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16 Commits

Author SHA1 Message Date
97ca8ac084 Move check valid hyperparameters to Classifier 2023-08-22 22:12:20 +02:00
1c1385b768 Fix maxModels mistake in BoostAODE if !repeatSp
Throw exception if wrong hyperparmeter is supplied
2023-08-22 21:55:17 +02:00
35432b6294 Fix time std was not saved in experiment 2023-08-22 12:30:27 +02:00
c59dd30e53 Complete Excel Report with data 2023-08-22 11:55:15 +02:00
d2da0ddb88 Create ReportExcel eq to ReportConsole 2023-08-21 17:51:49 +02:00
8066701c3c Refactor Report class into ReportBase & ReportCons 2023-08-21 17:16:29 +02:00
0f66ac73d0 Revert "Refactor Report into ReportBase & ReportConsole"
This reverts commit 4370bf51d7.
2023-08-21 17:15:14 +02:00
4370bf51d7 Refactor Report into ReportBase & ReportConsole 2023-08-21 17:14:23 +02:00
2b7353b9e0 Add default sorting by date in manage 2023-08-21 16:30:10 +02:00
b686b3c9c3 Enhance copy in Makefile 2023-08-21 12:18:23 +02:00
2dd04a6c44 enhance saving results and add Makefile copy 2023-08-21 11:57:45 +02:00
1da83662d0 Always save results 2023-08-21 10:55:20 +02:00
3ac9593c65 Fix mistake in sample 2023-08-20 20:36:46 +02:00
6b317accf1 Add hyperparameters and processing order to Boost 2023-08-20 20:31:23 +02:00
4964aab722 Add hyperparameters management in experiments 2023-08-20 17:57:38 +02:00
7a6ec73d63 Merge pull request 'boostAode' (#5) from boostAode into main
Reviewed-on: https://gitea.rmontanana.es:11000/rmontanana/BayesNet/pulls/5
Implement boostAODE
add list datasets
add manage results
2023-08-20 09:02:07 +00:00
36 changed files with 487 additions and 240 deletions

4
.vscode/launch.json vendored
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@@ -31,7 +31,9 @@
"--discretize",
"--stratified",
"-d",
"iris"
"glass",
"--hyperparameters",
"{\"repeatSparent\": true, \"maxModels\": 12}"
],
"cwd": "/Users/rmontanana/Code/discretizbench",
},

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@@ -55,6 +55,7 @@ endif (ENABLE_CLANG_TIDY)
add_git_submodule("lib/mdlp")
add_git_submodule("lib/argparse")
add_git_submodule("lib/json")
add_git_submodule("lib/openXLSX")
# Subdirectories
# --------------

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@@ -11,6 +11,16 @@ setup: ## Install dependencies for tests and coverage
pip install gcovr; \
fi
dest ?= ../discretizbench
copy: ## Copy binary files to selected folder
@echo "Destination folder: $(dest)"
make build
@echo ">>> Copying files to $(dest)"
@cp build/src/Platform/main $(dest)
@cp build/src/Platform/list $(dest)
@cp build/src/Platform/manage $(dest)
@echo ">>> Done"
dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
cd build && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png

