Compare commits

...

30 Commits

Author SHA1 Message Date
182b52a887 Add states as result in Proposal methods 2023-08-12 16:16:17 +02:00
405887f833 Solved Ld poor results 2023-08-12 11:49:18 +02:00
3a85481a5a Redo pass states to Network Fit needed in crossval
fix mistake in headerline (report)
2023-08-12 11:10:53 +02:00
0ad5505c16 Spodeld working with poor accuracy 2023-08-10 02:06:18 +02:00
323444b74a const functions 2023-08-08 01:53:41 +02:00
ef1bffcac3 Fixed normal classifiers 2023-08-07 13:50:11 +02:00
06db8f51ce Refactor library and models to lighten data stored
Refactro Ensemble to inherit from Classifier insted of BaseClassifier
2023-08-07 12:49:37 +02:00
e74565ba01 update clang-tidy 2023-08-07 00:44:12 +02:00
2da0fb5d8f Merge branch 'main' into TANNew 2023-08-06 11:40:10 +02:00
14ea51648a Complete AODELd 2023-08-06 11:31:44 +02:00
9e94f4e140 Rename suffix of proposal classifier to Ld 2023-08-05 23:23:31 +02:00
1d0fd629c9 Add SPODENew to models 2023-08-05 23:11:36 +02:00
506ef34c6f Add report output to main 2023-08-05 20:29:05 +02:00
7f45495837 Refactor New classifiers to extract predict 2023-08-05 18:39:48 +02:00
1a09ccca4c Add KDBNew fix computeCPT error 2023-08-05 14:40:42 +02:00
a1c6ab18f3 TANNew restructured with poor results 2023-08-04 20:11:22 +02:00
64ac8fb4f2 TANNew as a TAN variant working 2023-08-04 19:42:18 +02:00
c568ba111d Add Proposal class 2023-08-04 13:05:12 +02:00
45c1d052ac Compile TANNew with poor accuracy 2023-08-04 01:35:45 +02:00
eb1cec58a3 Complete nxm 2023-08-03 20:22:33 +02:00
f520b40016 Almost complete proposal in TANNew 2023-08-02 02:21:55 +02:00
cdfb45d2cb Add topological order to Network 2023-08-02 00:56:52 +02:00
f63a9a64f9 Update Makefile to add Release & Debug build 2023-08-01 19:02:37 +02:00
285f0938a6 Update mdlp library 2023-08-01 17:33:01 +02:00
8f8f9773ce Make TANNew same as TAN with local discretization 2023-08-01 13:17:12 +02:00
a9ba21560d Add environment platform to experiment result 2023-08-01 10:55:53 +02:00
a18fbe5594 Begin implementation 2023-07-31 19:53:55 +02:00
adf650d257 Max threading 2023-07-31 18:49:18 +02:00
43bb017d5d Fix problem with tensors way 2023-07-30 19:00:02 +02:00
53697648e7 Merge branch 'aftermath' into main 2023-07-30 01:05:31 +02:00
51 changed files with 1043 additions and 390 deletions

View File

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

18
.vscode/launch.json vendored
View File

@@ -10,12 +10,13 @@
"-d",
"iris",
"-m",
"TAN",
"KDB",
"-s",
"271",
"-p",
"../../data/",
"--tensors"
"/Users/rmontanana/Code/discretizbench/datasets/",
],
"cwd": "${workspaceFolder}/build/sample/",
//"cwd": "${workspaceFolder}/build/sample/",
},
{
"type": "lldb",
@@ -24,17 +25,14 @@
"program": "${workspaceFolder}/build/src/Platform/main",
"args": [
"-m",
"TAN",
"SPODELd",
"-p",
"/Users/rmontanana/Code/discretizbench/datasets",
"--discretize",
"--stratified",
"--title",
"Debug test",
"-d",
"ionosphere"
"iris"
],
"cwd": "${workspaceFolder}/build/src/Platform",
"cwd": "/Users/rmontanana/Code/discretizbench",
},
{
"name": "Build & debug active file",

View File

@@ -7,10 +7,14 @@ project(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
@@ -24,24 +28,31 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS}")
# Options
# -------
option(ENABLE_CLANG_TIDY "Enable to add clang tidy." OFF)
option(ENABLE_TESTING "Unit testing build" ON)
option(CODE_COVERAGE "Collect coverage from test library" ON)
set(CMAKE_BUILD_TYPE "Debug")
option(ENABLE_TESTING "Unit testing build" OFF)
option(CODE_COVERAGE "Collect coverage from test library" OFF)
# CMakes modules
# --------------
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
include(AddGitSubmodule)
include(StaticAnalyzers) # clang-tidy
include(CodeCoverage)
if (CODE_COVERAGE)
enable_testing()
include(CodeCoverage)
MESSAGE("Code coverage enabled")
set(CMAKE_C_FLAGS " ${CMAKE_C_FLAGS} -fprofile-arcs -ftest-coverage")
set(CMAKE_CXX_FLAGS " ${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
SET(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)
# 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")
@@ -59,18 +70,11 @@ file(GLOB Platform_SOURCES CONFIGURE_DEPENDS ${BayesNet_SOURCE_DIR}/src/Platform
# Testing
# -------
if (ENABLE_TESTING)
MESSAGE("Testing enabled")
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)
add_git_submodule("lib/catch2")
include(CTest)
#include(Catch)
add_subdirectory(tests)
endif (ENABLE_TESTING)

View File

@@ -14,16 +14,30 @@ setup: ## Install dependencies for tests and coverage
dependency: ## Create a dependency graph diagram of the project (build/dependency.png)
cd build && cmake .. --graphviz=dependency.dot && dot -Tpng dependency.dot -o dependency.png
build: ## Build the project
@echo ">>> Building BayesNet ...";
build: ## Build the main and BayesNetSample
cmake --build build -t main -t BayesNetSample -j 32
clean: ## Clean the debug info
@echo ">>> Cleaning Debug BayesNet ...";
find . -name "*.gcda" -print0 | xargs -0 rm
@echo ">>> Done";
debug: ## Build a debug version of the project
@echo ">>> Building Debug BayesNet ...";
@if [ -d ./build ]; then rm -rf ./build; fi
@mkdir build;
cmake -S . -B build; \
cd build; \
make; \
cmake -S . -B build -D CMAKE_BUILD_TYPE=Debug -D ENABLE_TESTING=ON -D CODE_COVERAGE=ON; \
cmake --build build -j 32;
@echo ">>> Done";
release: ## Build a Release version of the project
@echo ">>> Building Release BayesNet ...";
@if [ -d ./build ]; then rm -rf ./build; fi
@mkdir build;
cmake -S . -B build -D CMAKE_BUILD_TYPE=Release; \
cmake --build build -t main -t BayesNetSample -j 32;
@echo ">>> Done";
test: ## Run tests
@echo "* Running tests...";
find . -name "*.gcda" -print0 | xargs -0 rm

