Fix some issues in FeatureSelect

CHANGELOG.md

@@ -7,18 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
-## [1.1.1] - 2025-05-08
-
-### Internal
-
-- Fix the vcpkg configuration in building the library.
-- Fix the sample app to use the vcpkg configuration.
-
 ## [1.1.0] - 2025-04-27
 
 ### Internal
 
-- Add changes to .clang-format to adjust to vscode format style thanks to <https://clang-format-configurator.site/>
+- Add changes to .clang-format to ajust to vscode format style thanks to <https://clang-format-configurator.site/>
 - Remove all the dependencies as git submodules and add them as vcpkg dependencies.
 - Fix the dependencies versions for this specific BayesNet version.
 

CMakeLists.txt

@@ -1,19 +1,21 @@
-cmake_minimum_required(VERSION 3.27)
+cmake_minimum_required(VERSION 3.20)
 
-project(bayesnet
-  VERSION 1.1.1
+project(BayesNet
+  VERSION 1.1.0
   DESCRIPTION "Bayesian Network and basic classifiers Library."
   HOMEPAGE_URL "https://github.com/rmontanana/bayesnet"
   LANGUAGES CXX
 )
 
-set(CMAKE_CXX_STANDARD 17)
-cmake_policy(SET CMP0135 NEW)
+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 CONFIG REQUIRED)
-find_package(fimdlp CONFIG REQUIRED)
-find_package(nlohmann_json CONFIG REQUIRED)
-find_package(folding CONFIG REQUIRED)
+find_package(Torch REQUIRED)
+
+if (POLICY CMP0135)
+  cmake_policy(SET CMP0135 NEW)
+endif ()
 
 # Global CMake variables
 # ----------------------
@@ -31,83 +33,76 @@ endif()
 
 # Options
 # -------
-option(ENABLE_CLANG_TIDY "Enable to add clang tidy"              OFF)
-option(ENABLE_TESTING "Unit testing build"                       OFF)
-option(CODE_COVERAGE "Collect coverage from test library"        OFF)
-option(INSTALL_GTEST "Enable installation of googletest"         OFF)
+option(ENABLE_CLANG_TIDY "Enable to add clang tidy."              OFF)
+option(ENABLE_TESTING "Unit testing build"                        OFF)
+option(CODE_COVERAGE "Collect coverage from test library"         OFF)
+option(INSTALL_GTEST "Enable installation of googletest."         OFF)
 
-add_subdirectory(config)
+# CMakes modules
+# --------------
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules ${CMAKE_MODULE_PATH})
+
+if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+  MESSAGE("Debug mode")
+  set(ENABLE_TESTING ON)
+  set(CODE_COVERAGE ON)
+endif (CMAKE_BUILD_TYPE STREQUAL "Debug")
+
+get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
+message(STATUS "Languages=${LANGUAGES}")
+if (CODE_COVERAGE)
+  enable_testing()
+  include(CodeCoverage)
+  MESSAGE(STATUS "Code coverage enabled")
+  SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
+endif (CODE_COVERAGE)
 
 if (ENABLE_CLANG_TIDY)
-    include(StaticAnalyzers) # clang-tidy
+  include(StaticAnalyzers) # clang-tidy
 endif (ENABLE_CLANG_TIDY)
 
-# Add the library
-# ---------------
-include_directories(
-    ${bayesnet_SOURCE_DIR}
-    ${CMAKE_BINARY_DIR}/configured_files/include
-)
+# External libraries - dependencies of BayesNet
+# ---------------------------------------------
 
-file(GLOB_RECURSE Sources "bayesnet/*.cc")
+find_package(Torch CONFIG REQUIRED)
+find_package(fimdlp CONFIG REQUIRED)
+find_package(nlohmann_json CONFIG REQUIRED)
+find_package(folding CONFIG REQUIRED)
 
-add_library(bayesnet ${Sources})
-target_link_libraries(bayesnet fimdlp::fimdlp folding::folding "${TORCH_LIBRARIES}")
+# Subdirectories
+# --------------
+add_subdirectory(config)
+add_subdirectory(bayesnet)
 
 # Testing
 # -------
-if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-    MESSAGE("Debug mode")
-    set(ENABLE_TESTING ON)
-    set(CODE_COVERAGE ON)
-endif (CMAKE_BUILD_TYPE STREQUAL "Debug")
 if (ENABLE_TESTING)
-    MESSAGE(STATUS "Testing enabled")
-    find_package(Catch2 CONFIG REQUIRED)
-    find_package(arff-files CONFIG REQUIRED)
-    enable_testing()
-    include(CTest)
-    add_subdirectory(tests)
-else(ENABLE_TESTING)
-    message("Release mode")
+MESSAGE(STATUS "Testing enabled")
+  find_package(Catch2 CONFIG REQUIRED)
+  include(CTest)
+  add_subdirectory(tests)
 endif (ENABLE_TESTING)
 
