and second features to result
// First with its own score
auto first_feature = pop_first(featureOrderCopy);
selectedFeatures.push_back(first_feature);
selectedScores.push_back(suLabels.at(first_feature));
// Second with the score of the candidates
selectedFeatures.push_back(pop_first(featureOrderCopy));
auto merit = computeMeritCFS();
selectedScores.push_back(merit);
for (const auto feature : featureOrderCopy) {
selectedFeatures.push_back(feature);
// Compute merit with selectedFeatures
auto meritNew = computeMeritCFS();
double delta = merit != 0.0 ? abs(merit - meritNew) / merit : 0.0;
if (meritNew > merit || delta < threshold) {
if (meritNew > merit) {
merit = meritNew;
}
selectedScores.push_back(meritNew);
} else {
selectedFeatures.pop_back();
break;
}
if (selectedFeatures.size() == maxFeatures) {
break;
}
}
fitted = true;
}
}

View File

@@ -1,17 +0,0 @@
#ifndef IWSS_H
#define IWSS_H
#include <torch/torch.h>
#include <vector>
#include "FeatureSelect.h"
namespace bayesnet {
class IWSS : public FeatureSelect {
public:
// dataset is a n+1xm tensor of integers where dataset[-1] is the y std::vector
IWSS(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights, const double threshold);
virtual ~IWSS() {};
void fit() override;
private:
double threshold = -1;
};
}
#endif

View File

@@ -1,21 +1,10 @@
#include "KDB.h"
namespace bayesnet {
KDB::KDB(int k, float theta) : Classifier(Network()), k(k), theta(theta)
{
validHyperparameters = { "k", "theta" };
using namespace torch;
}
void KDB::setHyperparameters(const nlohmann::json& hyperparameters)
{
if (hyperparameters.contains("k")) {
k = hyperparameters["k"];
}
if (hyperparameters.contains("theta")) {
theta = hyperparameters["theta"];
}
}
void KDB::buildModel(const torch::Tensor& weights)
KDB::KDB(int k, float theta) : Classifier(Network()), k(k), theta(theta) {}
void KDB::train()
{
/*
1. For each feature Xi, compute mutual information, I(X;C),
@@ -38,25 +27,25 @@ namespace bayesnet {
*/
// 1. For each feature Xi, compute mutual information, I(X;C),
// where C is the class.
addNodes();
const torch::Tensor& y = dataset.index({ -1, "..." });
std::vector<double> mi;
vector <float> mi;
for (auto i = 0; i < features.size(); i++) {
torch::Tensor firstFeature = dataset.index({ i, "..." });
mi.push_back(metrics.mutualInformation(firstFeature, y, weights));
Tensor firstFeature = X.index({ "...", i });
mi.push_back(metrics.mutualInformation(firstFeature, y));
}
// 2. Compute class conditional mutual information I(Xi;XjIC), f or each
auto conditionalEdgeWeights = metrics.conditionalEdge(weights);
auto conditionalEdgeWeights = metrics.conditionalEdge();
// 3. Let the used variable list, S, be empty.
std::vector<int> S;
vector<int> S;
// 4. Let the DAG network being constructed, BN, begin with a single
// class node, C.
model.addNode(className, states[className].size());
// 5. Repeat until S includes all domain features
// 5.1. Select feature Xmax which is not in S and has the largest value
// I(Xmax;C).
auto order = argsort(mi);
for (auto idx : order) {
// 5.2. Add a node to BN representing Xmax.
model.addNode(features[idx], states[features[idx]].size());
// 5.3. Add an arc from C to Xmax in BN.
model.addEdge(className, features[idx]);
// 5.4. Add m = min(lSl,/c) arcs from m distinct features Xj in S with
@@ -66,9 +55,9 @@ namespace bayesnet {
S.push_back(idx);
}
}
void KDB::add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights)
void KDB::add_m_edges(int idx, vector<int>& S, Tensor& weights)
{
auto n_edges = std::min(k, static_cast<int>(S.size()));
auto n_edges = min(k, static_cast<int>(S.size()));
auto cond_w = clone(weights);
bool exit_cond = k == 0;
int num = 0;
@@ -80,7 +69,7 @@ namespace bayesnet {
model.addEdge(features[max_minfo], features[idx]);
num++;
}
catch (const std::invalid_argument& e) {
catch (const invalid_argument& e) {
// Loops are not allowed
}
}
@@ -90,12 +79,11 @@ namespace bayesnet {
exit_cond = num == n_edges || candidates.size(0) == 0;
}
}
std::vector<std::string> KDB::graph(const std::string& title) const
vector<string> KDB::graph(string title)
{
std::string header{ title };
if (title == "KDB") {
header += " (k=" + std::to_string(k) + ", theta=" + std::to_string(theta) + ")";
title += " (k=" + to_string(k) + ", theta=" + to_string(theta) + ")";
}
return model.graph(header);
return model.graph(title);
}
}

View File

@@ -1,21 +1,20 @@
#ifndef KDB_H
#define KDB_H
#include <torch/torch.h>
#include "Classifier.h"
#include "bayesnetUtils.h"
namespace bayesnet {
using namespace std;
using namespace torch;
class KDB : public Classifier {
private:
int k;
float theta;
void add_m_edges(int idx, std::vector<int>& S, torch::Tensor& weights);
void add_m_edges(int idx, vector<int>& S, Tensor& weights);
protected:
void buildModel(const torch::Tensor& weights) override;
void train() override;
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() = default;
void setHyperparameters(const nlohmann::json& hyperparameters) override;
std::vector<std::string> graph(const std::string& name = "KDB") const override;
vector<string> graph(string name = "KDB") override;
};
}
#endif

View File

@@ -1,29 +0,0 @@
#include "KDBLd.h"
namespace bayesnet {
KDBLd::KDBLd(int k) : KDB(k), Proposal(dataset, features, className) {}
KDBLd& KDBLd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal KDB structure, KDB::fit initializes the base Bayesian network
KDB::fit(dataset, features, className, states);
states = localDiscretizationProposal(states, model);
return *this;
}
torch::Tensor KDBLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return KDB::predict(Xt);
}
std::vector<std::string> KDBLd::graph(const std::string& name) const
{
return KDB::graph(name);
}
}

View File

@@ -1,18 +0,0 @@
#ifndef KDBLD_H
#define KDBLD_H
#include "KDB.h"
#include "Proposal.h"
namespace bayesnet {
class KDBLd : public KDB, public Proposal {
private:
public:
explicit KDBLd(int k);
virtual ~KDBLd() = default;
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states) override;
std::vector<std::string> graph(const std::string& name = "KDB") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !KDBLD_H

View File

@@ -1,13 +1,13 @@
#include "Mst.h"
#include <vector>
#include <list>
/*
Based on the code from https://www.softwaretestinghelp.com/minimum-spanning-tree-tutorial/
*/
namespace bayesnet {
Graph::Graph(int V) : V(V), parent(std::vector<int>(V))
using namespace std;
Graph::Graph(int V) : V(V), parent{ vector<int>(V) }
{
for (int i = 0; i < V; i++)
parent[i] = i;
@@ -33,46 +33,38 @@ namespace bayesnet {
}
void Graph::kruskal_algorithm()
{
int i;
// sort the edges ordered on decreasing weight
stable_sort(G.begin(), G.end(), [](const auto& left, const auto& right) {return left.first > right.first;});
for (int i = 0; i < G.size(); i++) {
sort(G.begin(), G.end(), [](const auto& left, const auto& right) {return left.first > right.first;});
for (i = 0; i < G.size(); i++) {
int uSt, vEd;
uSt = find_set(G[i].second.first);
vEd = find_set(G[i].second.second);
if (uSt != vEd) {
T.push_back(G[i]); // add to mst std::vector
T.push_back(G[i]); // add to mst vector
union_set(uSt, vEd);
}
}
}
void Graph::display_mst()
{
std::cout << "Edge :" << " Weight" << std::endl;
cout << "Edge :" << " Weight" << endl;
for (int i = 0; i < T.size(); i++) {
std::cout << T[i].second.first << " - " << T[i].second.second << " : "
cout << T[i].second.first << " - " << T[i].second.second << " : "
<< T[i].first;
std::cout << std::endl;
cout << endl;
}
}
void insertElement(std::list<int>& variables, int variable)
vector<pair<int, int>> reorder(vector<pair<float, pair<int, int>>> T, int root_original)
{
if (std::find(variables.begin(), variables.end(), variable) == variables.end()) {
variables.push_front(variable);
}
}
std::vector<std::pair<int, int>> reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original)
{
// Create the edges of a DAG from the MST
// replacing unordered_set with list because unordered_set cannot guarantee the order of the elements inserted
auto result = std::vector<std::pair<int, int>>();
auto visited = std::vector<int>();
auto nextVariables = std::list<int>();
nextVariables.push_front(root_original);
auto result = vector<pair<int, int>>();
auto visited = vector<int>();
auto nextVariables = unordered_set<int>();
nextVariables.emplace(root_original);
while (nextVariables.size() > 0) {
int root = nextVariables.front();
nextVariables.pop_front();
int root = *nextVariables.begin();
nextVariables.erase(nextVariables.begin());
for (int i = 0; i < T.size(); ++i) {
auto [weight, edge] = T[i];
auto [from, to] = edge;
@@ -80,10 +72,10 @@ namespace bayesnet {
visited.insert(visited.begin(), i);
if (from == root) {
result.push_back({ from, to });
insertElement(nextVariables, to);
nextVariables.emplace(to);
} else {
result.push_back({ to, from });
insertElement(nextVariables, from);
nextVariables.emplace(from);
}
}
}
@@ -103,11 +95,12 @@ namespace bayesnet {
return result;
}
MST::MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root) : features(features), weights(weights), root(root) {}
std::vector<std::pair<int, int>> MST::maximumSpanningTree()
MST::MST(vector<string>& features, Tensor& weights, int root) : features(features), weights(weights), root(root) {}
vector<pair<int, int>> MST::maximumSpanningTree()
{
auto num_features = features.size();
Graph g(num_features);
// Make a complete graph
for (int i = 0; i < num_features - 1; ++i) {
for (int j = i + 1; j < num_features; ++j) {

View File

@@ -4,22 +4,23 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
using namespace torch;
class MST {
private:
torch::Tensor weights;
std::vector<std::string> features;
int root = 0;
Tensor weights;
vector<string> features;
int root;
public:
MST() = default;
MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
std::vector<std::pair<int, int>> maximumSpanningTree();
MST(vector<string>& features, Tensor& weights, int root);
vector<pair<int, int>> maximumSpanningTree();
};
class Graph {
private:
int V; // number of nodes in graph
std::vector <std::pair<float, std::pair<int, int>>> G; // std::vector for graph
std::vector <std::pair<float, std::pair<int, int>>> T; // std::vector for mst
std::vector<int> parent;
vector <pair<float, pair<int, int>>> G; // vector for graph
vector <pair<float, pair<int, int>>> T; // vector for mst
vector<int> parent;
public:
explicit Graph(int V);
void addEdge(int u, int v, float wt);
@@ -27,7 +28,7 @@ namespace bayesnet {
void union_set(int u, int v);
void kruskal_algorithm();
void display_mst();
std::vector <std::pair<float, std::pair<int, int>>> get_mst() { return T; }
vector <pair<float, pair<int, int>>> get_mst() { return T; }
};
}
#endif