12
TAN_iris.dot Normal file
View File

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

View File

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

View File

@@ -1,7 +1,6 @@
#include <iostream>
#include <torch/torch.h>
#include <string>
#include <thread>
#include <map>
#include <argparse/argparse.hpp>
#include "ArffFiles.h"
@@ -42,7 +41,7 @@ bool file_exists(const std::string& name)
}
pair<vector<vector<int>>, vector<int>> extract_indices(vector<int> indices, vector<vector<int>> X, vector<int> y)
{
vector<vector<int>> Xr;
vector<vector<int>> Xr; // nxm
vector<int> yr;
for (int col = 0; col < X.size(); ++col) {
Xr.push_back(vector<int>());
@@ -96,6 +95,7 @@ int main(int argc, char** argv)
}
);
program.add_argument("--discretize").help("Discretize input dataset").default_value(false).implicit_value(true);
program.add_argument("--dumpcpt").help("Dump CPT Tables").default_value(false).implicit_value(true);
program.add_argument("--stratified").help("If Stratified KFold is to be done").default_value(false).implicit_value(true);
program.add_argument("--tensors").help("Use tensors to store samples").default_value(false).implicit_value(true);
program.add_argument("-f", "--folds").help("Number of folds").default_value(5).scan<'i', int>().action([](const string& value) {
@@ -113,7 +113,7 @@ 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;
bool class_last, stratified, tensors, dump_cpt;
string model_name, file_name, path, complete_file_name;
int nFolds, seed;
try {
@@ -126,6 +126,7 @@ int main(int argc, char** argv)
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");
@@ -161,61 +162,75 @@ int main(int argc, char** argv)
states[className] = vector<int>(maxes[className]);
auto clf = platform::Models::instance()->create(model_name);
clf->fit(Xd, y, features, className, states);
auto score = clf->score(Xd, y);
if (dump_cpt) {
cout << "--- CPT Tables ---" << endl;
clf->dump_cpt();
}
auto lines = clf->show();
auto graph = clf->graph();
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 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);
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);
}
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 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;
}

View File

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

View File

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

40
src/BayesNet/AODELd.cc Normal file
View File

@@ -0,0 +1,40 @@
#include "AODELd.h"
#include "Models.h"
namespace bayesnet {
using namespace std;
AODELd::AODELd() : Ensemble(), Proposal(dataset, features, className) {}
AODELd& AODELd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills 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()
{
models.clear();
for (int i = 0; i < features.size(); ++i) {
models.push_back(std::make_unique<SPODELd>(i));
}
n_models = models.size();
}
void AODELd::trainModel()
{
for (const auto& model : models) {
model->fit(Xf, y, features, className, states);
}
}
vector<string> AODELd::graph(const string& name) const
{
return Ensemble::graph(name);
}
}

21
src/BayesNet/AODELd.h Normal file
View File

@@ -0,0 +1,21 @@
#ifndef AODELD_H
#define AODELD_H
#include "Ensemble.h"
#include "Proposal.h"
#include "SPODELd.h"
namespace bayesnet {
using namespace std;
class AODELd : public Ensemble, public Proposal {
protected:
void trainModel() override;
void buildModel() override;
public:
AODELd();
AODELd& fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_) override;
virtual ~AODELd() = default;
vector<string> graph(const string& name = "AODE") const override;
static inline string version() { return "0.0.1"; };
};
}
#endif // !AODELD_H

View File

@@ -5,19 +5,27 @@
namespace bayesnet {
using namespace std;
class BaseClassifier {
protected:
virtual void trainModel() = 0;
public:
// X is nxm vector, y is nx1 vector
virtual BaseClassifier& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
// X is nxm tensor, y is nx1 tensor
virtual BaseClassifier& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
virtual BaseClassifier& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) = 0;
virtual ~BaseClassifier() = default;
torch::Tensor virtual predict(torch::Tensor& X) = 0;
vector<int> virtual predict(vector<vector<int>>& X) = 0;
float virtual score(vector<vector<int>>& X, vector<int>& y) = 0;
float virtual score(torch::Tensor& X, torch::Tensor& y) = 0;
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;
int virtual getNumberOfNodes()const = 0;
int virtual getNumberOfEdges()const = 0;
int virtual getNumberOfStates() const = 0;
vector<string> virtual show() const = 0;
vector<string> virtual graph(const string& title = "") const = 0;
const string inline getVersion() const { return "0.1.0"; };
vector<string> virtual topological_order() = 0;
void virtual dump_cpt()const = 0;
};
}
#endif

View File

@@ -1,13 +1,15 @@
#include "BayesMetrics.h"
#include "Mst.h"
namespace bayesnet {
Metrics::Metrics(torch::Tensor& samples, vector<string>& features, string& className, int classNumStates)
//samples is nxm tensor used to fit the model
Metrics::Metrics(const torch::Tensor& samples, const vector<string>& features, const string& className, const int classNumStates)
: samples(samples)
, features(features)
, className(className)
, classNumStates(classNumStates)
{
}
//samples is nxm vector used to fit the model
Metrics::Metrics(const vector<vector<int>>& vsamples, const vector<int>& labels, const vector<string>& features, const string& className, const int classNumStates)
: features(features)
, className(className)
@@ -15,9 +17,9 @@ namespace bayesnet {
, 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));
}
vector<pair<string, string>> Metrics::doCombinations(const vector<string>& source)
{
@@ -39,17 +41,17 @@ namespace bayesnet {
// Compute class prior
auto margin = torch::zeros({ classNumStates });
for (int value = 0; value < classNumStates; ++value) {
auto mask = samples.index({ "...", -1 }) == value;
margin[value] = mask.sum().item<float>() / samples.sizes()[0];
auto mask = samples.index({ -1, "..." }) == value;
margin[value] = mask.sum().item<float>() / samples.size(1);
}
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({ mask, index_first });
auto second_dataset = samples.index({ mask, index_second });
auto mask = samples.index({ -1, "..." }) == value;
auto first_dataset = samples.index({ index_first, mask });
auto second_dataset = samples.index({ index_second, mask });
auto mi = mutualInformation(first_dataset, second_dataset);
auto pb = margin[value].item<float>();
accumulated += pb * mi;
@@ -67,13 +69,14 @@ namespace bayesnet {
}
return matrix;
}
// To use in Python
vector<float> Metrics::conditionalEdgeWeights()
{
auto matrix = conditionalEdge();
std::vector<float> v(matrix.data_ptr<float>(), matrix.data_ptr<float>() + matrix.numel());
return v;
}
double Metrics::entropy(torch::Tensor& feature)
double Metrics::entropy(const torch::Tensor& feature)
{
torch::Tensor counts = feature.bincount();
int totalWeight = counts.sum().item<int>();
@@ -83,7 +86,7 @@ namespace bayesnet {
return entropy.nansum().item<double>();
}
// H(Y|X) = sum_{x in X} p(x) H(Y|X=x)
double Metrics::conditionalEntropy(torch::Tensor& firstFeature, torch::Tensor& secondFeature)
double Metrics::conditionalEntropy(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature)
{
int numSamples = firstFeature.sizes()[0];
torch::Tensor featureCounts = secondFeature.bincount();
@@ -112,7 +115,7 @@ namespace bayesnet {
return entropyValue;
}
// I(X;Y) = H(Y) - H(Y|X)
double Metrics::mutualInformation(torch::Tensor& firstFeature, torch::Tensor& secondFeature)
double Metrics::mutualInformation(const torch::Tensor& firstFeature, const torch::Tensor& secondFeature)
{
return entropy(firstFeature) - conditionalEntropy(firstFeature, secondFeature);
}
@@ -121,7 +124,7 @@ namespace bayesnet {
and the indices of the weights as nodes of this square matrix using
Kruskal algorithm
*/
vector<pair<int, int>> Metrics::maximumSpanningTree(vector<string> features, Tensor& weights, int root)
vector<pair<int, int>> Metrics::maximumSpanningTree(const vector<string>& features, const Tensor& weights, const int root)
{
auto mst = MST(features, weights, root);
return mst.maximumSpanningTree();

View File

@@ -8,21 +8,21 @@ namespace bayesnet {
using namespace torch;
class Metrics {
private:
Tensor samples;
Tensor samples; // nxm tensor used to fit the model
vector<string> features;
string className;
int classNumStates = 0;
public:
Metrics() = default;
Metrics(Tensor&, vector<string>&, string&, int);
Metrics(const Tensor&, const vector<string>&, const string&, const int);
Metrics(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&, const int);
double entropy(Tensor&);
double conditionalEntropy(Tensor&, Tensor&);
double mutualInformation(Tensor&, Tensor&);
vector<float> conditionalEdgeWeights();
double entropy(const Tensor&);
double conditionalEntropy(const Tensor&, const Tensor&);
double mutualInformation(const Tensor&, const Tensor&);
vector<float> conditionalEdgeWeights(); // To use in Python
Tensor conditionalEdge();
vector<pair<string, string>> doCombinations(const vector<string>&);
vector<pair<int, int>> maximumSpanningTree(vector<string> features, Tensor& weights, int root);
vector<pair<int, int>> maximumSpanningTree(const vector<string>& features, const Tensor& weights, const int root);
};
}
#endif