 # Installation
 # ------------
-include(CMakePackageConfigHelpers)
-write_basic_package_version_file(
-    "${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfigVersion.cmake"
-    VERSION ${PROJECT_VERSION}
-    COMPATIBILITY AnyNewerVersion
-)
-
-configure_package_config_file(
-    ${CMAKE_CURRENT_SOURCE_DIR}/bayesnetConfig.cmake.in
-    "${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfig.cmake"
-    INSTALL_DESTINATION share/bayesnet)
-
-install(TARGETS bayesnet
-        EXPORT bayesnetTargets
+install(TARGETS BayesNet
         ARCHIVE DESTINATION lib
         LIBRARY DESTINATION lib
         CONFIGURATIONS Release)
+install(DIRECTORY bayesnet/ DESTINATION include/bayesnet FILES_MATCHING CONFIGURATIONS Release PATTERN "*.h")
+install(FILES ${CMAKE_BINARY_DIR}/configured_files/include/bayesnet/config.h DESTINATION include/bayesnet CONFIGURATIONS Release)
 
-install(DIRECTORY bayesnet/ 
-    DESTINATION include/bayesnet 
-    FILES_MATCHING 
-    CONFIGURATIONS Release 
-    PATTERN "*.h")
-install(FILES ${CMAKE_BINARY_DIR}/configured_files/include/bayesnet/config.h 
-    DESTINATION include/bayesnet 
-    CONFIGURATIONS Release)
-
-install(EXPORT bayesnetTargets
-        FILE bayesnetTargets.cmake
-        NAMESPACE bayesnet::
-        DESTINATION share/bayesnet)
-
-install(FILES
-    "${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfig.cmake"
-    "${CMAKE_CURRENT_BINARY_DIR}/bayesnetConfigVersion.cmake"
-    DESTINATION share/bayesnet
-)
+# Documentation
+# -------------
+find_package(Doxygen)
+if (Doxygen_FOUND)
+  set(DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
+  set(doxyfile_in ${DOC_DIR}/Doxyfile.in)
+  set(doxyfile ${DOC_DIR}/Doxyfile)
+  configure_file(${doxyfile_in} ${doxyfile} @ONLY)
+  doxygen_add_docs(doxygen
+      WORKING_DIRECTORY ${DOC_DIR}
+    CONFIG_FILE ${doxyfile})
+else (Doxygen_FOUND) 
+  MESSAGE("* Doxygen not found")
+endif (Doxygen_FOUND)

Makefile

@@ -5,7 +5,7 @@ SHELL := /bin/bash
 f_release = build_Release
 f_debug = build_Debug
 f_diagrams = diagrams
-app_targets = bayesnet
+app_targets = BayesNet
 test_targets = TestBayesNet
 clang-uml = clang-uml
 plantuml = plantuml
@@ -86,13 +86,10 @@ init: ## Initialize the project installing dependencies
 
 clean: ## Clean the project
 	@echo ">>> Cleaning the project..."
+	@if test -d build_Debug ; then echo "- Deleting build_Debug folder" ; rm -rf build_Debug; fi
+	@if test -d build_Release ; then echo "- Deleting build_Release folder" ; rm -rf build_Release; fi
 	@if test -f CMakeCache.txt ; then echo "- Deleting CMakeCache.txt"; rm -f CMakeCache.txt; fi
-	@for folder in $(f_release) $(f_debug) vpcpkg_installed install_test ; do \
-	if test -d "$$folder" ; then \
-		echo "- Deleting $$folder folder" ; \
-		rm -rf "$$folder"; \
-	fi; \
-	done
+	@if test -d vcpkg_installed ; then echo "- Deleting vcpkg_installed folder" ; rm -rf vcpkg_installed; fi
 	@$(MAKE) clean-test
 	@echo ">>> Done";
 

bayesnet/feature_selection/FeatureSelect.cc

@@ -1,84 +1,141 @@
-// ***************************************************************
+// **
 // SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
 // SPDX-FileType: SOURCE
 // SPDX-License-Identifier: MIT
-// ***************************************************************
+// **
 
