rmontanana/BayesNet
rmontanana/BayesNet
1
0
Fork 0
Code Issues 2 Pull Requests Packages Projects Releases 3 Wiki Activity

Merge pull request 'gridsearch' (#13) from gridsearch into main

Browse Source 
Reviewed-on: #13
This commit is contained in:
Ricardo Montañana Gómez 2023-11-25 11:16:13 +00:00
commit ba2a3f9523
16 changed files with 393 additions and 35 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

3
.gitignore vendored
View File

@ -32,8 +32,7 @@
*.out
*.app
build/**
build_debug/**
build_release/**
build_*/**
*.dSYM/**
cmake-build*/**
.idea

12
Makefile
View File

@ -4,7 +4,7 @@ SHELL := /bin/bash
f_release = build_release
f_debug = build_debug
app_targets = b_best b_list b_main b_manage
app_targets = b_best b_list b_main b_manage b_grid
test_targets = unit_tests_bayesnet unit_tests_platform
n_procs = -j 16
@ -35,11 +35,13 @@ dest ?= ${HOME}/bin
install: ## Copy binary files to bin folder
@echo "Destination folder: $(dest)"
make buildr
@echo "*******************************************"
@echo ">>> Copying files to $(dest)"
@cp $(f_release)/src/Platform/b_main $(dest)
@cp $(f_release)/src/Platform/b_list $(dest)
@cp $(f_release)/src/Platform/b_manage $(dest)
@cp $(f_release)/src/Platform/b_best $(dest)
@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...";

2
sample/sample.cc
View File

@ -1,6 +1,6 @@
#include <iostream>
#include <torch/torch.h>
#include <std::string>
#include <string>
#include <map>
#include <argparse/argparse.hpp>
#include <nlohmann/json.hpp>

12
src/Platform/CMakeLists.txt
View File

@ -8,12 +8,14 @@ include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/libxlsxwriter/include)
include_directories(${Python3_INCLUDE_DIRS})
add_executable(b_best b_best.cc BestResults.cc Result.cc Statistics.cc BestResultsExcel.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
add_executable(b_grid b_grid.cc GridSearch.cc GridData.cc HyperParameters.cc Folding.cc Datasets.cc Dataset.cc)
add_executable(b_list b_list.cc Datasets.cc Dataset.cc)
add_executable(b_main b_main.cc Folding.cc Experiment.cc Datasets.cc Dataset.cc Models.cc HyperParameters.cc ReportConsole.cc ReportBase.cc)
add_executable(b_manage b_manage.cc Results.cc ManageResults.cc CommandParser.cc Result.cc ReportConsole.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
add_executable(b_list b_list.cc Datasets.cc Dataset.cc)
add_executable(b_best b_best.cc BestResults.cc Result.cc Statistics.cc BestResultsExcel.cc ReportExcel.cc ReportBase.cc Datasets.cc Dataset.cc ExcelFile.cc)
target_link_libraries(b_main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}" PyWrap)
target_link_libraries(b_manage "${TORCH_LIBRARIES}" "${XLSXWRITER_LIB}" ArffFiles mdlp)
target_link_libraries(b_best Boost::boost "${XLSXWRITER_LIB}" "${TORCH_LIBRARIES}" ArffFiles mdlp)
target_link_libraries(b_list ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(b_grid BayesNet PyWrap)
target_link_libraries(b_list ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(b_main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}" PyWrap)
target_link_libraries(b_manage "${TORCH_LIBRARIES}" "${XLSXWRITER_LIB}" ArffFiles mdlp)

2
src/Platform/Experiment.cc
View File

@ -133,7 +133,7 @@ namespace platform {
}
void Experiment::cross_validation(const std::string& fileName, bool quiet)
{
auto datasets = platform::Datasets(discretized, Paths::datasets());
auto datasets = Datasets(discretized, Paths::datasets());
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);