View File

@@ -3,24 +3,15 @@
#include "Network.h"
#include "bayesnetUtils.h"
namespace bayesnet {
Network::Network() : features(std::vector<std::string>()), className(""), classNumStates(0), fitted(false), laplaceSmoothing(0) {}
Network::Network(float maxT) : features(std::vector<std::string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false), laplaceSmoothing(0) {}
Network::Network(Network& other) : laplaceSmoothing(other.laplaceSmoothing), features(other.features), className(other.className), classNumStates(other.getClassNumStates()), maxThreads(other.
getmaxThreads()), fitted(other.fitted)
Network::Network() : laplaceSmoothing(1), features(vector<string>()), className(""), classNumStates(0), maxThreads(0.8), fitted(false) {}
Network::Network(const float maxT) : laplaceSmoothing(1), features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network(const float maxT, const int smoothing) : laplaceSmoothing(smoothing), features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network(const Network& other) : laplaceSmoothing(other.laplaceSmoothing), features(other.features), className(other.className), classNumStates(other.classNumStates), maxThreads(other.maxThreads), fitted(other.fitted)
{
for (const auto& node : other.nodes) {
nodes[node.first] = std::make_unique<Node>(*node.second);
for (const auto& pair : other.nodes) {
nodes[pair.first] = std::make_unique<Node>(*pair.second);
}
}
void Network::initialize()
{
features = std::vector<std::string>();
className = "";
classNumStates = 0;
fitted = false;
nodes.clear();
samples = torch::Tensor();
}
float Network::getmaxThreads()
{
return maxThreads;
@@ -29,28 +20,28 @@ namespace bayesnet {
{
return samples;
}
void Network::addNode(const std::string& name)
void Network::addNode(const string& name, const int numStates)
{
if (name == "") {
throw std::invalid_argument("Node name cannot be empty");
}
if (nodes.find(name) != nodes.end()) {
return;
}
if (find(features.begin(), features.end(), name) == features.end()) {
features.push_back(name);
}
nodes[name] = std::make_unique<Node>(name);
if (nodes.find(name) != nodes.end()) {
// if node exists update its number of states and remove parents, children and CPT
nodes[name]->clear();
nodes[name]->setNumStates(numStates);
return;
}
nodes[name] = std::make_unique<Node>(name, numStates);
}
std::vector<std::string> Network::getFeatures() const
vector<string> Network::getFeatures()
{
return features;
}
int Network::getClassNumStates() const
const int Network::getClassNumStates()
{
return classNumStates;
}
int Network::getStates() const
const int Network::getStates()
{
int result = 0;
for (auto& node : nodes) {
@@ -58,11 +49,11 @@ namespace bayesnet {
}
return result;
}
std::string Network::getClassName() const
const string Network::getClassName()
{
return className;
}
bool Network::isCyclic(const std::string& nodeId, std::unordered_set<std::string>& visited, std::unordered_set<std::string>& recStack)
bool Network::isCyclic(const string& nodeId, unordered_set<string>& visited, unordered_set<string>& recStack)
{
if (visited.find(nodeId) == visited.end()) // if node hasn't been visited yet
{
@@ -78,158 +69,124 @@ namespace bayesnet {
recStack.erase(nodeId); // remove node from recursion stack before function ends
return false;
}
void Network::addEdge(const std::string& parent, const std::string& child)
void Network::addEdge(const string& parent, const string& child)
{
if (nodes.find(parent) == nodes.end()) {
throw std::invalid_argument("Parent node " + parent + " does not exist");
throw invalid_argument("Parent node " + parent + " does not exist");
}
if (nodes.find(child) == nodes.end()) {
throw std::invalid_argument("Child node " + child + " does not exist");
throw invalid_argument("Child node " + child + " does not exist");
}
// Temporarily add edge to check for cycles
nodes[parent]->addChild(nodes[child].get());
nodes[child]->addParent(nodes[parent].get());
std::unordered_set<std::string> visited;
std::unordered_set<std::string> recStack;
unordered_set<string> visited;
unordered_set<string> recStack;
if (isCyclic(nodes[child]->getName(), visited, recStack)) // if adding this edge forms a cycle
{
// remove problematic edge
nodes[parent]->removeChild(nodes[child].get());
nodes[child]->removeParent(nodes[parent].get());
throw std::invalid_argument("Adding this edge forms a cycle in the graph.");
throw invalid_argument("Adding this edge forms a cycle in the graph.");
}
}
std::map<std::string, std::unique_ptr<Node>>& Network::getNodes()
map<string, std::unique_ptr<Node>>& Network::getNodes()
{
return nodes;
}
void Network::checkFitData(int n_samples, int n_features, int n_samples_y, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
void Network::fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& featureNames, const string& className)
{
if (weights.size(0) != n_samples) {
throw std::invalid_argument("Weights (" + std::to_string(weights.size(0)) + ") must have the same number of elements as samples (" + std::to_string(n_samples) + ") in Network::fit");
}
if (n_samples != n_samples_y) {
throw std::invalid_argument("X and y must have the same number of samples in Network::fit (" + std::to_string(n_samples) + " != " + std::to_string(n_samples_y) + ")");
}
if (n_features != featureNames.size()) {
throw std::invalid_argument("X and features must have the same number of features in Network::fit (" + std::to_string(n_features) + " != " + std::to_string(featureNames.size()) + ")");
}
if (n_features != features.size() - 1) {
throw std::invalid_argument("X and local features must have the same number of features in Network::fit (" + std::to_string(n_features) + " != " + std::to_string(features.size() - 1) + ")");
}
if (find(features.begin(), features.end(), className) == features.end()) {
throw std::invalid_argument("className not found in Network::features");
}
for (auto& feature : featureNames) {
if (find(features.begin(), features.end(), feature) == features.end()) {
throw std::invalid_argument("Feature " + feature + " not found in Network::features");
}
if (states.find(feature) == states.end()) {
throw std::invalid_argument("Feature " + feature + " not found in states");
}
}
}
void Network::setStates(const std::map<std::string, std::vector<int>>& states)
{
// Set states to every Node in the network
for_each(features.begin(), features.end(), [this, &states](const std::string& feature) {
nodes.at(feature)->setNumStates(states.at(feature).size());
});
classNumStates = nodes.at(className)->getNumStates();
}
// X comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
{
checkFitData(X.size(1), X.size(0), y.size(0), featureNames, className, states, weights);
features = featureNames;
this->className = className;
torch::Tensor ytmp = torch::transpose(y.view({ y.size(0), 1 }), 0, 1);
samples = torch::cat({ X , ytmp }, 0);
dataset.clear();
// Specific part
classNumStates = torch::max(y).item<int>() + 1;
samples = torch::cat({ X, y.view({ y.size(0), 1 }) }, 1);
for (int i = 0; i < featureNames.size(); ++i) {
auto row_feature = X.index({ i, "..." });
auto column = torch::flatten(X.index({ "...", i }));
auto k = vector<int>();
for (auto z = 0; z < X.size(0); ++z) {
k.push_back(column[z].item<int>());
}
dataset[featureNames[i]] = k;
}
completeFit(states, weights);
dataset[className] = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
completeFit();
}
void Network::fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
void Network::fit(const vector<vector<int>>& input_data, const vector<int>& labels, const vector<string>& featureNames, const string& className)
{
checkFitData(samples.size(1), samples.size(0) - 1, samples.size(1), featureNames, className, states, weights);
features = featureNames;
this->className = className;
this->samples = samples;
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 std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights_, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states)
{
const 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);
dataset.clear();
// Specific part
classNumStates = *max_element(labels.begin(), labels.end()) + 1;
// Build dataset & tensor of samples
samples = torch::zeros({ static_cast<int>(input_data[0].size()), static_cast<int>(input_data.size() + 1) }, torch::kInt32);
for (int i = 0; i < featureNames.size(); ++i) {
samples.index_put_({ i, "..." }, torch::tensor(input_data[i], torch::kInt32));
dataset[featureNames[i]] = input_data[i];
samples.index_put_({ "...", i }, torch::tensor(input_data[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
completeFit(states, weights);
dataset[className] = labels;
samples.index_put_({ "...", -1 }, torch::tensor(labels, torch::kInt32));
completeFit();
}
void Network::completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights)
void Network::completeFit()
{
setStates(states);
laplaceSmoothing = 1.0 / samples.size(1); // To use in CPT computation
std::vector<std::thread> threads;
for (auto& node : nodes) {
threads.emplace_back([this, &node, &weights]() {
node.second->computeCPT(samples, features, laplaceSmoothing, weights);
int maxThreadsRunning = static_cast<int>(std::thread::hardware_concurrency() * maxThreads);
if (maxThreadsRunning < 1) {
maxThreadsRunning = 1;
}
vector<thread> threads;
mutex mtx;
condition_variable cv;
int activeThreads = 0;
int nextNodeIndex = 0;
while (nextNodeIndex < nodes.size()) {
unique_lock<mutex> lock(mtx);
cv.wait(lock, [&activeThreads, &maxThreadsRunning]() { return activeThreads < maxThreadsRunning; });
if (nextNodeIndex >= nodes.size()) {
break; // No more work remaining
}
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(dataset, laplaceSmoothing);
lock.lock();
nodes[pair.first] = std::move(pair.second);
lock.unlock();
}
lock_guard<mutex> lock(mtx);
--activeThreads;
cv.notify_one();
});
++activeThreads;
}
for (auto& thread : threads) {
thread.join();
}
fitted = true;
}
torch::Tensor Network::predict_tensor(const torch::Tensor& samples, const bool proba)
vector<int> Network::predict(const vector<vector<int>>& tsamples)
{
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict()");
throw logic_error("You must call fit() before calling predict()");
}
torch::Tensor result;
result = torch::zeros({ samples.size(1), classNumStates }, torch::kFloat64);
for (int i = 0; i < samples.size(1); ++i) {
const torch::Tensor sample = samples.index({ "...", i });
auto psample = predict_sample(sample);
auto temp = torch::tensor(psample, torch::kFloat64);
// result.index_put_({ i, "..." }, torch::tensor(predict_sample(sample), torch::kFloat64));
result.index_put_({ i, "..." }, temp);
}
if (proba)
return result;
return result.argmax(1);
}
// Return mxn tensor of probabilities
torch::Tensor Network::predict_proba(const torch::Tensor& samples)
{
return predict_tensor(samples, true);
}
// Return mxn tensor of probabilities
torch::Tensor Network::predict(const torch::Tensor& samples)
{
return predict_tensor(samples, false);
}
// Return mx1 std::vector of predictions
// tsamples is nxm std::vector of samples
std::vector<int> Network::predict(const std::vector<std::vector<int>>& tsamples)
{
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict()");
}
std::vector<int> predictions;
std::vector<int> sample;
vector<int> predictions;
vector<int> sample;
for (int row = 0; row < tsamples[0].size(); ++row) {
sample.clear();
for (int col = 0; col < tsamples.size(); ++col) {
sample.push_back(tsamples[col][row]);
}
std::vector<double> classProbabilities = predict_sample(sample);
vector<double> classProbabilities = predict_sample(sample);
// Find the class with the maximum posterior probability
auto maxElem = max_element(classProbabilities.begin(), classProbabilities.end());
int predictedClass = distance(classProbabilities.begin(), maxElem);
@@ -237,14 +194,13 @@ namespace bayesnet {
}
return predictions;
}
// Return mxn std::vector of probabilities
std::vector<std::vector<double>> Network::predict_proba(const std::vector<std::vector<int>>& tsamples)
vector<vector<double>> Network::predict_proba(const vector<vector<int>>& tsamples)
{
if (!fitted) {
throw std::logic_error("You must call fit() before calling predict_proba()");
throw logic_error("You must call fit() before calling predict_proba()");
}
std::vector<std::vector<double>> predictions;
std::vector<int> sample;
vector<vector<double>> predictions;
vector<int> sample;
for (int row = 0; row < tsamples[0].size(); ++row) {
sample.clear();
for (int col = 0; col < tsamples.size(); ++col) {
@@ -254,9 +210,9 @@ namespace bayesnet {
}
return predictions;
}
double Network::score(const std::vector<std::vector<int>>& tsamples, const std::vector<int>& labels)
double Network::score(const vector<vector<int>>& tsamples, const vector<int>& labels)
{
std::vector<int> y_pred = predict(tsamples);
vector<int> y_pred = predict(tsamples);
int correct = 0;
for (int i = 0; i < y_pred.size(); ++i) {
if (y_pred[i] == labels[i]) {
@@ -265,35 +221,20 @@ namespace bayesnet {
}
return (double)correct / y_pred.size();
}
// Return 1xn std::vector of probabilities
std::vector<double> Network::predict_sample(const std::vector<int>& sample)
vector<double> Network::predict_sample(const vector<int>& sample)
{
// Ensure the sample size is equal to the number of features
if (sample.size() != features.size() - 1) {
throw std::invalid_argument("Sample size (" + std::to_string(sample.size()) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
if (sample.size() != features.size()) {
throw invalid_argument("Sample size (" + to_string(sample.size()) +
") does not match the number of features (" + to_string(features.size()) + ")");
}
std::map<std::string, int> evidence;
map<string, int> evidence;
for (int i = 0; i < sample.size(); ++i) {
evidence[features[i]] = sample[i];
}
return exactInference(evidence);
}
// Return 1xn std::vector of probabilities
std::vector<double> Network::predict_sample(const torch::Tensor& sample)
{
// Ensure the sample size is equal to the number of features
if (sample.size(0) != features.size() - 1) {
throw std::invalid_argument("Sample size (" + std::to_string(sample.size(0)) +
") does not match the number of features (" + std::to_string(features.size() - 1) + ")");
}
std::map<std::string, int> evidence;
for (int i = 0; i < sample.size(0); ++i) {
evidence[features[i]] = sample[i].item<int>();
}
return exactInference(evidence);
}
double Network::computeFactor(std::map<std::string, int>& completeEvidence)
double Network::computeFactor(map<string, int>& completeEvidence)
{
double result = 1.0;
for (auto& node : getNodes()) {
@@ -301,34 +242,35 @@ namespace bayesnet {
}
return result;
}
std::vector<double> Network::exactInference(std::map<std::string, int>& evidence)
vector<double> Network::exactInference(map<string, int>& evidence)
{
std::vector<double> result(classNumStates, 0.0);
std::vector<std::thread> threads;
std::mutex mtx;
vector<double> result(classNumStates, 0.0);
vector<thread> threads;
mutex mtx;
for (int i = 0; i < classNumStates; ++i) {
threads.emplace_back([this, &result, &evidence, i, &mtx]() {
auto completeEvidence = std::map<std::string, int>(evidence);
auto completeEvidence = map<string, int>(evidence);
completeEvidence[getClassName()] = i;
double factor = computeFactor(completeEvidence);
std::lock_guard<std::mutex> lock(mtx);
lock_guard<mutex> lock(mtx);
result[i] = factor;
});
}
for (auto& thread : threads) {
thread.join();
}
// Normalize result
double sum = accumulate(result.begin(), result.end(), 0.0);
transform(result.begin(), result.end(), result.begin(), [sum](const double& value) { return value / sum; });
transform(result.begin(), result.end(), result.begin(), [sum](double x) { return x / sum; });
return result;
}
std::vector<std::string> Network::show() const
vector<string> Network::show()
{
std::vector<std::string> result;
vector<string> result;
// Draw the network
for (auto& node : nodes) {
std::string line = node.first + " -> ";
string line = node.first + " -> ";
for (auto child : node.second->getChildren()) {
line += child->getName() + ", ";
}
@@ -336,12 +278,12 @@ namespace bayesnet {
}
return result;
}
std::vector<std::string> Network::graph(const std::string& title) const
vector<string> Network::graph(const string& title)
{
auto output = std::vector<std::string>();
auto output = vector<string>();
auto prefix = "digraph BayesNet {\nlabel=<BayesNet ";
auto suffix = ">\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n";
std::string header = prefix + title + suffix;
string header = prefix + title + suffix;
output.push_back(header);
for (auto& node : nodes) {
auto result = node.second->graph(className);
@@ -350,9 +292,9 @@ namespace bayesnet {
output.push_back("}\n");
return output;
}
std::vector<std::pair<std::string, std::string>> Network::getEdges() const
vector<pair<string, string>> Network::getEdges()
{
auto edges = std::vector<std::pair<std::string, std::string>>();
auto edges = vector<pair<string, string>>();
for (const auto& node : nodes) {
auto head = node.first;
for (const auto& child : node.second->getChildren()) {
@@ -362,52 +304,4 @@ namespace bayesnet {
}
return edges;
}
int Network::getNumEdges() const
{
return getEdges().size();
}
std::vector<std::string> Network::topological_sort()
{
/* Check if al the fathers of every node are before the node */
auto result = features;
result.erase(remove(result.begin(), result.end(), className), result.end());
bool ending{ false };
while (!ending) {
ending = true;
for (auto feature : features) {
auto fathers = nodes[feature]->getParents();
for (const auto& father : fathers) {
auto fatherName = father->getName();
if (fatherName == className) {
continue;
}
// Check if father is placed before the actual feature
auto it = find(result.begin(), result.end(), fatherName);
if (it != result.end()) {
auto it2 = find(result.begin(), result.end(), feature);
if (it2 != result.end()) {
if (distance(it, it2) < 0) {
// if it is not, insert it before the feature
result.erase(remove(result.begin(), result.end(), fatherName), result.end());
result.insert(it2, fatherName);
ending = false;
}
} else {
throw std::logic_error("Error in topological sort because of node " + feature + " is not in result");
}
} else {
throw std::logic_error("Error in topological sort because of node father " + fatherName + " is not in result");
}
}
}
}
return result;
}
void Network::dump_cpt() const
{
for (auto& node : nodes) {
std::cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << std::endl;
std::cout << node.second->getCPT() << std::endl;
}
}
}

View File

@@ -7,56 +7,49 @@
namespace bayesnet {
class Network {
private:
std::map<std::string, std::unique_ptr<Node>> nodes;
map<string, unique_ptr<Node>> nodes;
map<string, vector<int>> dataset;
bool fitted;
float maxThreads = 0.95;
float maxThreads;
int classNumStates;
std::vector<std::string> features; // Including classname
std::string className;
double laplaceSmoothing;
torch::Tensor samples; // nxm tensor used to fit the model
vector<string> features;
string className;
int laplaceSmoothing;
torch::Tensor samples;
bool isCyclic(const std::string&, std::unordered_set<std::string>&, std::unordered_set<std::string>&);
std::vector<double> predict_sample(const std::vector<int>&);
std::vector<double> predict_sample(const torch::Tensor&);
std::vector<double> exactInference(std::map<std::string, int>&);
double computeFactor(std::map<std::string, int>&);
void completeFit(const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
void checkFitData(int n_features, int n_samples, int n_samples_y, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights);
void setStates(const std::map<std::string, std::vector<int>>&);
vector<double> predict_sample(const vector<int>&);
vector<double> exactInference(map<string, int>&);
double computeFactor(map<string, int>&);
double mutual_info(torch::Tensor&, torch::Tensor&);
double entropy(torch::Tensor&);
double conditionalEntropy(torch::Tensor&, torch::Tensor&);
double mutualInformation(torch::Tensor&, torch::Tensor&);
void completeFit();
public:
Network();
explicit Network(float);
explicit Network(Network&);
~Network() = default;
explicit Network(const float, const int);
explicit Network(const float);
explicit Network(const Network&);
torch::Tensor& getSamples();
float getmaxThreads();
void addNode(const std::string&);
void addEdge(const std::string&, const std::string&);
std::map<std::string, std::unique_ptr<Node>>& getNodes();
std::vector<std::string> getFeatures() const;
int getStates() const;
std::vector<std::pair<std::string, std::string>> getEdges() const;
int getNumEdges() const;
int getClassNumStates() const;
std::string getClassName() const;
/*
Notice: Nodes have to be inserted in the same order as they are in the dataset, i.e., first node is first column and so on.
*/
void fit(const std::vector<std::vector<int>>& input_data, const std::vector<int>& labels, const std::vector<double>& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
void fit(const torch::Tensor& X, const torch::Tensor& y, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
void fit(const torch::Tensor& samples, const torch::Tensor& weights, const std::vector<std::string>& featureNames, const std::string& className, const std::map<std::string, std::vector<int>>& states);
std::vector<int> predict(const std::vector<std::vector<int>>&); // Return mx1 std::vector of predictions
torch::Tensor predict(const torch::Tensor&); // Return mx1 tensor of predictions
torch::Tensor predict_tensor(const torch::Tensor& samples, const bool proba);
std::vector<std::vector<double>> predict_proba(const std::vector<std::vector<int>>&); // Return mxn std::vector of probabilities
torch::Tensor predict_proba(const torch::Tensor&); // Return mxn tensor of probabilities
double score(const std::vector<std::vector<int>>&, const std::vector<int>&);
std::vector<std::string> topological_sort();
std::vector<std::string> show() const;
std::vector<std::string> graph(const std::string& title) const; // Returns a std::vector of std::strings representing the graph in graphviz format
void initialize();
void dump_cpt() const;
inline std::string version() { return "0.2.0"; }
void addNode(const string&, const int);
void addEdge(const string&, const string&);
map<string, std::unique_ptr<Node>>& getNodes();
vector<string> getFeatures();
const int getStates();
vector<pair<string, string>> getEdges();
const int getClassNumStates();
const string getClassName();
void fit(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&);
void fit(torch::Tensor&, torch::Tensor&, const vector<string>&, const string&);
vector<int> predict(const vector<vector<int>>&);
//Computes the conditional edge weight of variable index u and v conditioned on class_node
torch::Tensor conditionalEdgeWeight();
vector<vector<double>> predict_proba(const vector<vector<int>>&);
double score(const vector<vector<int>>&, const vector<int>&);
vector<string> show();
vector<string> graph(const string& title); // Returns a vector of strings representing the graph in graphviz format
inline string version() { return "0.1.0"; }
};
}
#endif