-#include <limits>
 #include "bayesnet/utils/bayesnetUtils.h"
 #include "FeatureSelect.h"
-namespace bayesnet {
-    FeatureSelect::FeatureSelect(const torch::Tensor& samples, const std::vector<std::string>& features, const std::string& className, const int maxFeatures, const int classNumStates, const torch::Tensor& weights) :
-        Metrics(samples, features, className, classNumStates), maxFeatures(maxFeatures == 0 ? samples.size(0) - 1 : maxFeatures), weights(weights)
 
+namespace bayesnet {
+
+    using namespace torch::indexing;          // for Ellipsis constant
+
+    //---------------------------------------------------------------------
+    // ctor
+    //---------------------------------------------------------------------
+    FeatureSelect::FeatureSelect(const torch::Tensor& samples,
+        const std::vector<std::string>& features,
+        const std::string& className,
+        int maxFeatures,
+        int classNumStates,
+        const torch::Tensor& weights)
+        : Metrics(samples, features, className, classNumStates),
+        maxFeatures(maxFeatures == 0 ? samples.size(0) - 1 : maxFeatures),
+        weights(weights)
     {
     }
+
+    //---------------------------------------------------------------------
+    // public helpers
+    //---------------------------------------------------------------------
     void FeatureSelect::initialize()
     {
         selectedFeatures.clear();
         selectedScores.clear();
+        suLabels.clear();
+        suFeatures.clear();
+
+        fitted = false;
     }
+
+    //---------------------------------------------------------------------
+    // Symmetrical Uncertainty (SU)
+    //---------------------------------------------------------------------
     double FeatureSelect::symmetricalUncertainty(int a, int b)
     {
         /*
-        Compute symmetrical uncertainty. Normalize* information gain (mutual
-        information) with the entropies of the features in order to compensate
-        the bias due to high cardinality features. *Range [0, 1]
-        (https://www.sciencedirect.com/science/article/pii/S0020025519303603)
-        */
-        auto x = samples.index({ a, "..." });
-        auto y = samples.index({ b, "..." });
-        auto mu = mutualInformation(x, y, weights);
-        auto hx = entropy(x, weights);
-        auto hy = entropy(y, weights);
-        return 2.0 * mu / (hx + hy);
+         * Compute symmetrical uncertainty. Normalises the information gain
+         * (mutual information) with the entropies of the variables to compensate
+         * the bias due to high‑cardinality features. Range: [0, 1]
+         * See: https://www.sciencedirect.com/science/article/pii/S0020025519303603
+         */
+
+        auto x = samples.index({ a, Ellipsis });             // row a => feature a
+        auto y = (b >= 0) ? samples.index({ b, Ellipsis })    // row b (>=0) => feature b
+            : samples.index({ -1, Ellipsis }); // ‑1 treated as last row = labels
+
+        double mu = mutualInformation(x, y, weights);
+        double hx = entropy(x, weights);
+        double hy = entropy(y, weights);
+
+        const double denom = hx + hy;
+        if (denom == 0.0) return 0.0;   // perfectly pure variables
+
+        return 2.0 * mu / denom;
     }
+
+    //---------------------------------------------------------------------
+    // SU feature–class
+    //---------------------------------------------------------------------
     void FeatureSelect::computeSuLabels()
     {
-        // Compute Simmetrical Uncertainty between features and labels
+        // Compute Symmetrical Uncertainty between each feature and the class labels
         // https://en.wikipedia.org/wiki/Symmetric_uncertainty
-        for (int i = 0; i < features.size(); ++i) {
-            suLabels.push_back(symmetricalUncertainty(i, -1));
+        const int classIdx = static_cast<int>(samples.size(0)) - 1; // labels in last row
+        suLabels.reserve(features.size());
+        for (int i = 0; i < static_cast<int>(features.size()); ++i) {
+            suLabels.emplace_back(symmetricalUncertainty(i, classIdx));
         }
     }
-    double FeatureSelect::computeSuFeatures(const int firstFeature, const int secondFeature)
+
+    //---------------------------------------------------------------------
+    // SU feature–feature with cache
+    //---------------------------------------------------------------------
+    double FeatureSelect::computeSuFeatures(int firstFeature, int secondFeature)
     {
-        // Compute Simmetrical Uncertainty between features
-        // https://en.wikipedia.org/wiki/Symmetric_uncertainty
-        try {
-            return suFeatures.at({ firstFeature, secondFeature });
-        }
-        catch (const std::out_of_range& e) {
-            double result = symmetricalUncertainty(firstFeature, secondFeature);
-            suFeatures[{firstFeature, secondFeature}] = result;
-            return result;
-        }
+        // Order the pair to exploit symmetry => only one entry in the map
+        auto ordered = std::minmax(firstFeature, secondFeature);
+        const std::pair<int, int> key{ ordered.first, ordered.second };
+
+        auto it = suFeatures.find(key);
+        if (it != suFeatures.end()) return it->second;
+
+        double result = symmetricalUncertainty(key.first, key.second);
+        suFeatures[key] = result;  // store once (symmetry handled by ordering)
+        return result;
     }
+
+    //---------------------------------------------------------------------
+    // Correlation‑based Feature Selection (CFS) merit
+    //---------------------------------------------------------------------
     double FeatureSelect::computeMeritCFS()
     {
-        double rcf = 0;
-        for (auto feature : selectedFeatures) {
-            rcf += suLabels[feature];
-        }
-        double rff = 0;
-        int n = selectedFeatures.size();
-        for (const auto& item : doCombinations(selectedFeatures)) {
-            rff += computeSuFeatures(item.first, item.second);
-        }
-        return rcf / sqrt(n + (n * n - n) * rff);
+        const int n = static_cast<int>(selectedFeatures.size());
+        if (n == 0) return 0.0;
+
+        // average r_cf (feature–class)
+        double rcf_sum = 0.0;
+        for (int f : selectedFeatures) rcf_sum += suLabels[f];
+        const double rcf_avg = rcf_sum / n;
+
+        // average r_ff (feature–feature)
+        double rff_sum = 0.0;
+        const auto& pairs = doCombinations(selectedFeatures); // generates each unordered pair once
+        for (const auto& p : pairs) rff_sum += computeSuFeatures(p.first, p.second);
+
+        const double numPairs = n * (n - 1) * 0.5;
+        const double rff_avg = (numPairs > 0) ? rff_sum / numPairs : 0.0;
+
+        // Merit_S = k * r_cf / sqrt( k + k*(k‑1) * r_ff )      (Hall, 1999)
+        const double k = static_cast<double>(n);
+        return (k * rcf_avg) / std::sqrt(k + k * (k - 1) * rff_avg);
     }
+
+    //---------------------------------------------------------------------
+    // getters
+    //---------------------------------------------------------------------
     std::vector<int> FeatureSelect::getFeatures() const
     {
-        if (!fitted) {
-            throw std::runtime_error("FeatureSelect not fitted");
-        }
+        if (!fitted) throw std::runtime_error("FeatureSelect not fitted");
         return selectedFeatures;
     }
+
     std::vector<double> FeatureSelect::getScores() const
     {
-        if (!fitted) {
-            throw std::runtime_error("FeatureSelect not fitted");
-        }
+        if (!fitted) throw std::runtime_error("FeatureSelect not fitted");
         return selectedScores;
     }
-}
+
+} // namespace bayesnet
+ 