1
lib/openXLSX Submodule

Submodule lib/openXLSX added at b80da42d14

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

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@@ -3,6 +3,7 @@
#include <string>
#include <map>
#include <argparse/argparse.hpp>
#include <nlohmann/json.hpp>
#include "ArffFiles.h"
#include "BayesMetrics.h"
#include "CPPFImdlp.h"
@@ -141,111 +142,96 @@ int main(int argc, char** argv)
/*
* Begin Processing
*/
auto ypred = torch::tensor({ 1,2,3,2,2,3,4,5,2,1 });
auto y = torch::tensor({ 0,0,0,0,2,3,4,0,0,0 });
auto weights = torch::ones({ 10 }, kDouble);
auto mask = ypred == y;
cout << "ypred:" << ypred << endl;
cout << "y:" << y << endl;
cout << "weights:" << weights << endl;
cout << "mask:" << mask << endl;
double value_to_add = 0.5;
weights += mask.to(torch::kDouble) * value_to_add;
cout << "New weights:" << weights << endl;
auto masked_weights = weights * mask.to(weights.dtype());
double sum_of_weights = masked_weights.sum().item<double>();
cout << "Sum of weights: " << sum_of_weights << endl;
//weights.index_put_({ mask }, weights + 10);
// auto handler = ArffFiles();
// handler.load(complete_file_name, class_last);
// // Get Dataset X, y
// vector<mdlp::samples_t>& X = handler.getX();
// mdlp::labels_t& y = handler.getY();
// // Get className & Features
// auto className = handler.getClassName();
// vector<string> features;
// auto attributes = handler.getAttributes();
// transform(attributes.begin(), attributes.end(), back_inserter(features),
// [](const pair<string, string>& item) { return item.first; });
// // Discretize Dataset
// auto [Xd, maxes] = discretize(X, y, features);
// maxes[className] = *max_element(y.begin(), y.end()) + 1;
// map<string, vector<int>> states;
// for (auto feature : features) {
// states[feature] = vector<int>(maxes[feature]);
// }
// states[className] = vector<int>(maxes[className]);
// auto clf = platform::Models::instance()->create(model_name);
// clf->fit(Xd, y, features, className, states);
// if (dump_cpt) {
// cout << "--- CPT Tables ---" << endl;
// clf->dump_cpt();
// }
// auto lines = clf->show();
// for (auto line : lines) {
// cout << line << endl;
// }
// cout << "--- Topological Order ---" << endl;
// auto order = clf->topological_order();
// for (auto name : order) {
// cout << name << ", ";
// }
// cout << "end." << endl;
// auto score = clf->score(Xd, y);
// cout << "Score: " << score << endl;
// auto graph = clf->graph();
// auto dot_file = model_name + "_" + file_name;
// ofstream file(dot_file + ".dot");
// file << graph;
// file.close();
// cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << endl;
// cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << endl;
// string stratified_string = stratified ? " Stratified" : "";
// cout << nFolds << " Folds" << stratified_string << " Cross validation" << endl;
// cout << "==========================================" << endl;
// torch::Tensor Xt = torch::zeros({ static_cast<int>(Xd.size()), static_cast<int>(Xd[0].size()) }, torch::kInt32);
// torch::Tensor yt = torch::tensor(y, torch::kInt32);
// for (int i = 0; i < features.size(); ++i) {
// Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
// }
// float total_score = 0, total_score_train = 0, score_train, score_test;
// Fold* fold;
// if (stratified)
// fold = new StratifiedKFold(nFolds, y, seed);
// else
// fold = new KFold(nFolds, y.size(), seed);
// for (auto i = 0; i < nFolds; ++i) {
// auto [train, test] = fold->getFold(i);
// cout << "Fold: " << i + 1 << endl;
// if (tensors) {
// auto ttrain = torch::tensor(train, torch::kInt64);
// auto ttest = torch::tensor(test, torch::kInt64);
// torch::Tensor Xtraint = torch::index_select(Xt, 1, ttrain);
// torch::Tensor ytraint = yt.index({ ttrain });
// torch::Tensor Xtestt = torch::index_select(Xt, 1, ttest);
// torch::Tensor ytestt = yt.index({ ttest });
// clf->fit(Xtraint, ytraint, features, className, states);
// auto temp = clf->predict(Xtraint);
// score_train = clf->score(Xtraint, ytraint);
// score_test = clf->score(Xtestt, ytestt);
// } else {
// auto [Xtrain, ytrain] = extract_indices(train, Xd, y);
// auto [Xtest, ytest] = extract_indices(test, Xd, y);
// clf->fit(Xtrain, ytrain, features, className, states);
// score_train = clf->score(Xtrain, ytrain);
// score_test = clf->score(Xtest, ytest);
// }
// if (dump_cpt) {
// cout << "--- CPT Tables ---" << endl;
// clf->dump_cpt();
// }
// total_score_train += score_train;
// total_score += score_test;
// cout << "Score Train: " << score_train << endl;
// cout << "Score Test : " << score_test << endl;
// cout << "-------------------------------------------------------------------------------" << endl;
// }
// cout << "**********************************************************************************" << endl;
// cout << "Average Score Train: " << total_score_train / nFolds << endl;
// cout << "Average Score Test : " << total_score / nFolds << endl;return 0;
auto handler = ArffFiles();
handler.load(complete_file_name, class_last);
// Get Dataset X, y
vector<mdlp::samples_t>& X = handler.getX();
mdlp::labels_t& y = handler.getY();
// Get className & Features
auto className = handler.getClassName();
vector<string> features;
auto attributes = handler.getAttributes();
transform(attributes.begin(), attributes.end(), back_inserter(features),
[](const pair<string, string>& item) { return item.first; });
// Discretize Dataset
auto [Xd, maxes] = discretize(X, y, features);
maxes[className] = *max_element(y.begin(), y.end()) + 1;
map<string, vector<int>> states;
for (auto feature : features) {
states[feature] = vector<int>(maxes[feature]);
}
states[className] = vector<int>(maxes[className]);
auto clf = platform::Models::instance()->create(model_name);
clf->fit(Xd, y, features, className, states);
if (dump_cpt) {
cout << "--- CPT Tables ---" << endl;
clf->dump_cpt();
}
auto lines = clf->show();
for (auto line : lines) {
cout << line << endl;
}
cout << "--- Topological Order ---" << endl;
auto order = clf->topological_order();
for (auto name : order) {
cout << name << ", ";
}
cout << "end." << endl;
auto score = clf->score(Xd, y);
cout << "Score: " << score << endl;
auto graph = clf->graph();
auto dot_file = model_name + "_" + file_name;
ofstream file(dot_file + ".dot");
file << graph;
file.close();
cout << "Graph saved in " << model_name << "_" << file_name << ".dot" << endl;
cout << "dot -Tpng -o " + dot_file + ".png " + dot_file + ".dot " << endl;
string stratified_string = stratified ? " Stratified" : "";
cout << nFolds << " Folds" << stratified_string << " Cross validation" << endl;
cout << "==========================================" << endl;
torch::Tensor Xt = torch::zeros({ static_cast<int>(Xd.size()), static_cast<int>(Xd[0].size()) }, torch::kInt32);
torch::Tensor yt = torch::tensor(y, torch::kInt32);
for (int i = 0; i < features.size(); ++i) {
Xt.index_put_({ i, "..." }, torch::tensor(Xd[i], torch::kInt32));
}
float total_score = 0, total_score_train = 0, score_train, score_test;
Fold* fold;
if (stratified)
fold = new StratifiedKFold(nFolds, y, seed);
else
fold = new KFold(nFolds, y.size(), seed);
for (auto i = 0; i < nFolds; ++i) {
auto [train, test] = fold->getFold(i);
cout << "Fold: " << i + 1 << endl;
if (tensors) {
auto ttrain = torch::tensor(train, torch::kInt64);
auto ttest = torch::tensor(test, torch::kInt64);
torch::Tensor Xtraint = torch::index_select(Xt, 1, ttrain);
torch::Tensor ytraint = yt.index({ ttrain });
torch::Tensor Xtestt = torch::index_select(Xt, 1, ttest);
torch::Tensor ytestt = yt.index({ ttest });
clf->fit(Xtraint, ytraint, features, className, states);
auto temp = clf->predict(Xtraint);
score_train = clf->score(Xtraint, ytraint);
score_test = clf->score(Xtestt, ytestt);
} else {
auto [Xtrain, ytrain] = extract_indices(train, Xd, y);
auto [Xtest, ytest] = extract_indices(test, Xd, y);
clf->fit(Xtrain, ytrain, features, className, states);
score_train = clf->score(Xtrain, ytrain);
score_test = clf->score(Xtest, ytest);
}
if (dump_cpt) {
cout << "--- CPT Tables ---" << endl;
clf->dump_cpt();
}
total_score_train += score_train;
total_score += score_test;
cout << "Score Train: " << score_train << endl;
cout << "Score Test : " << score_test << endl;
cout << "-------------------------------------------------------------------------------" << endl;
}
cout << "**********************************************************************************" << endl;
cout << "Average Score Train: " << total_score_train / nFolds << endl;
cout << "Average Score Test : " << total_score / nFolds << endl;return 0;
}