View File

@@ -2,8 +2,8 @@
namespace bayesnet {
Node::Node(const std::string& name)
: name(name), numStates(0), cpTable(torch::Tensor()), parents(std::vector<Node*>()), children(std::vector<Node*>())
Node::Node(const std::string& name, int numStates)
: name(name), numStates(numStates), cpTable(torch::Tensor()), parents(vector<Node*>()), children(vector<Node*>())
{
}
void Node::clear()
@@ -14,7 +14,7 @@ namespace bayesnet {
dimensions.clear();
numStates = 0;
}
std::string Node::getName() const
string Node::getName() const
{
return name;
}
@@ -34,11 +34,11 @@ namespace bayesnet {
{
children.push_back(child);
}
std::vector<Node*>& Node::getParents()
vector<Node*>& Node::getParents()
{
return parents;
}
std::vector<Node*>& Node::getChildren()
vector<Node*>& Node::getChildren()
{
return children;
}
@@ -63,73 +63,59 @@ namespace bayesnet {
*/
unsigned Node::minFill()
{
std::unordered_set<std::string> neighbors;
unordered_set<string> neighbors;
for (auto child : children) {
neighbors.emplace(child->getName());
}
for (auto parent : parents) {
neighbors.emplace(parent->getName());
}
auto source = std::vector<std::string>(neighbors.begin(), neighbors.end());
auto source = vector<string>(neighbors.begin(), neighbors.end());
return combinations(source).size();
}
std::vector<std::pair<std::string, std::string>> Node::combinations(const std::vector<std::string>& source)
vector<pair<string, string>> Node::combinations(const vector<string>& source)
{
std::vector<std::pair<std::string, std::string>> result;
vector<pair<string, string>> result;
for (int i = 0; i < source.size(); ++i) {
std::string temp = source[i];
string temp = source[i];
for (int j = i + 1; j < source.size(); ++j) {
result.push_back({ temp, source[j] });
}
}
return result;
}
void Node::computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double laplaceSmoothing, const torch::Tensor& weights)
void Node::computeCPT(map<string, vector<int>>& dataset, const int laplaceSmoothing)
{
dimensions.clear();
// Get dimensions of the CPT
dimensions.push_back(numStates);
transform(parents.begin(), parents.end(), back_inserter(dimensions), [](const auto& parent) { return parent->getNumStates(); });
transform(parents.begin(), parents.end(), back_inserter(dimensions), [](Node* parent) { return parent->getNumStates(); });
// Create a tensor of zeros with the dimensions of the CPT
cpTable = torch::zeros(dimensions, torch::kFloat) + laplaceSmoothing;
// Fill table with counts
auto pos = find(features.begin(), features.end(), name);
if (pos == features.end()) {
throw std::logic_error("Feature " + name + " not found in dataset");
}
int name_index = pos - features.begin();
for (int n_sample = 0; n_sample < dataset.size(1); ++n_sample) {
c10::List<c10::optional<at::Tensor>> coordinates;
coordinates.push_back(dataset.index({ name_index, n_sample }));
for (auto parent : parents) {
pos = find(features.begin(), features.end(), parent->getName());
if (pos == features.end()) {
throw std::logic_error("Feature parent " + parent->getName() + " not found in dataset");
}
int parent_index = pos - features.begin();
coordinates.push_back(dataset.index({ parent_index, n_sample }));
}
for (int n_sample = 0; n_sample < dataset[name].size(); ++n_sample) {
torch::List<c10::optional<torch::Tensor>> coordinates;
coordinates.push_back(torch::tensor(dataset[name][n_sample]));
transform(parents.begin(), parents.end(), back_inserter(coordinates), [&dataset, &n_sample](Node* parent) { return torch::tensor(dataset[parent->getName()][n_sample]); });
// Increment the count of the corresponding coordinate
cpTable.index_put_({ coordinates }, cpTable.index({ coordinates }) + weights.index({ n_sample }).item<double>());
cpTable.index_put_({ coordinates }, cpTable.index({ coordinates }) + 1);
}
// Normalize the counts
cpTable = cpTable / cpTable.sum(0);
}
float Node::getFactorValue(std::map<std::string, int>& evidence)
float Node::getFactorValue(map<string, int>& evidence)
{
c10::List<c10::optional<at::Tensor>> coordinates;
torch::List<c10::optional<torch::Tensor>> coordinates;
// following predetermined order of indices in the cpTable (see Node.h)
coordinates.push_back(at::tensor(evidence[name]));
transform(parents.begin(), parents.end(), std::back_inserter(coordinates), [&evidence](const auto& parent) { return at::tensor(evidence[parent->getName()]); });
coordinates.push_back(torch::tensor(evidence[name]));
transform(parents.begin(), parents.end(), back_inserter(coordinates), [&evidence](Node* parent) { return torch::tensor(evidence[parent->getName()]); });
return cpTable.index({ coordinates }).item<float>();
}
std::vector<std::string> Node::graph(const std::string& className)
vector<string> Node::graph(const string& className)
{
auto output = std::vector<std::string>();
auto output = vector<string>();
auto suffix = name == className ? ", fontcolor=red, fillcolor=lightblue, style=filled " : "";
output.push_back(name + " [shape=circle" + suffix + "] \n");
transform(children.begin(), children.end(), back_inserter(output), [this](const auto& child) { return name + " -> " + child->getName(); });
transform(children.begin(), children.end(), back_inserter(output), [this](Node* child) { return name + " -> " + child->getName() + "\n"; });
return output;
}
}

View File

@@ -5,32 +5,33 @@
#include <vector>
#include <string>
namespace bayesnet {
using namespace std;
class Node {
private:
std::string name;
std::vector<Node*> parents;
std::vector<Node*> children;
string name;
vector<Node*> parents;
vector<Node*> children;
int numStates; // number of states of the variable
torch::Tensor cpTable; // Order of indices is 0-> node variable, 1-> 1st parent, 2-> 2nd parent, ...
std::vector<int64_t> dimensions; // dimensions of the cpTable
std::vector<std::pair<std::string, std::string>> combinations(const std::vector<std::string>&);
vector<int64_t> dimensions; // dimensions of the cpTable
public:
explicit Node(const std::string&);
vector<pair<string, string>> combinations(const vector<string>&);
Node(const std::string&, int);
void clear();
void addParent(Node*);
void addChild(Node*);
void removeParent(Node*);
void removeChild(Node*);
std::string getName() const;
std::vector<Node*>& getParents();
std::vector<Node*>& getChildren();
string getName() const;
vector<Node*>& getParents();
vector<Node*>& getChildren();
torch::Tensor& getCPT();
void computeCPT(const torch::Tensor& dataset, const std::vector<std::string>& features, const double laplaceSmoothing, const torch::Tensor& weights);
void computeCPT(map<string, vector<int>>&, const int);
int getNumStates() const;
void setNumStates(int);
unsigned minFill();
std::vector<std::string> graph(const std::string& clasName); // Returns a std::vector of std::strings representing the graph in graphviz format
float getFactorValue(std::map<std::string, int>&);
vector<string> graph(const string& clasName); // Returns a vector of strings representing the graph in graphviz format
float getFactorValue(map<string, int>&);
};
}
#endif

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@@ -1,110 +0,0 @@
#include "Proposal.h"
#include "ArffFiles.h"
namespace bayesnet {
Proposal::Proposal(torch::Tensor& dataset_, std::vector<std::string>& features_, std::string& className_) : pDataset(dataset_), pFeatures(features_), pClassName(className_) {}
Proposal::~Proposal()
{
for (auto& [key, value] : discretizers) {
delete value;
}
}
void Proposal::checkInput(const torch::Tensor& X, const torch::Tensor& y)
{
if (!torch::is_floating_point(X)) {
throw std::invalid_argument("X must be a floating point tensor");
}
if (torch::is_floating_point(y)) {
throw std::invalid_argument("y must be an integer tensor");
}
}
map<std::string, std::vector<int>> Proposal::localDiscretizationProposal(const map<std::string, std::vector<int>>& oldStates, Network& model)
{
// order of local discretization is important. no good 0, 1, 2...
// although we rediscretize features after the local discretization of every feature
auto order = model.topological_sort();
auto& nodes = model.getNodes();
map<std::string, std::vector<int>> states = oldStates;
std::vector<int> indicesToReDiscretize;
bool upgrade = false; // Flag to check if we need to upgrade the model
for (auto feature : order) {
auto nodeParents = nodes[feature]->getParents();
if (nodeParents.size() < 2) continue; // Only has class as parent
upgrade = true;
int index = find(pFeatures.begin(), pFeatures.end(), feature) - pFeatures.begin();
indicesToReDiscretize.push_back(index); // We need to re-discretize this feature
std::vector<std::string> parents;
transform(nodeParents.begin(), nodeParents.end(), back_inserter(parents), [](const auto& p) { return p->getName(); });
// Remove class as parent as it will be added later
parents.erase(remove(parents.begin(), parents.end(), pClassName), parents.end());
// Get the indices of the parents
std::vector<int> indices;
indices.push_back(-1); // Add class index
transform(parents.begin(), parents.end(), back_inserter(indices), [&](const auto& p) {return find(pFeatures.begin(), pFeatures.end(), p) - pFeatures.begin(); });
// Now we fit the discretizer of the feature, conditioned on its parents and the class i.e. discretizer.fit(X[index], X[indices] + y)
std::vector<std::string> yJoinParents(Xf.size(1));
for (auto idx : indices) {
for (int i = 0; i < Xf.size(1); ++i) {
yJoinParents[i] += to_string(pDataset.index({ idx, i }).item<int>());
}
}
auto arff = ArffFiles();
auto yxv = arff.factorize(yJoinParents);
auto xvf_ptr = Xf.index({ index }).data_ptr<float>();
auto xvf = std::vector<mdlp::precision_t>(xvf_ptr, xvf_ptr + Xf.size(1));
discretizers[feature]->fit(xvf, yxv);
}
if (upgrade) {
// Discretize again X (only the affected indices) with the new fitted discretizers
for (auto index : indicesToReDiscretize) {
auto Xt_ptr = Xf.index({ index }).data_ptr<float>();
auto Xt = std::vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
pDataset.index_put_({ index, "..." }, torch::tensor(discretizers[pFeatures[index]]->transform(Xt)));
auto xStates = std::vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
//Update new states of the feature/node
states[pFeatures[index]] = xStates;
}
const torch::Tensor weights = torch::full({ pDataset.size(1) }, 1.0 / pDataset.size(1), torch::kDouble);
model.fit(pDataset, weights, pFeatures, pClassName, states);
}
return states;
}
map<std::string, std::vector<int>> Proposal::fit_local_discretization(const torch::Tensor& y)
{
// Discretize the continuous input data and build pDataset (Classifier::dataset)
int m = Xf.size(1);
int n = Xf.size(0);
map<std::string, std::vector<int>> states;
pDataset = torch::zeros({ n + 1, m }, torch::kInt32);
auto yv = std::vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
// discretize input data by feature(row)
for (auto i = 0; i < pFeatures.size(); ++i) {
auto* discretizer = new mdlp::CPPFImdlp();
auto Xt_ptr = Xf.index({ i }).data_ptr<float>();
auto Xt = std::vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
discretizer->fit(Xt, yv);
pDataset.index_put_({ i, "..." }, torch::tensor(discretizer->transform(Xt)));
auto xStates = std::vector<int>(discretizer->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
states[pFeatures[i]] = xStates;
discretizers[pFeatures[i]] = discretizer;
}
int n_classes = torch::max(y).item<int>() + 1;
auto yStates = std::vector<int>(n_classes);
iota(yStates.begin(), yStates.end(), 0);
states[pClassName] = yStates;
pDataset.index_put_({ n, "..." }, y);
return states;
}
torch::Tensor Proposal::prepareX(torch::Tensor& X)
{
auto Xtd = torch::zeros_like(X, torch::kInt32);
for (int i = 0; i < X.size(0); ++i) {
auto Xt = std::vector<float>(X[i].data_ptr<float>(), X[i].data_ptr<float>() + X.size(1));
auto Xd = discretizers[pFeatures[i]]->transform(Xt);
Xtd.index_put_({ i }, torch::tensor(Xd, torch::kInt32));
}
return Xtd;
}
}

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@@ -1,30 +0,0 @@
#ifndef PROPOSAL_H
#define PROPOSAL_H
#include <string>
#include <map>
#include <torch/torch.h>
#include "Network.h"
#include "CPPFImdlp.h"
#include "Classifier.h"
namespace bayesnet {
class Proposal {
public:
Proposal(torch::Tensor& pDataset, std::vector<std::string>& features_, std::string& className_);
virtual ~Proposal();
protected:
void checkInput(const torch::Tensor& X, const torch::Tensor& y);
torch::Tensor prepareX(torch::Tensor& X);
map<std::string, std::vector<int>> localDiscretizationProposal(const map<std::string, std::vector<int>>& states, Network& model);
map<std::string, std::vector<int>> fit_local_discretization(const torch::Tensor& y);
torch::Tensor Xf; // X continuous nxm tensor
torch::Tensor y; // y discrete nx1 tensor
map<std::string, mdlp::CPPFImdlp*> discretizers;
private:
torch::Tensor& pDataset; // (n+1)xm tensor
std::vector<std::string>& pFeatures;
std::string& pClassName;
};
}
#endif

View File

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

View File

@@ -1,17 +1,15 @@
#ifndef SPODE_H
#define SPODE_H
#include "Classifier.h"
namespace bayesnet {
class SPODE : public Classifier {
private:
int root;
protected:
void buildModel(const torch::Tensor& weights) override;
void train() override;
public:
explicit SPODE(int root);
virtual ~SPODE() = default;
std::vector<std::string> graph(const std::string& name = "SPODE") const override;
vector<string> graph(string name = "SPODE") override;
};
}
#endif

View File

@@ -1,47 +0,0 @@
#include "SPODELd.h"
namespace bayesnet {
SPODELd::SPODELd(int root) : SPODE(root), Proposal(dataset, features, className) {}
SPODELd& SPODELd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal SPODE structure, SPODE::fit initializes the base Bayesian network
SPODE::fit(dataset, features, className, states);
states = localDiscretizationProposal(states, model);
return *this;
}
SPODELd& SPODELd::fit(torch::Tensor& dataset, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
if (!torch::is_floating_point(dataset)) {
throw std::runtime_error("Dataset must be a floating point tensor");
}
Xf = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." }).clone();
y = dataset.index({ -1, "..." }).clone();
features = features_;
className = className_;
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal SPODE structure, SPODE::fit initializes the base Bayesian network
SPODE::fit(dataset, features, className, states);
states = localDiscretizationProposal(states, model);
return *this;
}
torch::Tensor SPODELd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return SPODE::predict(Xt);
}
std::vector<std::string> SPODELd::graph(const std::string& name) const
{
return SPODE::graph(name);
}
}

