Compare commits
1 Commits
| Author | SHA1 | Date | |
|---|---|---|---|
baa631dd66
|
@ -1,4 +1,4 @@
|
||||
compilation_database_dir: build_Debug
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compilation_database_dir: build_debug
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output_directory: diagrams
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diagrams:
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BayesNet:
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@ -1,6 +1,6 @@
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FROM mcr.microsoft.com/devcontainers/cpp:ubuntu22.04
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ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.29.3"
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ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="3.22.2"
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# Optionally install the cmake for vcpkg
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COPY ./reinstall-cmake.sh /tmp/
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@ -23,7 +23,7 @@ RUN add-apt-repository ppa:ubuntu-toolchain-r/test
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RUN apt-get update
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# Install GCC 13.1
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RUN apt-get install -y gcc-13 g++-13 doxygen
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RUN apt-get install -y gcc-13 g++-13
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|
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# Install lcov 2.1
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RUN wget --quiet https://github.com/linux-test-project/lcov/releases/download/v2.1/lcov-2.1.tar.gz && \
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8
.gitmodules
vendored
8
.gitmodules
vendored
@ -1,3 +1,8 @@
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[submodule "lib/mdlp"]
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path = lib/mdlp
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url = https://github.com/rmontanana/mdlp
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main = main
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update = merge
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[submodule "lib/json"]
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path = lib/json
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url = https://github.com/nlohmann/json.git
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@ -16,6 +21,3 @@
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[submodule "tests/lib/Files"]
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path = tests/lib/Files
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url = https://github.com/rmontanana/ArffFiles
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[submodule "lib/mdlp"]
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path = lib/mdlp
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url = https://github.com/rmontanana/mdlp
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|
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2
.vscode/launch.json
vendored
2
.vscode/launch.json
vendored
@ -16,7 +16,7 @@
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"name": "test",
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"program": "${workspaceFolder}/build_Debug/tests/TestBayesNet",
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"args": [
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"No features selected"
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"[Network]"
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],
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"cwd": "${workspaceFolder}/build_Debug/tests"
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},
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24
CHANGELOG.md
24
CHANGELOG.md
@ -7,15 +7,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [Unreleased]
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## [1.0.6] 2024-11-23
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### Fixed
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- Prevent existing edges to be added to the network in the `add_edge` method.
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- Don't allow to add nodes or edges on already fiited networks.
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- Number of threads spawned
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- Network class tests
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|
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### Added
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- Library logo generated with <https://openart.ai> to README.md
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@ -23,21 +14,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- *convergence_best* hyperparameter to the BoostAODE class, to control the way the prior accuracy is computed if convergence is set. Default value is *false*.
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- SPnDE model.
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- A2DE model.
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- BoostA2DE model.
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- A2DE & SPnDE tests.
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- Add tests to reach 99% of coverage.
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- Add tests to check the correct version of the mdlp, folding and json libraries.
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- Library documentation generated with Doxygen.
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- Link to documentation in the README.md.
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- Three types of smoothing the Bayesian Network ORIGINAL, LAPLACE and CESTNIK.
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- Three types of smoothing the Bayesian Network OLD_LAPLACE, LAPLACE and CESTNIK.
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|
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### Internal
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|
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- Fixed doxygen optional dependency
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- Add env parallel variable to Makefile
|
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- Add CountingSemaphore class to manage the number of threads spawned.
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- Ignore CUDA language in CMake CodeCoverage module.
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- Update mdlp library as a git submodule.
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- Create library ShuffleArffFile to limit the number of samples with a parameter and shuffle them.
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- Refactor catch2 library location to test/lib
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- Refactor loadDataset function in tests.
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@ -48,13 +33,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Add a Makefile target (doc) to generate the documentation.
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- Add a Makefile target (doc-install) to install the documentation.
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|
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### Libraries versions
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- mdlp: 2.0.1
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- Folding: 1.1.0
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- json: 3.11
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- ArffFiles: 1.1.0
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## [1.0.5] 2024-04-20
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### Added
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@ -49,13 +49,17 @@ if (CMAKE_BUILD_TYPE STREQUAL "Debug")
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set(CODE_COVERAGE ON)
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endif (CMAKE_BUILD_TYPE STREQUAL "Debug")
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get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
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message(STATUS "Languages=${LANGUAGES}")
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|
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if (CODE_COVERAGE)
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get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
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message("ALL LANGUAGES: ${LANGUAGES}")
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foreach(LANG ${LANGUAGES})
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message("${LANG} compiler is \"${CMAKE_${LANG}_COMPILER_ID}\"")
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endforeach()
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enable_testing()
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include(CodeCoverage)
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MESSAGE(STATUS "Code coverage enabled")
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SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
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#include(CodeCoverage)
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#MESSAGE("Code coverage enabled")
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#SET(GCC_COVERAGE_LINK_FLAGS " ${GCC_COVERAGE_LINK_FLAGS} -lgcov --coverage")
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endif (CODE_COVERAGE)
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if (ENABLE_CLANG_TIDY)
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@ -64,7 +68,6 @@ endif (ENABLE_CLANG_TIDY)
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# External libraries - dependencies of BayesNet
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# ---------------------------------------------
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# include(FetchContent)
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add_git_submodule("lib/json")
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add_git_submodule("lib/mdlp")
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@ -77,7 +80,7 @@ add_subdirectory(bayesnet)
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# Testing
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# -------
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if (ENABLE_TESTING)
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MESSAGE(STATUS "Testing enabled")
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MESSAGE("Testing enabled")
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add_subdirectory(tests/lib/catch2)
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include(CTest)
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add_subdirectory(tests)
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@ -95,14 +98,10 @@ install(FILES ${CMAKE_BINARY_DIR}/configured_files/include/bayesnet/config.h DES
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# Documentation
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# -------------
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find_package(Doxygen)
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if (Doxygen_FOUND)
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set(DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
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set(doxyfile_in ${DOC_DIR}/Doxyfile.in)
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set(doxyfile ${DOC_DIR}/Doxyfile)
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configure_file(${doxyfile_in} ${doxyfile} @ONLY)
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doxygen_add_docs(doxygen
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WORKING_DIRECTORY ${DOC_DIR}
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set(DOC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/docs)
|
||||
set(doxyfile_in ${DOC_DIR}/Doxyfile.in)
|
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set(doxyfile ${DOC_DIR}/Doxyfile)
|
||||
configure_file(${doxyfile_in} ${doxyfile} @ONLY)
|
||||
doxygen_add_docs(doxygen
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WORKING_DIRECTORY ${DOC_DIR}
|
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CONFIG_FILE ${doxyfile})
|
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else (Doxygen_FOUND)
|
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MESSAGE("* Doxygen not found")
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endif (Doxygen_FOUND)
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|
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10
Makefile
10
Makefile
@ -43,7 +43,7 @@ setup: ## Install dependencies for tests and coverage
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fi
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||||
@echo "* You should install plantuml & graphviz for the diagrams"
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diagrams: ## Create an UML class diagram & dependency of the project (diagrams/BayesNet.png)
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diagrams: ## Create an UML class diagram & depnendency of the project (diagrams/BayesNet.png)
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@which $(plantuml) || (echo ">>> Please install plantuml"; exit 1)
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||||
@which $(dot) || (echo ">>> Please install graphviz"; exit 1)
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||||
@which $(clang-uml) || (echo ">>> Please install clang-uml"; exit 1)
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||||
@ -58,10 +58,10 @@ diagrams: ## Create an UML class diagram & dependency of the project (diagrams/B
|
||||
@$(dot) -Tsvg $(f_debug)/dependency.dot.BayesNet -o $(f_diagrams)/dependency.svg
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|
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buildd: ## Build the debug targets
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cmake --build $(f_debug) -t $(app_targets) --parallel $(CMAKE_BUILD_PARALLEL_LEVEL)
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cmake --build $(f_debug) -t $(app_targets) --parallel
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|
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buildr: ## Build the release targets
|
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cmake --build $(f_release) -t $(app_targets) --parallel $(CMAKE_BUILD_PARALLEL_LEVEL)
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cmake --build $(f_release) -t $(app_targets) --parallel
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clean: ## Clean the tests info
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@echo ">>> Cleaning Debug BayesNet tests...";
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@ -105,7 +105,7 @@ opt = ""
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test: ## Run tests (opt="-s") to verbose output the tests, (opt="-c='Test Maximum Spanning Tree'") to run only that section
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@echo ">>> Running BayesNet tests...";
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@$(MAKE) clean
|
||||
@cmake --build $(f_debug) -t $(test_targets) --parallel $(CMAKE_BUILD_PARALLEL_LEVEL)
|
||||
@cmake --build $(f_debug) -t $(test_targets) --parallel
|
||||
@for t in $(test_targets); do \
|
||||
echo ">>> Running $$t...";\
|
||||
if [ -f $(f_debug)/tests/$$t ]; then \
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@ -172,7 +172,7 @@ docdir = ""
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||||
doc-install: ## Install documentation
|
||||
@echo ">>> Installing documentation..."
|
||||
@if [ "$(docdir)" = "" ]; then \
|
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echo "docdir parameter has to be set when calling doc-install, i.e. docdir=../bayesnet_help"; \
|
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echo "docdir parameter has to be set when calling doc-install"; \
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exit 1; \
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||||
fi
|
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@if [ ! -d $(docdir) ]; then \
|
||||
|
||||
@ -7,10 +7,9 @@
|
||||
[](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
|
||||
[](https://sonarcloud.io/summary/new_code?id=rmontanana_BayesNet)
|
||||
|
||||
[](html/index.html)
|
||||
[](https://doi.org/10.5281/zenodo.14210344)
|
||||
[](html/index.html)
|
||||
|
||||
Bayesian Network Classifiers library
|
||||
Bayesian Network Classifiers using libtorch from scratch
|
||||
|
||||
## Dependencies
|
||||
|
||||
@ -72,8 +71,6 @@ make sample fname=tests/data/glass.arff
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||||
|
||||
#### - AODE
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||||
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||||
#### - A2DE
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||||
|
||||
#### - [BoostAODE](docs/BoostAODE.md)
|
||||
|
||||
#### - BoostA2DE
|
||||
|
||||
@ -9,4 +9,4 @@ include_directories(
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file(GLOB_RECURSE Sources "*.cc")
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||||
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||||
add_library(BayesNet ${Sources})
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||||
target_link_libraries(BayesNet fimdlp "${TORCH_LIBRARIES}")
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||||
target_link_libraries(BayesNet mdlp "${TORCH_LIBRARIES}")
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||||
|
||||
@ -9,7 +9,15 @@
|
||||
#include "Classifier.h"
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||||
|
||||
namespace bayesnet {
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||||
Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false) {}