View File

@@ -1,2 +1,7 @@
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 "${TORCH_LIBRARIES}")
include_directories(${BayesNet_SOURCE_DIR}/lib/mdlp)
include_directories(${BayesNet_SOURCE_DIR}/lib/Files)
include_directories(${BayesNet_SOURCE_DIR}/src/BayesNet)
include_directories(${BayesNet_SOURCE_DIR}/src/Platform)
add_library(BayesNet bayesnetUtils.cc Network.cc Node.cc BayesMetrics.cc Classifier.cc
KDB.cc TAN.cc SPODE.cc Ensemble.cc AODE.cc TANLd.cc KDBLd.cc SPODELd.cc AODELd.cc Mst.cc Proposal.cc ${BayesNet_SOURCE_DIR}/src/Platform/Models.cc)
target_link_libraries(BayesNet mdlp ArffFiles "${TORCH_LIBRARIES}")

View File

@@ -7,54 +7,65 @@ namespace bayesnet {
Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false) {}
Classifier& Classifier::build(vector<string>& features, string className, map<string, vector<int>>& states)
{
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[className].size();
metrics = Metrics(dataset, features, className, n_classes);
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);
}
model.initialize();
buildModel();
trainModel();
fitted = true;
return *this;
}
void Classifier::buildDataset(Tensor& ytmp)
{
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';
cout << "X dimensions: " << dataset.sizes() << "\n";
cout << "y dimensions: " << ytmp.sizes() << "\n";
exit(1);
}
}
void Classifier::trainModel()
{
model.fit(dataset, features, className, states);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states)
{
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));
dataset = X;
buildDataset(y);
return build(features, className, states);
}
// X is nxm where n is the number of features and m the number of samples
Classifier& Classifier::fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states)
{
this->X = torch::zeros({ static_cast<int>(X[0].size()), static_cast<int>(X.size()) }, kInt32);
Xv = X;
dataset = torch::zeros({ static_cast<int>(X.size()), static_cast<int>(X[0].size()) }, kInt32);
for (int i = 0; i < X.size(); ++i) {
this->X.index_put_({ "...", i }, torch::tensor(X[i], kInt32));
dataset.index_put_({ i, "..." }, torch::tensor(X[i], kInt32));
}
this->y = torch::tensor(y, kInt32);
yv = y;
auto ytmp = torch::tensor(y, kInt32);
buildDataset(ytmp);
return build(features, className, states);
}
Classifier& Classifier::fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states)
{
this->dataset = dataset;
return build(features, className, states);
}
void Classifier::checkFitParameters()
{
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 invalid_argument("X and features must have the same number of features");
throw invalid_argument("X " + to_string(n) + " and features " + to_string(features.size()) + " must have the same number of features");
}
if (states.find(className) == states.end()) {
throw invalid_argument("className not found in states");
@@ -65,23 +76,12 @@ namespace bayesnet {
}
}
}
Tensor Classifier::predict(Tensor& X)
{
if (!fitted) {
throw logic_error("Classifier has not been fitted");
}
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;
return model.predict(X);
}
vector<int> Classifier::predict(vector<vector<int>>& X)
{
@@ -102,8 +102,7 @@ namespace bayesnet {
if (!fitted) {
throw logic_error("Classifier has not been fitted");
}
auto Xt = torch::transpose(X, 0, 1);
Tensor y_pred = predict(Xt);
Tensor y_pred = predict(X);
return (y_pred == y).sum().item<float>() / y.size(0);
}
float Classifier::score(vector<vector<int>>& X, vector<int>& y)
@@ -111,37 +110,39 @@ namespace bayesnet {
if (!fitted) {
throw logic_error("Classifier has not been fitted");
}
auto m_ = X[0].size();
auto n_ = X.size();
vector<vector<int>> Xd(n_, vector<int>(m_, 0));
for (auto i = 0; i < n_; i++) {
Xd[i] = vector<int>(X[i].begin(), X[i].end());
}
return model.score(Xd, y);
return model.score(X, y);
}
vector<string> Classifier::show()
vector<string> Classifier::show() const
{
return model.show();
}
void Classifier::addNodes()
{
// Add all nodes to the network
for (auto feature : features) {
model.addNode(feature, states[feature].size());
for (const auto& feature : features) {
model.addNode(feature);
}
model.addNode(className, states[className].size());
model.addNode(className);
}
int Classifier::getNumberOfNodes()
int Classifier::getNumberOfNodes() const
{
// Features does not include class
return fitted ? model.getFeatures().size() + 1 : 0;
}
int Classifier::getNumberOfEdges()
int Classifier::getNumberOfEdges() const
{
return fitted ? model.getEdges().size() : 0;
return fitted ? model.getNumEdges() : 0;
}
int Classifier::getNumberOfStates()
int Classifier::getNumberOfStates() const
{
return fitted ? model.getStates() : 0;
}
vector<string> Classifier::topological_order()
{
return model.topological_sort();
}
void Classifier::dump_cpt() const
{
model.dump_cpt();
}
}

View File

@@ -10,36 +10,37 @@ using namespace torch;
namespace bayesnet {
class Classifier : public BaseClassifier {
private:
bool fitted;
void buildDataset(torch::Tensor& y);
Classifier& build(vector<string>& features, string className, map<string, vector<int>>& states);
protected:
bool fitted;
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;
Tensor dataset; // (n+1)xm tensor
Metrics metrics;
vector<string> features;
string className;
map<string, vector<int>> states;
void checkFitParameters();
virtual void train() = 0;
virtual void buildModel() = 0;
void trainModel() override;
public:
Classifier(Network model);
virtual ~Classifier() = default;
Classifier& fit(vector<vector<int>>& X, vector<int>& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
Classifier& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) override;
void addNodes();
int getNumberOfNodes() override;
int getNumberOfEdges() override;
int getNumberOfStates() override;
Tensor predict(Tensor& X);
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
Tensor predict(Tensor& X) override;
vector<int> predict(vector<vector<int>>& X) override;
float score(Tensor& X, Tensor& y) override;
float score(vector<vector<int>>& X, vector<int>& y) override;
vector<string> show() override;
vector<string> show() const override;
vector<string> topological_order() override;
void dump_cpt() const override;
};
}
#endif

View File

@@ -3,69 +3,52 @@
namespace bayesnet {
using namespace torch;
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)
Ensemble::Ensemble() : Classifier(Network()) {}
void Ensemble::trainModel()
{
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) {
models[i]->fit(Xv, yv, features, className, states);
// fit with vectors
models[i]->fit(dataset, features, className, states);
}
fitted = true;
return *this;
}
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>();
vector<int> y_pred_final;
for (int i = 0; i < y_pred.size(0); ++i) {
vector<float> votes(states[className].size(), 0);
vector<float> votes(y_pred.size(1), 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;
}
Tensor Ensemble::predict(Tensor& X)
{
if (!fitted) {
throw logic_error("Ensemble has not been fitted");
}
Tensor y_pred = torch::zeros({ X.size(1), n_models }, kInt32);
//Create a threadpool
auto threads{ vector<thread>() };
mutex mtx;
for (auto i = 0; i < n_models; ++i) {
threads.push_back(thread([&, i]() {
auto ypredict = models[i]->predict(X);
lock_guard<mutex> lock(mtx);
y_pred.index_put_({ "...", i }, ypredict);
}));
}
for (auto& thread : threads) {
thread.join();
}
return torch::tensor(voting(y_pred));
}
vector<int> Ensemble::predict(vector<vector<int>>& X)
{
if (!fitted) {
@@ -110,9 +93,8 @@ namespace bayesnet {
}
}
return (double)correct / y_pred.size();
}
vector<string> Ensemble::show()
vector<string> Ensemble::show() const
{
auto result = vector<string>();
for (auto i = 0; i < n_models; ++i) {
@@ -121,7 +103,7 @@ namespace bayesnet {
}
return result;
}
vector<string> Ensemble::graph(string title)
vector<string> Ensemble::graph(const string& title) const
{
auto result = vector<string>();
for (auto i = 0; i < n_models; ++i) {
@@ -130,7 +112,7 @@ namespace bayesnet {
}
return result;
}
int Ensemble::getNumberOfNodes()
int Ensemble::getNumberOfNodes() const
{
int nodes = 0;
for (auto i = 0; i < n_models; ++i) {
@@ -138,7 +120,7 @@ namespace bayesnet {
}
return nodes;
}
int Ensemble::getNumberOfEdges()
int Ensemble::getNumberOfEdges() const
{
int edges = 0;
for (auto i = 0; i < n_models; ++i) {
@@ -146,7 +128,7 @@ namespace bayesnet {
}
return edges;
}
int Ensemble::getNumberOfStates()
int Ensemble::getNumberOfStates() const
{
int nstates = 0;
for (auto i = 0; i < n_models; ++i) {