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@@ -1,18 +0,0 @@
#ifndef SPODELD_H
#define SPODELD_H
#include "SPODE.h"
#include "Proposal.h"
namespace bayesnet {
class SPODELd : public SPODE, public Proposal {
public:
explicit SPODELd(int root);
virtual ~SPODELd() = default;
SPODELd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states) override;
SPODELd& fit(torch::Tensor& dataset, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states) override;
std::vector<std::string> graph(const std::string& name = "SPODE") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !SPODELD_H

View File

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

View File

@@ -2,14 +2,15 @@
#define TAN_H
#include "Classifier.h"
namespace bayesnet {
using namespace std;
using namespace torch;
class TAN : public Classifier {
private:
protected:
void buildModel(const torch::Tensor& weights) override;
void train() override;
public:
TAN();
virtual ~TAN() = default;
std::vector<std::string> graph(const std::string& name = "TAN") const override;
vector<string> graph(string name = "TAN") override;
};
}
#endif

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@@ -1,30 +0,0 @@
#include "TANLd.h"
namespace bayesnet {
TANLd::TANLd() : TAN(), Proposal(dataset, features, className) {}
TANLd& TANLd::fit(torch::Tensor& X_, torch::Tensor& y_, const std::vector<std::string>& features_, const std::string& className_, map<std::string, std::vector<int>>& states_)
{
checkInput(X_, y_);
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
states = fit_local_discretization(y);
// We have discretized the input data
// 1st we need to fit the model to build the normal TAN structure, TAN::fit initializes the base Bayesian network
TAN::fit(dataset, features, className, states);
states = localDiscretizationProposal(states, model);
return *this;
}
torch::Tensor TANLd::predict(torch::Tensor& X)
{
auto Xt = prepareX(X);
return TAN::predict(Xt);
}
std::vector<std::string> TANLd::graph(const std::string& name) const
{
return TAN::graph(name);
}
}

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@@ -1,18 +0,0 @@
#ifndef TANLD_H
#define TANLD_H
#include "TAN.h"
#include "Proposal.h"
namespace bayesnet {
class TANLd : public TAN, public Proposal {
private:
public:
TANLd();
virtual ~TANLd() = default;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, const std::vector<std::string>& features, const std::string& className, map<std::string, std::vector<int>>& states) override;
std::vector<std::string> graph(const std::string& name = "TAN") const override;
torch::Tensor predict(torch::Tensor& X) override;
static inline std::string version() { return "0.0.1"; };
};
}
#endif // !TANLD_H

View File

@@ -1,23 +1,24 @@
#include "bayesnetUtils.h"
namespace bayesnet {
// Return the indices in descending order
std::vector<int> argsort(std::vector<double>& nums)
using namespace std;
using namespace torch;
vector<int> argsort(vector<float>& nums)
{
int n = nums.size();
std::vector<int> indices(n);
vector<int> indices(n);
iota(indices.begin(), indices.end(), 0);
sort(indices.begin(), indices.end(), [&nums](int i, int j) {return nums[i] > nums[j];});
return indices;
}
std::vector<std::vector<int>> tensorToVector(torch::Tensor& tensor)
vector<vector<int>> tensorToVector(Tensor& tensor)
{
// convert mxn tensor to nxm std::vector
std::vector<std::vector<int>> result;
// convert mxn tensor to nxm vector
vector<vector<int>> result;
// Iterate over cols
for (int i = 0; i < tensor.size(1); ++i) {
auto col_tensor = tensor.index({ "...", i });
auto col = std::vector<int>(col_tensor.data_ptr<int>(), col_tensor.data_ptr<int>() + tensor.size(0));
auto col = vector<int>(col_tensor.data_ptr<int>(), col_tensor.data_ptr<int>() + tensor.size(0));
result.push_back(col);
}
return result;

View File

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

View File

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

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

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

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@@ -1,39 +0,0 @@
#ifndef BESTRESULTS_EXCEL_H
#define BESTRESULTS_EXCEL_H
#include "ExcelFile.h"
#include <vector>
#include <map>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
class BestResultsExcel : ExcelFile {
public:
BestResultsExcel(const std::string& score, const std::vector<std::string>& datasets);
~BestResultsExcel();
void reportAll(const std::vector<std::string>& models, const json& table, const std::map<std::string, std::map<std::string, float>>& ranks, bool friedman, double significance);
void reportSingle(const std::string& model, const std::string& fileName);
std::string getFileName();
private:
void build();
void header(bool ranks);
void body(bool ranks);
void footer(bool ranks);
void formatColumns();
void doFriedman();
void addConditionalFormat(std::string formula);
const std::string fileName = "BestResults.xlsx";
std::string score;
std::vector<std::string> models;
std::vector<std::string> datasets;
json table;
std::map<std::string, std::map<std::string, float>> ranksModels;
bool friedman;
double significance;
int modelNameSize = 12; // Min size of the column
int datasetNameSize = 25; // Min size of the column
};
}
#endif //BESTRESULTS_EXCEL_H

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@@ -1,28 +0,0 @@
#ifndef BESTSCORE_H
#define BESTSCORE_H
#include <string>
#include <map>
#include <utility>
#include "DotEnv.h"
namespace platform {
class BestScore {
public:
static std::pair<std::string, double> getScore(const std::string& metric)
{
static std::map<std::pair<std::string, std::string>, std::pair<std::string, double>> data = {
{{"discretiz", "accuracy"}, {"STree_default (linear-ovo)", 22.109799}},
{{"odte", "accuracy"}, {"STree_default (linear-ovo)", 22.109799}},
};
auto env = platform::DotEnv();
std::string experiment = env.get("experiment");
try {
return data[{experiment, metric}];
}
catch (...) {
return { "", 0.0 };
}
}
};
}
#endif

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@@ -1,22 +0,0 @@
#ifndef LOCALE_H
#define LOCALE_H
#include <locale>
#include <iostream>
#include <string>
namespace platform {
struct separation : std::numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
std::string do_grouping() const { return "\03"; }
};
class ConfigLocale {
public:
explicit ConfigLocale()
{
std::locale mylocale(std::cout.getloc(), new separation);
std::locale::global(mylocale);
std::cout.imbue(mylocale);
}
};
}
#endif

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@@ -1,22 +1,8 @@
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
include_directories(${BayesNet_SOURCE_DIR}/src/PyClassifiers)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/argparse/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/libxlsxwriter/include)
include_directories(${Python3_INCLUDE_DIRS})
include_directories(${MPI_CXX_INCLUDE_DIRS})
add_executable(b_best b_best.cc BestResults.cc Result.cc Statistics.cc BestResultsExcel.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
add_executable(b_grid b_grid.cc GridSearch.cc GridData.cc HyperParameters.cc Folding.cc Datasets.cc Dataset.cc)
add_executable(b_list b_list.cc Datasets.cc Dataset.cc)
add_executable(b_main b_main.cc Folding.cc Experiment.cc Datasets.cc Dataset.cc Models.cc HyperParameters.cc ReportConsole.cc ReportBase.cc)
add_executable(b_manage b_manage.cc Results.cc ManageResults.cc CommandParser.cc Result.cc ReportConsole.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
target_link_libraries(b_best Boost::boost "${XLSXWRITER_LIB}" "${TORCH_LIBRARIES}" ArffFiles mdlp)
target_link_libraries(b_grid BayesNet PyWrap ${MPI_CXX_LIBRARIES})
target_link_libraries(b_list ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(b_main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}" PyWrap)
target_link_libraries(b_manage "${TORCH_LIBRARIES}" "${XLSXWRITER_LIB}" ArffFiles mdlp)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc CrossValidation.cc Models.cc)
target_link_libraries(main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")

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@@ -1,15 +0,0 @@
#ifndef COLORS_H
#define COLORS_H
class Colors {
public:
static std::string MAGENTA() { return "\033[1;35m"; }
static std::string BLUE() { return "\033[1;34m"; }
static std::string CYAN() { return "\033[1;36m"; }
static std::string GREEN() { return "\033[1;32m"; }
static std::string YELLOW() { return "\033[1;33m"; }
static std::string RED() { return "\033[1;31m"; }
static std::string WHITE() { return "\033[1;37m"; }
static std::string IBLUE() { return "\033[0;94m"; }
static std::string RESET() { return "\033[0m"; }
};
#endif // COLORS_H

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@@ -1,87 +0,0 @@
#include "CommandParser.h"
#include <iostream>
#include <sstream>
#include <algorithm>
#include "Colors.h"
#include "Utils.h"
namespace platform {
void CommandParser::messageError(const std::string& message)
{
std::cout << Colors::RED() << message << Colors::RESET() << std::endl;
}
std::pair<char, int> CommandParser::parse(const std::string& color, const std::vector<std::tuple<std::string, char, bool>>& options, const char defaultCommand, const int maxIndex)
{
bool finished = false;
while (!finished) {
std::stringstream oss;
std::string line;
oss << color << "Choose option (";
bool first = true;
for (auto& option : options) {
if (first) {
first = false;
} else {
oss << ", ";
}
oss << std::get<char>(option) << "=" << std::get<std::string>(option);
}
oss << "): ";
std::cout << oss.str();
getline(std::cin, line);
std::cout << Colors::RESET();
line = trim(line);
if (line.size() == 0)
continue;
if (all_of(line.begin(), line.end(), ::isdigit)) {
command = defaultCommand;
index = stoi(line);
if (index > maxIndex || index < 0) {
messageError("Index out of range");
continue;
}
finished = true;
break;
}
bool found = false;
for (auto& option : options) {
if (line[0] == std::get<char>(option)) {
found = true;
// it's a match
line.erase(line.begin());
line = trim(line);
if (std::get<bool>(option)) {
// The option requires a value
if (line.size() == 0) {
messageError("Option " + std::get<std::string>(option) + " requires a value");
break;
}
try {
index = stoi(line);
if (index > maxIndex || index < 0) {
messageError("Index out of range");
break;
}
}
catch (const std::invalid_argument& ia) {
messageError("Invalid value: " + line);
break;
}
} else {
if (line.size() > 0) {
messageError("option " + std::get<std::string>(option) + " doesn't accept values");
break;
}
}
command = std::get<char>(option);
finished = true;
break;
}
}
if (!found) {
messageError("I don't know " + line);
}
}
return { command, index };
}
} /* namespace platform */

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@@ -1,20 +0,0 @@
#ifndef COMMAND_PARSER_H
#define COMMAND_PARSER_H
#include <string>
#include <vector>
#include <tuple>
namespace platform {
class CommandParser {
public:
CommandParser() = default;
std::pair<char, int> parse(const std::string& color, const std::vector<std::tuple<std::string, char, bool>>& options, const char defaultCommand, const int maxIndex);
char getCommand() const { return command; };
int getIndex() const { return index; };
private:
void messageError(const std::string& message);
char command;
int index;
};
} /* namespace platform */
#endif /* COMMAND_PARSER_H */

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@@ -0,0 +1,79 @@
#include "CrossValidation.h"
#include "Models.h"
namespace platform {
using json = nlohmann::json;
using namespace std::chrono;
CrossValidation::CrossValidation(const string& modelName, bool stratified, int nfolds, const vector<int>& randomSeeds, platform::Datasets& datasets) : modelName(modelName), stratified(stratified), nfolds(nfolds), randomSeeds(randomSeeds), datasets(datasets)
{
}
Result CrossValidation::crossValidate(const string& fileName)
{
auto [Xt, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
auto className = datasets.getClassName(fileName);
auto features = datasets.getFeatures(fileName);
auto samples = datasets.getNSamples(fileName);
auto result = Result();
auto [values, counts] = at::_unique(y);
result.setSamples(Xt.size(1)).setFeatures(Xt.size(0)).setClasses(values.size(0));
int nSeeds = static_cast<int>(randomSeeds.size());
auto accuracy_test = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto accuracy_train = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto train_time = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto test_time = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto nodes = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto edges = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
auto num_states = torch::zeros({ nfolds * nSeeds }, torch::kFloat64);
Timer train_timer, test_timer;
int item = 0;
for (auto seed : randomSeeds) {
cout << "(" << seed << ") " << flush;
Fold* fold;
if (stratified)
fold = new StratifiedKFold(nfolds, y, seed);
else
fold = new KFold(nfolds, samples, seed);
cout << "Fold: " << flush;
for (int nfold = 0; nfold < nfolds; nfold++) {
bayesnet::BaseClassifier* model = Models::get(modelName);
result.setModelVersion(model->getVersion());
train_timer.start();
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
auto X_train = Xt.index({ "...", train_t });
auto y_train = y.index({ train_t });
auto X_test = Xt.index({ "...", test_t });
auto y_test = y.index({ test_t });
cout << nfold + 1 << ", " << flush;
model->fit(X_train, y_train, features, className, states);
nodes[item] = model->getNumberOfNodes();
edges[item] = model->getNumberOfEdges();
num_states[item] = model->getNumberOfStates();
train_time[item] = train_timer.getDuration();
auto accuracy_train_value = model->score(X_train, y_train);
test_timer.start();
auto accuracy_test_value = model->score(X_test, y_test);
test_time[item] = test_timer.getDuration();
accuracy_train[item] = accuracy_train_value;
accuracy_test[item] = accuracy_test_value;
// Store results and times in vector
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++;
}
delete fold;
}
cout << "end." << endl;
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.setNodes(torch::mean(nodes).item<double>()).setLeaves(torch::mean(edges).item<double>()).setDepth(torch::mean(num_states).item<double>());
return result;
}
} // namespace platform

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@@ -0,0 +1,25 @@
#ifndef CROSSVALIDATION_H
#define CROSSVALIDATION_H
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <string>
#include <chrono>
#include "Folding.h"
#include "Datasets.h"
#include "Experiment.h"
namespace platform {
class CrossValidation {
private:
bool stratified;
int nfolds;
string modelName;
vector<int> randomSeeds;
platform::Datasets& datasets;
public:
CrossValidation(const string& modelName, bool stratified, int nfolds, const vector<int>& randomSeeds, platform::Datasets& datasets);
~CrossValidation() = default;
Result crossValidate(const string& fileName);
};
}
#endif // !CROSSVALIDATION_H

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

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@@ -1,78 +0,0 @@
#ifndef DATASET_H
#define DATASET_H
#include <torch/torch.h>
#include <map>
#include <vector>
#include <string>
#include "CPPFImdlp.h"
#include "Utils.h"
namespace platform {
enum fileType_t { CSV, ARFF, RDATA };
class SourceData {
public:
SourceData(std::string source)
{
if (source == "Surcov") {
path = "datasets/";
fileType = CSV;
} else if (source == "Arff") {
path = "datasets/";
fileType = ARFF;
} else if (source == "Tanveer") {
path = "data/";
fileType = RDATA;
} else {
throw std::invalid_argument("Unknown source.");
}
}
std::string getPath()
{
return path;
}
fileType_t getFileType()
{
return fileType;
}
private:
std::string path;
fileType_t fileType;
};
class Dataset {
private:
std::string path;
std::string name;
fileType_t fileType;
std::string className;
int n_samples{ 0 }, n_features{ 0 };
std::vector<std::string> features;
std::map<std::string, std::vector<int>> states;
bool loaded;
bool discretize;
torch::Tensor X, y;
std::vector<std::vector<float>> Xv;
std::vector<std::vector<int>> Xd;
std::vector<int> yv;
void buildTensors();
void load_csv();
void load_arff();
void load_rdata();
void computeStates();
std::vector<mdlp::labels_t> discretizeDataset(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y);
public:
Dataset(const std::string& path, const std::string& name, const std::string& className, bool discretize, fileType_t fileType) : path(path), name(name), className(className), discretize(discretize), loaded(false), fileType(fileType) {};
explicit Dataset(const Dataset&);
std::string getName() const;
std::string getClassName() const;
std::vector<string> getFeatures() const;
std::map<std::string, std::vector<int>> getStates() const;
std::pair<vector<std::vector<float>>&, std::vector<int>&> getVectors();
std::pair<vector<std::vector<int>>&, std::vector<int>&> getVectorsDiscretized();
std::pair<torch::Tensor&, torch::Tensor&> getTensors();
int getNFeatures() const;
int getNSamples() const;
void load();
const bool inline isLoaded() const { return loaded; };
};
};
#endif