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@@ -10,6 +10,7 @@ namespace bayesnet {
AODE();
virtual ~AODE() {};
vector<string> graph(const string& title = "AODE") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override {};
};
}
#endif

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@@ -16,6 +16,7 @@ namespace bayesnet {
virtual ~AODELd() = default;
vector<string> graph(const string& name = "AODE") const override;
static inline string version() { return "0.0.1"; };
void setHyperparameters(nlohmann::json& hyperparameters) override {};
};
}
#endif // !AODELD_H

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@@ -1,6 +1,7 @@
#ifndef BASE_H
#define BASE_H
#include <torch/torch.h>
#include <nlohmann/json.hpp>
#include <vector>
namespace bayesnet {
using namespace std;
@@ -27,6 +28,7 @@ namespace bayesnet {
const string inline getVersion() const { return "0.1.0"; };
vector<string> virtual topological_order() = 0;
void virtual dump_cpt()const = 0;
virtual void setHyperparameters(nlohmann::json& hyperparameters) = 0;
};
}
#endif

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@@ -21,25 +21,39 @@ namespace bayesnet {
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
}
vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, unsigned k)
vector<int> Metrics::SelectKBestWeighted(const torch::Tensor& weights, bool ascending, unsigned k)
{
// Return the K Best features
auto n = samples.size(0) - 1;
if (k == 0) {
k = n;
}
// compute scores
scoresKBest.reserve(n);
scoresKBest.clear();
featuresKBest.clear();
auto label = samples.index({ -1, "..." });
for (int i = 0; i < n; ++i) {
scoresKBest.push_back(mutualInformation(label, samples.index({ i, "..." }), weights));
featuresKBest.push_back(i);
}
// sort & reduce scores and features
if (ascending) {
sort(featuresKBest.begin(), featuresKBest.end(), [&](int i, int j)
{ return scoresKBest[i] < scoresKBest[j]; });
sort(scoresKBest.begin(), scoresKBest.end(), std::less<double>());
if (k < n) {
for (int i = 0; i < n - k; ++i) {
featuresKBest.erase(featuresKBest.begin());
scoresKBest.erase(scoresKBest.begin());
}
}
} else {
sort(featuresKBest.begin(), featuresKBest.end(), [&](int i, int j)
{ return scoresKBest[i] > scoresKBest[j]; });
sort(scoresKBest.begin(), scoresKBest.end(), std::greater<double>());
featuresKBest.resize(k);
scoresKBest.resize(k);
}
return featuresKBest;
}
vector<double> Metrics::getScoresKBest() const

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@@ -21,7 +21,7 @@ namespace bayesnet {
Metrics() = default;
Metrics(const torch::Tensor& samples, const vector<string>& features, const string& className, const int classNumStates);
Metrics(const vector<vector<int>>& vsamples, const vector<int>& labels, const vector<string>& features, const string& className, const int classNumStates);
vector<int> SelectKBestWeighted(const torch::Tensor& weights, unsigned k = 0);
vector<int> SelectKBestWeighted(const torch::Tensor& weights, bool ascending=false, unsigned k = 0);
vector<double> getScoresKBest() const;
double mutualInformation(const Tensor& firstFeature, const Tensor& secondFeature, const Tensor& weights);
vector<float> conditionalEdgeWeights(vector<float>& weights); // To use in Python