16
src/Platform/Experiment.h
View File

@ -3,30 +3,16 @@
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <string>
#include <chrono>
#include "Folding.h"
#include "BaseClassifier.h"
#include "HyperParameters.h"
#include "TAN.h"
#include "KDB.h"
#include "AODE.h"
#include "Timer.h"
namespace platform {
using json = nlohmann::json;
class Timer {
private:
std::chrono::high_resolution_clock::time_point begin;
public:
Timer() = default;
~Timer() = default;
void start() { begin = std::chrono::high_resolution_clock::now(); }
double getDuration()
{
std::chrono::high_resolution_clock::time_point end = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> time_span = std::chrono::duration_cast<std::chrono::duration<double >> (end - begin);
return time_span.count();
}
};
class Result {
private:
std::string dataset, model_version;

55
src/Platform/GridData.cc Normal file
View File

@ -0,0 +1,55 @@
#include "GridData.h"
#include <fstream>
namespace platform {
GridData::GridData(const std::string& fileName)
{
std::ifstream resultData(fileName);
if (resultData.is_open()) {
grid = json::parse(resultData);
} else {
throw std::invalid_argument("Unable to open input file. [" + fileName + "]");
}
}
int GridData::computeNumCombinations(const json& line)
{
int numCombinations = 1;
for (const auto& item : line.items()) {
numCombinations *= item.value().size();
}
return numCombinations;
}
int GridData::getNumCombinations()
{
int numCombinations = 0;
for (const auto& line : grid) {
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()
{
auto result = std::vector<json>();
for (json line : grid) {
generateCombinations(line.begin(), line.end(), result, json({}));
}
return result;
}
} /* namespace platform */

22
src/Platform/GridData.h Normal file
View File

@ -0,0 +1,22 @@
#ifndef GRIDDATA_H
#define GRIDDATA_H
#include <string>
#include <vector>
#include <map>
#include <nlohmann/json.hpp>
namespace platform {
using json = nlohmann::json;
class GridData {
public:
explicit GridData(const std::string& fileName);
~GridData() = default;
std::vector<json> getGrid();
int getNumCombinations();
private:
json generateCombinations(json::iterator index, const json::iterator last, std::vector<json>& output, json currentCombination);
int computeNumCombinations(const json& line);
json grid;
};
} /* namespace platform */
#endif /* GRIDDATA_H */

130
src/Platform/GridSearch.cc Normal file
View File

@ -0,0 +1,130 @@
#include <iostream>
#include <torch/torch.h>
#include "GridSearch.h"
#include "Models.h"
#include "Paths.h"
#include "Folding.h"
#include "Colors.h"
namespace platform {
GridSearch::GridSearch(struct ConfigGrid& config) : config(config)
{
this->config.output_file = config.path + "grid_" + config.model + "_output.json";
this->config.input_file = config.path + "grid_" + config.model + "_input.json";
}
void showProgressComb(const int num, const int total, const std::string& color)
{
int spaces = int(log(total) / log(10)) + 1;
int magic = 37 + 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();
}
}
double GridSearch::processFile(std::string fileName, Datasets& datasets, HyperParameters& hyperparameters)
{
// 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);
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);
double bestScore = 0.0;
for (int nfold = 0; nfold < config.n_folds; nfold++) {
auto clf = Models::instance()->create(config.model);
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;
}
return numItems == 0 ? 0.0 : totalScore / numItems;
}
void GridSearch::go()
{
// Load datasets
auto datasets = Datasets(config.discretize, Paths::datasets());
// Create model
std::cout << "***************** Starting Gridsearch *****************" << std::endl;
std::cout << "input file=" << config.input_file << std::endl;
auto grid = GridData(config.input_file);
auto totalComb = grid.getNumCombinations();
std::cout << "* Doing " << totalComb << " combinations for each dataset/seed/fold" << std::endl;
// Generate hyperparameters grid & run gridsearch
// Check each combination of hyperparameters for each dataset and each seed
for (const auto& dataset : datasets.getNames()) {
if (!config.quiet)
std::cout << "- " << setw(20) << left << dataset << " " << right << flush;
int num = 0;
double bestScore = 0.0;
json bestHyperparameters;
for (const auto& hyperparam_line : grid.getGrid()) {
if (!config.quiet)
showProgressComb(++num, totalComb, Colors::CYAN());
auto hyperparameters = platform::HyperParameters(datasets.getNames(), hyperparam_line);
double score = processFile(dataset, datasets, hyperparameters);
if (score > bestScore) {
bestScore = score;
bestHyperparameters = hyperparam_line;
}
}
if (!config.quiet) {
std::cout << "end." << " Score: " << setw(9) << setprecision(7) << fixed
<< bestScore << " [" << bestHyperparameters.dump() << "]" << std::endl;
}
results[dataset]["score"] = bestScore;
results[dataset]["hyperparameters"] = bestHyperparameters;
}
// Save results
save();
std::cout << "***************** Ending Gridsearch *******************" << std::endl;
}
void GridSearch::save() const
{
std::ofstream file(config.output_file);
file << results.dump(4);
file.close();
}
} /* namespace platform */