View File

@@ -1,129 +1,239 @@
#include "Datasets.h"
#include <fstream>
#include "platformUtils.h"
#include "ArffFiles.h"
namespace platform {
vector<string> split(const string& text, char delimiter)
{
vector<string> result;
stringstream ss(text);
string token;
while (getline(ss, token, delimiter)) {
result.push_back(token);
}
return result;
}
void Datasets::load()
{
auto sd = SourceData(sfileType);
fileType = sd.getFileType();
path = sd.getPath();
ifstream catalog(path + "all.txt");
ifstream catalog(path + "/all.txt");
if (catalog.is_open()) {
std::string line;
string line;
while (getline(catalog, line)) {
if (line.empty() || line[0] == '#') {
continue;
}
std::vector<std::string> tokens = split(line, ',');
std::string name = tokens[0];
std::string className;
if (tokens.size() == 1) {
className = "-1";
} else {
className = tokens[1];
}
vector<string> tokens = split(line, ',');
string name = tokens[0];
string className = tokens[1];
datasets[name] = make_unique<Dataset>(path, name, className, discretize, fileType);
}
catalog.close();
} else {
throw std::invalid_argument("Unable to open catalog file. [" + path + "all.txt" + "]");
throw invalid_argument("Unable to open catalog file. [" + path + "/all.txt" + "]");
}
}
std::vector<std::string> Datasets::getNames()
vector<string> Datasets::getNames()
{
std::vector<std::string> result;
vector<string> result;
transform(datasets.begin(), datasets.end(), back_inserter(result), [](const auto& d) { return d.first; });
return result;
}
std::vector<std::string> Datasets::getFeatures(const std::string& name) const
vector<string> Datasets::getFeatures(const string& name)
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getFeatures();
if (datasets[name]->isLoaded()) {
return datasets[name]->getFeatures();
} else {
throw std::invalid_argument("Dataset not loaded.");
throw invalid_argument("Dataset not loaded.");
}
}
map<std::string, std::vector<int>> Datasets::getStates(const std::string& name) const
map<string, vector<int>> Datasets::getStates(const string& name)
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getStates();
if (datasets[name]->isLoaded()) {
return datasets[name]->getStates();
} else {
throw std::invalid_argument("Dataset not loaded.");
throw invalid_argument("Dataset not loaded.");
}
}
void Datasets::loadDataset(const std::string& name) const
string Datasets::getClassName(const string& name)
{
if (datasets.at(name)->isLoaded()) {
return;
if (datasets[name]->isLoaded()) {
return datasets[name]->getClassName();
} else {
datasets.at(name)->load();
throw invalid_argument("Dataset not loaded.");
}
}
std::string Datasets::getClassName(const std::string& name) const
int Datasets::getNSamples(const string& name)
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getClassName();
if (datasets[name]->isLoaded()) {
return datasets[name]->getNSamples();
} else {
throw std::invalid_argument("Dataset not loaded.");
throw invalid_argument("Dataset not loaded.");
}
}
int Datasets::getNSamples(const std::string& name) const
{
if (datasets.at(name)->isLoaded()) {
return datasets.at(name)->getNSamples();
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
int Datasets::getNClasses(const std::string& name)
{
if (datasets.at(name)->isLoaded()) {
auto className = datasets.at(name)->getClassName();
if (discretize) {
auto states = getStates(name);
return states.at(className).size();
}
auto [Xv, yv] = getVectors(name);
return *std::max_element(yv.begin(), yv.end()) + 1;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
std::vector<int> Datasets::getClassesCounts(const std::string& name) const
{
if (datasets.at(name)->isLoaded()) {
auto [Xv, yv] = datasets.at(name)->getVectors();
std::vector<int> counts(*std::max_element(yv.begin(), yv.end()) + 1);
for (auto y : yv) {
counts[y]++;
}
return counts;
} else {
throw std::invalid_argument("Dataset not loaded.");
}
}
pair<std::vector<std::vector<float>>&, std::vector<int>&> Datasets::getVectors(const std::string& name)
pair<vector<vector<float>>&, vector<int>&> Datasets::getVectors(const string& name)
{
if (!datasets[name]->isLoaded()) {
datasets[name]->load();
}
return datasets[name]->getVectors();
}
pair<std::vector<std::vector<int>>&, std::vector<int>&> Datasets::getVectorsDiscretized(const std::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(const std::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 std::string& name) const
bool Datasets::isDataset(const string& name)
{
return datasets.find(name) != datasets.end();
}
Dataset::Dataset(Dataset& dataset) : path(dataset.path), name(dataset.name), className(dataset.className), n_samples(dataset.n_samples), n_features(dataset.n_features), features(dataset.features), states(dataset.states), loaded(dataset.loaded), discretize(dataset.discretize), X(dataset.X), y(dataset.y), Xv(dataset.Xv), Xd(dataset.Xd), yv(dataset.yv), fileType(dataset.fileType) {}
string Dataset::getName()
{
return name;
}
string Dataset::getClassName()
{
return className;
}
vector<string> Dataset::getFeatures()
{
if (loaded) {
return features;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNFeatures()
{
if (loaded) {
return n_features;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
int Dataset::getNSamples()
{
if (loaded) {
return n_samples;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
map<string, vector<int>> Dataset::getStates()
{
if (loaded) {
return states;
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<float>>&, vector<int>&> Dataset::getVectors()
{
if (loaded) {
return { Xv, yv };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<vector<vector<int>>&, vector<int>&> Dataset::getVectorsDiscretized()
{
if (loaded) {
return { Xd, yv };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
pair<torch::Tensor&, torch::Tensor&> Dataset::getTensors()
{
if (loaded) {
buildTensors();
return { X, y };
} else {
throw invalid_argument("Dataset not loaded.");
}
}
void Dataset::load_csv()
{
ifstream file(path + "/" + name + ".csv");
if (file.is_open()) {
string line;
getline(file, line);
vector<string> tokens = split(line, ',');
features = vector<string>(tokens.begin(), tokens.end() - 1);
className = tokens.back();
for (auto i = 0; i < features.size(); ++i) {
Xv.push_back(vector<float>());
}
while (getline(file, line)) {
tokens = split(line, ',');
for (auto i = 0; i < features.size(); ++i) {
Xv[i].push_back(stof(tokens[i]));
}
yv.push_back(stoi(tokens.back()));
}
file.close();
} else {
throw invalid_argument("Unable to open dataset file.");
}
}
void Dataset::computeStates()
{
for (int i = 0; i < features.size(); ++i) {
states[features[i]] = vector<int>(*max_element(Xd[i].begin(), Xd[i].end()) + 1);
iota(begin(states[features[i]]), end(states[features[i]]), 0);
}
states[className] = vector<int>(*max_element(yv.begin(), yv.end()) + 1);
iota(begin(states[className]), end(states[className]), 0);
}
void Dataset::load_arff()
{
auto arff = ArffFiles();
arff.load(path + "/" + name + ".arff", className);
// Get Dataset X, y
Xv = arff.getX();
yv = arff.getY();
// Get className & Features
className = arff.getClassName();
auto attributes = arff.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features), [](const auto& f) { return f.first; });
}
void Dataset::load()
{
if (loaded) {
return;
}
if (fileType == CSV) {
load_csv();
} else if (fileType == ARFF) {
load_arff();
}
if (discretize) {
Xd = discretizeDataset(Xv, yv);
computeStates();
n_samples = Xd[0].size();
n_features = Xd.size();
}
loaded = true;
}
void Dataset::buildTensors()
{
if (discretize) {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kInt32);
} else {
X = torch::zeros({ static_cast<int>(n_features), static_cast<int>(n_samples) }, torch::kFloat32);
}
for (int i = 0; i < features.size(); ++i) {
if (discretize) {
X.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
} else {
X.index_put_({ i, "..." }, torch::tensor(Xv[i], torch::kFloat32));
}
}
y = torch::tensor(yv, torch::kInt32);
}
}

View File

@@ -1,30 +1,66 @@
#ifndef DATASETS_H
#define DATASETS_H
#include "Dataset.h"
#include <torch/torch.h>
#include <map>
#include <vector>
#include <string>
namespace platform {
using namespace std;
enum fileType_t { CSV, ARFF };
class Dataset {
private:
string path;
string name;
fileType_t fileType;
string className;
int n_samples, n_features;
vector<string> features;
map<string, vector<int>> states;
bool loaded;
bool discretize;
torch::Tensor X, y;
vector<vector<float>> Xv;
vector<vector<int>> Xd;
vector<int> yv;
void buildTensors();
void load_csv();
void load_arff();
void computeStates();
public:
Dataset(const string& path, const string& name, const string& className, bool discretize, fileType_t fileType) : path(path), name(name), className(className), discretize(discretize), loaded(false), fileType(fileType), n_samples(0), n_features(0) {};
explicit Dataset(Dataset&);
string getName();
string getClassName();
vector<string> getFeatures();
map<string, vector<int>> getStates();
pair<vector<vector<float>>&, vector<int>&> getVectors();
pair<vector<vector<int>>&, vector<int>&> getVectorsDiscretized();
pair<torch::Tensor&, torch::Tensor&> getTensors();
int getNFeatures();
int getNSamples();
void load();
const bool inline isLoaded() const { return loaded; };
};
class Datasets {
private:
std::string path;
string path;
fileType_t fileType;
std::string sfileType;
std::map<std::string, std::unique_ptr<Dataset>> datasets;
map<string, unique_ptr<Dataset>> datasets;
bool discretize;
void load(); // Loads the list of datasets
public:
explicit Datasets(bool discretize, std::string sfileType) : discretize(discretize), sfileType(sfileType) { load(); };
std::vector<string> getNames();
std::vector<string> getFeatures(const std::string& name) const;
int getNSamples(const std::string& name) const;
std::string getClassName(const std::string& name) const;
int getNClasses(const std::string& name);
std::vector<int> getClassesCounts(const std::string& name) const;
std::map<std::string, std::vector<int>> getStates(const std::string& name) const;
std::pair<std::vector<std::vector<float>>&, std::vector<int>&> getVectors(const std::string& name);
std::pair<std::vector<std::vector<int>>&, std::vector<int>&> getVectorsDiscretized(const std::string& name);
std::pair<torch::Tensor&, torch::Tensor&> getTensors(const std::string& name);
bool isDataset(const std::string& name) const;
void loadDataset(const std::string& name) const;
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(const string& name);
int getNSamples(const string& name);
string getClassName(const string& name);
map<string, vector<int>> getStates(const string& name);
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);
};
vector<string> split(const string&, char);
};
#endif

View File

@@ -4,52 +4,64 @@
#include <map>
#include <fstream>
#include <sstream>
#include <algorithm>
#include <iostream>
#include "Utils.h"
//#include "Dataset.h"
namespace platform {
class DotEnv {
private:
std::map<std::string, std::string> env;
public:
DotEnv()
{
std::ifstream file(".env");
if (!file.is_open()) {
std::cerr << "File .env not found" << std::endl;
exit(1);
}
std::string line;
while (std::getline(file, line)) {
line = trim(line);
if (line.empty() || line[0] == '#') {
continue;
}
std::istringstream iss(line);
std::string key, value;
if (std::getline(iss, key, '=') && std::getline(iss, value)) {
env[key] = value;
}
}
}
std::string get(const std::string& key)
{
return env.at(key);
}
std::vector<int> getSeeds()
{
auto seeds = std::vector<int>();
auto seeds_str = env["seeds"];
seeds_str = trim(seeds_str);
seeds_str = seeds_str.substr(1, seeds_str.size() - 2);
auto seeds_str_split = split(seeds_str, ',');
transform(seeds_str_split.begin(), seeds_str_split.end(), back_inserter(seeds), [](const std::string& str) {
return stoi(str);
});
return seeds;
}
};
std::vector<std::string> split(std::string text, char delimiter)
{
std::vector<std::string> result;
std::stringstream ss(text);
std::string token;
while (getline(ss, token, delimiter)) {
result.push_back(token);
}
return result;
}
class DotEnv {
private:
std::map<std::string, std::string> env;
std::string trim(const std::string& str)
{
std::string result = str;
result.erase(result.begin(), std::find_if(result.begin(), result.end(), [](int ch) {
return !std::isspace(ch);
}));
result.erase(std::find_if(result.rbegin(), result.rend(), [](int ch) {
return !std::isspace(ch);
}).base(), result.end());
return result;
}
public:
DotEnv()
{
std::ifstream file(".env");
if (!file.is_open()) {
std::cerr << "File .env not found" << std::endl;
exit(1);
}
std::string line;
while (std::getline(file, line)) {
line = trim(line);
if (line.empty() || line[0] == '#') {
continue;
}
std::istringstream iss(line);
std::string key, value;
if (std::getline(iss, key, '=') && std::getline(iss, value)) {
env[key] = value;
}
}
}
std::string get(const std::string& key)
{
return env[key];
}
std::vector<int> getSeeds()
{
auto seeds = std::vector<int>();
auto seeds_str = env["seeds"];
seeds_str = trim(seeds_str);
seeds_str = seeds_str.substr(1, seeds_str.size() - 2);
auto seeds_str_split = split(seeds_str, ',');
transform(seeds_str_split.begin(), seeds_str_split.end(), back_inserter(seeds), [](const auto& s) { return stoi(s); });
return seeds;
}
};
#endif