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Classifier::Classifier(Network model) : model(model), m(0), n(0), metrics(Metrics()), fitted(false), device(torch::kCPU)
|
||||
{
|
||||
if (torch::cuda::is_available()) {
|
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device = torch::Device(torch::kCUDA);
|
||||
std::cout << "CUDA is available! Using GPU." << std::endl;
|
||||
} else {
|
||||
std::cout << "CUDA is not available. Using CPU." << std::endl;
|
||||
}
|
||||
}
|
||||
const std::string CLASSIFIER_NOT_FITTED = "Classifier has not been fitted";
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Classifier& Classifier::build(const std::vector<std::string>& features, const std::string& className, std::map<std::string, std::vector<int>>& states, const torch::Tensor& weights, const Smoothing_t smoothing)
|
||||
{
|
||||
@ -31,7 +39,7 @@ namespace bayesnet {
|
||||
{
|
||||
try {
|
||||
auto yresized = torch::transpose(ytmp.view({ ytmp.size(0), 1 }), 0, 1);
|
||||
dataset = torch::cat({ dataset, yresized }, 0);
|
||||
dataset = torch::cat({ dataset, yresized }, 0).to(device);
|
||||
}
|
||||
catch (const std::exception& e) {
|
||||
std::stringstream oss;
|
||||
@ -50,7 +58,7 @@ namespace bayesnet {
|
||||
{
|
||||
dataset = X;
|
||||
buildDataset(y);
|
||||
const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble);
|
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const torch::Tensor weights = torch::full({ dataset.size(1) }, 1.0 / dataset.size(1), torch::kDouble).to(device);
|
||||
return build(features, className, states, weights, smoothing);
|
||||
}
|
||||
// X is nxm where n is the number of features and m the number of samples
|
||||
|
||||
@ -38,6 +38,7 @@ namespace bayesnet {
|
||||
std::string dump_cpt() const override;
|
||||
void setHyperparameters(const nlohmann::json& hyperparameters) override; //For classifiers that don't have hyperparameters
|
||||
protected:
|
||||
torch::Device device;
|
||||
bool fitted;
|
||||
unsigned int m, n; // m: number of samples, n: number of features
|
||||
Network model;
|
||||
|
||||
@ -20,8 +20,7 @@ namespace bayesnet {
|
||||
// Fills std::vectors Xv & yv with the data from tensors X_ (discretized) & y
|
||||
states = fit_local_discretization(y);
|
||||
// We have discretized the input data
|
||||
// 1st we need to fit the model to build the normal AODE structure, Ensemble::fit
|
||||
// calls buildModel to initialize the base models
|
||||
// 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, smoothing);
|
||||
return *this;
|
||||
|
||||
|
||||
@ -59,9 +59,6 @@ namespace bayesnet {
|
||||
std::vector<int> featuresUsed;
|
||||
if (selectFeatures) {
|
||||
featuresUsed = initializeModels(smoothing);
|
||||
if (featuresUsed.size() == 0) {
|
||||
return;
|
||||
}
|
||||
auto ypred = predict(X_train);
|
||||
std::tie(weights_, alpha_t, finished) = update_weights(y_train, ypred, weights_);
|
||||
// Update significance of the models
|
||||
|
||||
@ -209,7 +209,7 @@ namespace bayesnet {
|
||||
pthread_setname_np(threadName.c_str());
|
||||
#endif
|
||||
double numStates = static_cast<double>(node.second->getNumStates());
|
||||
double smoothing_factor;
|
||||
double smoothing_factor = 0.0;
|
||||
switch (smoothing) {
|
||||
case Smoothing_t::ORIGINAL:
|
||||
smoothing_factor = 1.0 / n_samples;
|
||||
@ -221,7 +221,7 @@ namespace bayesnet {
|
||||
smoothing_factor = 1 / numStates;
|
||||
break;
|
||||
default:
|
||||
smoothing_factor = 0.0; // No smoothing
|
||||
throw std::invalid_argument("Smoothing method not recognized " + std::to_string(static_cast<int>(smoothing)));
|
||||
}
|
||||
node.second->computeCPT(samples, features, smoothing_factor, weights);
|
||||
semaphore.release();
|
||||
@ -234,6 +234,16 @@ namespace bayesnet {
|
||||
for (auto& thread : threads) {
|
||||
thread.join();
|
||||
}
|
||||
// std::fstream file;
|
||||
// file.open("cpt.txt", std::fstream::out | std::fstream::app);
|
||||
// file << std::string(80, '*') << std::endl;
|
||||
// for (const auto& item : graph("Test")) {
|
||||
// file << item << std::endl;
|
||||
// }
|
||||
// file << std::string(80, '-') << std::endl;
|
||||
// file << dump_cpt() << std::endl;
|
||||
// file << std::string(80, '=') << std::endl;
|
||||
// file.close();
|
||||
fitted = true;
|
||||
}
|
||||
torch::Tensor Network::predict_tensor(const torch::Tensor& samples, const bool proba)
|
||||
|
||||
@ -97,7 +97,7 @@ namespace bayesnet {
|
||||
dimensions.push_back(numStates);
|
||||
transform(parents.begin(), parents.end(), back_inserter(dimensions), [](const auto& parent) { return parent->getNumStates(); });
|
||||
// Create a tensor of zeros with the dimensions of the CPT
|
||||
cpTable = torch::zeros(dimensions, torch::kDouble) + smoothing;
|
||||
cpTable = torch::zeros(dimensions, torch::kDouble).to(device) + smoothing;
|
||||
// Fill table with counts
|
||||
auto pos = find(features.begin(), features.end(), name);
|
||||
if (pos == features.end()) {
|
||||
|
||||
@ -53,14 +53,14 @@ namespace bayesnet {
|
||||
}
|
||||
}
|
||||
|
||||
void MST::insertElement(std::list<int>& variables, int variable)
|
||||
void insertElement(std::list<int>& variables, int variable)
|
||||
{
|
||||
if (std::find(variables.begin(), variables.end(), variable) == variables.end()) {
|
||||
variables.push_front(variable);
|
||||
}
|
||||
}
|
||||
|
||||
std::vector<std::pair<int, int>> MST::reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original)
|
||||
std::vector<std::pair<int, int>> reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original)
|
||||
{
|
||||
// Create the edges of a DAG from the MST
|
||||
// replacing unordered_set with list because unordered_set cannot guarantee the order of the elements inserted
|
||||
|
||||
@ -14,8 +14,6 @@ namespace bayesnet {
|
||||
public:
|
||||
MST() = default;
|
||||
MST(const std::vector<std::string>& features, const torch::Tensor& weights, const int root);
|
||||
void insertElement(std::list<int>& variables, int variable);
|
||||
std::vector<std::pair<int, int>> reorder(std::vector<std::pair<float, std::pair<int, int>>> T, int root_original);
|
||||
std::vector<std::pair<int, int>> maximumSpanningTree();
|
||||
private:
|
||||
torch::Tensor weights;
|
||||
|
||||
@ -137,7 +137,7 @@
|
||||
|
||||
include(CMakeParseArguments)
|
||||
|
||||
option(CODE_COVERAGE_VERBOSE "Verbose information" TRUE)
|
||||
option(CODE_COVERAGE_VERBOSE "Verbose information" FALSE)
|
||||
|
||||
# Check prereqs
|
||||
find_program( GCOV_PATH gcov )
|
||||
@ -160,11 +160,7 @@ foreach(LANG ${LANGUAGES})
|
||||
endif()
|
||||
elseif(NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "GNU"
|
||||
AND NOT "${CMAKE_${LANG}_COMPILER_ID}" MATCHES "(LLVM)?[Ff]lang")
|
||||
if ("${LANG}" MATCHES "CUDA")
|
||||
message(STATUS "Ignoring CUDA")
|
||||
else()
|
||||
message(FATAL_ERROR "Compiler is not GNU or Flang! Aborting...")
|
||||
endif()
|
||||
message(FATAL_ERROR "Compiler is not GNU or Flang! Aborting...")
|
||||
endif()
|
||||
endforeach()
|
||||
|
||||
|
||||
@ -1,16 +1,36 @@
|
||||
@startuml
|
||||
title clang-uml class diagram model
|
||||
class "bayesnet::Node" as C_0010428199432536647474
|
||||
class C_0010428199432536647474 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::Metrics" as C_0000736965376885623323
|
||||
class C_0000736965376885623323 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Metrics() = default : void
|
||||
+Metrics(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
|
||||
+Metrics(const std::vector<std::vector<int>> & vsamples, const std::vector<int> & labels, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
|
||||
..
|
||||
+SelectKBestWeighted(const torch::Tensor & weights, bool ascending = false, unsigned int k = 0) : std::vector<int>
|
||||
+conditionalEdge(const torch::Tensor & weights) : torch::Tensor
|
||||
+conditionalEdgeWeights(std::vector<float> & weights) : std::vector<float>
|
||||
#doCombinations<T>(const std::vector<T> & source) : std::vector<std::pair<T, T> >
|
||||
#entropy(const torch::Tensor & feature, const torch::Tensor & weights) : double
|
||||
+getScoresKBest() const : std::vector<double>
|
||||
+maximumSpanningTree(const std::vector<std::string> & features, const torch::Tensor & weights, const int root) : std::vector<std::pair<int,int>>
|
||||
+mutualInformation(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & weights) : double
|
||||
#pop_first<T>(std::vector<T> & v) : T
|
||||
__
|
||||
#className : std::string
|
||||
#features : std::vector<std::string>
|
||||
#samples : torch::Tensor
|
||||
}
|
||||
class "bayesnet::Node" as C_0001303524929067080934
|
||||
class C_0001303524929067080934 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Node(const std::string &) : void
|
||||
..
|
||||
+addChild(Node *) : void
|
||||
+addParent(Node *) : void
|
||||
+clear() : void
|
||||
+computeCPT(const torch::Tensor & dataset, const std::vector<std::string> & features, const double smoothing, const torch::Tensor & weights) : void
|
||||
+computeCPT(const torch::Tensor & dataset, const std::vector<std::string> & features, const double laplaceSmoothing, const torch::Tensor & weights) : void
|
||||
+getCPT() : torch::Tensor &
|
||||
+getChildren() : std::vector<Node *> &
|
||||
+getFactorValue(std::map<std::string,int> &) : double
|
||||
+getFactorValue(std::map<std::string,int> &) : float
|
||||
+getName() const : std::string
|
||||
+getNumStates() const : int
|
||||
+getParents() : std::vector<Node *> &
|
||||
@ -21,29 +41,24 @@ class C_0010428199432536647474 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+setNumStates(int) : void
|
||||
__
|
||||
}
|
||||
enum "bayesnet::Smoothing_t" as C_0013393078277439680282
|
||||
enum C_0013393078277439680282 {
|
||||
NONE
|
||||
ORIGINAL
|
||||
LAPLACE
|
||||
CESTNIK
|
||||
}
|
||||
class "bayesnet::Network" as C_0009493661199123436603
|
||||
class C_0009493661199123436603 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::Network" as C_0001186707649890429575
|
||||
class C_0001186707649890429575 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Network() : void
|
||||
+Network(float) : void
|
||||
+Network(const Network &) : void
|
||||
+~Network() = default : void
|
||||
..
|
||||
+addEdge(const std::string &, const std::string &) : void
|
||||
+addNode(const std::string &) : void
|
||||
+dump_cpt() const : std::string
|
||||
+fit(const torch::Tensor & samples, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
|
||||
+fit(const torch::Tensor & X, const torch::Tensor & y, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
|
||||
+fit(const std::vector<std::vector<int>> & input_data, const std::vector<int> & labels, const std::vector<double> & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : void
|
||||
+fit(const torch::Tensor & samples, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states) : void
|
||||
+fit(const torch::Tensor & X, const torch::Tensor & y, const torch::Tensor & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states) : void
|
||||
+fit(const std::vector<std::vector<int>> & input_data, const std::vector<int> & labels, const std::vector<double> & weights, const std::vector<std::string> & featureNames, const std::string & className, const std::map<std::string,std::vector<int>> & states) : void
|
||||
+getClassName() const : std::string
|
||||
+getClassNumStates() const : int
|
||||
+getEdges() const : std::vector<std::pair<std::string,std::string>>
|
||||
+getFeatures() const : std::vector<std::string>
|
||||
+getMaxThreads() const : float
|
||||
+getNodes() : std::map<std::string,std::unique_ptr<Node>> &
|
||||
+getNumEdges() const : int
|
||||
+getSamples() : torch::Tensor &
|
||||
@ -61,21 +76,21 @@ class C_0009493661199123436603 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+version() : std::string
|
||||
__
|
||||
}
|
||||
enum "bayesnet::status_t" as C_0005907365846270811004
|
||||
enum C_0005907365846270811004 {
|
||||
enum "bayesnet::status_t" as C_0000738420730783851375
|
||||
enum C_0000738420730783851375 {
|
||||
NORMAL
|
||||
WARNING
|
||||
ERROR
|
||||
}
|
||||
abstract "bayesnet::BaseClassifier" as C_0002617087915615796317
|
||||
abstract C_0002617087915615796317 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
abstract "bayesnet::BaseClassifier" as C_0000327135989451974539
|
||||
abstract C_0000327135989451974539 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+~BaseClassifier() = default : void
|
||||
..
|
||||
{abstract} +dump_cpt() const = 0 : std::string
|
||||
{abstract} +fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
|
||||
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
|
||||
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights, const Smoothing_t smoothing) = 0 : BaseClassifier &
|
||||
{abstract} +fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) = 0 : BaseClassifier &
|
||||
{abstract} +fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) = 0 : BaseClassifier &
|
||||
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) = 0 : BaseClassifier &
|
||||
{abstract} +fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights) = 0 : BaseClassifier &
|
||||
{abstract} +fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) = 0 : BaseClassifier &
|
||||
{abstract} +getClassNumStates() const = 0 : int
|
||||
{abstract} +getNotes() const = 0 : std::vector<std::string>
|
||||
{abstract} +getNumberOfEdges() const = 0 : int
|
||||
@ -94,35 +109,12 @@ abstract C_0002617087915615796317 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
{abstract} +setHyperparameters(const nlohmann::json & hyperparameters) = 0 : void
|
||||
{abstract} +show() const = 0 : std::vector<std::string>
|
||||
{abstract} +topological_order() = 0 : std::vector<std::string>
|
||||
{abstract} #trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) = 0 : void
|
||||
{abstract} #trainModel(const torch::Tensor & weights) = 0 : void
|
||||
__
|
||||
#validHyperparameters : std::vector<std::string>
|
||||
}
|
||||
class "bayesnet::Metrics" as C_0005895723015084986588
|
||||
class C_0005895723015084986588 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Metrics() = default : void
|
||||
+Metrics(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
|
||||
+Metrics(const std::vector<std::vector<int>> & vsamples, const std::vector<int> & labels, const std::vector<std::string> & features, const std::string & className, const int classNumStates) : void
|
||||
..
|
||||
+SelectKBestWeighted(const torch::Tensor & weights, bool ascending = false, unsigned int k = 0) : std::vector<int>
|
||||
+SelectKPairs(const torch::Tensor & weights, std::vector<int> & featuresExcluded, bool ascending = false, unsigned int k = 0) : std::vector<std::pair<int,int>>
|
||||
+conditionalEdge(const torch::Tensor & weights) : torch::Tensor
|
||||
+conditionalEntropy(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & labels, const torch::Tensor & weights) : double
|
||||
+conditionalMutualInformation(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & labels, const torch::Tensor & weights) : double
|
||||
#doCombinations<T>(const std::vector<T> & source) : std::vector<std::pair<T, T> >
|
||||
+entropy(const torch::Tensor & feature, const torch::Tensor & weights) : double
|
||||
+getScoresKBest() const : std::vector<double>
|
||||
+getScoresKPairs() const : std::vector<std::pair<std::pair<int,int>,double>>
|
||||
+maximumSpanningTree(const std::vector<std::string> & features, const torch::Tensor & weights, const int root) : std::vector<std::pair<int,int>>
|
||||
+mutualInformation(const torch::Tensor & firstFeature, const torch::Tensor & secondFeature, const torch::Tensor & weights) : double
|
||||
#pop_first<T>(std::vector<T> & v) : T
|
||||
__
|
||||
#className : std::string
|
||||
#features : std::vector<std::string>
|
||||
#samples : torch::Tensor
|
||||
}
|
||||
abstract "bayesnet::Classifier" as C_0016351972983202413152
|
||||
abstract C_0016351972983202413152 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
abstract "bayesnet::Classifier" as C_0002043996622900301644
|
||||
abstract C_0002043996622900301644 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Classifier(Network model) : void
|
||||
+~Classifier() = default : void
|
||||
..
|
||||
@ -131,10 +123,10 @@ abstract C_0016351972983202413152 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
{abstract} #buildModel(const torch::Tensor & weights) = 0 : void
|
||||
#checkFitParameters() : void
|
||||
+dump_cpt() const : std::string
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
|
||||
+fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : Classifier &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights, const Smoothing_t smoothing) : Classifier &
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : Classifier &
|
||||
+fit(std::vector<std::vector<int>> & X, std::vector<int> & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : Classifier &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : Classifier &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const torch::Tensor & weights) : Classifier &
|
||||
+getClassNumStates() const : int
|
||||
+getNotes() const : std::vector<std::string>
|
||||
+getNumberOfEdges() const : int
|
||||
@ -151,7 +143,7 @@ abstract C_0016351972983202413152 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters) : void
|
||||
+show() const : std::vector<std::string>
|
||||
+topological_order() : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
|
||||
#trainModel(const torch::Tensor & weights) : void
|
||||
__
|
||||
#className : std::string
|
||||
#dataset : torch::Tensor
|
||||
@ -165,8 +157,8 @@ __
|
||||
#states : std::map<std::string,std::vector<int>>
|
||||
#status : status_t
|
||||
}
|
||||
class "bayesnet::KDB" as C_0008902920152122000044
|
||||
class C_0008902920152122000044 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::KDB" as C_0001112865019015250005
|
||||
class C_0001112865019015250005 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+KDB(int k, float theta = 0.03) : void
|
||||
+~KDB() = default : void
|
||||
..