View File

@@ -8,39 +8,33 @@ using namespace std;
using namespace torch;
namespace bayesnet {
class Ensemble : public BaseClassifier {
class Ensemble : public Classifier {
private:
bool fitted;
long n_models;
Ensemble& build(vector<string>& features, string className, map<string, vector<int>>& states);
protected:
unsigned n_models;
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;
void trainModel() override;
vector<int> voting(Tensor& y_pred);
public:
Ensemble();
virtual ~Ensemble() = default;
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);
Tensor predict(Tensor& X) override;
vector<int> predict(vector<vector<int>>& X) override;
float score(Tensor& X, Tensor& y) override;
float score(vector<vector<int>>& X, vector<int>& y) override;
int getNumberOfNodes() override;
int getNumberOfEdges() override;
int getNumberOfStates() override;
vector<string> show() override;
vector<string> graph(string title) override;
int getNumberOfNodes() const override;
int getNumberOfEdges() const override;
int getNumberOfStates() const override;
vector<string> show() const override;
vector<string> graph(const string& title) const override;
vector<string> topological_order() override
{
return vector<string>();
}
void dump_cpt() const override
{
}
};
}
#endif

View File

@@ -4,7 +4,7 @@ namespace bayesnet {
using namespace torch;
KDB::KDB(int k, float theta) : Classifier(Network()), k(k), theta(theta) {}
void KDB::train()
void KDB::buildModel()
{
/*
1. For each feature Xi, compute mutual information, I(X;C),
@@ -27,9 +27,11 @@ namespace bayesnet {
*/
// 1. For each feature Xi, compute mutual information, I(X;C),
// where C is the class.
addNodes();
const Tensor& y = dataset.index({ -1, "..." });
vector <float> mi;
for (auto i = 0; i < features.size(); i++) {
Tensor firstFeature = X.index({ "...", i });
Tensor firstFeature = dataset.index({ i, "..." });
mi.push_back(metrics.mutualInformation(firstFeature, y));
}
// 2. Compute class conditional mutual information I(Xi;XjIC), f or each
@@ -38,14 +40,12 @@ namespace bayesnet {
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
@@ -79,11 +79,12 @@ namespace bayesnet {
exit_cond = num == n_edges || candidates.size(0) == 0;
}
}
vector<string> KDB::graph(string title)
vector<string> KDB::graph(const string& title) const
{
string header{ title };
if (title == "KDB") {
title += " (k=" + to_string(k) + ", theta=" + to_string(theta) + ")";
header += " (k=" + to_string(k) + ", theta=" + to_string(theta) + ")";
}
return model.graph(title);
return model.graph(header);
}
}

View File

@@ -11,11 +11,11 @@ namespace bayesnet {
float theta;
void add_m_edges(int idx, vector<int>& S, Tensor& weights);
protected:
void train() override;
void buildModel() override;
public:
explicit KDB(int k, float theta = 0.03);
virtual ~KDB() {};
vector<string> graph(string name = "KDB") override;
vector<string> graph(const string& name = "KDB") const override;
};
}
#endif

30
src/BayesNet/KDBLd.cc Normal file
View File

@@ -0,0 +1,30 @@
#include "KDBLd.h"
namespace bayesnet {
using namespace std;
KDBLd::KDBLd(int k) : KDB(k), Proposal(dataset, features, className) {}
KDBLd& KDBLd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills 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;
}
Tensor KDBLd::predict(Tensor& X)
{
auto Xt = prepareX(X);
return KDB::predict(Xt);
}
vector<string> KDBLd::graph(const string& name) const
{
return KDB::graph(name);
}
}

19
src/BayesNet/KDBLd.h Normal file
View File

@@ -0,0 +1,19 @@
#ifndef KDBLD_H
#define KDBLD_H
#include "KDB.h"
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class KDBLd : public KDB, public Proposal {
private:
public:
explicit KDBLd(int k);
virtual ~KDBLd() = default;
KDBLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "KDB") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
};
}
#endif // !KDBLD_H

View File

@@ -94,7 +94,7 @@ namespace bayesnet {
return result;
}
MST::MST(vector<string>& features, Tensor& weights, int root) : features(features), weights(weights), root(root) {}
MST::MST(const vector<string>& features, const Tensor& weights, const int root) : features(features), weights(weights), root(root) {}
vector<pair<int, int>> MST::maximumSpanningTree()
{
auto num_features = features.size();

View File

@@ -13,7 +13,7 @@ namespace bayesnet {
int root = 0;
public:
MST() = default;
MST(vector<string>& features, Tensor& weights, int root);
MST(const vector<string>& features, const Tensor& weights, const int root);
vector<pair<int, int>> maximumSpanningTree();
};
class Graph {