View File

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

View File

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

View File

@@ -1,12 +1,8 @@
#include <fstream>
#include "Experiment.h"
#include "Datasets.h"
#include "Models.h"
#include "ReportConsole.h"
#include "Paths.h"
namespace platform {
using json = nlohmann::json;
std::string get_date()
string get_date()
{
time_t rawtime;
tm* timeinfo;
@@ -16,7 +12,7 @@ namespace platform {
oss << std::put_time(timeinfo, "%Y-%m-%d");
return oss.str();
}
std::string get_time()
string get_time()
{
time_t rawtime;
tm* timeinfo;
@@ -26,9 +22,9 @@ namespace platform {
oss << std::put_time(timeinfo, "%H:%M:%S");
return oss.str();
}
std::string Experiment::get_file_name()
string Experiment::get_file_name()
{
std::string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
return result;
}
@@ -47,7 +43,7 @@ namespace platform {
result["discretized"] = discretized;
result["stratified"] = stratified;
result["folds"] = nfolds;
result["seeds"] = randomSeeds;
result["seeds"] = random_seeds;
result["duration"] = duration;
result["results"] = json::array();
for (const auto& r : results) {
@@ -80,147 +76,17 @@ namespace platform {
}
return result;
}
void Experiment::save(const std::string& path)
void Experiment::save(const string& path)
{
json data = build_json();
ofstream file(path + "/" + get_file_name());
file << data;
file.close();
}
void Experiment::report()
{
json data = build_json();
ReportConsole report(data);
report.show();
}
void Experiment::show()
{
json data = build_json();
std::cout << data.dump(4) << std::endl;
cout << data.dump(4) << endl;
}
void Experiment::go(std::vector<std::string> filesToProcess, bool quiet)
{
std::cout << "*** Starting experiment: " << title << " ***" << std::endl;
for (auto fileName : filesToProcess) {
std::cout << "- " << setw(20) << left << fileName << " " << right << flush;
cross_validation(fileName, quiet);
std::cout << std::endl;
}
}
std::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 std::string& color, const std::string& phase)
{
std::string prefix = phase == "a" ? "" : "\b\b\b\b";
std::cout << prefix << color << fold << Colors::RESET() << "(" << color << phase << Colors::RESET() << ")" << flush;
}
void Experiment::cross_validation(const std::string& fileName, bool quiet)
{
auto datasets = Datasets(discretized, Paths::datasets());
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
auto features = datasets.getFeatures(fileName);
auto samples = datasets.getNSamples(fileName);
auto className = datasets.getClassName(fileName);
if (!quiet) {
std::cout << " (" << setw(5) << samples << "," << setw(3) << features.size() << ") " << flush;
}
// Prepare Result
auto result = Result();
auto [values, counts] = at::_unique(y);
result.setSamples(X.size(1)).setFeatures(X.size(0)).setClasses(values.size(0));
result.setHyperparameters(hyperparameters.get(fileName));
// Initialize results std::vectors
int nResults = nfolds * static_cast<int>(randomSeeds.size());
auto accuracy_test = torch::zeros({ nResults }, torch::kFloat64);
auto accuracy_train = torch::zeros({ nResults }, torch::kFloat64);
auto train_time = torch::zeros({ nResults }, torch::kFloat64);
auto test_time = torch::zeros({ nResults }, torch::kFloat64);
auto nodes = torch::zeros({ nResults }, torch::kFloat64);
auto edges = torch::zeros({ nResults }, torch::kFloat64);
auto num_states = torch::zeros({ nResults }, torch::kFloat64);
Timer train_timer, test_timer;
int item = 0;
for (auto seed : randomSeeds) {
if (!quiet)
std::cout << "(" << seed << ") doing Fold: " << flush;
Fold* fold;
if (stratified)
fold = new StratifiedKFold(nfolds, y, seed);
else
fold = new KFold(nfolds, y.size(0), seed);
for (int nfold = 0; nfold < nfolds; nfold++) {
auto clf = Models::instance()->create(model);
setModelVersion(clf->getVersion());
auto valid = clf->getValidHyperparameters();
hyperparameters.check(valid, fileName);
clf->setHyperparameters(hyperparameters.get(fileName));
// Split train - test dataset
train_timer.start();
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
auto X_train = X.index({ "...", train_t });
auto y_train = y.index({ train_t });
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "a");
// Train model
clf->fit(X_train, y_train, features, className, states);
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "b");
nodes[item] = clf->getNumberOfNodes();
edges[item] = clf->getNumberOfEdges();
num_states[item] = clf->getNumberOfStates();
train_time[item] = train_timer.getDuration();
// Score train
auto accuracy_train_value = clf->score(X_train, y_train);
// Test model
if (!quiet)
showProgress(nfold + 1, getColor(clf->getStatus()), "c");
test_timer.start();
auto accuracy_test_value = clf->score(X_test, y_test);
test_time[item] = test_timer.getDuration();
accuracy_train[item] = accuracy_train_value;
accuracy_test[item] = accuracy_test_value;
if (!quiet)
std::cout << "\b\b\b, " << flush;
// Store results and times in std::vector
result.addScoreTrain(accuracy_train_value);
result.addScoreTest(accuracy_test_value);
result.addTimeTrain(train_time[item].item<double>());
result.addTimeTest(test_time[item].item<double>());
item++;
}
if (!quiet)
std::cout << "end. " << flush;
delete fold;
}
result.setScoreTest(torch::mean(accuracy_test).item<double>()).setScoreTrain(torch::mean(accuracy_train).item<double>());
result.setScoreTestStd(torch::std(accuracy_test).item<double>()).setScoreTrainStd(torch::std(accuracy_train).item<double>());
result.setTrainTime(torch::mean(train_time).item<double>()).setTestTime(torch::mean(test_time).item<double>());
result.setTestTimeStd(torch::std(test_time).item<double>()).setTrainTimeStd(torch::std(train_time).item<double>());
result.setNodes(torch::mean(nodes).item<double>()).setLeaves(torch::mean(edges).item<double>()).setDepth(torch::mean(num_states).item<double>());
result.setDataset(fileName);
addResult(result);
}
}

View File

@@ -3,50 +3,59 @@
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <string>
#include "Folding.h"
#include "BaseClassifier.h"
#include "HyperParameters.h"
#include "TAN.h"
#include "KDB.h"
#include "AODE.h"
#include "Timer.h"
#include <chrono>
using namespace std;
namespace platform {
using json = nlohmann::json;
class Timer {
private:
chrono::high_resolution_clock::time_point begin;
public:
Timer() = default;
~Timer() = default;
void start() { begin = chrono::high_resolution_clock::now(); }
double getDuration()
{
chrono::high_resolution_clock::time_point end = chrono::high_resolution_clock::now();
chrono::duration<double> time_span = chrono::duration_cast<chrono::duration<double>>(end - begin);
return time_span.count();
}
};
class Result {
private:
std::string dataset, model_version;
json hyperparameters;
string dataset = "", hyperparameters = "", model_version = "";
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 };
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;
vector<double> scores_train{}, scores_test{}, times_train{}, times_test{};
float nodes{ 0 }, leaves{ 0 }, depth{ 0 };
std::vector<double> scores_train, scores_test, times_train, times_test;
public:
Result() = default;
Result& setDataset(const std::string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setSamples(int samples) { this->samples = samples; return *this; }
Result& setFeatures(int features) { this->features = features; return *this; }
Result& setClasses(int classes) { this->classes = classes; return *this; }
Result& setScoreTrain(double score) { this->score_train = score; return *this; }
Result& setScoreTest(double score) { this->score_test = score; return *this; }
Result& setScoreTrainStd(double score_std) { this->score_train_std = score_std; return *this; }
Result& setScoreTestStd(double score_std) { this->score_test_std = score_std; return *this; }
Result& setTrainTime(double train_time) { this->train_time = train_time; return *this; }
Result& setTrainTimeStd(double train_time_std) { this->train_time_std = train_time_std; return *this; }
Result& setTestTime(double test_time) { this->test_time = test_time; return *this; }
Result& setTestTimeStd(double test_time_std) { this->test_time_std = test_time_std; return *this; }
Result& setNodes(float nodes) { this->nodes = nodes; return *this; }
Result& setLeaves(float leaves) { this->leaves = leaves; return *this; }
Result& setDepth(float depth) { this->depth = depth; return *this; }
Result& addScoreTrain(double score) { scores_train.push_back(score); return *this; }
Result& addScoreTest(double score) { scores_test.push_back(score); return *this; }
Result& addTimeTrain(double time) { times_train.push_back(time); return *this; }
Result& addTimeTest(double time) { times_test.push_back(time); return *this; }
Result& setDataset(const string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const string& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setSamples(const int samples) { this->samples = samples; return *this; }
Result& setFeatures(const int features) { this->features = features; return *this; }
Result& setClasses(const int classes) { this->classes = classes; return *this; }
Result& setScoreTrain(const double score) { this->score_train = score; return *this; }
Result& setScoreTest(const double score) { this->score_test = score; return *this; }
Result& setScoreTrainStd(const double score_std) { this->score_train_std = score_std; return *this; }
Result& setScoreTestStd(const double score_std) { this->score_test_std = score_std; return *this; }
Result& setTrainTime(const double train_time) { this->train_time = train_time; return *this; }
Result& setTrainTimeStd(const double train_time_std) { this->train_time_std = train_time_std; return *this; }
Result& setTestTime(const double test_time) { this->test_time = test_time; return *this; }
Result& setTestTimeStd(const double test_time_std) { this->test_time_std = test_time_std; return *this; }
Result& setNodes(const float nodes) { this->nodes = nodes; return *this; }
Result& setLeaves(const float leaves) { this->leaves = leaves; return *this; }
Result& setDepth(const float depth) { this->depth = depth; return *this; }
Result& setModelVersion(const string& model_version) { this->model_version = model_version; return *this; }
Result& addScoreTrain(const double score) { scores_train.push_back(score); return *this; }
Result& addScoreTest(const double score) { scores_test.push_back(score); return *this; }
Result& addTimeTrain(const double time) { times_train.push_back(time); return *this; }
Result& addTimeTest(const double time) { times_test.push_back(time); return *this; }
const float get_score_train() const { return score_train; }
float get_score_test() { return score_test; }
const std::string& getDataset() const { return dataset; }
const json& getHyperparameters() const { return hyperparameters; }
const string& getDataset() const { return dataset; }
const string& getHyperparameters() const { return hyperparameters; }
const int getSamples() const { return samples; }
const int getFeatures() const { return features; }
const int getClasses() const { return classes; }
@@ -61,43 +70,39 @@ namespace platform {
const float getNodes() const { return nodes; }
const float getLeaves() const { return leaves; }
const float getDepth() const { return depth; }
const std::vector<double>& getScoresTrain() const { return scores_train; }
const std::vector<double>& getScoresTest() const { return scores_test; }
const std::vector<double>& getTimesTrain() const { return times_train; }
const std::vector<double>& getTimesTest() const { return times_test; }
const vector<double>& getScoresTrain() const { return scores_train; }
const vector<double>& getScoresTest() const { return scores_test; }
const vector<double>& getTimesTrain() const { return times_train; }
const vector<double>& getTimesTest() const { return times_test; }
const string& getModelVersion() const { return model_version; }
};
class Experiment {
private:
string title{""}, model{""}, platform{""}, score_name{""}, model_version{""}, language_version{""}, language{""};
bool discretized{false}, stratified{false};
vector<Result> results;
vector<int> random_seeds;
int nfolds{0};
float duration{0};
json build_json();
public:
Experiment() = default;
Experiment& setTitle(const std::string& title) { this->title = title; return *this; }
Experiment& setModel(const std::string& model) { this->model = model; return *this; }
Experiment& setPlatform(const std::string& platform) { this->platform = platform; return *this; }
Experiment& setScoreName(const std::string& score_name) { this->score_name = score_name; return *this; }
Experiment& setModelVersion(const std::string& model_version) { this->model_version = model_version; return *this; }
Experiment& setLanguage(const std::string& language) { this->language = language; return *this; }
Experiment& setLanguageVersion(const std::string& language_version) { this->language_version = language_version; return *this; }
Experiment& setDiscretized(bool discretized) { this->discretized = discretized; return *this; }
Experiment& setStratified(bool stratified) { this->stratified = stratified; return *this; }
Experiment& setNFolds(int nfolds) { this->nfolds = nfolds; return *this; }
Experiment& setTitle(const string& title) { this->title = title; return *this; }
Experiment& setModel(const string& model) { this->model = model; return *this; }
Experiment& setPlatform(const string& platform) { this->platform = platform; return *this; }
Experiment& setScoreName(const string& score_name) { this->score_name = score_name; return *this; }
Experiment& setModelVersion(const string& model_version) { this->model_version = model_version; return *this; }
Experiment& setLanguage(const string& language) { this->language = language; return *this; }
Experiment& setLanguageVersion(const string& language_version) { this->language_version = language_version; return *this; }
Experiment& setDiscretized(const bool discretized) { this->discretized = discretized; return *this; }
Experiment& setStratified(const bool stratified) { this->stratified = stratified; return *this; }
Experiment& setNFolds(const int nfolds) { this->nfolds = nfolds; return *this; }
Experiment& addResult(Result result) { results.push_back(result); return *this; }
Experiment& addRandomSeed(int randomSeed) { randomSeeds.push_back(randomSeed); return *this; }
Experiment& setDuration(float duration) { this->duration = duration; return *this; }
Experiment& setHyperparameters(const HyperParameters& hyperparameters_) { this->hyperparameters = hyperparameters_; return *this; }
std::string get_file_name();
void save(const std::string& path);
void cross_validation(const std::string& fileName, bool quiet);
void go(std::vector<std::string> filesToProcess, bool quiet);
Experiment& addRandomSeed(const int random_seed) { random_seeds.push_back(random_seed); return *this; }
Experiment& setDuration(const float duration) { this->duration = duration; return *this; }
string get_file_name();
void save(const string& path);
void show();
void report();
private:
std::string title, model, platform, score_name, model_version, language_version, language;
bool discretized{ false }, stratified{ false };
std::vector<Result> results;
std::vector<int> randomSeeds;
HyperParameters hyperparameters;
int nfolds{ 0 };
float duration{ 0 };
json build_json();
};
}
#endif

View File

@@ -1,104 +1,95 @@
#include "Folding.h"
#include <algorithm>
#include <map>
namespace platform {
Fold::Fold(int k, int n, int seed) : k(k), n(n), seed(seed)
{
std::random_device rd;
random_seed = std::default_random_engine(seed == -1 ? rd() : seed);
std::srand(seed == -1 ? time(0) : seed);
Fold::Fold(int k, int n, int seed) : k(k), n(n), seed(seed)
{
random_device rd;
random_seed = default_random_engine(seed == -1 ? rd() : seed);
srand(seed == -1 ? time(0) : seed);
}
KFold::KFold(int k, int n, int seed) : Fold(k, n, seed), indices(vector<int>())
{
iota(begin(indices), end(indices), 0); // fill with 0, 1, ..., n - 1
shuffle(indices.begin(), indices.end(), random_seed);
}
pair<vector<int>, vector<int>> KFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw out_of_range("nFold (" + to_string(nFold) + ") must be less than k (" + to_string(k) + ")");
}
KFold::KFold(int k, int n, int seed) : Fold(k, n, seed), indices(std::vector<int>(n))
{
std::iota(begin(indices), end(indices), 0); // fill with 0, 1, ..., n - 1
int nTest = n / k;
auto train = vector<int>();
auto test = vector<int>();
for (int i = 0; i < n; i++) {
if (i >= nTest * nFold && i < nTest * (nFold + 1)) {
test.push_back(indices[i]);
} else {
train.push_back(indices[i]);
}
}
return { train, test };
}
StratifiedKFold::StratifiedKFold(int k, torch::Tensor& y, int seed) : Fold(k, y.numel(), seed)
{
n = y.numel();
this->y = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + n);
build();
}
StratifiedKFold::StratifiedKFold(int k, const vector<int>& y, int seed)
: Fold(k, y.size(), seed)
{
this->y = y;
n = y.size();
build();
}
void StratifiedKFold::build()
{
stratified_indices = vector<vector<int>>(k);
int fold_size = n / k;
// Compute class counts and indices
auto class_indices = map<int, vector<int>>();
vector<int> class_counts(*max_element(y.begin(), y.end()) + 1, 0);
for (auto i = 0; i < n; ++i) {
class_counts[y[i]]++;
class_indices[y[i]].push_back(i);
}
// Shuffle class indices
for (auto& [cls, indices] : class_indices) {
shuffle(indices.begin(), indices.end(), random_seed);
}
std::pair<std::vector<int>, std::vector<int>> KFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw std::out_of_range("nFold (" + std::to_string(nFold) + ") must be less than k (" + std::to_string(k) + ")");
// Assign indices to folds
for (auto label = 0; label < class_counts.size(); ++label) {
auto num_samples_to_take = class_counts[label] / k;
if (num_samples_to_take == 0)
continue;
auto remainder_samples_to_take = class_counts[label] % k;
for (auto fold = 0; fold < k; ++fold) {
auto it = next(class_indices[label].begin(), num_samples_to_take);
move(class_indices[label].begin(), it, back_inserter(stratified_indices[fold])); // ##
class_indices[label].erase(class_indices[label].begin(), it);
}
int nTest = n / k;
auto train = std::vector<int>();
auto test = std::vector<int>();
for (int i = 0; i < n; i++) {
if (i >= nTest * nFold && i < nTest * (nFold + 1)) {
test.push_back(indices[i]);
} else {
train.push_back(indices[i]);
}
}
return { train, test };
}
StratifiedKFold::StratifiedKFold(int k, torch::Tensor& y, int seed) : Fold(k, y.numel(), seed)
{
n = y.numel();
this->y = std::vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + n);
build();
}
StratifiedKFold::StratifiedKFold(int k, const std::vector<int>& y, int seed)
: Fold(k, y.size(), seed)
{
this->y = y;
n = y.size();
build();
}
void StratifiedKFold::build()
{
stratified_indices = std::vector<std::vector<int>>(k);
int fold_size = n / k;
// Compute class counts and indices
auto class_indices = std::map<int, std::vector<int>>();
std::vector<int> class_counts(*max_element(y.begin(), y.end()) + 1, 0);
for (auto i = 0; i < n; ++i) {
class_counts[y[i]]++;
class_indices[y[i]].push_back(i);
}
// Shuffle class indices
for (auto& [cls, indices] : class_indices) {
shuffle(indices.begin(), indices.end(), random_seed);
}
// Assign indices to folds
for (auto label = 0; label < class_counts.size(); ++label) {
auto num_samples_to_take = class_counts.at(label) / k;
if (num_samples_to_take == 0) {
std::cerr << "Warning! The number of samples in class " << label << " (" << class_counts.at(label)
<< ") is less than the number of folds (" << k << ")." << std::endl;
faulty = true;
while (remainder_samples_to_take > 0) {
int fold = (rand() % static_cast<int>(k));
if (stratified_indices[fold].size() == fold_size + 1) {
continue;
}
auto remainder_samples_to_take = class_counts[label] % k;
for (auto fold = 0; fold < k; ++fold) {
auto it = next(class_indices[label].begin(), num_samples_to_take);
move(class_indices[label].begin(), it, back_inserter(stratified_indices[fold])); // ##
class_indices[label].erase(class_indices[label].begin(), it);
}
auto chosen = std::vector<bool>(k, false);
while (remainder_samples_to_take > 0) {
int fold = (rand() % static_cast<int>(k));
if (chosen.at(fold)) {
continue;
}
chosen[fold] = true;
auto it = next(class_indices[label].begin(), 1);
stratified_indices[fold].push_back(*class_indices[label].begin());
class_indices[label].erase(class_indices[label].begin(), it);
remainder_samples_to_take--;
}
auto it = next(class_indices[label].begin(), 1);
stratified_indices[fold].push_back(*class_indices[label].begin());
class_indices[label].erase(class_indices[label].begin(), it);
remainder_samples_to_take--;
}
}
std::pair<std::vector<int>, std::vector<int>> StratifiedKFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw std::out_of_range("nFold (" + std::to_string(nFold) + ") must be less than k (" + std::to_string(k) + ")");
}
std::vector<int> test_indices = stratified_indices[nFold];
std::vector<int> train_indices;
for (int i = 0; i < k; ++i) {
if (i == nFold) continue;
train_indices.insert(train_indices.end(), stratified_indices[i].begin(), stratified_indices[i].end());
}
return { train_indices, test_indices };
}
}
pair<vector<int>, vector<int>> StratifiedKFold::getFold(int nFold)
{
if (nFold >= k || nFold < 0) {
throw out_of_range("nFold (" + to_string(nFold) + ") must be less than k (" + to_string(k) + ")");
}
vector<int> test_indices = stratified_indices[nFold];
vector<int> train_indices;
for (int i = 0; i < k; ++i) {
if (i == nFold) continue;
train_indices.insert(train_indices.end(), stratified_indices[i].begin(), stratified_indices[i].end());
}
return { train_indices, test_indices };
}