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

@ -0,0 +1,36 @@
#ifndef GRIDSEARCH_H
#define GRIDSEARCH_H
#include <string>
#include <vector>
#include <nlohmann/json.hpp>
#include "Datasets.h"
#include "HyperParameters.h"
#include "GridData.h"
namespace platform {
using json = nlohmann::json;
struct ConfigGrid {
std::string model;
std::string score;
std::string path;
std::string input_file;
std::string output_file;
bool quiet;
bool discretize;
bool stratified;
int n_folds;
std::vector<int> seeds;
};
class GridSearch {
public:
explicit GridSearch(struct ConfigGrid& config);
void go();
void save() const;
~GridSearch() = default;
private:
double processFile(std::string fileName, Datasets& datasets, HyperParameters& hyperparameters);
json results;
struct ConfigGrid config;
};
} /* namespace platform */
#endif /* GRIDSEARCH_H */

13
src/Platform/Paths.h
View File

@ -1,6 +1,7 @@
#ifndef PATHS_H
#define PATHS_H
#include <string>
#include <filesystem>
#include "DotEnv.h"
namespace platform {
class Paths {
@ -8,12 +9,22 @@ namespace platform {
static std::string results() { return "results/"; }
static std::string hiddenResults() { return "hidden_results/"; }
static std::string excel() { return "excel/"; }
static std::string cfs() { return "cfs/"; }
static std::string grid() { return "grid/"; }
static std::string datasets()
{
auto env = platform::DotEnv();
return env.get("source_data");
}
static void createPath(const std::string& path)
{
// Create directory if it does not exist
try {
std::filesystem::create_directory(path);
}
catch (std::exception& e) {
throw std::runtime_error("Could not create directory " + path);
}
}
static std::string excelResults() { return "some_results.xlsx"; }
};
}

34
src/Platform/Timer.h Normal file
View File

@ -0,0 +1,34 @@
#ifndef TIMER_H
#define TIMER_H
#include <chrono>
#include <string>
#include <sstream>
namespace platform {
class Timer {
private:
std::chrono::high_resolution_clock::time_point begin;
std::chrono::high_resolution_clock::time_point end;
public:
Timer() = default;
~Timer() = default;
void start() { begin = std::chrono::high_resolution_clock::now(); }
void stop() { end = std::chrono::high_resolution_clock::now(); }
double getDuration()
{
stop();
std::chrono::duration<double> time_span = std::chrono::duration_cast<std::chrono::duration<double >> (end - begin);
return time_span.count();
}
std::string getDurationString()
{
double duration = getDuration();
double durationShow = duration > 3600 ? duration / 3600 : duration > 60 ? duration / 60 : duration;
std::string durationUnit = duration > 3600 ? "h" : duration > 60 ? "m" : "s";
std::stringstream ss;
ss << std::setw(7) << std::setprecision(2) << std::fixed << durationShow << " " << durationUnit << " ";
return ss.str();
}
};
} /* namespace platform */
#endif /* TIMER_H */

2
src/Platform/b_best.cc
View File

@ -7,7 +7,7 @@
argparse::ArgumentParser manageArguments(int argc, char** argv)
{
argparse::ArgumentParser program("best");
argparse::ArgumentParser program("b_sbest");
program.add_argument("-m", "--model").default_value("").help("Filter results of the selected model) (any for all models)");
program.add_argument("-s", "--score").default_value("").help("Filter results of the score name supplied");
program.add_argument("--build").help("build best score results file").default_value(false).implicit_value(true);