|
||||
@ -175,26 +167,8 @@ class C_0008902920152122000044 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::SPODE" as C_0004096182510460307610
|
||||
class C_0004096182510460307610 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+SPODE(int root) : void
|
||||
+~SPODE() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & name = "SPODE") const : std::vector<std::string>
|
||||
__
|
||||
}
|
||||
class "bayesnet::SPnDE" as C_0016268916386101512883
|
||||
class C_0016268916386101512883 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+SPnDE(std::vector<int> parents) : void
|
||||
+~SPnDE() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & name = "SPnDE") const : std::vector<std::string>
|
||||
__
|
||||
}
|
||||
class "bayesnet::TAN" as C_0014087955399074584137
|
||||
class C_0014087955399074584137 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::TAN" as C_0001760994424884323017
|
||||
class C_0001760994424884323017 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+TAN() : void
|
||||
+~TAN() = default : void
|
||||
..
|
||||
@ -202,8 +176,8 @@ class C_0014087955399074584137 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+graph(const std::string & name = "TAN") const : std::vector<std::string>
|
||||
__
|
||||
}
|
||||
class "bayesnet::Proposal" as C_0017759964713298103839
|
||||
class C_0017759964713298103839 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::Proposal" as C_0002219995589162262979
|
||||
class C_0002219995589162262979 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Proposal(torch::Tensor & pDataset, std::vector<std::string> & features_, std::string & className_) : void
|
||||
+~Proposal() : void
|
||||
..
|
||||
@ -216,42 +190,74 @@ __
|
||||
#discretizers : map<std::string,mdlp::CPPFImdlp *>
|
||||
#y : torch::Tensor
|
||||
}
|
||||
class "bayesnet::KDBLd" as C_0002756018222998454702
|
||||
class C_0002756018222998454702 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+KDBLd(int k) : void
|
||||
+~KDBLd() = default : void
|
||||
..
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : KDBLd &
|
||||
+graph(const std::string & name = "KDB") const : std::vector<std::string>
|
||||
+predict(torch::Tensor & X) : torch::Tensor
|
||||
{static} +version() : std::string
|
||||
__
|
||||
}
|
||||
class "bayesnet::SPODELd" as C_0010957245114062042836
|
||||
class C_0010957245114062042836 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+SPODELd(int root) : void
|
||||
+~SPODELd() = default : void
|
||||
..
|
||||
+commonFit(const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : SPODELd &
|
||||
+graph(const std::string & name = "SPODELd") const : std::vector<std::string>
|
||||
+predict(torch::Tensor & X) : torch::Tensor
|
||||
{static} +version() : std::string
|
||||
__
|
||||
}
|
||||
class "bayesnet::TANLd" as C_0013350632773616302678
|
||||
class C_0013350632773616302678 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::TANLd" as C_0001668829096702037834
|
||||
class C_0001668829096702037834 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+TANLd() : void
|
||||
+~TANLd() = default : void
|
||||
..
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states, const Smoothing_t smoothing) : TANLd &
|
||||
+graph(const std::string & name = "TANLd") const : std::vector<std::string>
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : TANLd &
|
||||
+graph(const std::string & name = "TAN") const : std::vector<std::string>
|
||||
+predict(torch::Tensor & X) : torch::Tensor
|
||||
{static} +version() : std::string
|
||||
__
|
||||
}
|
||||
class "bayesnet::Ensemble" as C_0015881931090842884611
|
||||
class C_0015881931090842884611 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
abstract "bayesnet::FeatureSelect" as C_0001695326193250580823
|
||||
abstract C_0001695326193250580823 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+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) : void
|
||||
+~FeatureSelect() : void
|
||||
..
|
||||
#computeMeritCFS() : double
|
||||
#computeSuFeatures(const int a, const int b) : double
|
||||
#computeSuLabels() : void
|
||||
{abstract} +fit() = 0 : void
|
||||
+getFeatures() const : std::vector<int>
|
||||
+getScores() const : std::vector<double>
|
||||
#initialize() : void
|
||||
#symmetricalUncertainty(int a, int b) : double
|
||||
__
|
||||
#fitted : bool
|
||||
#maxFeatures : int
|
||||
#selectedFeatures : std::vector<int>
|
||||
#selectedScores : std::vector<double>
|
||||
#suFeatures : std::map<std::pair<int,int>,double>
|
||||
#suLabels : std::vector<double>
|
||||
#weights : const torch::Tensor &
|
||||
}
|
||||
class "bayesnet::CFS" as C_0000011627355691342494
|
||||
class C_0000011627355691342494 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+CFS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights) : void
|
||||
+~CFS() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::FCBF" as C_0000144682015341746929
|
||||
class C_0000144682015341746929 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+FCBF(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
|
||||
+~FCBF() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::IWSS" as C_0000008268514674428553
|
||||
class C_0000008268514674428553 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+IWSS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
|
||||
+~IWSS() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::SPODE" as C_0000512022813807538451
|
||||
class C_0000512022813807538451 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+SPODE(int root) : void
|
||||
+~SPODE() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & name = "SPODE") const : std::vector<std::string>
|
||||
__
|
||||
}
|
||||
class "bayesnet::Ensemble" as C_0001985241386355360576
|
||||
class C_0001985241386355360576 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Ensemble(bool predict_voting = true) : void
|
||||
+~Ensemble() = default : void
|
||||
..
|
||||
@ -274,7 +280,7 @@ class C_0015881931090842884611 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+score(torch::Tensor & X, torch::Tensor & y) : float
|
||||
+show() const : std::vector<std::string>
|
||||
+topological_order() : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
|
||||
#trainModel(const torch::Tensor & weights) : void
|
||||
#voting(torch::Tensor & votes) : torch::Tensor
|
||||
__
|
||||
#models : std::vector<std::unique_ptr<Classifier>>
|
||||
@ -282,223 +288,41 @@ __
|
||||
#predict_voting : bool
|
||||
#significanceModels : std::vector<double>
|
||||
}
|
||||
class "bayesnet::A2DE" as C_0001410789567057647859
|
||||
class C_0001410789567057647859 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+A2DE(bool predict_voting = false) : void
|
||||
+~A2DE() : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & title = "A2DE") const : std::vector<std::string>
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::AODE" as C_0006288892608974306258
|
||||
class C_0006288892608974306258 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+AODE(bool predict_voting = false) : void
|
||||
+~AODE() : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & title = "AODE") const : std::vector<std::string>
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters) : void
|
||||
__
|
||||
}
|
||||
abstract "bayesnet::FeatureSelect" as C_0013562609546004646591
|
||||
abstract C_0013562609546004646591 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+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) : void
|
||||
+~FeatureSelect() : void
|
||||
..
|
||||
#computeMeritCFS() : double
|
||||
#computeSuFeatures(const int a, const int b) : double
|
||||
#computeSuLabels() : void
|
||||
{abstract} +fit() = 0 : void
|
||||
+getFeatures() const : std::vector<int>
|
||||
+getScores() const : std::vector<double>
|
||||
#initialize() : void
|
||||
#symmetricalUncertainty(int a, int b) : double
|
||||
__
|
||||
#fitted : bool
|
||||
#maxFeatures : int
|
||||
#selectedFeatures : std::vector<int>
|
||||
#selectedScores : std::vector<double>
|
||||
#suFeatures : std::map<std::pair<int,int>,double>
|
||||
#suLabels : std::vector<double>
|
||||
#weights : const torch::Tensor &
|
||||
}
|
||||
class "bayesnet::(anonymous_60342586)" as C_0005584545181746538542
|
||||
class C_0005584545181746538542 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::(anonymous_45089536)" as C_0001186398587753535158
|
||||
class C_0001186398587753535158 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60343240)" as C_0016227156982041949444
|
||||
class C_0016227156982041949444 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::(anonymous_45090163)" as C_0000602764946063116717
|
||||
class C_0000602764946063116717 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::Boost" as C_0009819322948617116148
|
||||
class C_0009819322948617116148 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Boost(bool predict_voting = false) : void
|
||||
+~Boost() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
#featureSelection(torch::Tensor & weights_) : std::vector<int>
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
|
||||
#update_weights(torch::Tensor & ytrain, torch::Tensor & ypred, torch::Tensor & weights) : std::tuple<torch::Tensor &,double,bool>
|
||||
#update_weights_block(int k, torch::Tensor & ytrain, torch::Tensor & weights) : std::tuple<torch::Tensor &,double,bool>
|
||||
__
|
||||
#X_test : torch::Tensor
|
||||
#X_train : torch::Tensor
|
||||
#bisection : bool
|
||||
#block_update : bool
|
||||
#convergence : bool
|
||||
#convergence_best : bool
|
||||
#featureSelector : FeatureSelect *
|
||||
#maxTolerance : int
|
||||
#order_algorithm : std::string
|
||||
#selectFeatures : bool
|
||||
#select_features_algorithm : std::string
|
||||
#threshold : double
|
||||
#y_test : torch::Tensor
|
||||
#y_train : torch::Tensor
|
||||
}
|
||||
class "bayesnet::AODELd" as C_0003898187834670349177
|
||||
class C_0003898187834670349177 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+AODELd(bool predict_voting = true) : void
|
||||
+~AODELd() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+fit(torch::Tensor & X_, torch::Tensor & y_, const std::vector<std::string> & features_, const std::string & className_, std::map<std::string,std::vector<int>> & states_, const Smoothing_t smoothing) : AODELd &
|
||||
+graph(const std::string & name = "AODELd") const : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::(anonymous_60275628)" as C_0009086919615463763584
|
||||
class C_0009086919615463763584 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60276282)" as C_0015251985607563196159
|
||||
class C_0015251985607563196159 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::BoostA2DE" as C_0000272055465257861326
|
||||
class C_0000272055465257861326 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+BoostA2DE(bool predict_voting = false) : void
|
||||
+~BoostA2DE() = default : void
|
||||
..
|
||||
+graph(const std::string & title = "BoostA2DE") const : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::(anonymous_60275502)" as C_0016033655851510053155
|
||||
class C_0016033655851510053155 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60276156)" as C_0000379522761622473555
|
||||
class C_0000379522761622473555 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::BoostAODE" as C_0002867772739198819061
|
||||
class C_0002867772739198819061 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::BoostAODE" as C_0000358471592399852382
|
||||
class C_0000358471592399852382 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+BoostAODE(bool predict_voting = false) : void
|
||||
+~BoostAODE() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & title = "BoostAODE") const : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights, const Smoothing_t smoothing) : void
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters_) : void
|
||||
#trainModel(const torch::Tensor & weights) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::CFS" as C_0000093018845530739957
|
||||
class C_0000093018845530739957 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+CFS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights) : void
|
||||
+~CFS() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::FCBF" as C_0001157456122733975432
|
||||
class C_0001157456122733975432 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+FCBF(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
|
||||
+~FCBF() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::IWSS" as C_0000066148117395428429
|
||||
class C_0000066148117395428429 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+IWSS(const torch::Tensor & samples, const std::vector<std::string> & features, const std::string & className, const int maxFeatures, const int classNumStates, const torch::Tensor & weights, const double threshold) : void
|
||||
+~IWSS() : void
|
||||
..
|
||||
+fit() : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::(anonymous_60730495)" as C_0004857727320042830573
|
||||
class C_0004857727320042830573 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60731150)" as C_0000076541533312623385
|
||||
class C_0000076541533312623385 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60653004)" as C_0001444063444142949758
|
||||
class C_0001444063444142949758 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60653658)" as C_0007139277546931322856
|
||||
class C_0007139277546931322856 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60731375)" as C_0010493853592456211189
|
||||
class C_0010493853592456211189 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+CFS : std::string
|
||||
+FCBF : std::string
|
||||
+IWSS : std::string
|
||||
}
|
||||
class "bayesnet::(anonymous_60732030)" as C_0007011438637915849564
|
||||
class C_0007011438637915849564 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
__
|
||||
+ASC : std::string
|
||||
+DESC : std::string
|
||||
+RAND : std::string
|
||||
}
|
||||
class "bayesnet::MST" as C_0001054867409378333602
|
||||
class C_0001054867409378333602 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::MST" as C_0000131858426172291700
|
||||
class C_0000131858426172291700 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+MST() = default : void
|
||||
+MST(const std::vector<std::string> & features, const torch::Tensor & weights, const int root) : void
|
||||
..
|
||||
+insertElement(std::list<int> & variables, int variable) : void
|
||||
+maximumSpanningTree() : std::vector<std::pair<int,int>>
|
||||
+reorder(std::vector<std::pair<float,std::pair<int,int>>> T, int root_original) : std::vector<std::pair<int,int>>
|
||||
__
|
||||
}
|
||||
class "bayesnet::Graph" as C_0009576333456015187741
|
||||
class C_0009576333456015187741 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
class "bayesnet::Graph" as C_0001197041682001898467
|
||||
class C_0001197041682001898467 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+Graph(int V) : void
|
||||
..
|
||||
+addEdge(int u, int v, float wt) : void
|
||||
@ -508,73 +332,81 @@ class C_0009576333456015187741 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+union_set(int u, int v) : void
|
||||
__
|
||||
}
|
||||
C_0010428199432536647474 --> C_0010428199432536647474 : -parents
|
||||
C_0010428199432536647474 --> C_0010428199432536647474 : -children
|
||||
C_0009493661199123436603 ..> C_0013393078277439680282
|
||||
C_0009493661199123436603 o-- C_0010428199432536647474 : -nodes
|
||||
C_0002617087915615796317 ..> C_0013393078277439680282
|
||||
C_0002617087915615796317 ..> C_0005907365846270811004
|
||||
C_0016351972983202413152 ..> C_0013393078277439680282
|
||||
C_0016351972983202413152 o-- C_0009493661199123436603 : #model
|
||||
C_0016351972983202413152 o-- C_0005895723015084986588 : #metrics
|
||||
C_0016351972983202413152 o-- C_0005907365846270811004 : #status
|
||||
C_0002617087915615796317 <|-- C_0016351972983202413152
|
||||
class "bayesnet::KDBLd" as C_0000344502277874806837
|
||||
class C_0000344502277874806837 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+KDBLd(int k) : void
|
||||
+~KDBLd() = default : void
|
||||
..