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@@ -1,4 +1,5 @@
#include "BoostAODE.h"
#include <set>
#include "BayesMetrics.h"
namespace bayesnet {
@@ -7,40 +8,49 @@ namespace bayesnet {
{
// Models shall be built in trainModel
}
void BoostAODE::setHyperparameters(nlohmann::json& hyperparameters)
{
// Check if hyperparameters are valid
const vector<string> validKeys = { "repeatSparent", "maxModels", "ascending" };
checkHyperparameters(validKeys, hyperparameters);
if (hyperparameters.contains("repeatSparent")) {
repeatSparent = hyperparameters["repeatSparent"];
}
if (hyperparameters.contains("maxModels")) {
maxModels = hyperparameters["maxModels"];
}
if (hyperparameters.contains("ascending")) {
ascending = hyperparameters["ascending"];
}
}
void BoostAODE::trainModel(const torch::Tensor& weights)
{
models.clear();
n_models = 0;
int max_models = .1 * n > 10 ? .1 * n : n;
if (maxModels == 0)
maxModels = .1 * n > 10 ? .1 * n : n;
Tensor weights_ = torch::full({ m }, 1.0 / m, torch::kFloat64);
auto X_ = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." });
auto y_ = dataset.index({ -1, "..." });
bool exitCondition = false;
bool repeatSparent = false;
vector<int> featuresUsed;
unordered_set<int> featuresUsed;
// Step 0: Set the finish condition
// if not repeatSparent a finish condition is run out of features
// n_models == max_models
// n_models == maxModels
int numClasses = states[className].size();
while (!exitCondition) {
// Step 1: Build ranking with mutual information
auto featureSelection = metrics.SelectKBestWeighted(weights_, n); // Get all the features sorted
auto feature = featureSelection[0];
auto featureSelection = metrics.SelectKBestWeighted(weights_, ascending, n); // Get all the features sorted
unique_ptr<Classifier> model;
if (!repeatSparent) {
if (n_models == 0) {
models.resize(n); // Resize for n==nfeatures SPODEs
significanceModels.resize(n);
}
auto feature = featureSelection[0];
if (!repeatSparent || featuresUsed.size() < featureSelection.size()) {
bool found = false;
for (int i = 0; i < featureSelection.size(); ++i) {
if (find(featuresUsed.begin(), featuresUsed.end(), i) != featuresUsed.end()) {
for (auto feat : featureSelection) {
if (find(featuresUsed.begin(), featuresUsed.end(), feat) != featuresUsed.end()) {
continue;
}
found = true;
feature = i;
featuresUsed.push_back(feature);
n_models++;
feature = feat;
break;
}
if (!found) {
@@ -48,7 +58,9 @@ namespace bayesnet {
continue;
}
}
featuresUsed.insert(feature);
model = std::make_unique<SPODE>(feature);
n_models++;
model->fit(dataset, features, className, states, weights_);
auto ypred = model->predict(X_);
// Step 3.1: Compute the classifier amout of say
@@ -63,15 +75,12 @@ namespace bayesnet {
double totalWeights = torch::sum(weights_).item<double>();
weights_ = weights_ / totalWeights;
// Step 3.4: Store classifier and its accuracy to weigh its future vote
if (!repeatSparent) {
models[feature] = std::move(model);
significanceModels[feature] = significance;
} else {
models.push_back(std::move(model));
significanceModels.push_back(significance);
n_models++;
exitCondition = n_models == maxModels && repeatSparent;
}
exitCondition = n_models == max_models;
if (featuresUsed.size() != features.size()) {
cout << "Warning: BoostAODE did not use all the features" << endl;
}
weights.copy_(weights_);
}

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@@ -4,13 +4,18 @@
#include "SPODE.h"
namespace bayesnet {
class BoostAODE : public Ensemble {
protected:
void buildModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights) override;
public:
BoostAODE();
virtual ~BoostAODE() {};
vector<string> graph(const string& title = "BoostAODE") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override;
protected:
void buildModel(const torch::Tensor& weights) override;
void trainModel(const torch::Tensor& weights) override;
private:
bool repeatSparent=false;
int maxModels=0;
bool ascending=false; //Process KBest features ascending or descending order
};
}
#endif

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@@ -1,5 +1,6 @@
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
add_library(BayesNet bayesnetUtils.cc Network.cc Node.cc BayesMetrics.cc Classifier.cc

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@@ -152,4 +152,12 @@ namespace bayesnet {
{
model.dump_cpt();
}
void Classifier::checkHyperparameters(const vector<string>& validKeys, nlohmann::json& hyperparameters)
{
for (const auto& item : hyperparameters.items()) {
if (find(validKeys.begin(), validKeys.end(), item.key()) == validKeys.end()) {
throw invalid_argument("Hyperparameter " + item.key() + " is not valid");
}
}
}
}

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@@ -24,6 +24,7 @@ namespace bayesnet {
void checkFitParameters();
virtual void buildModel(const torch::Tensor& weights) = 0;
void trainModel(const torch::Tensor& weights) override;
void checkHyperparameters(const vector<string>& validKeys, nlohmann::json& hyperparameters);
public:
Classifier(Network model);
virtual ~Classifier() = default;

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@@ -16,6 +16,7 @@ namespace bayesnet {
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() {};
void setHyperparameters(nlohmann::json& hyperparameters) override {};
vector<string> graph(const string& name = "KDB") const override;
};
}

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@@ -13,6 +13,7 @@ namespace bayesnet {
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "KDB") const override;
Tensor predict(Tensor& X) override;
void setHyperparameters(nlohmann::json& hyperparameters) override {};
static inline string version() { return "0.0.1"; };
};
}

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@@ -12,6 +12,7 @@ namespace bayesnet {
explicit SPODE(int root);
virtual ~SPODE() {};
vector<string> graph(const string& name = "SPODE") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override {};
};
}
#endif

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@@ -13,6 +13,7 @@ namespace bayesnet {
SPODELd& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "SPODE") const override;
Tensor predict(Tensor& X) override;
void setHyperparameters(nlohmann::json& hyperparameters) override {};
static inline string version() { return "0.0.1"; };
};
}