81
src/Platform/b_grid.cc Normal file
View File

@ -0,0 +1,81 @@
#include <iostream>
#include <argparse/argparse.hpp>
#include "DotEnv.h"
#include "Models.h"
#include "modelRegister.h"
#include "GridSearch.h"
#include "Paths.h"
#include "Timer.h"
argparse::ArgumentParser manageArguments(std::string program_name)
{
auto env = platform::DotEnv();
argparse::ArgumentParser program(program_name);
program.add_argument("-m", "--model")
.help("Model to use " + platform::Models::instance()->tostring())
.action([](const std::string& value) {
static const std::vector<std::string> choices = platform::Models::instance()->getNames();
if (find(choices.begin(), choices.end(), value) != choices.end()) {
return value;
}
throw std::runtime_error("Model must be one of " + platform::Models::instance()->tostring());
}
);
program.add_argument("--discretize").help("Discretize input datasets").default_value((bool)stoi(env.get("discretize"))).implicit_value(true);
program.add_argument("--quiet").help("Don't display detailed progress").default_value(false).implicit_value(true);
program.add_argument("--stratified").help("If Stratified KFold is to be done").default_value((bool)stoi(env.get("stratified"))).implicit_value(true);
program.add_argument("--score").help("Score used in gridsearch").default_value("accuracy");
program.add_argument("-f", "--folds").help("Number of folds").default_value(stoi(env.get("n_folds"))).scan<'i', int>().action([](const std::string& value) {
try {
auto k = stoi(value);
if (k < 2) {
throw std::runtime_error("Number of folds must be greater than 1");
}
return k;
}
catch (const runtime_error& err) {
throw std::runtime_error(err.what());
}
catch (...) {
throw std::runtime_error("Number of folds must be an integer");
}});
auto seed_values = env.getSeeds();
program.add_argument("-s", "--seeds").nargs(1, 10).help("Random seeds. Set to -1 to have pseudo random").scan<'i', int>().default_value(seed_values);
return program;
}
int main(int argc, char** argv)
{
auto program = manageArguments("b_grid");
struct platform::ConfigGrid config;
try {
program.parse_args(argc, argv);
config.model = program.get<std::string>("model");
config.score = program.get<std::string>("score");
config.discretize = program.get<bool>("discretize");
config.stratified = program.get<bool>("stratified");
config.n_folds = program.get<int>("folds");
config.quiet = program.get<bool>("quiet");
config.seeds = program.get<std::vector<int>>("seeds");
}
catch (const exception& err) {
cerr << err.what() << std::endl;
cerr << program;
exit(1);
}
/*
* Begin Processing
*/
auto env = platform::DotEnv();
platform::Paths::createPath(platform::Paths::grid());
config.path = platform::Paths::grid();
auto grid_search = platform::GridSearch(config);
platform::Timer timer;
timer.start();
grid_search.go();
std::cout << "Process took " << timer.getDurationString() << std::endl;
grid_search.save();
std::cout << "Done!" << std::endl;
return 0;
}

6
src/Platform/b_main.cc
View File

@ -11,10 +11,10 @@
using json = nlohmann::json;
argparse::ArgumentParser manageArguments()
argparse::ArgumentParser manageArguments(std::string program_name)
{
auto env = platform::DotEnv();
argparse::ArgumentParser program("main");
argparse::ArgumentParser program(program_name);
program.add_argument("-d", "--dataset").default_value("").help("Dataset file name");
program.add_argument("--hyperparameters").default_value("{}").help("Hyperparameters passed to the model in Experiment");
program.add_argument("--hyper-file").default_value("").help("Hyperparameters file name." \
@ -61,7 +61,7 @@ int main(int argc, char** argv)
std::vector<int> seeds;
std::vector<std::string> filesToTest;
int n_folds;
auto program = manageArguments();
auto program = manageArguments("b_main");
try {
program.parse_args(argc, argv);
file_name = program.get<std::string>("dataset");

2
src/Platform/b_manage.cc
View File

@ -5,7 +5,7 @@
argparse::ArgumentParser manageArguments(int argc, char** argv)
{
argparse::ArgumentParser program("manage");
argparse::ArgumentParser program("b_manage");
program.add_argument("-n", "--number").default_value(0).help("Number of results to show (0 = all)").scan<'i', int>();
program.add_argument("-m", "--model").default_value("any").help("Filter results of the selected model)");
program.add_argument("-s", "--score").default_value("any").help("Filter results of the score name supplied");