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : KDBLd &
|
||||
+graph(const std::string & name = "KDB") const : std::vector<std::string>
|
||||
+predict(torch::Tensor & X) : torch::Tensor
|
||||
{static} +version() : std::string
|
||||
__
|
||||
}
|
||||
class "bayesnet::AODE" as C_0000786111576121788282
|
||||
class C_0000786111576121788282 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+AODE(bool predict_voting = false) : void
|
||||
+~AODE() : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+graph(const std::string & title = "AODE") const : std::vector<std::string>
|
||||
+setHyperparameters(const nlohmann::json & hyperparameters) : void
|
||||
__
|
||||
}
|
||||
class "bayesnet::SPODELd" as C_0001369655639257755354
|
||||
class C_0001369655639257755354 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+SPODELd(int root) : void
|
||||
+~SPODELd() = default : void
|
||||
..
|
||||
+commonFit(const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : SPODELd &
|
||||
+fit(torch::Tensor & X, torch::Tensor & y, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : SPODELd &
|
||||
+fit(torch::Tensor & dataset, const std::vector<std::string> & features, const std::string & className, std::map<std::string,std::vector<int>> & states) : SPODELd &
|
||||
+graph(const std::string & name = "SPODE") const : std::vector<std::string>
|
||||
+predict(torch::Tensor & X) : torch::Tensor
|
||||
{static} +version() : std::string
|
||||
__
|
||||
}
|
||||
class "bayesnet::AODELd" as C_0000487273479333793647
|
||||
class C_0000487273479333793647 #aliceblue;line:blue;line.dotted;text:blue {
|
||||
+AODELd(bool predict_voting = true) : void
|
||||
+~AODELd() = default : void
|
||||
..
|
||||
#buildModel(const torch::Tensor & weights) : void
|
||||
+fit(torch::Tensor & X_, torch::Tensor & y_, const std::vector<std::string> & features_, const std::string & className_, std::map<std::string,std::vector<int>> & states_) : AODELd &
|
||||
+graph(const std::string & name = "AODELd") const : std::vector<std::string>
|
||||
#trainModel(const torch::Tensor & weights) : void
|
||||
__
|
||||
}
|
||||
C_0001303524929067080934 --> C_0001303524929067080934 : -parents
|
||||
C_0001303524929067080934 --> C_0001303524929067080934 : -children
|
||||
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Before Width: | Height: | Size: 18 KiB After Width: | Height: | Size: 7.1 KiB |
2
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|
||||
Subproject commit 7d62d6af4a6ca944a3bbde0b61f651fd4b2d3f57
|
||||
Subproject commit 2db60e007d70da876379373c53b6421f281daeac
|
||||
@ -5,21 +5,15 @@ project(bayesnet_sample)
|
||||
set(CMAKE_CXX_STANDARD 17)
|
||||
|
||||
find_package(Torch REQUIRED)
|
||||
find_library(BayesNet NAMES libBayesNet BayesNet libBayesNet.a REQUIRED)
|
||||
find_path(Bayesnet_INCLUDE_DIRS REQUIRED NAMES bayesnet)
|
||||
find_library(FImdlp NAMES libfimdlp.a PATHS REQUIRED)
|
||||
|
||||
message(STATUS "FImdlp=${FImdlp}")
|
||||
message(STATUS "FImdlp_INCLUDE_DIRS=${FImdlp_INCLUDE_DIRS}")
|
||||
message(STATUS "BayesNet=${BayesNet}")
|
||||
message(STATUS "Bayesnet_INCLUDE_DIRS=${Bayesnet_INCLUDE_DIRS}")
|
||||
find_library(BayesNet NAMES BayesNet.a libBayesNet.a REQUIRED)
|
||||
|
||||
include_directories(
|
||||
../tests/lib/Files
|
||||
lib/mdlp
|
||||
lib/json/include
|
||||
/usr/local/include
|
||||
${FImdlp_INCLUDE_DIRS}
|
||||
)
|
||||
|
||||
add_subdirectory(lib/mdlp)
|
||||
add_executable(bayesnet_sample sample.cc)
|
||||
target_link_libraries(bayesnet_sample fimdlp "${TORCH_LIBRARIES}" "${BayesNet}")
|
||||
target_link_libraries(bayesnet_sample mdlp "${TORCH_LIBRARIES}" "${BayesNet}")
|
||||
11
sample/lib/mdlp/CMakeLists.txt
Normal file
11
sample/lib/mdlp/CMakeLists.txt
Normal file
@ -0,0 +1,11 @@
|
||||
cmake_minimum_required(VERSION 3.20)
|
||||
project(mdlp)
|
||||
|
||||
if (POLICY CMP0135)
|
||||
cmake_policy(SET CMP0135 NEW)
|
||||
endif ()
|
||||
|
||||
set(CMAKE_CXX_STANDARD 11)
|
||||
|
||||
add_library(mdlp CPPFImdlp.cpp Metrics.cpp)
|
||||
|
||||
222
sample/lib/mdlp/CPPFImdlp.cpp
Normal file
222
sample/lib/mdlp/CPPFImdlp.cpp
Normal file
@ -0,0 +1,222 @@
|
||||
#include <numeric>
|
||||
#include <algorithm>
|
||||
#include <set>
|
||||
#include <cmath>
|
||||
#include "CPPFImdlp.h"
|
||||
#include "Metrics.h"
|
||||
|
||||
namespace mdlp {
|
||||
|
||||
CPPFImdlp::CPPFImdlp(size_t min_length_, int max_depth_, float proposed) : min_length(min_length_),
|
||||
max_depth(max_depth_),
|
||||
proposed_cuts(proposed)
|
||||
{
|
||||
}
|
||||
|
||||
CPPFImdlp::CPPFImdlp() = default;
|
||||
|
||||
CPPFImdlp::~CPPFImdlp() = default;
|
||||
|
||||
size_t CPPFImdlp::compute_max_num_cut_points() const
|
||||
{
|
||||
// Set the actual maximum number of cut points as a number or as a percentage of the number of samples
|
||||
if (proposed_cuts == 0) {
|
||||
return numeric_limits<size_t>::max();
|
||||
}
|
||||
if (proposed_cuts < 0 || proposed_cuts > static_cast<float>(X.size())) {
|
||||
throw invalid_argument("wrong proposed num_cuts value");
|
||||
}
|
||||
if (proposed_cuts < 1)
|
||||
return static_cast<size_t>(round(static_cast<float>(X.size()) * proposed_cuts));
|
||||
return static_cast<size_t>(proposed_cuts);
|
||||
}
|
||||
|
||||
void CPPFImdlp::fit(samples_t& X_, labels_t& y_)
|
||||
{
|
||||
X = X_;
|
||||
y = y_;
|
||||
num_cut_points = compute_max_num_cut_points();
|
||||
depth = 0;
|
||||
discretizedData.clear();
|
||||
cutPoints.clear();
|
||||
if (X.size() != y.size()) {
|
||||
throw invalid_argument("X and y must have the same size");
|
||||
}
|
||||
if (X.empty() || y.empty()) {
|
||||
throw invalid_argument("X and y must have at least one element");
|
||||
}
|
||||
if (min_length < 3) {
|
||||
throw invalid_argument("min_length must be greater than 2");
|
||||
}
|
||||
if (max_depth < 1) {
|
||||
throw invalid_argument("max_depth must be greater than 0");
|
||||
}
|
||||
indices = sortIndices(X_, y_);
|
||||
metrics.setData(y, indices);
|
||||
computeCutPoints(0, X.size(), 1);
|
||||
sort(cutPoints.begin(), cutPoints.end());
|
||||
if (num_cut_points > 0) {
|
||||
// Select the best (with lower entropy) cut points
|
||||
while (cutPoints.size() > num_cut_points) {
|
||||
resizeCutPoints();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
pair<precision_t, size_t> CPPFImdlp::valueCutPoint(size_t start, size_t cut, size_t end)
|
||||
{
|
||||
size_t n;
|
||||
size_t m;
|
||||
size_t idxPrev = cut - 1 >= start ? cut - 1 : cut;
|
||||
size_t idxNext = cut + 1 < end ? cut + 1 : cut;
|
||||
bool backWall; // true if duplicates reach beginning of the interval
|
||||
precision_t previous;
|
||||
precision_t actual;
|
||||
precision_t next;
|
||||
previous = X[indices[idxPrev]];
|
||||
actual = X[indices[cut]];
|
||||
next = X[indices[idxNext]];
|
||||
// definition 2 of the paper => X[t-1] < X[t]
|
||||
// get the first equal value of X in the interval
|
||||
while (idxPrev > start && actual == previous) {
|
||||
previous = X[indices[--idxPrev]];
|
||||
}
|
||||
backWall = idxPrev == start && actual == previous;
|
||||
// get the last equal value of X in the interval
|
||||
while (idxNext < end - 1 && actual == next) {
|
||||
next = X[indices[++idxNext]];
|
||||
}
|
||||
// # of duplicates before cutpoint
|
||||
n = cut - 1 - idxPrev;
|
||||
// # of duplicates after cutpoint
|
||||
m = idxNext - cut - 1;
|
||||
// Decide which values to use
|
||||
cut = cut + (backWall ? m + 1 : -n);
|
||||
actual = X[indices[cut]];
|
||||
return { (actual + previous) / 2, cut };
|
||||
}
|
||||
|
||||
void CPPFImdlp::computeCutPoints(size_t start, size_t end, int depth_)
|
||||
{
|
||||
size_t cut;
|
||||
pair<precision_t, size_t> result;
|
||||
// Check if the interval length and the depth are Ok
|
||||
if (end - start < min_length || depth_ > max_depth)
|
||||
return;
|
||||
depth = depth_ > depth ? depth_ : depth;
|
||||
cut = getCandidate(start, end);
|
||||
if (cut == numeric_limits<size_t>::max())
|
||||
return;
|
||||
if (mdlp(start, cut, end)) {
|
||||
result = valueCutPoint(start, cut, end);
|
||||
cut = result.second;
|
||||
cutPoints.push_back(result.first);
|
||||
computeCutPoints(start, cut, depth_ + 1);
|
||||
computeCutPoints(cut, end, depth_ + 1);
|
||||
}
|
||||
}
|
||||
|
||||
size_t CPPFImdlp::getCandidate(size_t start, size_t end)
|
||||
{
|
||||
/* Definition 1: A binary discretization for A is determined by selecting the cut point TA for which
|
||||
E(A, TA; S) is minimal amongst all the candidate cut points. */
|
||||
size_t candidate = numeric_limits<size_t>::max();
|
||||
size_t elements = end - start;
|
||||
bool sameValues = true;
|
||||
precision_t entropy_left;
|
||||
precision_t entropy_right;
|
||||
precision_t minEntropy;
|
||||
// Check if all the values of the variable in the interval are the same
|
||||
for (size_t idx = start + 1; idx < end; idx++) {
|
||||
if (X[indices[idx]] != X[indices[start]]) {
|
||||
sameValues = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
if (sameValues)
|
||||
return candidate;
|
||||
minEntropy = metrics.entropy(start, end);
|
||||
for (size_t idx = start + 1; idx < end; idx++) {
|
||||
// Cutpoints are always on boundaries (definition 2)
|
||||
if (y[indices[idx]] == y[indices[idx - 1]])
|
||||
continue;
|
||||
entropy_left = precision_t(idx - start) / static_cast<precision_t>(elements) * metrics.entropy(start, idx);
|
||||
entropy_right = precision_t(end - idx) / static_cast<precision_t>(elements) * metrics.entropy(idx, end);
|
||||
if (entropy_left + entropy_right < minEntropy) {
|
||||
minEntropy = entropy_left + entropy_right;
|
||||
candidate = idx;
|
||||
}
|
||||
}
|
||||
return candidate;
|
||||
}
|
||||
|
||||
bool CPPFImdlp::mdlp(size_t start, size_t cut, size_t end)
|
||||
{
|
||||
int k;
|
||||
int k1;
|
||||
int k2;
|
||||
precision_t ig;
|
||||
precision_t delta;
|
||||
precision_t ent;
|
||||
precision_t ent1;
|
||||
precision_t ent2;
|
||||
auto N = precision_t(end - start);
|
||||