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@@ -3,7 +3,6 @@
#include "Classifier.h"
namespace bayesnet {
using namespace std;
using namespace torch;
class TAN : public Classifier {
private:
protected:
@@ -12,6 +11,7 @@ namespace bayesnet {
TAN();
virtual ~TAN() {};
vector<string> graph(const string& name = "TAN") const override;
void setHyperparameters(nlohmann::json& hyperparameters) override {};
};
}
#endif

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@@ -14,6 +14,7 @@ namespace bayesnet {
vector<string> graph(const string& name = "TAN") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
void setHyperparameters(nlohmann::json& hyperparameters) override {};
};
}
#endif // !TANLD_H

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@@ -4,9 +4,9 @@ include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/argparse/include)
include_directories(${BayesNet_SOURCE_DIR}/lib/json/include)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc Models.cc Report.cc)
add_executable(manage manage.cc Results.cc Report.cc)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc Models.cc ReportConsole.cc ReportBase.cc)
add_executable(manage manage.cc Results.cc ReportConsole.cc ReportExcel.cc ReportBase.cc)
add_executable(list list.cc platformUtils Datasets.cc)
target_link_libraries(main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")
target_link_libraries(manage "${TORCH_LIBRARIES}")
target_link_libraries(manage "${TORCH_LIBRARIES}" OpenXLSX::OpenXLSX)
target_link_libraries(list ArffFiles mdlp "${TORCH_LIBRARIES}")

View File

@@ -1,7 +1,7 @@
#include "Experiment.h"
#include "Datasets.h"
#include "Models.h"
#include "Report.h"
#include "ReportConsole.h"
namespace platform {
using json = nlohmann::json;
@@ -25,6 +25,7 @@ namespace platform {
oss << std::put_time(timeinfo, "%H:%M:%S");
return oss.str();
}
Experiment::Experiment() : hyperparameters(json::parse("{}")) {}
string Experiment::get_file_name()
{
string result = "results_" + score_name + "_" + model + "_" + platform + "_" + get_date() + "_" + get_time() + "_" + (stratified ? "1" : "0") + ".json";
@@ -90,7 +91,7 @@ namespace platform {
void Experiment::report()
{
json data = build_json();
Report report(data);
ReportConsole report(data);
report.show();
}
@@ -124,6 +125,8 @@ namespace platform {
auto result = Result();
auto [values, counts] = at::_unique(y);
result.setSamples(X.size(1)).setFeatures(X.size(0)).setClasses(values.size(0));
result.setHyperparameters(hyperparameters);
// Initialize results vectors
int nResults = nfolds * static_cast<int>(randomSeeds.size());
auto accuracy_test = torch::zeros({ nResults }, torch::kFloat64);
auto accuracy_train = torch::zeros({ nResults }, torch::kFloat64);
@@ -144,6 +147,10 @@ namespace platform {
for (int nfold = 0; nfold < nfolds; nfold++) {
auto clf = Models::instance()->create(model);
setModelVersion(clf->getVersion());
if (hyperparameters.size() != 0) {
clf->setHyperparameters(hyperparameters);
}
// Split train - test dataset
train_timer.start();
auto [train, test] = fold->getFold(nfold);
auto train_t = torch::tensor(train);
@@ -153,12 +160,14 @@ namespace platform {
auto X_test = X.index({ "...", test_t });
auto y_test = y.index({ test_t });
cout << nfold + 1 << ", " << flush;
// Train model
clf->fit(X_train, y_train, features, className, states);
nodes[item] = clf->getNumberOfNodes();
edges[item] = clf->getNumberOfEdges();
num_states[item] = clf->getNumberOfStates();
train_time[item] = train_timer.getDuration();
auto accuracy_train_value = clf->score(X_train, y_train);
// Test model
test_timer.start();
auto accuracy_test_value = clf->score(X_test, y_test);
test_time[item] = test_timer.getDuration();
@@ -172,11 +181,11 @@ namespace platform {
item++;
}
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

@@ -29,7 +29,8 @@ namespace platform {
};
class Result {
private:
string dataset, hyperparameters, model_version;
string dataset, model_version;
json hyperparameters;
int samples{ 0 }, features{ 0 }, classes{ 0 };
double score_train{ 0 }, score_test{ 0 }, score_train_std{ 0 }, score_test_std{ 0 }, train_time{ 0 }, train_time_std{ 0 }, test_time{ 0 }, test_time_std{ 0 };
float nodes{ 0 }, leaves{ 0 }, depth{ 0 };
@@ -37,7 +38,7 @@ namespace platform {
public:
Result() = default;
Result& setDataset(const string& dataset) { this->dataset = dataset; return *this; }
Result& setHyperparameters(const string& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
Result& setSamples(int samples) { this->samples = samples; return *this; }
Result& setFeatures(int features) { this->features = features; return *this; }
Result& setClasses(int classes) { this->classes = classes; return *this; }
@@ -59,7 +60,7 @@ namespace platform {
const float get_score_train() const { return score_train; }
float get_score_test() { return score_test; }
const string& getDataset() const { return dataset; }
const string& getHyperparameters() const { return hyperparameters; }
const json& getHyperparameters() const { return hyperparameters; }
const int getSamples() const { return samples; }
const int getFeatures() const { return features; }
const int getClasses() const { return classes; }
@@ -85,11 +86,12 @@ namespace platform {
bool discretized{ false }, stratified{ false };
vector<Result> results;
vector<int> randomSeeds;
json hyperparameters = "{}";
int nfolds{ 0 };
float duration{ 0 };
json build_json();
public:
Experiment() = default;
Experiment();
Experiment& setTitle(const string& title) { this->title = title; return *this; }
Experiment& setModel(const string& model) { this->model = model; return *this; }
Experiment& setPlatform(const string& platform) { this->platform = platform; return *this; }
@@ -103,6 +105,7 @@ namespace platform {
Experiment& addResult(Result result) { results.push_back(result); return *this; }
Experiment& addRandomSeed(int randomSeed) { randomSeeds.push_back(randomSeed); return *this; }
Experiment& setDuration(float duration) { this->duration = duration; return *this; }
Experiment& setHyperparameters(const json& hyperparameters) { this->hyperparameters = hyperparameters; return *this; }
string get_file_name();
void save(const string& path);
void cross_validation(const string& path, const string& fileName);