View File

@@ -3,15 +3,25 @@
#include "Network.h"
#include "bayesnetUtils.h"
namespace bayesnet {
Network::Network() : laplaceSmoothing(1), features(vector<string>()), className(""), classNumStates(0), maxThreads(0.8), fitted(false) {}
Network::Network(float maxT) : laplaceSmoothing(1), features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network() : features(vector<string>()), className(""), classNumStates(0), fitted(false) {}
Network::Network(float maxT) : features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network(float maxT, int smoothing) : laplaceSmoothing(smoothing), features(vector<string>()), className(""), classNumStates(0), maxThreads(maxT), fitted(false) {}
Network::Network(Network& other) : laplaceSmoothing(other.laplaceSmoothing), features(other.features), className(other.className), classNumStates(other.getClassNumStates()), maxThreads(other.getmaxThreads()), fitted(other.fitted)
Network::Network(Network& other) : laplaceSmoothing(other.laplaceSmoothing), features(other.features), className(other.className), classNumStates(other.getClassNumStates()), maxThreads(other.
getmaxThreads()), fitted(other.fitted)
{
for (const auto& pair : other.nodes) {
nodes[pair.first] = std::make_unique<Node>(*pair.second);
}
}
void Network::initialize()
{
features = vector<string>();
className = "";
classNumStates = 0;
fitted = false;
nodes.clear();
samples = torch::Tensor();
}
float Network::getmaxThreads()
{
return maxThreads;
@@ -20,28 +30,28 @@ namespace bayesnet {
{
return samples;
}
void Network::addNode(const string& name, int numStates)
void Network::addNode(const string& name)
{
if (name == "") {
throw 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);
}
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);
nodes[name] = std::make_unique<Node>(name);
}
vector<string> Network::getFeatures()
vector<string> Network::getFeatures() const
{
return features;
}
int Network::getClassNumStates()
int Network::getClassNumStates() const
{
return classNumStates;
}
int Network::getStates()
int Network::getStates() const
{
int result = 0;
for (auto& node : nodes) {
@@ -49,7 +59,7 @@ namespace bayesnet {
}
return result;
}
string Network::getClassName()
string Network::getClassName() const
{
return className;
}
@@ -94,45 +104,72 @@ namespace bayesnet {
{
return nodes;
}
void Network::fit(torch::Tensor& X, torch::Tensor& y, const vector<string>& featureNames, const string& className)
void Network::checkFitData(int n_samples, int n_features, int n_samples_y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states)
{
features = featureNames;
this->className = className;
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 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>());
if (n_samples != n_samples_y) {
throw invalid_argument("X and y must have the same number of samples in Network::fit (" + to_string(n_samples) + " != " + to_string(n_samples_y) + ")");
}
if (n_features != featureNames.size()) {
throw invalid_argument("X and features must have the same number of features in Network::fit (" + to_string(n_features) + " != " + to_string(featureNames.size()) + ")");
}
if (n_features != features.size() - 1) {
throw invalid_argument("X and local features must have the same number of features in Network::fit (" + to_string(n_features) + " != " + to_string(features.size() - 1) + ")");
}
if (find(features.begin(), features.end(), className) == features.end()) {
throw invalid_argument("className not found in Network::features");
}
for (auto& feature : featureNames) {
if (find(features.begin(), features.end(), feature) == features.end()) {
throw invalid_argument("Feature " + feature + " not found in Network::features");
}
if (states.find(feature) == states.end()) {
throw invalid_argument("Feature " + feature + " not found in states");
}
dataset[featureNames[i]] = k;
}
dataset[className] = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
completeFit();
}
void Network::fit(const vector<vector<int>>& input_data, const vector<int>& labels, const vector<string>& featureNames, const string& className)
void Network::setStates(const map<string, vector<int>>& states)
{
features = featureNames;
// Set states to every Node in the network
for (int i = 0; i < features.size(); ++i) {
nodes[features[i]]->setNumStates(states.at(features[i]).size());
}
classNumStates = nodes[className]->getNumStates();
}
// X comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const torch::Tensor& X, const torch::Tensor& y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states)
{
checkFitData(X.size(1), X.size(0), y.size(0), featureNames, className, states);
this->className = className;
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);
Tensor ytmp = torch::transpose(y.view({ y.size(0), 1 }), 0, 1);
samples = torch::cat({ X , ytmp }, 0);
for (int i = 0; i < featureNames.size(); ++i) {
dataset[featureNames[i]] = input_data[i];
samples.index_put_({ "...", i }, torch::tensor(input_data[i], torch::kInt32));
auto row_feature = X.index({ i, "..." });
}
dataset[className] = labels;
samples.index_put_({ "...", -1 }, torch::tensor(labels, torch::kInt32));
completeFit();
completeFit(states);
}
void Network::completeFit()
void Network::fit(const torch::Tensor& samples, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states)
{
checkFitData(samples.size(1), samples.size(0) - 1, samples.size(1), featureNames, className, states);
this->className = className;
this->samples = samples;
completeFit(states);
}
// input_data comes in nxm, where n is the number of features and m the number of samples
void Network::fit(const vector<vector<int>>& input_data, const vector<int>& labels, const vector<string>& featureNames, const string& className, const map<string, vector<int>>& states)
{
checkFitData(input_data[0].size(), input_data.size(), labels.size(), featureNames, className, states);
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);
for (int i = 0; i < featureNames.size(); ++i) {
samples.index_put_({ i, "..." }, torch::tensor(input_data[i], torch::kInt32));
}
samples.index_put_({ -1, "..." }, torch::tensor(labels, torch::kInt32));
completeFit(states);
}
void Network::completeFit(const map<string, vector<int>>& states)
{
setStates(states);
int maxThreadsRunning = static_cast<int>(std::thread::hardware_concurrency() * maxThreads);
if (maxThreadsRunning < 1) {
maxThreadsRunning = 1;
@@ -154,7 +191,7 @@ namespace bayesnet {
auto& pair = *std::next(nodes.begin(), nextNodeIndex);
++nextNodeIndex;
lock.unlock();
pair.second->computeCPT(dataset, laplaceSmoothing);
pair.second->computeCPT(samples, features, laplaceSmoothing);
lock.lock();
nodes[pair.first] = std::move(pair.second);
lock.unlock();
@@ -170,7 +207,39 @@ namespace bayesnet {
}
fitted = true;
}
torch::Tensor Network::predict_tensor(const torch::Tensor& samples, const bool proba)
{
if (!fitted) {
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 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;
else
return result.argmax(1);
}
// Return mxn tensor of probabilities
Tensor Network::predict_proba(const Tensor& samples)
{
return predict_tensor(samples, true);
}
// Return mxn tensor of probabilities
Tensor Network::predict(const Tensor& samples)
{
return predict_tensor(samples, false);
}
// Return mx1 vector of predictions
// tsamples is nxm vector of samples
vector<int> Network::predict(const vector<vector<int>>& tsamples)
{
if (!fitted) {
@@ -191,6 +260,7 @@ namespace bayesnet {
}
return predictions;
}
// Return mxn vector of probabilities
vector<vector<double>> Network::predict_proba(const vector<vector<int>>& tsamples)
{
if (!fitted) {
@@ -218,12 +288,13 @@ namespace bayesnet {
}
return (double)correct / y_pred.size();
}
// Return 1xn vector of probabilities
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()) {
if (sample.size() != features.size() - 1) {
throw invalid_argument("Sample size (" + to_string(sample.size()) +
") does not match the number of features (" + to_string(features.size()) + ")");
") does not match the number of features (" + to_string(features.size() - 1) + ")");
}
map<string, int> evidence;
for (int i = 0; i < sample.size(); ++i) {
@@ -231,6 +302,20 @@ namespace bayesnet {
}
return exactInference(evidence);
}
// Return 1xn vector of probabilities
vector<double> Network::predict_sample(const Tensor& sample)
{
// Ensure the sample size is equal to the number of features
if (sample.size(0) != features.size() - 1) {
throw invalid_argument("Sample size (" + to_string(sample.size(0)) +
") does not match the number of features (" + to_string(features.size() - 1) + ")");
}
map<string, int> evidence;
for (int i = 0; i < sample.size(0); ++i) {
evidence[features[i]] = sample[i].item<int>();
}
return exactInference(evidence);
}
double Network::computeFactor(map<string, int>& completeEvidence)
{
double result = 1.0;
@@ -256,13 +341,12 @@ namespace bayesnet {
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](double& value) { return value / sum; });
return result;
}
vector<string> Network::show()
vector<string> Network::show() const
{
vector<string> result;
// Draw the network
@@ -275,7 +359,7 @@ namespace bayesnet {
}
return result;
}
vector<string> Network::graph(const string& title)
vector<string> Network::graph(const string& title) const
{
auto output = vector<string>();
auto prefix = "digraph BayesNet {\nlabel=<BayesNet ";
@@ -289,7 +373,7 @@ namespace bayesnet {
output.push_back("}\n");
return output;
}
vector<pair<string, string>> Network::getEdges()
vector<pair<string, string>> Network::getEdges() const
{
auto edges = vector<pair<string, string>>();
for (const auto& node : nodes) {
@@ -301,4 +385,52 @@ namespace bayesnet {
}
return edges;
}
int Network::getNumEdges() const
{
return getEdges().size();
}
vector<string> Network::topological_sort()
{
/* Check if al the fathers of every node are before the node */
auto result = features;
result.erase(remove(result.begin(), result.end(), className), result.end());
bool ending{ false };
int idx = 0;
while (!ending) {
ending = true;
for (auto feature : features) {
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 logic_error("Error in topological sort because of node " + feature + " is not in result");
}
} else {
throw logic_error("Error in topological sort because of node father " + fatherName + " is not in result");
}
}
}
}
return result;
}
void Network::dump_cpt() const
{
for (auto& node : nodes) {
cout << "* " << node.first << ": (" << node.second->getNumStates() << ") : " << node.second->getCPT().sizes() << endl;
}
}
}