k = metrics.computeNumClasses(start, end);
|
||||
k1 = metrics.computeNumClasses(start, cut);
|
||||
k2 = metrics.computeNumClasses(cut, end);
|
||||
ent = metrics.entropy(start, end);
|
||||
ent1 = metrics.entropy(start, cut);
|
||||
ent2 = metrics.entropy(cut, end);
|
||||
ig = metrics.informationGain(start, cut, end);
|
||||
delta = static_cast<precision_t>(log2(pow(3, precision_t(k)) - 2) -
|
||||
(precision_t(k) * ent - precision_t(k1) * ent1 - precision_t(k2) * ent2));
|
||||
precision_t term = 1 / N * (log2(N - 1) + delta);
|
||||
return ig > term;
|
||||
}
|
||||
|
||||
// Argsort from https://stackoverflow.com/questions/1577475/c-sorting-and-keeping-track-of-indexes
|
||||
indices_t CPPFImdlp::sortIndices(samples_t& X_, labels_t& y_)
|
||||
{
|
||||
indices_t idx(X_.size());
|
||||
iota(idx.begin(), idx.end(), 0);
|
||||
stable_sort(idx.begin(), idx.end(), [&X_, &y_](size_t i1, size_t i2) {
|
||||
if (X_[i1] == X_[i2])
|
||||
return y_[i1] < y_[i2];
|
||||
else
|
||||
return X_[i1] < X_[i2];
|
||||
});
|
||||
return idx;
|
||||
}
|
||||
|
||||
void CPPFImdlp::resizeCutPoints()
|
||||
{
|
||||
//Compute entropy of each of the whole cutpoint set and discards the biggest value
|
||||
precision_t maxEntropy = 0;
|
||||
precision_t entropy;
|
||||
size_t maxEntropyIdx = 0;
|
||||
size_t begin = 0;
|
||||
size_t end;
|
||||
for (size_t idx = 0; idx < cutPoints.size(); idx++) {
|
||||
end = begin;
|
||||
while (X[indices[end]] < cutPoints[idx] && end < X.size())
|
||||
end++;
|
||||
entropy = metrics.entropy(begin, end);
|
||||
if (entropy > maxEntropy) {
|
||||
maxEntropy = entropy;
|
||||
maxEntropyIdx = idx;
|
||||
}
|
||||
begin = end;
|
||||
}
|
||||
cutPoints.erase(cutPoints.begin() + static_cast<long>(maxEntropyIdx));
|
||||
}
|
||||
labels_t& CPPFImdlp::transform(const samples_t& data)
|
||||
{
|
||||
discretizedData.clear();
|
||||
discretizedData.reserve(data.size());
|
||||
for (const precision_t& item : data) {
|
||||
auto upper = upper_bound(cutPoints.begin(), cutPoints.end(), item);
|
||||
discretizedData.push_back(upper - cutPoints.begin());
|
||||
}
|
||||
return discretizedData;
|
||||
}
|
||||
}
|
||||
51
sample/lib/mdlp/CPPFImdlp.h
Normal file
51
sample/lib/mdlp/CPPFImdlp.h
Normal file
@ -0,0 +1,51 @@
|
||||
// ***************************************************************
|
||||
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
|
||||
// SPDX-FileType: SOURCE
|
||||
// SPDX-License-Identifier: MIT
|
||||
// ***************************************************************
|
||||
|
||||
#ifndef CPPFIMDLP_H
|
||||
#define CPPFIMDLP_H
|
||||
|
||||
#include "typesFImdlp.h"
|
||||
#include "Metrics.h"
|
||||
#include <limits>
|
||||
#include <utility>
|
||||
#include <string>
|
||||
|
||||
namespace mdlp {
|
||||
class CPPFImdlp {
|
||||
protected:
|
||||
size_t min_length = 3;
|
||||
int depth = 0;
|
||||
int max_depth = numeric_limits<int>::max();
|
||||
float proposed_cuts = 0;
|
||||
indices_t indices = indices_t();
|
||||
samples_t X = samples_t();
|
||||
labels_t y = labels_t();
|
||||
Metrics metrics = Metrics(y, indices);
|
||||
cutPoints_t cutPoints;
|
||||
size_t num_cut_points = numeric_limits<size_t>::max();
|
||||
labels_t discretizedData = labels_t();
|
||||
|
||||
static indices_t sortIndices(samples_t&, labels_t&);
|
||||
|
||||
void computeCutPoints(size_t, size_t, int);
|
||||
void resizeCutPoints();
|
||||
bool mdlp(size_t, size_t, size_t);
|
||||
size_t getCandidate(size_t, size_t);
|
||||
size_t compute_max_num_cut_points() const;
|
||||
pair<precision_t, size_t> valueCutPoint(size_t, size_t, size_t);
|
||||
|
||||
public:
|
||||
CPPFImdlp();
|
||||
CPPFImdlp(size_t, int, float);
|
||||
~CPPFImdlp();
|
||||
void fit(samples_t&, labels_t&);
|
||||
inline cutPoints_t getCutPoints() const { return cutPoints; };
|
||||
labels_t& transform(const samples_t&);
|
||||
inline int get_depth() const { return depth; };
|
||||
static inline string version() { return "1.1.2"; };
|
||||
};
|
||||
}
|
||||
#endif
|
||||
21
sample/lib/mdlp/LICENSE
Normal file
21
sample/lib/mdlp/LICENSE
Normal file
@ -0,0 +1,21 @@
|
||||
MIT License
|
||||
|
||||
Copyright (c) 2022 Ricardo Montañana Gómez
|
||||
|
||||
Permission is hereby granted, free of charge, to any person obtaining a copy
|
||||
of this software and associated documentation files (the "Software"), to deal
|
||||
in the Software without restriction, including without limitation the rights
|
||||
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
copies of the Software, and to permit persons to whom the Software is
|
||||
furnished to do so, subject to the following conditions:
|
||||
|
||||
The above copyright notice and this permission notice shall be included in all
|
||||
copies or substantial portions of the Software.
|
||||
|
||||
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
||||
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
||||
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
||||
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
||||
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
||||
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
||||
SOFTWARE.
|
||||
78
sample/lib/mdlp/Metrics.cpp
Normal file
78
sample/lib/mdlp/Metrics.cpp
Normal file
@ -0,0 +1,78 @@
|
||||
#include "Metrics.h"
|
||||
#include <set>
|
||||
#include <cmath>
|
||||
|
||||
using namespace std;
|
||||
namespace mdlp {
|
||||
Metrics::Metrics(labels_t& y_, indices_t& indices_): y(y_), indices(indices_),
|
||||
numClasses(computeNumClasses(0, indices.size()))
|
||||
{
|
||||
}
|
||||
|
||||
int Metrics::computeNumClasses(size_t start, size_t end)
|
||||
{
|
||||
set<int> nClasses;
|
||||
for (auto i = start; i < end; ++i) {
|
||||
nClasses.insert(y[indices[i]]);
|
||||
}
|
||||
return static_cast<int>(nClasses.size());
|
||||
}
|
||||
|
||||
void Metrics::setData(const labels_t& y_, const indices_t& indices_)
|
||||
{
|
||||
indices = indices_;
|
||||
y = y_;
|
||||
numClasses = computeNumClasses(0, indices.size());
|
||||
entropyCache.clear();
|
||||
igCache.clear();
|
||||
}
|
||||
|
||||
precision_t Metrics::entropy(size_t start, size_t end)
|
||||
{
|
||||
precision_t p;
|
||||
precision_t ventropy = 0;
|
||||
int nElements = 0;
|
||||
labels_t counts(numClasses + 1, 0);
|
||||
if (end - start < 2)
|
||||
return 0;
|
||||
if (entropyCache.find({ start, end }) != entropyCache.end()) {
|
||||
return entropyCache[{start, end}];
|
||||
}
|
||||
for (auto i = &indices[start]; i != &indices[end]; ++i) {
|
||||
counts[y[*i]]++;
|
||||
nElements++;
|
||||
}
|
||||
for (auto count : counts) {
|
||||
if (count > 0) {
|
||||
p = static_cast<precision_t>(count) / static_cast<precision_t>(nElements);
|
||||
ventropy -= p * log2(p);
|
||||
}
|
||||
}
|
||||
entropyCache[{start, end}] = ventropy;
|
||||
return ventropy;
|
||||
}
|
||||
|
||||
precision_t Metrics::informationGain(size_t start, size_t cut, size_t end)
|
||||
{
|
||||
precision_t iGain;
|
||||
precision_t entropyInterval;
|
||||
precision_t entropyLeft;
|
||||
precision_t entropyRight;
|
||||
size_t nElementsLeft = cut - start;
|
||||
size_t nElementsRight = end - cut;
|
||||
size_t nElements = end - start;
|
||||
if (igCache.find(make_tuple(start, cut, end)) != igCache.end()) {
|
||||
return igCache[make_tuple(start, cut, end)];
|
||||
}
|
||||
entropyInterval = entropy(start, end);
|
||||
entropyLeft = entropy(start, cut);
|
||||
entropyRight = entropy(cut, end);
|
||||
iGain = entropyInterval -
|
||||
(static_cast<precision_t>(nElementsLeft) * entropyLeft +
|
||||
static_cast<precision_t>(nElementsRight) * entropyRight) /
|
||||
static_cast<precision_t>(nElements);
|
||||
igCache[make_tuple(start, cut, end)] = iGain;
|
||||
return iGain;
|
||||
}
|
||||
|
||||
}
|
||||
28
sample/lib/mdlp/Metrics.h
Normal file
28
sample/lib/mdlp/Metrics.h
Normal file
@ -0,0 +1,28 @@
|
||||
// ***************************************************************
|
||||
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
|
||||
// SPDX-FileType: SOURCE
|
||||
// SPDX-License-Identifier: MIT
|
||||
// ***************************************************************
|
||||
|
||||
#ifndef CCMETRICS_H
|
||||
#define CCMETRICS_H
|
||||
|
||||
#include "typesFImdlp.h"
|
||||
|
||||
namespace mdlp {
|
||||
class Metrics {
|
||||
protected:
|
||||
labels_t& y;
|
||||
indices_t& indices;
|
||||
int numClasses;
|
||||
cacheEnt_t entropyCache = cacheEnt_t();
|
||||
cacheIg_t igCache = cacheIg_t();
|
||||
public:
|
||||
Metrics(labels_t&, indices_t&);
|
||||
void setData(const labels_t&, const indices_t&);
|
||||
int computeNumClasses(size_t, size_t);
|
||||
precision_t entropy(size_t, size_t);
|
||||
precision_t informationGain(size_t, size_t, size_t);
|
||||
};
|
||||
}
|
||||
#endif
|
||||
41
sample/lib/mdlp/README.md
Normal file
41
sample/lib/mdlp/README.md
Normal file
@ -0,0 +1,41 @@
|
||||
[](https://github.com/rmontanana/mdlp/actions/workflows/build.yml)
|
||||
[](https://sonarcloud.io/summary/new_code?id=rmontanana_mdlp)
|
||||
[](https://sonarcloud.io/summary/new_code?id=rmontanana_mdlp)
|
||||
|
||||
# mdlp
|
||||
|
||||
Discretization algorithm based on the paper by Fayyad & Irani [Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning](https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf)
|
||||
|
||||
The implementation tries to mitigate the problem of different label values with the same value of the variable:
|
||||
|
||||
- Sorts the values of the variable using the label values as a tie-breaker
|
||||
- Once found a valid candidate for the split, it checks if the previous value is the same as actual one, and tries to get previous one, or next if the former is not possible.
|
||||
|
||||
Other features:
|
||||
|
||||
- Intervals with the same value of the variable are not taken into account for cutpoints.
|
||||
- Intervals have to have more than two examples to be evaluated.
|
||||
|
||||
The algorithm returns the cut points for the variable.