View File

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

View File

@@ -1,75 +0,0 @@
#include "GridData.h"
#include <fstream>
namespace platform {
GridData::GridData(const std::string& fileName)
{
json grid_file;
std::ifstream resultData(fileName);
if (resultData.is_open()) {
grid_file = json::parse(resultData);
} else {
throw std::invalid_argument("Unable to open input file. [" + fileName + "]");
}
for (const auto& item : grid_file.items()) {
auto key = item.key();
auto value = item.value();
grid[key] = value;
}
}
int GridData::computeNumCombinations(const json& line)
{
int numCombinations = 1;
for (const auto& item : line.items()) {
numCombinations *= item.value().size();
}
return numCombinations;
}
int GridData::getNumCombinations(const std::string& dataset)
{
int numCombinations = 0;
auto selected = decide_dataset(dataset);
for (const auto& line : grid.at(selected)) {
numCombinations += computeNumCombinations(line);
}
return numCombinations;
}
json GridData::generateCombinations(json::iterator index, const json::iterator last, std::vector<json>& output, json currentCombination)
{
if (index == last) {
// If we reached the end of input, store the current combination
output.push_back(currentCombination);
return currentCombination;
}
const auto& key = index.key();
const auto& values = index.value();
for (const auto& value : values) {
auto combination = currentCombination;
combination[key] = value;
json::iterator nextIndex = index;
generateCombinations(++nextIndex, last, output, combination);
}
return currentCombination;
}
std::vector<json> GridData::getGrid(const std::string& dataset)
{
auto selected = decide_dataset(dataset);
auto result = std::vector<json>();
for (json line : grid.at(selected)) {
generateCombinations(line.begin(), line.end(), result, json({}));
}
return result;
}
json& GridData::getInputGrid(const std::string& dataset)
{
auto selected = decide_dataset(dataset);
return grid.at(selected);
}
std::string GridData::decide_dataset(const std::string& dataset)
{
if (grid.find(dataset) != grid.end())
return dataset;
return ALL_DATASETS;
}
} /* namespace platform */

View File

@@ -1,26 +0,0 @@
#ifndef GRIDDATA_H
#define GRIDDATA_H
#include <string>
#include <vector>
#include <map>
#include <nlohmann/json.hpp>
namespace platform {
using json = nlohmann::json;
const std::string ALL_DATASETS = "all";
class GridData {
public:
explicit GridData(const std::string& fileName);
~GridData() = default;
std::vector<json> getGrid(const std::string& dataset = ALL_DATASETS);
int getNumCombinations(const std::string& dataset = ALL_DATASETS);
json& getInputGrid(const std::string& dataset = ALL_DATASETS);
std::map<std::string, json>& getGridFile() { return grid; }
private:
std::string decide_dataset(const std::string& dataset);
json generateCombinations(json::iterator index, const json::iterator last, std::vector<json>& output, json currentCombination);
int computeNumCombinations(const json& line);
std::map<std::string, json> grid;
};
} /* namespace platform */
#endif /* GRIDDATA_H */