View File

@@ -8,23 +8,21 @@ namespace bayesnet {
class Network {
private:
map<string, unique_ptr<Node>> nodes;
map<string, vector<int>> dataset;
bool fitted;
float maxThreads;
float maxThreads = 0.95;
int classNumStates;
vector<string> features;
vector<string> features; // Including classname
string className;
int laplaceSmoothing;
torch::Tensor samples;
int laplaceSmoothing = 1;
torch::Tensor samples; // nxm tensor used to fit the model
bool isCyclic(const std::string&, std::unordered_set<std::string>&, std::unordered_set<std::string>&);
vector<double> predict_sample(const vector<int>&);
vector<double> predict_sample(const torch::Tensor&);
vector<double> exactInference(map<string, int>&);
double computeFactor(map<string, int>&);
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();
void completeFit(const map<string, vector<int>>&);
void checkFitData(int n_features, int n_samples, int n_samples_y, const vector<string>& featureNames, const string& className, const map<string, vector<int>>&);
void setStates(const map<string, vector<int>>&);
public:
Network();
explicit Network(float, int);
@@ -32,23 +30,29 @@ namespace bayesnet {
explicit Network(Network&);
torch::Tensor& getSamples();
float getmaxThreads();
void addNode(const string&, int);
void addNode(const string&);
void addEdge(const string&, const string&);
map<string, std::unique_ptr<Node>>& getNodes();
vector<string> getFeatures();
int getStates();
vector<pair<string, string>> getEdges();
int getClassNumStates();
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>>&);
vector<string> getFeatures() const;
int getStates() const;
vector<pair<string, string>> getEdges() const;
int getNumEdges() const;
int getClassNumStates() const;
string getClassName() const;
void fit(const vector<vector<int>>&, const vector<int>&, const vector<string>&, const string&, const map<string, vector<int>>&);
void fit(const torch::Tensor&, const torch::Tensor&, const vector<string>&, const string&, const map<string, vector<int>>&);
void fit(const torch::Tensor&, const vector<string>&, const string&, const map<string, vector<int>>&);
vector<int> predict(const vector<vector<int>>&); // Return mx1 vector of predictions
torch::Tensor predict(const torch::Tensor&); // Return mx1 tensor of predictions
torch::Tensor predict_tensor(const torch::Tensor& samples, const bool proba);
vector<vector<double>> predict_proba(const vector<vector<int>>&); // Return mxn vector of probabilities
torch::Tensor predict_proba(const torch::Tensor&); // Return mxn tensor of probabilities
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
vector<string> topological_sort();
vector<string> show() const;
vector<string> graph(const string& title) const; // Returns a vector of strings representing the graph in graphviz format
void initialize();
void dump_cpt() const;
inline string version() { return "0.1.0"; }
};
}

View File

@@ -2,8 +2,8 @@
namespace bayesnet {
Node::Node(const std::string& name, int numStates)
: name(name), numStates(numStates), cpTable(torch::Tensor()), parents(vector<Node*>()), children(vector<Node*>())
Node::Node(const std::string& name)
: name(name), numStates(0), cpTable(torch::Tensor()), parents(vector<Node*>()), children(vector<Node*>())
{
}
void Node::clear()
@@ -84,8 +84,9 @@ namespace bayesnet {
}
return result;
}
void Node::computeCPT(map<string, vector<int>>& dataset, const int laplaceSmoothing)
void Node::computeCPT(const torch::Tensor& dataset, const vector<string>& features, 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(); });
@@ -93,10 +94,22 @@ namespace bayesnet {
// Create a tensor of zeros with the dimensions of the CPT
cpTable = torch::zeros(dimensions, torch::kFloat) + laplaceSmoothing;
// Fill table with counts
for (int n_sample = 0; n_sample < dataset[name].size(); ++n_sample) {
auto pos = find(features.begin(), features.end(), name);
if (pos == features.end()) {
throw logic_error("Feature " + name + " not found in dataset");
}
int name_index = pos - features.begin();
for (int n_sample = 0; n_sample < dataset.size(1); ++n_sample) {
torch::List<c10::optional<torch::Tensor>> coordinates;
coordinates.push_back(torch::tensor(dataset[name][n_sample]));
transform(parents.begin(), parents.end(), back_inserter(coordinates), [&dataset, &n_sample](const auto& parent) { return torch::tensor(dataset[parent->getName()][n_sample]); });
coordinates.push_back(dataset.index({ name_index, n_sample }));
for (auto parent : parents) {
pos = find(features.begin(), features.end(), parent->getName());
if (pos == features.end()) {
throw logic_error("Feature parent " + parent->getName() + " not found in dataset");
}
int parent_index = pos - features.begin();
coordinates.push_back(dataset.index({ parent_index, n_sample }));
}
// Increment the count of the corresponding coordinate
cpTable.index_put_({ coordinates }, cpTable.index({ coordinates }) + 1);
}

View File

@@ -16,7 +16,7 @@ namespace bayesnet {
vector<int64_t> dimensions; // dimensions of the cpTable
public:
vector<pair<string, string>> combinations(const vector<string>&);
Node(const string&, int);
explicit Node(const string&);
void clear();
void addParent(Node*);
void addChild(Node*);
@@ -26,7 +26,7 @@ namespace bayesnet {
vector<Node*>& getParents();
vector<Node*>& getChildren();
torch::Tensor& getCPT();
void computeCPT(map<string, vector<int>>&, const int);
void computeCPT(const torch::Tensor&, const vector<string>&, const int);
int getNumStates() const;
void setNumStates(int);
unsigned minFill();

109
src/BayesNet/Proposal.cc Normal file
View File

@@ -0,0 +1,109 @@
#include "Proposal.h"
#include "ArffFiles.h"
namespace bayesnet {
Proposal::Proposal(torch::Tensor& dataset_, vector<string>& features_, string& className_) : pDataset(dataset_), pFeatures(features_), pClassName(className_) {}
Proposal::~Proposal()
{
for (auto& [key, value] : discretizers) {
delete value;
}
}
map<string, vector<int>> Proposal::localDiscretizationProposal(const map<string, vector<int>>& oldStates, Network& model)
{
// order of local discretization is important. no good 0, 1, 2...
// although we rediscretize features after the local discretization of every feature
auto order = model.topological_sort();
auto& nodes = model.getNodes();
map<string, vector<int>> states = oldStates;
vector<int> indicesToReDiscretize;
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
vector<string> parents;
transform(nodeParents.begin(), nodeParents.end(), back_inserter(parents), [](const auto& p) { return p->getName(); });
// Remove class as parent as it will be added later
parents.erase(remove(parents.begin(), parents.end(), pClassName), parents.end());
// Get the indices of the parents
vector<int> indices;
indices.push_back(-1); // Add class index
transform(parents.begin(), parents.end(), back_inserter(indices), [&](const auto& p) {return find(pFeatures.begin(), pFeatures.end(), p) - pFeatures.begin(); });
// Now we fit the discretizer of the feature, conditioned on its parents and the class i.e. discretizer.fit(X[index], X[indices] + y)
vector<string> yJoinParents(Xf.size(1));
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 = vector<mdlp::precision_t>(xvf_ptr, xvf_ptr + Xf.size(1));
discretizers[feature]->fit(xvf, yxv);
//
//
//
// auto tmp = discretizers[feature]->transform(xvf);
// Xv[index] = tmp;
// auto xStates = vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
// iota(xStates.begin(), xStates.end(), 0);
// //Update new states of the feature/node
// states[feature] = xStates;
}
if (upgrade) {
// Discretize again X (only the affected indices) with the new fitted discretizers
for (auto index : indicesToReDiscretize) {
auto Xt_ptr = Xf.index({ index }).data_ptr<float>();
auto Xt = vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
pDataset.index_put_({ index, "..." }, torch::tensor(discretizers[pFeatures[index]]->transform(Xt)));
auto xStates = vector<int>(discretizers[pFeatures[index]]->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
//Update new states of the feature/node
states[pFeatures[index]] = xStates;
}
model.fit(pDataset, pFeatures, pClassName, states);
}
return states;
}
map<string, vector<int>> Proposal::fit_local_discretization(const torch::Tensor& y)
{
// Discretize the continuous input data and build pDataset (Classifier::dataset)
int m = Xf.size(1);
int n = Xf.size(0);
map<string, vector<int>> states;
pDataset = torch::zeros({ n + 1, m }, kInt32);
auto yv = vector<int>(y.data_ptr<int>(), y.data_ptr<int>() + y.size(0));
// discretize input data by feature(row)
for (auto i = 0; i < pFeatures.size(); ++i) {
auto* discretizer = new mdlp::CPPFImdlp();
auto Xt_ptr = Xf.index({ i }).data_ptr<float>();
auto Xt = vector<float>(Xt_ptr, Xt_ptr + Xf.size(1));
discretizer->fit(Xt, yv);
pDataset.index_put_({ i, "..." }, torch::tensor(discretizer->transform(Xt)));
auto xStates = vector<int>(discretizer->getCutPoints().size() + 1);
iota(xStates.begin(), xStates.end(), 0);
states[pFeatures[i]] = xStates;
discretizers[pFeatures[i]] = discretizer;
}
int n_classes = torch::max(y).item<int>() + 1;
auto yStates = vector<int>(n_classes);
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 = 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;
}
}