|
||||
|
||||
## Sample
|
||||
|
||||
To run the sample, just execute the following commands:
|
||||
|
||||
```bash
|
||||
cd sample
|
||||
cmake -B build
|
||||
cd build
|
||||
make
|
||||
./sample -f iris -m 2
|
||||
./sample -h
|
||||
```
|
||||
|
||||
## Test
|
||||
|
||||
To run the tests and see coverage (llvm & gcovr have to be installed), execute the following commands:
|
||||
|
||||
```bash
|
||||
cd tests
|
||||
./test
|
||||
```
|
||||
24
sample/lib/mdlp/typesFImdlp.h
Normal file
24
sample/lib/mdlp/typesFImdlp.h
Normal file
@ -0,0 +1,24 @@
|
||||
// ***************************************************************
|
||||
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
|
||||
// SPDX-FileType: SOURCE
|
||||
// SPDX-License-Identifier: MIT
|
||||
// ***************************************************************
|
||||
|
||||
#ifndef TYPES_H
|
||||
#define TYPES_H
|
||||
|
||||
#include <vector>
|
||||
#include <map>
|
||||
#include <stdexcept>
|
||||
|
||||
using namespace std;
|
||||
namespace mdlp {
|
||||
typedef float precision_t;
|
||||
typedef vector<precision_t> samples_t;
|
||||
typedef vector<int> labels_t;
|
||||
typedef vector<size_t> indices_t;
|
||||
typedef vector<precision_t> cutPoints_t;
|
||||
typedef map<pair<int, int>, precision_t> cacheEnt_t;
|
||||
typedef map<tuple<int, int, int>, precision_t> cacheIg_t;
|
||||
}
|
||||
#endif
|
||||
@ -7,6 +7,7 @@
|
||||
#include <ArffFiles.hpp>
|
||||
#include <CPPFImdlp.h>
|
||||
#include <bayesnet/ensembles/BoostAODE.h>
|
||||
#include <torch/torch.h>
|
||||
|
||||
std::vector<mdlp::labels_t> discretizeDataset(std::vector<mdlp::samples_t>& X, mdlp::labels_t& y)
|
||||
{
|
||||
@ -19,7 +20,8 @@ std::vector<mdlp::labels_t> discretizeDataset(std::vector<mdlp::samples_t>& X, m
|
||||
}
|
||||
return Xd;
|
||||
}
|
||||
tuple<torch::Tensor, torch::Tensor, std::vector<std::string>, std::string, map<std::string, std::vector<int>>> loadDataset(const std::string& name, bool class_last)
|
||||
|
||||
tuple<torch::Tensor, torch::Tensor, std::vector<std::string>, std::string, map<std::string, std::vector<int>>> loadDataset(const std::string& name, bool class_last, torch::Device device)
|
||||
{
|
||||
auto handler = ArffFiles();
|
||||
handler.load(name, class_last);
|
||||
@ -34,16 +36,16 @@ tuple<torch::Tensor, torch::Tensor, std::vector<std::string>, std::string, map<s
|
||||
torch::Tensor Xd;
|
||||
auto states = map<std::string, std::vector<int>>();
|
||||
auto Xr = discretizeDataset(X, y);
|
||||
Xd = torch::zeros({ static_cast<int>(Xr.size()), static_cast<int>(Xr[0].size()) }, torch::kInt32);
|
||||
Xd = torch::zeros({ static_cast<int>(Xr.size()), static_cast<int>(Xr[0].size()) }, torch::kInt32).to(device);
|
||||
for (int i = 0; i < features.size(); ++i) {
|
||||
states[features[i]] = std::vector<int>(*max_element(Xr[i].begin(), Xr[i].end()) + 1);
|
||||
auto item = states.at(features[i]);
|
||||
iota(begin(item), end(item), 0);
|
||||
Xd.index_put_({ i, "..." }, torch::tensor(Xr[i], torch::kInt32));
|
||||
Xd.index_put_({ i, "..." }, torch::tensor(Xr[i], torch::kInt32).to(device));
|
||||
}
|
||||
states[className] = std::vector<int>(*max_element(y.begin(), y.end()) + 1);
|
||||
iota(begin(states.at(className)), end(states.at(className)), 0);
|
||||
return { Xd, torch::tensor(y, torch::kInt32), features, className, states };
|
||||
return { Xd, torch::tensor(y, torch::kInt32).to(device), features, className, states };
|
||||
}
|
||||
|
||||
int main(int argc, char* argv[])
|
||||
@ -53,16 +55,22 @@ int main(int argc, char* argv[])
|
||||
return 1;
|
||||
}
|
||||
std::string file_name = argv[1];
|
||||
torch::Device device(torch::kCPU);
|
||||
if (torch::cuda::is_available()) {
|
||||
device = torch::Device(torch::kCUDA);
|
||||
std::cout << "CUDA is available! Using GPU." << std::endl;
|
||||
} else {
|
||||
std::cout << "CUDA is not available. Using CPU." << std::endl;
|
||||
}
|
||||
torch::Tensor X, y;
|
||||
std::vector<std::string> features;
|
||||
std::string className;
|
||||
map<std::string, std::vector<int>> states;
|
||||
auto clf = bayesnet::BoostAODE(false); // false for not using voting in predict
|
||||
std::cout << "Library version: " << clf.getVersion() << std::endl;
|
||||
tie(X, y, features, className, states) = loadDataset(file_name, true);
|
||||
tie(X, y, features, className, states) = loadDataset(file_name, true, device);
|
||||
clf.fit(X, y, features, className, states, bayesnet::Smoothing_t::LAPLACE);
|
||||
auto score = clf.score(X, y);
|
||||
std::cout << "File: " << file_name << " Model: BoostAODE score: " << score << std::endl;
|
||||
return 0;
|
||||
}
|
||||
|
||||
}
|
||||
@ -10,8 +10,8 @@ if(ENABLE_TESTING)
|
||||
file(GLOB_RECURSE BayesNet_SOURCES "${BayesNet_SOURCE_DIR}/bayesnet/*.cc")
|
||||
add_executable(TestBayesNet TestBayesNetwork.cc TestBayesNode.cc TestBayesClassifier.cc
|
||||
TestBayesModels.cc TestBayesMetrics.cc TestFeatureSelection.cc TestBoostAODE.cc TestA2DE.cc
|
||||
TestUtils.cc TestBayesEnsemble.cc TestModulesVersions.cc TestBoostA2DE.cc TestMST.cc ${BayesNet_SOURCES})
|
||||
target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" fimdlp PRIVATE Catch2::Catch2WithMain)
|
||||
TestUtils.cc TestBayesEnsemble.cc TestModulesVersions.cc TestBoostA2DE.cc ${BayesNet_SOURCES})
|
||||
target_link_libraries(TestBayesNet PUBLIC "${TORCH_LIBRARIES}" mdlp PRIVATE Catch2::Catch2WithMain)
|
||||
add_test(NAME BayesNetworkTest COMMAND TestBayesNet)
|
||||
add_test(NAME A2DE COMMAND TestBayesNet "[A2DE]")
|
||||
add_test(NAME BoostA2DE COMMAND TestBayesNet "[BoostA2DE]")
|
||||
@ -24,5 +24,4 @@ if(ENABLE_TESTING)
|
||||
add_test(NAME Modules COMMAND TestBayesNet "[Modules]")
|
||||
add_test(NAME Network COMMAND TestBayesNet "[Network]")
|
||||
add_test(NAME Node COMMAND TestBayesNet "[Node]")
|
||||
add_test(NAME MST COMMAND TestBayesNet "[MST]")
|
||||
endif(ENABLE_TESTING)
|
||||
|
||||
@ -45,5 +45,5 @@ TEST_CASE("Test graph", "[A2DE]")
|
||||
auto graph = clf.graph();
|
||||
REQUIRE(graph.size() == 78);
|
||||
REQUIRE(graph[0] == "digraph BayesNet {\nlabel=<BayesNet A2DE_0>\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n");
|
||||
REQUIRE(graph[1] == "\"class\" [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ] \n");
|
||||
REQUIRE(graph[1] == "class [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ] \n");
|
||||
}
|
||||
|
||||
@ -85,7 +85,7 @@ TEST_CASE("Dump_cpt", "[Classifier]")
|
||||
auto raw = RawDatasets("iris", true);
|
||||
model.fit(raw.Xt, raw.yt, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
auto cpt = model.dump_cpt();
|
||||
REQUIRE(cpt.size() == 1718);
|
||||
REQUIRE(cpt.size() == 1713);
|
||||
}
|
||||
TEST_CASE("Not fitted model", "[Classifier]")
|
||||
{
|
||||
|
||||
@ -27,13 +27,13 @@ TEST_CASE("Test Bayesian Classifiers score & version", "[Models]")
|
||||
map <pair<std::string, std::string>, float> scores{
|
||||
// Diabetes
|
||||
{{"diabetes", "AODE"}, 0.82161}, {{"diabetes", "KDB"}, 0.852865}, {{"diabetes", "SPODE"}, 0.802083}, {{"diabetes", "TAN"}, 0.821615},
|
||||
{{"diabetes", "AODELd"}, 0.8125f}, {{"diabetes", "KDBLd"}, 0.80208f}, {{"diabetes", "SPODELd"}, 0.7890625f}, {{"diabetes", "TANLd"}, 0.803385437f}, {{"diabetes", "BoostAODE"}, 0.83984f},
|
||||
{{"diabetes", "AODELd"}, 0.8138f}, {{"diabetes", "KDBLd"}, 0.80208f}, {{"diabetes", "SPODELd"}, 0.78646f}, {{"diabetes", "TANLd"}, 0.8099f}, {{"diabetes", "BoostAODE"}, 0.83984f},
|
||||
// Ecoli
|
||||
{{"ecoli", "AODE"}, 0.889881}, {{"ecoli", "KDB"}, 0.889881}, {{"ecoli", "SPODE"}, 0.880952}, {{"ecoli", "TAN"}, 0.892857},
|
||||
{{"ecoli", "AODELd"}, 0.875f}, {{"ecoli", "KDBLd"}, 0.880952358f}, {{"ecoli", "SPODELd"}, 0.839285731f}, {{"ecoli", "TANLd"}, 0.848214269f}, {{"ecoli", "BoostAODE"}, 0.89583f},
|
||||
{{"ecoli", "AODELd"}, 0.8869f}, {{"ecoli", "KDBLd"}, 0.875f}, {{"ecoli", "SPODELd"}, 0.84226f}, {{"ecoli", "TANLd"}, 0.86905f}, {{"ecoli", "BoostAODE"}, 0.89583f},
|
||||
// Glass
|
||||
{{"glass", "AODE"}, 0.79439}, {{"glass", "KDB"}, 0.827103}, {{"glass", "SPODE"}, 0.775701}, {{"glass", "TAN"}, 0.827103},
|
||||
{{"glass", "AODELd"}, 0.799065411f}, {{"glass", "KDBLd"}, 0.82710278f}, {{"glass", "SPODELd"}, 0.780373812f}, {{"glass", "TANLd"}, 0.869158864f}, {{"glass", "BoostAODE"}, 0.84579f},
|
||||
{{"glass", "AODELd"}, 0.79439f}, {{"glass", "KDBLd"}, 0.85047f}, {{"glass", "SPODELd"}, 0.79439f}, {{"glass", "TANLd"}, 0.86449f}, {{"glass", "BoostAODE"}, 0.84579f},
|
||||
// Iris
|
||||
{{"iris", "AODE"}, 0.973333}, {{"iris", "KDB"}, 0.973333}, {{"iris", "SPODE"}, 0.973333}, {{"iris", "TAN"}, 0.973333},
|
||||
{{"iris", "AODELd"}, 0.973333}, {{"iris", "KDBLd"}, 0.973333}, {{"iris", "SPODELd"}, 0.96f}, {{"iris", "TANLd"}, 0.97333f}, {{"iris", "BoostAODE"}, 0.98f}
|
||||
@ -71,10 +71,10 @@ TEST_CASE("Test Bayesian Classifiers score & version", "[Models]")
|
||||
TEST_CASE("Models features & Graph", "[Models]")
|
||||
{
|
||||
auto graph = std::vector<std::string>({ "digraph BayesNet {\nlabel=<BayesNet Test>\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n",
|
||||
"\"class\" [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ] \n",
|
||||
"\"class\" -> \"sepallength\"", "\"class\" -> \"sepalwidth\"", "\"class\" -> \"petallength\"", "\"class\" -> \"petalwidth\"", "\"petallength\" [shape=circle] \n",
|
||||
"\"petallength\" -> \"sepallength\"", "\"petalwidth\" [shape=circle] \n", "\"sepallength\" [shape=circle] \n",
|
||||
"\"sepallength\" -> \"sepalwidth\"", "\"sepalwidth\" [shape=circle] \n", "\"sepalwidth\" -> \"petalwidth\"", "}\n"
|
||||
"class [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ] \n",
|
||||
"class -> sepallength", "class -> sepalwidth", "class -> petallength", "class -> petalwidth", "petallength [shape=circle] \n",
|
||||
"petallength -> sepallength", "petalwidth [shape=circle] \n", "sepallength [shape=circle] \n",
|
||||
"sepallength -> sepalwidth", "sepalwidth [shape=circle] \n", "sepalwidth -> petalwidth", "}\n"
|
||||
}
|
||||
);
|
||||
SECTION("Test TAN")
|
||||
@ -96,7 +96,7 @@ TEST_CASE("Models features & Graph", "[Models]")
|
||||
clf.fit(raw.Xt, raw.yt, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 5);
|
||||
REQUIRE(clf.getNumberOfEdges() == 7);
|
||||
REQUIRE(clf.getNumberOfStates() == 27);
|
||||
REQUIRE(clf.getNumberOfStates() == 19);
|
||||
REQUIRE(clf.getClassNumStates() == 3);
|
||||
REQUIRE(clf.show() == std::vector<std::string>{"class -> sepallength, sepalwidth, petallength, petalwidth, ", "petallength -> sepallength, ", "petalwidth -> ", "sepallength -> sepalwidth, ", "sepalwidth -> petalwidth, "});
|
||||
REQUIRE(clf.graph("Test") == graph);
|
||||
|
||||
@ -186,11 +186,11 @@ TEST_CASE("Test Bayesian Network", "[Network]")
|
||||
auto str = net.graph("Test Graph");
|
||||
REQUIRE(str.size() == 7);
|
||||
REQUIRE(str[0] == "digraph BayesNet {\nlabel=<BayesNet Test Graph>\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n");
|
||||
REQUIRE(str[1] == "\"A\" [shape=circle] \n");
|
||||
REQUIRE(str[2] == "\"A\" -> \"B\"");
|
||||
REQUIRE(str[3] == "\"A\" -> \"C\"");
|
||||
REQUIRE(str[4] == "\"B\" [shape=circle] \n");
|
||||
REQUIRE(str[5] == "\"C\" [shape=circle] \n");
|
||||
REQUIRE(str[1] == "A [shape=circle] \n");
|
||||
REQUIRE(str[2] == "A -> B");
|
||||
REQUIRE(str[3] == "A -> C");
|
||||
REQUIRE(str[4] == "B [shape=circle] \n");
|
||||
REQUIRE(str[5] == "C [shape=circle] \n");
|
||||
REQUIRE(str[6] == "}\n");
|
||||
}
|
||||
SECTION("Test predict")
|
||||
@ -257,9 +257,9 @@ TEST_CASE("Test Bayesian Network", "[Network]")
|
||||
REQUIRE(node->getCPT().equal(node2->getCPT()));
|
||||
}
|
||||
}
|
||||
SECTION("Network oddities")
|
||||
SECTION("Test oddities")
|
||||
{
|
||||
INFO("Network oddities");
|
||||
INFO("Test oddities");
|
||||
buildModel(net, raw.features, raw.className);
|
||||
// predict without fitting
|
||||
std::vector<std::vector<int>> test = { {1, 2, 0, 1, 1}, {0, 1, 2, 0, 1}, {0, 0, 0, 0, 1}, {2, 2, 2, 2, 1} };
|
||||
@ -329,14 +329,6 @@ TEST_CASE("Test Bayesian Network", "[Network]")
|
||||