View File

@@ -6,6 +6,7 @@ namespace platform {
public:
static std::string datasets() { return "datasets/"; }
static std::string results() { return "results/"; }
static std::string excel() { return "excel/"; }
};
}
#endif

View File

@@ -1,26 +0,0 @@
#ifndef REPORT_H
#define REPORT_H
#include <string>
#include <iostream>
#include <nlohmann/json.hpp>
#include "Colors.h"
using json = nlohmann::json;
const int MAXL = 128;
namespace platform {
using namespace std;
class Report {
public:
explicit Report(json data_) { data = data_; };
virtual ~Report() = default;
void show();
private:
void header();
void body();
void footer();
string fromVector(const string& key);
json data;
double totalScore; // Total score of all results in a report
};
};
#endif

View File

@@ -0,0 +1,37 @@
#include <sstream>
#include <locale>
#include "ReportBase.h"
#include "BestResult.h"
namespace platform {
string ReportBase::fromVector(const string& key)
{
stringstream oss;
string sep = "";
oss << "[";
for (auto& item : data[key]) {
oss << sep << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
string ReportBase::fVector(const string& title, const json& data, const int width, const int precision)
{
stringstream oss;
string sep = "";
oss << title << "[";
for (const auto& item : data) {
oss << sep << fixed << setw(width) << setprecision(precision) << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
void ReportBase::show()
{
header();
body();
}
}

23
src/Platform/ReportBase.h Normal file
View File

@@ -0,0 +1,23 @@
#ifndef REPORTBASE_H
#define REPORTBASE_H
#include <string>
#include <iostream>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
namespace platform {
using namespace std;
class ReportBase {
public:
explicit ReportBase(json data_) { data = data_; };
virtual ~ReportBase() = default;
void show();
protected:
json data;
string fromVector(const string& key);
string fVector(const string& title, const json& data, const int width, const int precision);
virtual void header() = 0;
virtual void body() = 0;
};
};
#endif

View File

@@ -1,52 +1,24 @@
#include <sstream>
#include <locale>
#include "Report.h"
#include "ReportConsole.h"
#include "BestResult.h"
namespace platform {
string headerLine(const string& text)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + string(n, ' ') + "*\n";
}
string Report::fromVector(const string& key)
{
stringstream oss;
string sep = "";
oss << "[";
for (auto& item : data[key]) {
oss << sep << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
string fVector(const string& title, const json& data, const int width, const int precision)
{
stringstream oss;
string sep = "";
oss << title << "[";
for (const auto& item : data) {
oss << sep << fixed << setw(width) << setprecision(precision) << item.get<double>();
sep = ", ";
}
oss << "]";
return oss.str();
}
void Report::show()
{
header();
body();
footer();
}
struct separated : numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
string do_grouping() const { return "\03"; }
};
void Report::header()
string ReportConsole::headerLine(const string& text)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + string(n, ' ') + "*\n";
}
void ReportConsole::header()
{
locale mylocale(cout.getloc(), new separated);
locale::global(mylocale);
@@ -62,12 +34,12 @@ namespace platform {
cout << string(MAXL, '*') << endl;
cout << endl;
}
void Report::body()
void ReportConsole::body()
{
cout << Colors::GREEN() << "Dataset Sampl. Feat. Cls Nodes Edges States Score Time Hyperparameters" << endl;
cout << "============================== ====== ===== === ========= ========= ========= =============== ================== ===============" << endl;
json lastResult;
totalScore = 0;
double totalScore = 0.0;
bool odd = true;
for (const auto& r : data["results"]) {
auto color = odd ? Colors::CYAN() : Colors::BLUE();
@@ -98,9 +70,11 @@ namespace platform {
cout << headerLine(fVector("Train times: ", lastResult["times_train"], 10, 3));
cout << headerLine(fVector("Test times: ", lastResult["times_test"], 10, 3));
cout << string(MAXL, '*') << endl;
} else {
footer(totalScore);
}
}
void Report::footer()
void ReportConsole::footer(double totalScore)
{
cout << Colors::MAGENTA() << string(MAXL, '*') << endl;
auto score = data["score_name"].get<string>();
@@ -110,6 +84,5 @@ namespace platform {
cout << headerLine(oss.str());
}
cout << string(MAXL, '*') << endl << Colors::RESET();
}
}