29
src/BayesNet/Proposal.h Normal file
View File

@@ -0,0 +1,29 @@
#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, vector<string>& features_, string& className_);
virtual ~Proposal();
protected:
torch::Tensor prepareX(torch::Tensor& X);
map<string, vector<int>> localDiscretizationProposal(const map<string, vector<int>>& states, Network& model);
map<string, vector<int>> fit_local_discretization(const torch::Tensor& y);
torch::Tensor Xf; // X continuous nxm tensor
torch::Tensor y; // y discrete nx1 tensor
map<string, mdlp::CPPFImdlp*> discretizers;
private:
torch::Tensor& pDataset; // (n+1)xm tensor
vector<string>& pFeatures;
string& pClassName;
};
}
#endif

View File

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

View File

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

47
src/BayesNet/SPODELd.cc Normal file
View File

@@ -0,0 +1,47 @@
#include "SPODELd.h"
namespace bayesnet {
using namespace std;
SPODELd::SPODELd(int root) : SPODE(root), Proposal(dataset, features, className) {}
SPODELd& SPODELd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills 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, vector<string>& features_, string className_, map<string, vector<int>>& states_)
{
Xf = dataset.index({ torch::indexing::Slice(0, dataset.size(0) - 1), "..." }).clone();
cout << "Xf " << Xf.sizes() << " dtype: " << Xf.dtype() << endl;
y = dataset.index({ -1, "..." }).clone();
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
// Fills vectors Xv & yv with the data from tensors X_ (discretized) & y
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;
}
Tensor SPODELd::predict(Tensor& X)
{
auto Xt = prepareX(X);
return SPODE::predict(Xt);
}
vector<string> SPODELd::graph(const string& name) const
{
return SPODE::graph(name);
}
}

19
src/BayesNet/SPODELd.h Normal file
View File

@@ -0,0 +1,19 @@
#ifndef SPODELD_H
#define SPODELD_H
#include "SPODE.h"
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class SPODELd : public SPODE, public Proposal {
public:
explicit SPODELd(int root);
virtual ~SPODELd() = default;
SPODELd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
SPODELd& fit(torch::Tensor& dataset, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "SPODE") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
};
}
#endif // !SPODELD_H

View File

@@ -5,16 +5,16 @@ namespace bayesnet {
TAN::TAN() : Classifier(Network()) {}
void TAN::train()
void TAN::buildModel()
{
// 0. Add all nodes to the model
addNodes();
// 1. Compute mutual information between each feature and the class and set the root node
// as the highest mutual information with the class
auto mi = vector <pair<int, float >>();
Tensor class_dataset = dataset.index({ "...", -1 });
Tensor class_dataset = dataset.index({ -1, "..." });
for (int i = 0; i < static_cast<int>(features.size()); ++i) {
Tensor feature_dataset = dataset.index({ "...", i });
Tensor feature_dataset = dataset.index({ i, "..." });
auto mi_value = metrics.mutualInformation(class_dataset, feature_dataset);
mi.push_back({ i, mi_value });
}
@@ -34,7 +34,7 @@ namespace bayesnet {
model.addEdge(className, feature);
}
}
vector<string> TAN::graph(string title)
vector<string> TAN::graph(const string& title) const
{
return model.graph(title);
}

View File

@@ -7,11 +7,11 @@ namespace bayesnet {
class TAN : public Classifier {
private:
protected:
void train() override;
void buildModel() override;
public:
TAN();
virtual ~TAN() {};
vector<string> graph(string name = "TAN") override;
vector<string> graph(const string& name = "TAN") const override;
};
}
#endif

31
src/BayesNet/TANLd.cc Normal file
View File

@@ -0,0 +1,31 @@
#include "TANLd.h"
namespace bayesnet {
using namespace std;
TANLd::TANLd() : TAN(), Proposal(dataset, features, className) {}
TANLd& TANLd::fit(torch::Tensor& X_, torch::Tensor& y_, vector<string>& features_, string className_, map<string, vector<int>>& states_)
{
// This first part should go in a Classifier method called fit_local_discretization o fit_float...
features = features_;
className = className_;
Xf = X_;
y = y_;
// Fills 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;
}
Tensor TANLd::predict(Tensor& X)
{
auto Xt = prepareX(X);
return TAN::predict(Xt);
}
vector<string> TANLd::graph(const string& name) const
{
return TAN::graph(name);
}
}

19
src/BayesNet/TANLd.h Normal file
View File

@@ -0,0 +1,19 @@
#ifndef TANLD_H
#define TANLD_H
#include "TAN.h"
#include "Proposal.h"
namespace bayesnet {
using namespace std;
class TANLd : public TAN, public Proposal {
private:
public:
TANLd();
virtual ~TANLd() = default;
TANLd& fit(torch::Tensor& X, torch::Tensor& y, vector<string>& features, string className, map<string, vector<int>>& states) override;
vector<string> graph(const string& name = "TAN") const override;
Tensor predict(Tensor& X) override;
static inline string version() { return "0.0.1"; };
};
}
#endif // !TANLD_H

View File

@@ -3,6 +3,7 @@
namespace bayesnet {
using namespace std;
using namespace torch;
// Return the indices in descending order
vector<int> argsort(vector<float>& nums)
{
int n = nums.size();

View File

@@ -4,5 +4,5 @@ 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)
add_executable(main main.cc Folding.cc platformUtils.cc Experiment.cc Datasets.cc Models.cc Report.cc)
target_link_libraries(main BayesNet ArffFiles mdlp "${TORCH_LIBRARIES}")

View File

@@ -207,9 +207,9 @@ namespace platform {
if (discretize) {
Xd = discretizeDataset(Xv, yv);
computeStates();
n_samples = Xd[0].size();
n_features = Xd.size();
}
n_samples = Xv[0].size();
n_features = Xv.size();
loaded = true;
}
void Dataset::buildTensors()