View File

@@ -1,599 +0,0 @@
#include <iostream>
#include <torch/torch.h>
#include "GridSearch.h"
#include "Models.h"
#include "Paths.h"
#include "Folding.h"
#include "Colors.h"
namespace platform {
std::string get_date()
{
time_t rawtime;
tm* timeinfo;
time(&rawtime);
timeinfo = std::localtime(&rawtime);
std::ostringstream oss;
oss << std::put_time(timeinfo, "%Y-%m-%d");
return oss.str();
}
std::string get_time()
{
time_t rawtime;
tm* timeinfo;
time(&rawtime);
timeinfo = std::localtime(&rawtime);
std::ostringstream oss;
oss << std::put_time(timeinfo, "%H:%M:%S");
return oss.str();
}
GridSearch::GridSearch(struct ConfigGrid& config) : config(config)
{
}
json GridSearch::getResults()
{
std::ifstream file(Paths::grid_output(config.model));
if (file.is_open()) {
return json::parse(file);
}
return json();
}
vector<std::string> GridSearch::processDatasets(Datasets& datasets)
{
// Load datasets
auto datasets_names = datasets.getNames();
if (config.continue_from != NO_CONTINUE()) {
// Continue previous execution:
if (std::find(datasets_names.begin(), datasets_names.end(), config.continue_from) == datasets_names.end()) {
throw std::invalid_argument("Dataset " + config.continue_from + " not found");
}
// Remove datasets already processed
vector< string >::iterator it = datasets_names.begin();
while (it != datasets_names.end()) {
if (*it != config.continue_from) {
it = datasets_names.erase(it);
} else {
if (config.only)
++it;
else
break;
}
}
}
// Exclude datasets
for (const auto& name : config.excluded) {
auto dataset = name.get<std::string>();
auto it = std::find(datasets_names.begin(), datasets_names.end(), dataset);
if (it == datasets_names.end()) {
throw std::invalid_argument("Dataset " + dataset + " already excluded or doesn't exist!");
}
datasets_names.erase(it);
}
return datasets_names;
}
void showProgressComb(const int num, const int n_folds, const int total, const std::string& color)
{
int spaces = int(log(total) / log(10)) + 1;
int magic = n_folds * 3 + 22 + 2 * spaces;
std::string prefix = num == 1 ? "" : string(magic, '\b') + string(magic + 1, ' ') + string(magic + 1, '\b');
std::cout << prefix << color << "(" << setw(spaces) << num << "/" << setw(spaces) << total << ") " << Colors::RESET() << flush;
}
void showProgressFold(int fold, const std::string& color, const std::string& phase)
{
std::string prefix = phase == "a" ? "" : "\b\b\b\b";
std::cout << prefix << color << fold << Colors::RESET() << "(" << color << phase << Colors::RESET() << ")" << flush;
}
std::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();
}
}
json GridSearch::build_tasks_mpi()
{
auto tasks = json::array();
auto grid = GridData(Paths::grid_input(config.model));
auto datasets = Datasets(false, Paths::datasets());
auto datasets_names = processDatasets(datasets);
for (const auto& dataset : datasets_names) {
for (const auto& seed : config.seeds) {
auto combinations = grid.getGrid(dataset);
for (int n_fold = 0; n_fold < config.n_folds; n_fold++) {
json task = {
{ "dataset", dataset },
{ "seed", seed },
{ "fold", n_fold}
};
tasks.push_back(task);
}
}
}
// It's important to shuffle the array so heavy datasets are spread across the Workers
std::mt19937 g{ 271 }; // Use fixed seed to obtain the same shuffle
std::shuffle(tasks.begin(), tasks.end(), g);
std::cout << "Tasks size: " << tasks.size() << std::endl;
std::cout << "|";
for (int i = 0; i < tasks.size(); ++i) {
std::cout << (i + 1) % 10;
}
std::cout << "|" << std::endl << "|" << std::flush;
return tasks;
}
std::pair<int, int> GridSearch::part_range_mpi(int n_tasks, int nprocs, int rank)
{
int assigned = 0;
int remainder = n_tasks % nprocs;
int start = 0;
if (rank < remainder) {
assigned = n_tasks / nprocs + 1;
} else {
assigned = n_tasks / nprocs;
start = remainder;
}
start += rank * assigned;
int end = start + assigned;
if (rank == nprocs - 1) {
end = n_tasks;
}
return { start, end };
}
std::string get_color_rank(int rank)
{
auto colors = { Colors::RED(), Colors::GREEN(), Colors::BLUE(), Colors::MAGENTA(), Colors::CYAN() };
return *(colors.begin() + rank % colors.size());
}
void GridSearch::process_task_mpi(struct ConfigMPI& config_mpi, json& task, Datasets& datasets, json& results)
{
// Process the task and store the result in the results json
Timer timer;
timer.start();
auto grid = GridData(Paths::grid_input(config.model));
auto dataset = task["dataset"].get<std::string>();
auto seed = task["seed"].get<int>();
auto n_fold = task["fold"].get<int>();
// Generate the hyperparamters combinations
auto combinations = grid.getGrid(dataset);
auto [X, y] = datasets.getTensors(dataset);
auto states = datasets.getStates(dataset);
auto features = datasets.getFeatures(dataset);
auto className = datasets.getClassName(dataset);
//
// Start working on task
//
Fold* fold;
if (config.stratified)
fold = new StratifiedKFold(config.n_folds, y, seed);
else
fold = new KFold(config.n_folds, y.size(0), seed);
auto [train, test] = fold->getFold(n_fold);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
auto X_train = X.index({ "...", train_t });
auto y_train = y.index({ train_t });
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
auto num = 0;
double best_fold_score = 0.0;
json best_fold_hyper;
for (const auto& hyperparam_line : combinations) {
auto hyperparameters = platform::HyperParameters(datasets.getNames(), hyperparam_line);
Fold* nested_fold;
if (config.stratified)
nested_fold = new StratifiedKFold(config.nested, y_train, seed);
else
nested_fold = new KFold(config.nested, y_train.size(0), seed);
double score = 0.0;
for (int n_nested_fold = 0; n_nested_fold < config.nested; n_nested_fold++) {
// Nested level fold
auto [train_nested, test_nested] = nested_fold->getFold(n_nested_fold);
auto train_nested_t = torch::tensor(train_nested);
auto test_nested_t = torch::tensor(test_nested);
auto X_nested_train = X_train.index({ "...", train_nested_t });
auto y_nested_train = y_train.index({ train_nested_t });
auto X_nested_test = X_train.index({ "...", test_nested_t });
auto y_nested_test = y_train.index({ test_nested_t });
// Build Classifier with selected hyperparameters
auto clf = Models::instance()->create(config.model);
auto valid = clf->getValidHyperparameters();
hyperparameters.check(valid, dataset);
clf->setHyperparameters(hyperparameters.get(dataset));
// Train model
clf->fit(X_nested_train, y_nested_train, features, className, states);
// Test model
score += clf->score(X_nested_test, y_nested_test);
}
delete nested_fold;
score /= config.nested;
if (score > best_fold_score) {
best_fold_score = score;
best_fold_hyper = hyperparam_line;
}
}
delete fold;
// Build Classifier with the best hyperparameters to obtain the best score
auto hyperparameters = platform::HyperParameters(datasets.getNames(), best_fold_hyper);
auto clf = Models::instance()->create(config.model);
auto valid = clf->getValidHyperparameters();
hyperparameters.check(valid, dataset);
clf->setHyperparameters(best_fold_hyper);
clf->fit(X_train, y_train, features, className, states);
best_fold_score = clf->score(X_test, y_test);
// Save results
results[dataset][std::to_string(n_fold)]["score"] = best_fold_score;
results[dataset][std::to_string(n_fold)]["hyperparameters"] = best_fold_hyper;
results[dataset][std::to_string(n_fold)]["seed"] = seed;
results[dataset][std::to_string(n_fold)]["duration"] = timer.getDuration();
std::cout << get_color_rank(config_mpi.rank) << "*" << std::flush;
}
void GridSearch::go_mpi(struct ConfigMPI& config_mpi)
{
/*
* Each task is a json object with the following structure:
* {
* "dataset": "dataset_name",
* "seed": # of seed to use,
* "model": "model_name",
* "Fold": # of fold to process
* }
*
* The overall process consists in these steps:
* 1. Manager will broadcast the tasks to all the processes
* 1.1 Broadcast the number of tasks
* 1.2 Broadcast the length of the following string
* 1.2 Broadcast the tasks as a char* string
* 2. Workers will receive the tasks and start the process
* 2.1 A method will tell each worker the range of tasks to process
* 2.2 Each worker will process the tasks and generate the best score for each task
* 3. Manager gather the scores from all the workers and find out the best hyperparameters for each dataset
* 3.1 Obtain the maximum size of the results message of all the workers
* 3.2 Gather all the results from the workers into the manager
* 3.3 Compile the results from all the workers
* 3.4 Filter the best hyperparameters for each dataset
*/
char* msg;
int tasks_size;
if (config_mpi.rank == config_mpi.manager) {
timer.start();
auto tasks = build_tasks_mpi();
auto tasks_str = tasks.dump();
tasks_size = tasks_str.size();
msg = new char[tasks_size + 1];
strcpy(msg, tasks_str.c_str());
}
//
// 1. Manager will broadcast the tasks to all the processes
//
MPI_Bcast(&tasks_size, 1, MPI_INT, config_mpi.manager, MPI_COMM_WORLD);
if (config_mpi.rank != config_mpi.manager) {
msg = new char[tasks_size + 1];
}
MPI_Bcast(msg, tasks_size + 1, MPI_CHAR, config_mpi.manager, MPI_COMM_WORLD);
json tasks = json::parse(msg);
delete[] msg;
//
// 2. All Workers will receive the tasks and start the process
//
int num_tasks = tasks.size();
// 2.1 A method will tell each worker the range of tasks to process
auto [start, end] = part_range_mpi(num_tasks, config_mpi.n_procs, config_mpi.rank);
// 2.2 Each worker will process the tasks and return the best scores obtained
auto datasets = Datasets(config.discretize, Paths::datasets());
json results;
for (int i = start; i < end; ++i) {
// Process task
process_task_mpi(config_mpi, tasks[i], datasets, results);
}
int size = results.dump().size() + 1;
int max_size = 0;
//
// 3. Manager gather the scores from all the workers and find out the best hyperparameters for each dataset
//
//3.1 Obtain the maximum size of the results message of all the workers
MPI_Allreduce(&size, &max_size, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
// Assign the memory to the message and initialize it to 0s
char* total = NULL;
msg = new char[max_size];
strncpy(msg, results.dump().c_str(), size);
if (config_mpi.rank == config_mpi.manager) {
total = new char[max_size * config_mpi.n_procs];
}
// 3.2 Gather all the results from the workers into the manager
MPI_Gather(msg, max_size, MPI_CHAR, total, max_size, MPI_CHAR, config_mpi.manager, MPI_COMM_WORLD);
delete[] msg;
if (config_mpi.rank == config_mpi.manager) {
std::cout << Colors::RESET() << "|" << std::endl;
json total_results;
json best_results;
// 3.3 Compile the results from all the workers
for (int i = 0; i < config_mpi.n_procs; ++i) {
json partial_results = json::parse(total + i * max_size);
for (auto& [dataset, folds] : partial_results.items()) {
for (auto& [fold, result] : folds.items()) {
total_results[dataset][fold] = result;
}
}
}
delete[] total;
// 3.4 Filter the best hyperparameters for each dataset
auto grid = GridData(Paths::grid_input(config.model));
for (auto& [dataset, folds] : total_results.items()) {
double best_score = 0.0;
double duration = 0.0;
json best_hyper;
for (auto& [fold, result] : folds.items()) {
duration += result["duration"].get<double>();
if (result["score"] > best_score) {
best_score = result["score"];
best_hyper = result["hyperparameters"];
}
}
auto timer = Timer();
json result = {
{ "score", best_score },
{ "hyperparameters", best_hyper },
{ "date", get_date() + " " + get_time() },
{ "grid", grid.getInputGrid(dataset) },
{ "duration", timer.translate2String(duration) }
};
best_results[dataset] = result;
}
save(best_results);
}
}
void GridSearch::go()
{
timer.start();
auto grid_type = config.nested == 0 ? "Single" : "Nested";
auto datasets = Datasets(config.discretize, Paths::datasets());
auto datasets_names = processDatasets(datasets);
json results = initializeResults();
std::cout << "***************** Starting " << grid_type << " Gridsearch *****************" << std::endl;
std::cout << "input file=" << Paths::grid_input(config.model) << std::endl;
auto grid = GridData(Paths::grid_input(config.model));
Timer timer_dataset;
double bestScore = 0;
json bestHyperparameters;
for (const auto& dataset : datasets_names) {
if (!config.quiet)
std::cout << "- " << setw(20) << left << dataset << " " << right << flush;
auto combinations = grid.getGrid(dataset);
timer_dataset.start();
if (config.nested == 0)
// for dataset // for hyperparameters // for seed // for fold
tie(bestScore, bestHyperparameters) = processFileSingle(dataset, datasets, combinations);
else
// for dataset // for seed // for fold // for hyperparameters // for nested fold
tie(bestScore, bestHyperparameters) = processFileNested(dataset, datasets, combinations);
if (!config.quiet) {
std::cout << "end." << " Score: " << Colors::IBLUE() << setw(9) << setprecision(7) << fixed
<< bestScore << Colors::BLUE() << " [" << bestHyperparameters.dump() << "]"
<< Colors::RESET() << ::endl;
}
json result = {
{ "score", bestScore },
{ "hyperparameters", bestHyperparameters },
{ "date", get_date() + " " + get_time() },
{ "grid", grid.getInputGrid(dataset) },
{ "duration", timer_dataset.getDurationString() }
};
results[dataset] = result;
// Save partial results
save(results);
}
// Save final results
save(results);
std::cout << "***************** Ending " << grid_type << " Gridsearch *******************" << std::endl;
}
pair<double, json> GridSearch::processFileSingle(std::string fileName, Datasets& datasets, vector<json>& combinations)
{
int num = 0;
double bestScore = 0.0;
json bestHyperparameters;
auto totalComb = combinations.size();
for (const auto& hyperparam_line : combinations) {
if (!config.quiet)
showProgressComb(++num, config.n_folds, totalComb, Colors::CYAN());
auto hyperparameters = platform::HyperParameters(datasets.getNames(), hyperparam_line);
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
auto features = datasets.getFeatures(fileName);
auto className = datasets.getClassName(fileName);
double totalScore = 0.0;
int numItems = 0;
for (const auto& seed : config.seeds) {
if (!config.quiet)
std::cout << "(" << seed << ") doing Fold: " << flush;
Fold* fold;
if (config.stratified)
fold = new StratifiedKFold(config.n_folds, y, seed);
else
fold = new KFold(config.n_folds, y.size(0), seed);
for (int nfold = 0; nfold < config.n_folds; nfold++) {
auto clf = Models::instance()->create(config.model);
auto valid = clf->getValidHyperparameters();
hyperparameters.check(valid, fileName);
clf->setHyperparameters(hyperparameters.get(fileName));
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
auto X_train = X.index({ "...", train_t });
auto y_train = y.index({ train_t });
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
// Train model
if (!config.quiet)
showProgressFold(nfold + 1, getColor(clf->getStatus()), "a");
clf->fit(X_train, y_train, features, className, states);
// Test model
if (!config.quiet)
showProgressFold(nfold + 1, getColor(clf->getStatus()), "b");
totalScore += clf->score(X_test, y_test);
numItems++;
if (!config.quiet)
std::cout << "\b\b\b, \b" << flush;
}
delete fold;
}
double score = numItems == 0 ? 0.0 : totalScore / numItems;
if (score > bestScore) {
bestScore = score;
bestHyperparameters = hyperparam_line;
}
}
return { bestScore, bestHyperparameters };
}
pair<double, json> GridSearch::processFileNested(std::string fileName, Datasets& datasets, vector<json>& combinations)
{
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
auto features = datasets.getFeatures(fileName);
auto className = datasets.getClassName(fileName);
int spcs_combinations = int(log(combinations.size()) / log(10)) + 1;
double goatScore = 0.0;
json goatHyperparameters;
// for dataset // for seed // for fold // for hyperparameters // for nested fold
for (const auto& seed : config.seeds) {
Fold* fold;
if (config.stratified)
fold = new StratifiedKFold(config.n_folds, y, seed);
else
fold = new KFold(config.n_folds, y.size(0), seed);
double bestScore = 0.0;
json bestHyperparameters;
std::cout << "(" << seed << ") doing Fold: " << flush;
for (int nfold = 0; nfold < config.n_folds; nfold++) {
if (!config.quiet)
std::cout << Colors::GREEN() << nfold + 1 << " " << flush;
// First level fold
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
auto test_t = torch::tensor(test);
auto X_train = X.index({ "...", train_t });
auto y_train = y.index({ train_t });
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
auto num = 0;
json result_fold;
double hypScore = 0.0;
double bestHypScore = 0.0;
json bestHypHyperparameters;
for (const auto& hyperparam_line : combinations) {
std::cout << "[" << setw(spcs_combinations) << ++num << "/" << setw(spcs_combinations)
<< combinations.size() << "] " << std::flush;
Fold* nested_fold;
if (config.stratified)
nested_fold = new StratifiedKFold(config.nested, y_train, seed);
else
nested_fold = new KFold(config.nested, y_train.size(0), seed);
for (int n_nested_fold = 0; n_nested_fold < config.nested; n_nested_fold++) {
// Nested level fold
auto [train_nested, test_nested] = nested_fold->getFold(n_nested_fold);
auto train_nested_t = torch::tensor(train_nested);
auto test_nested_t = torch::tensor(test_nested);
auto X_nexted_train = X_train.index({ "...", train_nested_t });
auto y_nested_train = y_train.index({ train_nested_t });
auto X_nested_test = X_train.index({ "...", test_nested_t });
auto y_nested_test = y_train.index({ test_nested_t });
// Build Classifier with selected hyperparameters
auto hyperparameters = platform::HyperParameters(datasets.getNames(), hyperparam_line);
auto clf = Models::instance()->create(config.model);
auto valid = clf->getValidHyperparameters();
hyperparameters.check(valid, fileName);
clf->setHyperparameters(hyperparameters.get(fileName));
// Train model
if (!config.quiet)
showProgressFold(n_nested_fold + 1, getColor(clf->getStatus()), "a");
clf->fit(X_nexted_train, y_nested_train, features, className, states);
// Test model
if (!config.quiet)
showProgressFold(n_nested_fold + 1, getColor(clf->getStatus()), "b");
hypScore += clf->score(X_nested_test, y_nested_test);
if (!config.quiet)
std::cout << "\b\b\b, \b" << flush;
}
int magic = 3 * config.nested + 2 * spcs_combinations + 4;
std::cout << string(magic, '\b') << string(magic, ' ') << string(magic, '\b') << flush;
delete nested_fold;
hypScore /= config.nested;
if (hypScore > bestHypScore) {
bestHypScore = hypScore;
bestHypHyperparameters = hyperparam_line;
}
}
// Build Classifier with selected hyperparameters
auto clf = Models::instance()->create(config.model);
clf->setHyperparameters(bestHypHyperparameters);
// Train model
if (!config.quiet)
showProgressFold(nfold + 1, getColor(clf->getStatus()), "a");
clf->fit(X_train, y_train, features, className, states);
// Test model
if (!config.quiet)
showProgressFold(nfold + 1, getColor(clf->getStatus()), "b");
double score = clf->score(X_test, y_test);
if (!config.quiet)
std::cout << string(2 * config.nested - 1, '\b') << "," << string(2 * config.nested, ' ') << string(2 * config.nested - 1, '\b') << flush;
if (score > bestScore) {
bestScore = score;
bestHyperparameters = bestHypHyperparameters;
}
}
if (bestScore > goatScore) {
goatScore = bestScore;
goatHyperparameters = bestHyperparameters;
}
delete fold;
}
return { goatScore, goatHyperparameters };
}
json GridSearch::initializeResults()
{
// Load previous results
json results;
if (config.continue_from != NO_CONTINUE()) {
if (!config.quiet)
std::cout << "* Loading previous results" << std::endl;
try {
std::ifstream file(Paths::grid_output(config.model));
if (file.is_open()) {
results = json::parse(file);
results = results["results"];
}
}
catch (const std::exception& e) {
std::cerr << "* There were no previous results" << std::endl;
std::cerr << "* Initizalizing new results" << std::endl;
results = json();
}
}
return results;
}
void GridSearch::save(json& results)
{
std::ofstream file(Paths::grid_output(config.model));
json output = {
{ "model", config.model },
{ "score", config.score },
{ "discretize", config.discretize },
{ "stratified", config.stratified },
{ "n_folds", config.n_folds },
{ "seeds", config.seeds },
{ "date", get_date() + " " + get_time()},
{ "nested", config.nested},
{ "platform", config.platform },
{ "duration", timer.getDurationString(true)},
{ "results", results }
};
file << output.dump(4);
}
} /* namespace platform */

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@@ -1,54 +0,0 @@
#ifndef GRIDSEARCH_H
#define GRIDSEARCH_H
#include <string>
#include <map>
#include <mpi.h>
#include <nlohmann/json.hpp>
#include "Datasets.h"
#include "HyperParameters.h"
#include "GridData.h"
#include "Timer.h"
namespace platform {
using json = nlohmann::json;
struct ConfigGrid {
std::string model;
std::string score;
std::string continue_from;
std::string platform;
bool quiet;
bool only; // used with continue_from to only compute that dataset
bool discretize;
bool stratified;
int nested;
int n_folds;
json excluded;
std::vector<int> seeds;
};
struct ConfigMPI {
int rank;
int n_procs;
int manager;
};
class GridSearch {
public:
explicit GridSearch(struct ConfigGrid& config);
void go();
void go_mpi(struct ConfigMPI& config_mpi);
~GridSearch() = default;
json getResults();
static inline std::string NO_CONTINUE() { return "NO_CONTINUE"; }
private:
void save(json& results);
json initializeResults();
vector<std::string> processDatasets(Datasets& datasets);
pair<double, json> processFileSingle(std::string fileName, Datasets& datasets, std::vector<json>& combinations);
pair<double, json> processFileNested(std::string fileName, Datasets& datasets, std::vector<json>& combinations);
struct ConfigGrid config;
pair<int, int> part_range_mpi(int n_tasks, int nprocs, int rank);
json build_tasks_mpi();
void process_task_mpi(struct ConfigMPI& config_mpi, json& task, Datasets& datasets, json& results);
Timer timer; // used to measure the time of the whole process
};
} /* namespace platform */
#endif /* GRIDSEARCH_H */

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@@ -1,55 +0,0 @@
#include "HyperParameters.h"
#include <fstream>
#include <sstream>
#include <iostream>
namespace platform {
HyperParameters::HyperParameters(const std::vector<std::string>& datasets, const json& hyperparameters_)
{
// Initialize all datasets with the given hyperparameters
for (const auto& item : datasets) {
hyperparameters[item] = hyperparameters_;
}
}
// https://www.techiedelight.com/implode-a-vector-of-strings-into-a-comma-separated-string-in-cpp/
std::string join(std::vector<std::string> const& strings, std::string delim)
{
std::stringstream ss;
std::copy(strings.begin(), strings.end(),
std::ostream_iterator<std::string>(ss, delim.c_str()));
return ss.str();
}
HyperParameters::HyperParameters(const std::vector<std::string>& datasets, const std::string& hyperparameters_file)
{
// Check if file exists
std::ifstream file(hyperparameters_file);
if (!file.is_open()) {
throw std::runtime_error("File " + hyperparameters_file + " not found");
}
// Check if file is a json
json input_hyperparameters = json::parse(file);
// Check if hyperparameters are valid
for (const auto& dataset : datasets) {
if (!input_hyperparameters.contains(dataset)) {
std::cerr << "*Warning: Dataset " << dataset << " not found in hyperparameters file" << " assuming default hyperparameters" << std::endl;
hyperparameters[dataset] = json({});
continue;
}
hyperparameters[dataset] = input_hyperparameters[dataset]["hyperparameters"].get<json>();
}
}
void HyperParameters::check(const std::vector<std::string>& valid, const std::string& fileName)
{
json result = hyperparameters.at(fileName);
for (const auto& item : result.items()) {
if (find(valid.begin(), valid.end(), item.key()) == valid.end()) {
throw std::invalid_argument("Hyperparameter " + item.key() + " is not valid. Passed Hyperparameters are: "
+ result.dump(4) + "\n Valid hyperparameters are: {" + join(valid, ",") + "}");
}
}
}
json HyperParameters::get(const std::string& fileName)
{
return hyperparameters.at(fileName);
}
} /* namespace platform */

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@@ -1,23 +0,0 @@
#ifndef HYPERPARAMETERS_H
#define HYPERPARAMETERS_H
#include <string>
#include <map>
#include <vector>
#include <nlohmann/json.hpp>
namespace platform {
using json = nlohmann::json;
class HyperParameters {
public:
HyperParameters() = default;
explicit HyperParameters(const std::vector<std::string>& datasets, const json& hyperparameters_);
explicit HyperParameters(const std::vector<std::string>& datasets, const std::string& hyperparameters_file);
~HyperParameters() = default;
bool notEmpty(const std::string& key) const { return !hyperparameters.at(key).empty(); }
void check(const std::vector<std::string>& valid, const std::string& fileName);
json get(const std::string& fileName);
private:
std::map<std::string, json> hyperparameters;
};
} /* namespace platform */
#endif /* HYPERPARAMETERS_H */

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

View File

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

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