std::string invalid_state = "Feature sepallength not found in states";
|
||||
REQUIRE_THROWS_AS(net4.fit(raw.Xv, raw.yv, raw.weightsv, raw.features, raw.className, std::map<std::string, std::vector<int>>(), raw.smoothing), std::invalid_argument);
|
||||
REQUIRE_THROWS_WITH(net4.fit(raw.Xv, raw.yv, raw.weightsv, raw.features, raw.className, std::map<std::string, std::vector<int>>(), raw.smoothing), invalid_state);
|
||||
// Try to add node or edge to a fitted network
|
||||
auto net5 = bayesnet::Network();
|
||||
buildModel(net5, raw.features, raw.className);
|
||||
net5.fit(raw.Xv, raw.yv, raw.weightsv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE_THROWS_AS(net5.addNode("A"), std::logic_error);
|
||||
REQUIRE_THROWS_WITH(net5.addNode("A"), "Cannot add node to a fitted network. Initialize first.");
|
||||
REQUIRE_THROWS_AS(net5.addEdge("A", "B"), std::logic_error);
|
||||
REQUIRE_THROWS_WITH(net5.addEdge("A", "B"), "Cannot add edge to a fitted network. Initialize first.");
|
||||
}
|
||||
|
||||
}
|
||||
@ -381,7 +373,7 @@ TEST_CASE("Dump CPT", "[Network]")
|
||||
0.3333
|
||||
0.3333
|
||||
0.3333
|
||||
[ CPUDoubleType{3} ]
|
||||
[ CPUFloatType{3} ]
|
||||
* petallength: (4) : [4, 3, 3]
|
||||
(1,.,.) =
|
||||
0.9388 0.1000 0.2000
|
||||
@ -402,7 +394,7 @@ TEST_CASE("Dump CPT", "[Network]")
|
||||
0.0204 0.1000 0.2000
|
||||
0.1250 0.0526 0.1667
|
||||
0.2000 0.0606 0.8235
|
||||
[ CPUDoubleType{4,3,3} ]
|
||||
[ CPUFloatType{4,3,3} ]
|
||||
* petalwidth: (3) : [3, 6, 3]
|
||||
(1,.,.) =
|
||||
0.5000 0.0417 0.0714
|
||||
@ -427,12 +419,12 @@ TEST_CASE("Dump CPT", "[Network]")
|
||||
0.1111 0.0909 0.8000
|
||||
0.0667 0.2000 0.8667
|
||||
0.0303 0.2500 0.7500
|
||||
[ CPUDoubleType{3,6,3} ]
|
||||
[ CPUFloatType{3,6,3} ]
|
||||
* sepallength: (3) : [3, 3]
|
||||
0.8679 0.1321 0.0377
|
||||
0.0943 0.3019 0.0566
|
||||
0.0377 0.5660 0.9057
|
||||
[ CPUDoubleType{3,3} ]
|
||||
[ CPUFloatType{3,3} ]
|
||||
* sepalwidth: (6) : [6, 3, 3]
|
||||
(1,.,.) =
|
||||
0.0392 0.5000 0.2857
|
||||
@ -463,7 +455,7 @@ TEST_CASE("Dump CPT", "[Network]")
|
||||
0.5098 0.0833 0.1429
|
||||
0.5000 0.0476 0.1250
|
||||
0.2857 0.0571 0.1132
|
||||
[ CPUDoubleType{6,3,3} ]
|
||||
[ CPUFloatType{6,3,3} ]
|
||||
)";
|
||||
REQUIRE(res == expected);
|
||||
}
|
||||
@ -533,7 +525,6 @@ TEST_CASE("Test Smoothing A", "[Network]")
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("Test Smoothing B", "[Network]")
|
||||
{
|
||||
auto net = bayesnet::Network();
|
||||
@ -558,41 +549,19 @@ TEST_CASE("Test Smoothing B", "[Network]")
|
||||
{ "C", {0, 1} }
|
||||
};
|
||||
auto weights = std::vector<double>(C.size(), 1);
|
||||
// See https://www.overleaf.com/read/tfnhpfysfkfx#2d576c example for calculations
|
||||
INFO("Test Smoothing B - Laplace");
|
||||
// Simple
|
||||
std::cout << "LAPLACE\n";
|
||||
net.fit(Data, C, weights, { "X", "Y", "Z" }, "C", states, bayesnet::Smoothing_t::LAPLACE);
|
||||
auto laplace_values = std::vector<std::vector<float>>({ {0.377418, 0.622582}, {0.217821, 0.782179} });
|
||||
auto laplace_score = net.predict_proba({ {0, 1}, {1, 2}, {2, 3} });
|
||||
for (auto i = 0; i < 2; ++i) {
|
||||
for (auto j = 0; j < 2; ++j) {
|
||||
REQUIRE(laplace_score.at(i).at(j) == Catch::Approx(laplace_values.at(i).at(j)).margin(threshold));
|
||||
}
|
||||
}
|
||||
INFO("Test Smoothing B - Original");
|
||||
std::cout << net.dump_cpt();
|
||||
std::cout << "Predict proba of {0, 1, 2} y {1, 2, 3} = " << net.predict_proba({ {0, 1}, {1, 2}, {2, 3} }) << std::endl;
|
||||
std::cout << "ORIGINAL\n";
|
||||
net.fit(Data, C, weights, { "X", "Y", "Z" }, "C", states, bayesnet::Smoothing_t::ORIGINAL);
|
||||
auto original_values = std::vector<std::vector<float>>({ {0.344769, 0.655231}, {0.0421263, 0.957874} });
|
||||
auto original_score = net.predict_proba({ {0, 1}, {1, 2}, {2, 3} });
|
||||
for (auto i = 0; i < 2; ++i) {
|
||||
for (auto j = 0; j < 2; ++j) {
|
||||
REQUIRE(original_score.at(i).at(j) == Catch::Approx(original_values.at(i).at(j)).margin(threshold));
|
||||
}
|
||||
}
|
||||
INFO("Test Smoothing B - Cestnik");
|
||||
std::cout << net.dump_cpt();
|
||||
std::cout << "Predict proba of {0, 1, 2} y {1, 2, 3} = " << net.predict_proba({ {0, 1}, {1, 2}, {2, 3} }) << std::endl;
|
||||
std::cout << "CESTNIK\n";
|
||||
net.fit(Data, C, weights, { "X", "Y", "Z" }, "C", states, bayesnet::Smoothing_t::CESTNIK);
|
||||
auto cestnik_values = std::vector<std::vector<float>>({ {0.353422, 0.646578}, {0.12364, 0.87636} });
|
||||
auto cestnik_score = net.predict_proba({ {0, 1}, {1, 2}, {2, 3} });
|
||||
for (auto i = 0; i < 2; ++i) {
|
||||
for (auto j = 0; j < 2; ++j) {
|
||||
REQUIRE(cestnik_score.at(i).at(j) == Catch::Approx(cestnik_values.at(i).at(j)).margin(threshold));
|
||||
}
|
||||
}
|
||||
INFO("Test Smoothing B - No smoothing");
|
||||
net.fit(Data, C, weights, { "X", "Y", "Z" }, "C", states, bayesnet::Smoothing_t::NONE);
|
||||
auto nosmooth_values = std::vector<std::vector<float>>({ {0.342465753, 0.65753424}, {0.0, 1.0} });
|
||||
auto nosmooth_score = net.predict_proba({ {0, 1}, {1, 2}, {2, 3} });
|
||||
for (auto i = 0; i < 2; ++i) {
|
||||
for (auto j = 0; j < 2; ++j) {
|
||||
REQUIRE(nosmooth_score.at(i).at(j) == Catch::Approx(nosmooth_values.at(i).at(j)).margin(threshold));
|
||||
}
|
||||
}
|
||||
}
|
||||
std::cout << net.dump_cpt();
|
||||
std::cout << "Predict proba of {0, 1, 2} y {1, 2, 3} = " << net.predict_proba({ {0, 1}, {1, 2}, {2, 3} }) << std::endl;
|
||||
|
||||
|
||||
}
|
||||
|
||||
@ -62,17 +62,15 @@ TEST_CASE("Test Node computeCPT", "[Node]")
|
||||
// Create a vector with the names of the classes
|
||||
auto className = std::string("Class");
|
||||
// weights
|
||||
auto weights = torch::tensor({ 1.0, 1.0, 1.0, 1.0 }, torch::kDouble);
|
||||
auto weights = torch::tensor({ 1.0, 1.0, 1.0, 1.0 });
|
||||
std::vector<bayesnet::Node> nodes;
|
||||
for (int i = 0; i < features.size(); i++) {
|
||||
auto node = bayesnet::Node(features[i]);
|
||||
node.setNumStates(states[i]);
|
||||
nodes.push_back(node);
|
||||
}
|
||||
// Create node class with 2 states
|
||||
nodes.push_back(bayesnet::Node(className));
|
||||
nodes[features.size()].setNumStates(2);
|
||||
// The network is c->f1, f2, f3 y f1->f2, f3
|
||||
for (int i = 0; i < features.size(); i++) {
|
||||
// Add class node as parent of all feature nodes
|
||||
nodes[i].addParent(&nodes[features.size()]);
|
||||
|
||||
@ -27,192 +27,189 @@ TEST_CASE("Build basic model", "[BoostA2DE]")
|
||||
auto score = clf.score(raw.Xv, raw.yv);
|
||||
REQUIRE(score == Catch::Approx(0.919271).epsilon(raw.epsilon));
|
||||
}
|
||||
TEST_CASE("Feature_select IWSS", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("glass", true);
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
clf.setHyperparameters({ {"select_features", "IWSS"}, {"threshold", 0.5 } });
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 140);
|
||||
REQUIRE(clf.getNumberOfEdges() == 294);
|
||||
REQUIRE(clf.getNotes().size() == 4);
|
||||
REQUIRE(clf.getNotes()[0] == "Used features in initialization: 4 of 9 with IWSS");
|
||||
REQUIRE(clf.getNotes()[1] == "Convergence threshold reached & 15 models eliminated");
|
||||
REQUIRE(clf.getNotes()[2] == "Pairs not used in train: 2");
|
||||
REQUIRE(clf.getNotes()[3] == "Number of models: 14");
|
||||
}
|
||||
TEST_CASE("Feature_select FCBF", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("glass", true);
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
clf.setHyperparameters({ {"select_features", "FCBF"}, {"threshold", 1e-7 } });
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 110);
|
||||
REQUIRE(clf.getNumberOfEdges() == 231);
|
||||
REQUIRE(clf.getNotes()[0] == "Used features in initialization: 4 of 9 with FCBF");
|
||||
REQUIRE(clf.getNotes()[1] == "Convergence threshold reached & 15 models eliminated");
|
||||
REQUIRE(clf.getNotes()[2] == "Pairs not used in train: 2");
|
||||
REQUIRE(clf.getNotes()[3] == "Number of models: 11");
|
||||
}
|
||||
TEST_CASE("Test used features in train note and score", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("diabetes", true);
|
||||
auto clf = bayesnet::BoostA2DE(true);
|
||||
clf.setHyperparameters({
|
||||
{"order", "asc"},
|
||||
{"convergence", true},
|
||||
{"select_features","CFS"},
|
||||
});
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 144);
|
||||
REQUIRE(clf.getNumberOfEdges() == 288);
|
||||
REQUIRE(clf.getNotes().size() == 2);
|
||||
REQUIRE(clf.getNotes()[0] == "Used features in initialization: 6 of 8 with CFS");
|
||||
REQUIRE(clf.getNotes()[1] == "Number of models: 16");
|
||||
auto score = clf.score(raw.Xv, raw.yv);
|
||||
auto scoret = clf.score(raw.Xt, raw.yt);
|
||||
REQUIRE(score == Catch::Approx(0.856771).epsilon(raw.epsilon));
|
||||
REQUIRE(scoret == Catch::Approx(0.856771).epsilon(raw.epsilon));
|
||||
}
|
||||
TEST_CASE("Voting vs proba", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("iris", true);
|
||||
auto clf = bayesnet::BoostA2DE(false);
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
auto score_proba = clf.score(raw.Xv, raw.yv);
|
||||
auto pred_proba = clf.predict_proba(raw.Xv);
|
||||
clf.setHyperparameters({
|
||||
{"predict_voting",true},
|
||||
});
|
||||
auto score_voting = clf.score(raw.Xv, raw.yv);
|
||||
auto pred_voting = clf.predict_proba(raw.Xv);
|
||||
REQUIRE(score_proba == Catch::Approx(0.98).epsilon(raw.epsilon));
|
||||
REQUIRE(score_voting == Catch::Approx(0.946667).epsilon(raw.epsilon));
|
||||
REQUIRE(pred_voting[83][2] == Catch::Approx(0.53508).epsilon(raw.epsilon));
|
||||
REQUIRE(pred_proba[83][2] == Catch::Approx(0.48394).epsilon(raw.epsilon));
|
||||
REQUIRE(clf.dump_cpt() == "");
|
||||
REQUIRE(clf.topological_order() == std::vector<std::string>());
|
||||
}
|
||||
TEST_CASE("Order asc, desc & random", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("glass", true);
|
||||
std::map<std::string, double> scores{
|
||||
{"asc", 0.752336f }, { "desc", 0.813084f }, { "rand", 0.850467 }
|
||||
};
|
||||
for (const std::string& order : { "asc", "desc", "rand" }) {
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
clf.setHyperparameters({
|
||||
{"order", order},
|
||||
{"bisection", false},
|
||||
{"maxTolerance", 1},
|
||||
{"convergence", false},
|
||||
});
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
auto score = clf.score(raw.Xv, raw.yv);
|
||||
auto scoret = clf.score(raw.Xt, raw.yt);
|
||||
INFO("BoostA2DE order: " + order);
|
||||
REQUIRE(score == Catch::Approx(scores[order]).epsilon(raw.epsilon));
|
||||
REQUIRE(scoret == Catch::Approx(scores[order]).epsilon(raw.epsilon));
|
||||
}
|
||||
}
|
||||
TEST_CASE("Oddities2", "[BoostA2DE]")
|
||||
{
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
auto raw = RawDatasets("iris", true);
|
||||
auto bad_hyper = nlohmann::json{
|
||||
{ { "order", "duck" } },
|
||||
{ { "select_features", "duck" } },
|
||||
{ { "maxTolerance", 0 } },
|
||||
{ { "maxTolerance", 5 } },
|
||||
};
|
||||
for (const auto& hyper : bad_hyper.items()) {
|
||||
INFO("BoostA2DE hyper: " + hyper.value().dump());
|
||||
REQUIRE_THROWS_AS(clf.setHyperparameters(hyper.value()), std::invalid_argument);
|
||||
}
|
||||
REQUIRE_THROWS_AS(clf.setHyperparameters({ {"maxTolerance", 0 } }), std::invalid_argument);
|
||||
auto bad_hyper_fit = nlohmann::json{
|
||||
{ { "select_features","IWSS" }, { "threshold", -0.01 } },
|
||||
{ { "select_features","IWSS" }, { "threshold", 0.51 } },
|
||||
{ { "select_features","FCBF" }, { "threshold", 1e-8 } },
|
||||
{ { "select_features","FCBF" }, { "threshold", 1.01 } },
|
||||
};
|
||||
for (const auto& hyper : bad_hyper_fit.items()) {
|
||||
INFO("BoostA2DE hyper: " + hyper.value().dump());
|
||||
clf.setHyperparameters(hyper.value());
|
||||
REQUIRE_THROWS_AS(clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing), std::invalid_argument);
|
||||
}
|
||||
}
|
||||
TEST_CASE("No features selected", "[BoostA2DE]")
|
||||
{
|
||||
// Check that the note "No features selected in initialization" is added
|
||||
//
|
||||
auto raw = RawDatasets("iris", true);
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