View File

@@ -1,6 +1,7 @@
#include "Experiment.h"
#include "Datasets.h"
#include "Models.h"
#include "Report.h"
namespace platform {
using json = nlohmann::json;
@@ -86,6 +87,13 @@ namespace platform {
file.close();
}
void Experiment::report()
{
json data = build_json();
Report report(data);
report.show();
}
void Experiment::show()
{
json data = build_json();
@@ -104,7 +112,7 @@ namespace platform {
void Experiment::cross_validation(const string& path, const string& fileName)
{
auto datasets = platform::Datasets(path, true, platform::ARFF);
auto datasets = platform::Datasets(path, discretized, platform::ARFF);
// Get dataset
auto [X, y] = datasets.getTensors(fileName);
auto states = datasets.getStates(fileName);
@@ -114,7 +122,7 @@ namespace platform {
cout << " (" << setw(5) << samples << "," << setw(3) << features.size() << ") " << flush;
// Prepare Result
auto result = Result();
auto [values, counts] = at::_unique(y);;
auto [values, counts] = at::_unique(y);
result.setSamples(X.size(1)).setFeatures(X.size(0)).setClasses(values.size(0));
int nResults = nfolds * static_cast<int>(randomSeeds.size());
auto accuracy_test = torch::zeros({ nResults }, torch::kFloat64);

View File

@@ -108,6 +108,7 @@ namespace platform {
void cross_validation(const string& path, const string& fileName);
void go(vector<string> filesToProcess, const string& path);
void show();
void report();
};
}
#endif

View File

@@ -6,6 +6,10 @@
#include "TAN.h"
#include "KDB.h"
#include "SPODE.h"
#include "TANLd.h"
#include "KDBLd.h"
#include "SPODELd.h"
#include "AODELd.h"
namespace platform {
class Models {
private:

67
src/Platform/Report.cc Normal file
View File

@@ -0,0 +1,67 @@
#include "Report.h"
namespace platform {
string headerLine(const string& text)
{
int n = MAXL - text.length() - 3;
n = n < 0 ? 0 : n;
return "* " + text + string(n, ' ') + "*\n";
}
string Report::fromVector(const string& key)
{
string result = "";
for (auto& item : data[key]) {
result += to_string(item) + ", ";
}
return "[" + result.substr(0, result.size() - 2) + "]";
}
string fVector(const json& data)
{
string result = "";
for (const auto& item : data) {
result += to_string(item) + ", ";
}
return "[" + result.substr(0, result.size() - 2) + "]";
}
void Report::show()
{
header();
body();
}
void Report::header()
{
cout << string(MAXL, '*') << endl;
cout << headerLine("Report " + data["model"].get<string>() + " ver. " + data["version"].get<string>() + " with " + to_string(data["folds"].get<int>()) + " Folds cross validation and " + to_string(data["seeds"].size()) + " random seeds. " + data["date"].get<string>() + " " + data["time"].get<string>());
cout << headerLine(data["title"].get<string>());
cout << headerLine("Random seeds: " + fromVector("seeds") + " Stratified: " + (data["stratified"].get<bool>() ? "True" : "False"));
cout << headerLine("Execution took " + to_string(data["duration"].get<float>()) + " seconds, " + to_string(data["duration"].get<float>() / 3600) + " hours, on " + data["platform"].get<string>());
cout << headerLine("Score is " + data["score_name"].get<string>());
cout << string(MAXL, '*') << endl;
cout << endl;
}
void Report::body()
{
cout << "Dataset Sampl. Feat. Cls Nodes Edges States Score Time Hyperparameters" << endl;
cout << "============================== ====== ===== === ======= ======= ======= =============== ================= ===============" << endl;
for (const auto& r : data["results"]) {
cout << setw(30) << left << r["dataset"].get<string>() << " ";
cout << setw(6) << right << r["samples"].get<int>() << " ";
cout << setw(5) << right << r["features"].get<int>() << " ";
cout << setw(3) << right << r["classes"].get<int>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["nodes"].get<float>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["leaves"].get<float>() << " ";
cout << setw(7) << setprecision(2) << fixed << r["depth"].get<float>() << " ";
cout << setw(8) << right << setprecision(6) << fixed << r["score_test"].get<double>() << "±" << setw(6) << setprecision(4) << fixed << r["score_test_std"].get<double>() << " ";
cout << setw(10) << right << setprecision(6) << fixed << r["test_time"].get<double>() << "±" << setw(6) << setprecision(4) << fixed << r["test_time_std"].get<double>() << " ";
cout << " " << r["hyperparameters"].get<string>();
cout << endl;
cout << string(MAXL, '*') << endl;
cout << headerLine("Train scores: " + fVector(r["scores_train"]));
cout << headerLine("Test scores: " + fVector(r["scores_test"]));
cout << headerLine("Train times: " + fVector(r["times_train"]));
cout << headerLine("Test times: " + fVector(r["times_test"]));
cout << string(MAXL, '*') << endl;
}
}
}

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

@@ -0,0 +1,23 @@
#ifndef REPORT_H
#define REPORT_H
#include <string>
#include <iostream>
#include <nlohmann/json.hpp>
using json = nlohmann::json;
const int MAXL = 121;
namespace platform {
using namespace std;
class Report {
public:
explicit Report(json data_) { data = data_; };
virtual ~Report() = default;
void show();
private:
void header();
void body();
string fromVector(const string& key);
json data;
};
};
#endif

View File

@@ -99,13 +99,13 @@ int main(int argc, char** argv)
filesToTest = platform::Datasets(path, true, platform::ARFF).getNames();
saveResults = true;
}
/*
* Begin Processing
*/
auto env = platform::DotEnv();
auto experiment = platform::Experiment();
experiment.setTitle(title).setLanguage("cpp").setLanguageVersion("1.0.0");
experiment.setDiscretized(discretize_dataset).setModel(model_name).setPlatform("BayesNet");
experiment.setDiscretized(discretize_dataset).setModel(model_name).setPlatform(env.get("platform"));
experiment.setStratified(stratified).setNFolds(n_folds).setScoreName("accuracy");
for (auto seed : seeds) {
experiment.addRandomSeed(seed);
@@ -117,7 +117,7 @@ int main(int argc, char** argv)
if (saveResults)
experiment.save(PATH_RESULTS);
else
experiment.show();
experiment.report();
cout << "Done!" << endl;
return 0;
}

View File

@@ -2,10 +2,18 @@
#define MODEL_REGISTER_H
static platform::Registrar registrarT("TAN",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::TAN();});
static platform::Registrar registrarTLD("TANLd",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::TANLd();});
static platform::Registrar registrarS("SPODE",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::SPODE(2);});
static platform::Registrar registrarSLD("SPODELd",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::SPODELd(2);});
static platform::Registrar registrarK("KDB",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::KDB(2);});
static platform::Registrar registrarKLD("KDBLd",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::KDBLd(2);});
static platform::Registrar registrarA("AODE",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::AODE();});
static platform::Registrar registrarALD("AODELd",
[](void) -> bayesnet::BaseClassifier* { return new bayesnet::AODELd();});
#endif

View File

@@ -9,29 +9,21 @@ TEST_CASE("Test Bayesian Network")
{
auto [Xd, y, features, className, states] = loadFile("iris");
SECTION("Test Update Nodes")
{
auto net = bayesnet::Network();
net.addNode("A", 3);
REQUIRE(net.getStates() == 3);
net.addNode("A", 5);
REQUIRE(net.getStates() == 5);
}
SECTION("Test get features")
{
auto net = bayesnet::Network();
net.addNode("A", 3);
net.addNode("B", 5);
net.addNode("A");
net.addNode("B");
REQUIRE(net.getFeatures() == vector<string>{"A", "B"});
net.addNode("C", 2);
net.addNode("C");
REQUIRE(net.getFeatures() == vector<string>{"A", "B", "C"});
}
SECTION("Test get edges")
{
auto net = bayesnet::Network();
net.addNode("A", 3);
net.addNode("B", 5);
net.addNode("C", 2);
net.addNode("A");
net.addNode("B");
net.addNode("C");
net.addEdge("A", "B");
net.addEdge("B", "C");
REQUIRE(net.getEdges() == vector<pair<string, string>>{ {"A", "B"}, { "B", "C" } });