bayesnetConfig.cmake.in

@@ -1,4 +0,0 @@
-@PACKAGE_INIT@
-
-include("${CMAKE_CURRENT_LIST_DIR}/bayesnetTargets.cmake")
-

config/config.h.in

@@ -11,4 +11,4 @@ static constexpr std::string_view project_name = "@PROJECT_NAME@";
 static constexpr std::string_view project_version = "@PROJECT_VERSION@";
 static constexpr std::string_view project_description = "@PROJECT_DESCRIPTION@";
 static constexpr std::string_view git_sha = "@GIT_SHA@";
-static constexpr std::string_view data_path = "@bayesnet_SOURCE_DIR@/tests/data/";
+static constexpr std::string_view data_path = "@BayesNet_SOURCE_DIR@/tests/data/";

sample/CMakeLists.txt

@@ -1,16 +1,15 @@
 cmake_minimum_required(VERSION 3.20)
 
-project(bayesnet_sample VERSION 0.1.0 LANGUAGES CXX)
+project(bayesnet_sample)
 
 set(CMAKE_CXX_STANDARD 17)
 
-set(CMAKE_BUILD_TYPE Release)
-
 find_package(Torch CONFIG REQUIRED)
+find_package(bayesnet CONFIG REQUIRED)
 find_package(fimdlp CONFIG REQUIRED)
 find_package(folding CONFIG REQUIRED)
 find_package(arff-files CONFIG REQUIRED)
-find_package(bayesnet CONFIG REQUIRED)
+find_package(nlohman_json CONFIG REQUIRED)
 
 add_executable(bayesnet_sample sample.cc) 
 target_link_libraries(bayesnet_sample PRIVATE 
@@ -18,5 +17,6 @@ target_link_libraries(bayesnet_sample PRIVATE
     arff-files::arff-files 
     "${TORCH_LIBRARIES}" 
     bayesnet::bayesnet 
+    nlohmann_json::nlohmann_json
     folding::folding
 )