View File

@@ -0,0 +1,22 @@
#ifndef REPORTCONSOLE_H
#define REPORTCONSOLE_H
#include <string>
#include <iostream>
#include "ReportBase.h"
#include "Colors.h"
namespace platform {
using namespace std;
const int MAXL = 128;
class ReportConsole : public ReportBase{
public:
explicit ReportConsole(json data_) : ReportBase(data_) {};
virtual ~ReportConsole() = default;
private:
string headerLine(const string& text);
void header() override;
void body() override;
void footer(double totalScore);
};
};
#endif

109
src/Platform/ReportExcel.cc Normal file
View File

@@ -0,0 +1,109 @@
#include <sstream>
#include <locale>
#include "ReportExcel.h"
#include "BestResult.h"
namespace platform {
struct separated : numpunct<char> {
char do_decimal_point() const { return ','; }
char do_thousands_sep() const { return '.'; }
string do_grouping() const { return "\03"; }
};
void ReportExcel::createFile()
{
doc.create(Paths::excel() + "some_results.xlsx");
wks = doc.workbook().worksheet("Sheet1");
wks.setName(data["model"].get<string>());
}
void ReportExcel::closeFile()
{
doc.save();
doc.close();
}
void ReportExcel::header()
{
locale mylocale(cout.getloc(), new separated);
locale::global(mylocale);
cout.imbue(mylocale);
stringstream oss;
wks.cell("A1").value().set(
"Report " + data["model"].get<string>() + " ver. " + data["version"].get<string>() + " with " +
to_string(data["folds"].get<int>()) + " Folds cross validation and " + to_string(data["seeds"].size()) +
" random seeds. " + data["date"].get<string>() + " " + data["time"].get<string>());
wks.cell("A2").value() = data["title"].get<string>();
wks.cell("A3").value() = "Random seeds: " + fromVector("seeds") + " Stratified: " +
(data["stratified"].get<bool>() ? "True" : "False");
oss << "Execution took " << setprecision(2) << fixed << data["duration"].get<float>() << " seconds, "
<< data["duration"].get<float>() / 3600 << " hours, on " << data["platform"].get<string>();
wks.cell("A4").value() = oss.str();
wks.cell("A5").value() = "Score is " + data["score_name"].get<string>();
}
void ReportExcel::body()
{
auto header = vector<string>(
{ "Dataset", "Samples", "Features", "Classes", "Nodes", "Edges", "States", "Score", "Score Std.", "Time",
"Time Std.", "Hyperparameters" });
int col = 1;
for (const auto& item : header) {
wks.cell(8, col++).value() = item;
}
int row = 9;
col = 1;
json lastResult;
double totalScore = 0.0;
string hyperparameters;
for (const auto& r : data["results"]) {
wks.cell(row, col).value() = r["dataset"].get<string>();
wks.cell(row, col + 1).value() = r["samples"].get<int>();
wks.cell(row, col + 2).value() = r["features"].get<int>();
wks.cell(row, col + 3).value() = r["classes"].get<int>();
wks.cell(row, col + 4).value() = r["nodes"].get<float>();
wks.cell(row, col + 5).value() = r["leaves"].get<float>();
wks.cell(row, col + 6).value() = r["depth"].get<float>();
wks.cell(row, col + 7).value() = r["score"].get<double>();
wks.cell(row, col + 8).value() = r["score_std"].get<double>();
wks.cell(row, col + 9).value() = r["time"].get<double>();
wks.cell(row, col + 10).value() = r["time_std"].get<double>();
try {
hyperparameters = r["hyperparameters"].get<string>();
}
catch (const exception& err) {
stringstream oss;
oss << r["hyperparameters"];
hyperparameters = oss.str();
}
wks.cell(row, col + 11).value() = hyperparameters;
lastResult = r;
totalScore += r["score"].get<double>();
row++;
}
if (data["results"].size() == 1) {
for (const string& group : { "scores_train", "scores_test", "times_train", "times_test" }) {
row++;
col = 1;
wks.cell(row, col).value() = group;
for (double item : lastResult[group]) {
wks.cell(row, ++col).value() = item;
}
}
} else {
footer(totalScore, row);
}
}
void ReportExcel::footer(double totalScore, int row)
{
auto score = data["score_name"].get<string>();
if (score == BestResult::scoreName()) {
wks.cell(row + 2, 1).value() = score + " compared to " + BestResult::title() + " .: ";
wks.cell(row + 2, 5).value() = totalScore / BestResult::score();
}
}
}

View File

@@ -0,0 +1,25 @@
#ifndef REPORTEXCEL_H
#define REPORTEXCEL_H
#include <OpenXLSX.hpp>
#include "ReportBase.h"
#include "Paths.h"
#include "Colors.h"
namespace platform {
using namespace std;
using namespace OpenXLSX;
const int MAXLL = 128;
class ReportExcel : public ReportBase{
public:
explicit ReportExcel(json data_) : ReportBase(data_) {createFile();};
virtual ~ReportExcel() {closeFile();};
private:
void createFile();
void closeFile();
XLDocument doc;
XLWorksheet wks;
void header() override;
void body() override;
void footer(double totalScore, int row);
};
};
#endif // !REPORTEXCEL_H

View File

@@ -1,7 +1,8 @@
#include <filesystem>
#include "platformUtils.h"
#include "Results.h"
#include "Report.h"
#include "ReportConsole.h"
#include "ReportExcel.h"
#include "BestResult.h"
#include "Colors.h"
namespace platform {
@@ -94,21 +95,26 @@ namespace platform {
cout << "Invalid index" << endl;
return -1;
}
void Results::report(const int index) const
void Results::report(const int index, const bool excelReport) const
{
cout << Colors::YELLOW() << "Reporting " << files.at(index).getFilename() << endl;
auto data = files.at(index).load();
Report report(data);
if (excelReport) {
ReportExcel report(data);
report.show();
} else {
ReportConsole report(data);
report.show();
}
}
void Results::menu()
{
char option;
int index;
bool finished = false;
string filename, line, options = "qldhsr";
string filename, line, options = "qldhsre";
while (!finished) {
cout << Colors::RESET() << "Choose option (quit='q', list='l', delete='d', hide='h', sort='s', report='r'): ";
cout << Colors::RESET() << "Choose option (quit='q', list='l', delete='d', hide='h', sort='s', report='r', excel='e'): ";
getline(cin, line);
if (line.size() == 0)
continue;
@@ -119,12 +125,14 @@ namespace platform {
}
option = line[0];
} else {
if (all_of(line.begin(), line.end(), ::isdigit)) {
index = stoi(line);
if (index >= 0 && index < files.size()) {
report(index);
} else {
cout << "Invalid option" << endl;
report(index, false);
continue;
}
}
cout << "Invalid option" << endl;
continue;
}
switch (option) {
@@ -164,7 +172,13 @@ namespace platform {
index = getIndex("report");
if (index == -1)
break;
report(index);
report(index, false);
break;
case 'e':
index = getIndex("excel");
if (index == -1)
break;
report(index, true);
break;
default:
cout << "Invalid option" << endl;
@@ -231,6 +245,7 @@ namespace platform {
cout << "No results found!" << endl;
exit(0);
}
sortDate();
show();
menu();
cout << "Done!" << endl;

View File

@@ -42,7 +42,7 @@ namespace platform {
vector<Result> files;
void load(); // Loads the list of results
void show() const;
void report(const int index) const;
void report(const int index, const bool excelReport) const;
int getIndex(const string& intent) const;
void menu();
void sortList();

View File

@@ -1,5 +1,6 @@
#include <iostream>
#include <argparse/argparse.hpp>
#include <nlohmann/json.hpp>
#include "platformUtils.h"
#include "Experiment.h"
#include "Datasets.h"
@@ -10,12 +11,14 @@
using namespace std;
using json = nlohmann::json;
argparse::ArgumentParser manageArguments(int argc, char** argv)
{
auto env = platform::DotEnv();
argparse::ArgumentParser program("main");
program.add_argument("-d", "--dataset").default_value("").help("Dataset file name");
program.add_argument("--hyperparameters").default_value("{}").help("Hyperparamters passed to the model in Experiment");
program.add_argument("-p", "--path")
.help("folder where the data files are located, default")
.default_value(string{ platform::Paths::datasets() });
@@ -31,6 +34,7 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
);
program.add_argument("--title").default_value("").help("Experiment title");
program.add_argument("--discretize").help("Discretize input dataset").default_value((bool)stoi(env.get("discretize"))).implicit_value(true);
program.add_argument("--save").help("Save result (always save if no dataset is supplied)").default_value(false).implicit_value(true);
program.add_argument("--stratified").help("If Stratified KFold is to be done").default_value((bool)stoi(env.get("stratified"))).implicit_value(true);
program.add_argument("-f", "--folds").help("Number of folds").default_value(stoi(env.get("n_folds"))).scan<'i', int>().action([](const string& value) {
try {
@@ -59,6 +63,8 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
auto seeds = program.get<vector<int>>("seeds");
auto complete_file_name = path + file_name + ".arff";
auto title = program.get<string>("title");
auto hyperparameters = program.get<string>("hyperparameters");
auto saveResults = program.get<bool>("save");
if (title == "" && file_name == "") {
throw runtime_error("title is mandatory if dataset is not provided");
}
@@ -74,7 +80,6 @@ argparse::ArgumentParser manageArguments(int argc, char** argv)
int main(int argc, char** argv)
{
auto program = manageArguments(argc, argv);
bool saveResults = false;
auto file_name = program.get<string>("dataset");
auto path = program.get<string>("path");
auto model_name = program.get<string>("model");
@@ -82,9 +87,11 @@ int main(int argc, char** argv)
auto stratified = program.get<bool>("stratified");
auto n_folds = program.get<int>("folds");
auto seeds = program.get<vector<int>>("seeds");
auto hyperparameters =program.get<string>("hyperparameters");
vector<string> filesToTest;
auto datasets = platform::Datasets(path, true, platform::ARFF);
auto title = program.get<string>("title");
auto saveResults = program.get<bool>("save");
if (file_name != "") {
if (!datasets.isDataset(file_name)) {
cerr << "Dataset " << file_name << " not found" << endl;
@@ -106,6 +113,7 @@ int main(int argc, char** argv)
experiment.setTitle(title).setLanguage("cpp").setLanguageVersion("14.0.3");
experiment.setDiscretized(discretize_dataset).setModel(model_name).setPlatform(env.get("platform"));
experiment.setStratified(stratified).setNFolds(n_folds).setScoreName("accuracy");
experiment.setHyperparameters(json::parse(hyperparameters));
for (auto seed : seeds) {
experiment.addRandomSeed(seed);
}
@@ -113,9 +121,9 @@ int main(int argc, char** argv)
timer.start();
experiment.go(filesToTest, path);
experiment.setDuration(timer.getDuration());
if (saveResults)
if (saveResults) {
experiment.save(platform::Paths::results());
else
}
experiment.report();
cout << "Done!" << endl;
return 0;