sample/vcpkg-configuration.json

@@ -1,21 +1,21 @@
 {
-    "default-registry": {
-        "kind": "git",
-        "baseline": "760bfd0c8d7c89ec640aec4df89418b7c2745605",
-        "repository": "https://github.com/microsoft/vcpkg"
-    },
     "registries": [
         {
             "kind": "git",
             "repository": "https://github.com/rmontanana/vcpkg-stash",
-            "baseline": "1ea69243c0e8b0de77c9d1dd6e1d7593ae7f3627",
+            "baseline": "393efa4e74e053b6f02c4ab03738c8fe796b28e5",
             "packages": [
-                "arff-files",
-                "bayesnet",
-                "fimdlp",
                 "folding",
+                "bayesnet",
+                "arff-files",
+                "fimdlp",
                 "libtorch-bin"
             ]
         }
-    ]
+    ],
+    "default-registry": {
+        "kind": "git",
+        "repository": "https://github.com/microsoft/vcpkg",
+        "baseline": "760bfd0c8d7c89ec640aec4df89418b7c2745605"
+    }
 }

sample/vcpkg.json

@@ -2,32 +2,11 @@
     "name": "sample-project",
     "version-string": "0.1.0",
     "dependencies": [
+        "bayesnet",
+        "folding",
         "arff-files",
         "fimdlp",
-        "libtorch-bin",
-        "folding",
-        "bayesnet"
-    ],
-    "overrides": [
-        {
-            "name": "arff-files",
-            "version": "1.1.0"
-        },
-        {
-            "name": "fimdlp",
-            "version": "2.0.1"
-        },
-        {
-            "name": "libtorch-bin",
-            "version": "2.7.0"
-        },
-        {
-            "name": "bayesnet",
-            "version": "1.1.1"
-        },
-        {
-            "name": "folding",
-            "version": "1.1.1"
-        }
+        "nlohmann-json",
+        "libtorch-bin"
     ]
 }

tests/CMakeLists.txt

@@ -1,13 +1,18 @@
 if(ENABLE_TESTING)
     include_directories(
+        ${BayesNet_SOURCE_DIR}/tests/lib/Files
+        ${BayesNet_SOURCE_DIR}/lib/folding
+        ${BayesNet_SOURCE_DIR}/lib/mdlp/src
+        ${BayesNet_SOURCE_DIR}/lib/log
+        ${BayesNet_SOURCE_DIR}/lib/json/include
         ${BayesNet_SOURCE_DIR}
         ${CMAKE_BINARY_DIR}/configured_files/include
     )
-    file(GLOB_RECURSE BayesNet_SOURCES "${bayesnet_SOURCE_DIR}/bayesnet/*.cc")
+    file(GLOB_RECURSE BayesNet_SOURCES "${BayesNet_SOURCE_DIR}/bayesnet/*.cc")
     add_executable(TestBayesNet TestBayesNetwork.cc TestBayesNode.cc TestBayesClassifier.cc TestXSPnDE.cc TestXBA2DE.cc 
         TestBayesModels.cc TestBayesMetrics.cc TestFeatureSelection.cc TestBoostAODE.cc TestXBAODE.cc TestA2DE.cc 
         TestUtils.cc TestBayesEnsemble.cc TestModulesVersions.cc TestBoostA2DE.cc TestMST.cc TestXSPODE.cc ${BayesNet_SOURCES})
-    target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" fimdlp::fimdlp PRIVATE Catch2::Catch2WithMain)
+    target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" fimdlp PRIVATE Catch2::Catch2WithMain)
     add_test(NAME BayesNetworkTest COMMAND TestBayesNet)
     add_test(NAME A2DE COMMAND TestBayesNet "[A2DE]")
     add_test(NAME BoostA2DE COMMAND TestBayesNet "[BoostA2DE]")

tests/TestBayesModels.cc

@@ -20,7 +20,7 @@
 #include "bayesnet/ensembles/AODELd.h"
 #include "bayesnet/ensembles/BoostAODE.h"
 
-const std::string ACTUAL_VERSION = "1.1.1";
+const std::string ACTUAL_VERSION = "1.1.0";
 
 TEST_CASE("Test Bayesian Classifiers score & version", "[Models]")
 {

vcpkg-configuration.json

@@ -8,7 +8,7 @@
     {
       "kind": "git",
       "repository": "https://github.com/rmontanana/vcpkg-stash",
-      "baseline": "1ea69243c0e8b0de77c9d1dd6e1d7593ae7f3627",
+      "baseline": "393efa4e74e053b6f02c4ab03738c8fe796b28e5",
       "packages": [
         "arff-files",
         "fimdlp",