clf.setHyperparameters({ {"select_features","FCBF"}, {"threshold", 1 } });
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNotes().size() == 1);
|
||||
REQUIRE(clf.getNotes()[0] == "No features selected in initialization");
|
||||
}
|
||||
TEST_CASE("Bisection Best", "[BoostA2DE]")
|
||||
{
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
auto raw = RawDatasets("kdd_JapaneseVowels", true, 1200, true, false);
|
||||
clf.setHyperparameters({
|
||||
{"bisection", true},
|
||||
{"maxTolerance", 3},
|
||||
{"convergence", true},
|
||||
{"block_update", false},
|
||||
{"convergence_best", false},
|
||||
});
|
||||
clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 480);
|
||||
REQUIRE(clf.getNumberOfEdges() == 1152);
|
||||
REQUIRE(clf.getNotes().size() == 3);
|
||||
REQUIRE(clf.getNotes().at(0) == "Convergence threshold reached & 15 models eliminated");
|
||||
REQUIRE(clf.getNotes().at(1) == "Pairs not used in train: 83");
|
||||
REQUIRE(clf.getNotes().at(2) == "Number of models: 32");
|
||||
auto score = clf.score(raw.X_test, raw.y_test);
|
||||
auto scoret = clf.score(raw.X_test, raw.y_test);
|
||||
REQUIRE(score == Catch::Approx(0.966667f).epsilon(raw.epsilon));
|
||||
REQUIRE(scoret == Catch::Approx(0.966667f).epsilon(raw.epsilon));
|
||||
}
|
||||
TEST_CASE("Block Update", "[BoostA2DE]")
|
||||
{
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
auto raw = RawDatasets("spambase", true, 500);
|
||||
clf.setHyperparameters({
|
||||
{"bisection", true},
|
||||
{"block_update", true},
|
||||
{"maxTolerance", 3},
|
||||
{"convergence", true},
|
||||
});
|
||||
clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
REQUIRE(clf.getNumberOfNodes() == 58);
|
||||
REQUIRE(clf.getNumberOfEdges() == 165);
|
||||
REQUIRE(clf.getNotes().size() == 3);
|
||||
REQUIRE(clf.getNotes()[0] == "Convergence threshold reached & 15 models eliminated");
|
||||
REQUIRE(clf.getNotes()[1] == "Pairs not used in train: 1588");
|
||||
REQUIRE(clf.getNotes()[2] == "Number of models: 1");
|
||||
auto score = clf.score(raw.X_test, raw.y_test);
|
||||
auto scoret = clf.score(raw.X_test, raw.y_test);
|
||||
REQUIRE(score == Catch::Approx(1.0f).epsilon(raw.epsilon));
|
||||
REQUIRE(scoret == Catch::Approx(1.0f).epsilon(raw.epsilon));
|
||||
//
|
||||
// std::cout << "Number of nodes " << clf.getNumberOfNodes() << std::endl;
|
||||
// std::cout << "Number of edges " << clf.getNumberOfEdges() << std::endl;
|
||||
// std::cout << "Notes size " << clf.getNotes().size() << std::endl;
|
||||
// for (auto note : clf.getNotes()) {
|
||||
// std::cout << note << std::endl;
|
||||
// }
|
||||
// std::cout << "Score " << score << std::endl;
|
||||
}
|
||||
TEST_CASE("Test graph b2a2de", "[BoostA2DE]")
|
||||
{
|
||||
auto raw = RawDatasets("iris", true);
|
||||
auto clf = bayesnet::BoostA2DE();
|
||||
clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
auto graph = clf.graph();
|
||||
REQUIRE(graph.size() == 26);
|
||||
REQUIRE(graph[0] == "digraph BayesNet {\nlabel=<BayesNet BoostA2DE_0>\nfontsize=30\nfontcolor=blue\nlabelloc=t\nlayout=circo\n");
|
||||
REQUIRE(graph[1] == "\"class\" [shape=circle, fontcolor=red, fillcolor=lightblue, style=filled ] \n");
|
||||
}
|
||||
// TEST_CASE("Feature_select IWSS", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("glass", true);
|
||||
// auto clf = bayesnet::BoostAODE();
|
||||
// clf.setHyperparameters({ {"select_features", "IWSS"}, {"threshold", 0.5 } });
|
||||
// clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// REQUIRE(clf.getNumberOfNodes() == 90);
|
||||
// REQUIRE(clf.getNumberOfEdges() == 153);
|
||||
// REQUIRE(clf.getNotes().size() == 2);
|
||||
// REQUIRE(clf.getNotes()[0] == "Used features in initialization: 4 of 9 with IWSS");
|
||||
// REQUIRE(clf.getNotes()[1] == "Number of models: 9");
|
||||
// }
|
||||
// TEST_CASE("Feature_select FCBF", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("glass", true);
|
||||
// auto clf = bayesnet::BoostAODE();
|
||||
// clf.setHyperparameters({ {"select_features", "FCBF"}, {"threshold", 1e-7 } });
|
||||
// clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// REQUIRE(clf.getNumberOfNodes() == 90);
|
||||
// REQUIRE(clf.getNumberOfEdges() == 153);
|
||||
// REQUIRE(clf.getNotes().size() == 2);
|
||||
// REQUIRE(clf.getNotes()[0] == "Used features in initialization: 4 of 9 with FCBF");
|
||||
// REQUIRE(clf.getNotes()[1] == "Number of models: 9");
|
||||
// }
|
||||
// TEST_CASE("Test used features in train note and score", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("diabetes", true);
|
||||
// auto clf = bayesnet::BoostAODE(true);
|
||||
// clf.setHyperparameters({
|
||||
// {"order", "asc"},
|
||||
// {"convergence", true},
|
||||
// {"select_features","CFS"},
|
||||
// });
|
||||
// clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// REQUIRE(clf.getNumberOfNodes() == 72);
|
||||
// REQUIRE(clf.getNumberOfEdges() == 120);
|
||||
// REQUIRE(clf.getNotes().size() == 2);
|
||||
// REQUIRE(clf.getNotes()[0] == "Used features in initialization: 6 of 8 with CFS");
|
||||
// REQUIRE(clf.getNotes()[1] == "Number of models: 8");
|
||||
// auto score = clf.score(raw.Xv, raw.yv);
|
||||
// auto scoret = clf.score(raw.Xt, raw.yt);
|
||||
// REQUIRE(score == Catch::Approx(0.809895813).epsilon(raw.epsilon));
|
||||
// REQUIRE(scoret == Catch::Approx(0.809895813).epsilon(raw.epsilon));
|
||||
// }
|
||||
// TEST_CASE("Voting vs proba", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("iris", true);
|
||||
// auto clf = bayesnet::BoostAODE(false);
|
||||
// clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// auto score_proba = clf.score(raw.Xv, raw.yv);
|
||||
// auto pred_proba = clf.predict_proba(raw.Xv);
|
||||
// clf.setHyperparameters({
|
||||
// {"predict_voting",true},
|
||||
// });
|
||||
// auto score_voting = clf.score(raw.Xv, raw.yv);
|
||||
// auto pred_voting = clf.predict_proba(raw.Xv);
|
||||
// REQUIRE(score_proba == Catch::Approx(0.97333).epsilon(raw.epsilon));
|
||||
// REQUIRE(score_voting == Catch::Approx(0.98).epsilon(raw.epsilon));
|
||||
// REQUIRE(pred_voting[83][2] == Catch::Approx(1.0).epsilon(raw.epsilon));
|
||||
// REQUIRE(pred_proba[83][2] == Catch::Approx(0.86121525).epsilon(raw.epsilon));
|
||||
// REQUIRE(clf.dump_cpt() == "");
|
||||
// REQUIRE(clf.topological_order() == std::vector<std::string>());
|
||||
// }
|
||||
// TEST_CASE("Order asc, desc & random", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("glass", true);
|
||||
// std::map<std::string, double> scores{
|
||||
// {"asc", 0.83645f }, { "desc", 0.84579f }, { "rand", 0.84112 }
|
||||
// };
|
||||
// for (const std::string& order : { "asc", "desc", "rand" }) {
|
||||
// auto clf = bayesnet::BoostAODE();
|
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// clf.setHyperparameters({
|
||||
// {"order", order},
|
||||
// {"bisection", false},
|
||||
// {"maxTolerance", 1},
|
||||
// {"convergence", false},
|
||||
// });
|
||||
// clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing);
|
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// auto score = clf.score(raw.Xv, raw.yv);
|
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// auto scoret = clf.score(raw.Xt, raw.yt);
|
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// INFO("BoostAODE order: " + order);
|
||||
// REQUIRE(score == Catch::Approx(scores[order]).epsilon(raw.epsilon));
|
||||
// REQUIRE(scoret == Catch::Approx(scores[order]).epsilon(raw.epsilon));
|
||||
// }
|
||||
// }
|
||||
// TEST_CASE("Oddities", "[BoostAODE]")
|
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// {
|
||||
// auto clf = bayesnet::BoostAODE();
|
||||
// auto raw = RawDatasets("iris", true);
|
||||
// auto bad_hyper = nlohmann::json{
|
||||
// { { "order", "duck" } },
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||||
// { { "select_features", "duck" } },
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// { { "maxTolerance", 0 } },
|
||||
// { { "maxTolerance", 5 } },
|
||||
// };
|
||||
// for (const auto& hyper : bad_hyper.items()) {
|
||||
// INFO("BoostAODE hyper: " + hyper.value().dump());
|
||||
// REQUIRE_THROWS_AS(clf.setHyperparameters(hyper.value()), std::invalid_argument);
|
||||
// }
|
||||
// REQUIRE_THROWS_AS(clf.setHyperparameters({ {"maxTolerance", 0 } }), std::invalid_argument);
|
||||
// auto bad_hyper_fit = nlohmann::json{
|
||||
// { { "select_features","IWSS" }, { "threshold", -0.01 } },
|
||||
// { { "select_features","IWSS" }, { "threshold", 0.51 } },
|
||||
// { { "select_features","FCBF" }, { "threshold", 1e-8 } },
|
||||
// { { "select_features","FCBF" }, { "threshold", 1.01 } },
|
||||
// };
|
||||
// for (const auto& hyper : bad_hyper_fit.items()) {
|
||||
// INFO("BoostAODE hyper: " + hyper.value().dump());
|
||||
// clf.setHyperparameters(hyper.value());
|
||||
// REQUIRE_THROWS_AS(clf.fit(raw.Xv, raw.yv, raw.features, raw.className, raw.states, raw.smoothing, std::invalid_argument);
|
||||
// }
|
||||
// }
|
||||
|
||||
// TEST_CASE("Bisection Best", "[BoostAODE]")
|
||||
// {
|
||||
// auto clf = bayesnet::BoostAODE();
|
||||
// auto raw = RawDatasets("kdd_JapaneseVowels", true, 1200, true, false);
|
||||
// clf.setHyperparameters({
|
||||
// {"bisection", true},
|
||||
// {"maxTolerance", 3},
|
||||
// {"convergence", true},
|
||||
// {"block_update", false},
|
||||
// {"convergence_best", false},
|
||||
// });
|
||||
// clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// REQUIRE(clf.getNumberOfNodes() == 210);
|
||||
// REQUIRE(clf.getNumberOfEdges() == 378);
|
||||
// REQUIRE(clf.getNotes().size() == 1);
|
||||
// REQUIRE(clf.getNotes().at(0) == "Number of models: 14");
|
||||
// auto score = clf.score(raw.X_test, raw.y_test);
|
||||
// auto scoret = clf.score(raw.X_test, raw.y_test);
|
||||
// REQUIRE(score == Catch::Approx(0.991666675f).epsilon(raw.epsilon));
|
||||
// REQUIRE(scoret == Catch::Approx(0.991666675f).epsilon(raw.epsilon));
|
||||
// }
|
||||
// TEST_CASE("Bisection Best vs Last", "[BoostAODE]")
|
||||
// {
|
||||
// auto raw = RawDatasets("kdd_JapaneseVowels", true, 1500, true, false);
|
||||
// auto clf = bayesnet::BoostAODE(true);
|
||||
// auto hyperparameters = nlohmann::json{
|
||||
// {"bisection", true},
|
||||
// {"maxTolerance", 3},
|
||||
// {"convergence", true},
|
||||
// {"convergence_best", true},
|
||||
// };
|
||||
// clf.setHyperparameters(hyperparameters);
|
||||
// clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// auto score_best = clf.score(raw.X_test, raw.y_test);
|
||||
// REQUIRE(score_best == Catch::Approx(0.980000019f).epsilon(raw.epsilon));
|
||||
// // Now we will set the hyperparameter to use the last accuracy
|
||||
// hyperparameters["convergence_best"] = false;
|
||||
// clf.setHyperparameters(hyperparameters);
|
||||
// clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// auto score_last = clf.score(raw.X_test, raw.y_test);
|
||||
// REQUIRE(score_last == Catch::Approx(0.976666689f).epsilon(raw.epsilon));
|
||||
// }
|
||||
|
||||
// TEST_CASE("Block Update", "[BoostAODE]")
|
||||
// {
|
||||
// auto clf = bayesnet::BoostAODE();
|
||||
// auto raw = RawDatasets("mfeat-factors", true, 500);
|
||||
// clf.setHyperparameters({
|
||||
// {"bisection", true},
|
||||
// {"block_update", true},
|
||||
// {"maxTolerance", 3},
|
||||
// {"convergence", true},
|
||||
// });
|
||||
// clf.fit(raw.X_train, raw.y_train, raw.features, raw.className, raw.states, raw.smoothing);
|
||||
// REQUIRE(clf.getNumberOfNodes() == 868);
|
||||
// REQUIRE(clf.getNumberOfEdges() == 1724);
|
||||
// REQUIRE(clf.getNotes().size() == 3);
|
||||
// REQUIRE(clf.getNotes()[0] == "Convergence threshold reached & 15 models eliminated");
|
||||
// REQUIRE(clf.getNotes()[1] == "Used features in train: 19 of 216");
|
||||
// REQUIRE(clf.getNotes()[2] == "Number of models: 4");
|
||||
// auto score = clf.score(raw.X_test, raw.y_test);
|
||||
// auto scoret = clf.score(raw.X_test, raw.y_test);
|
||||
// REQUIRE(score == Catch::Approx(0.99f).epsilon(raw.epsilon));
|
||||
// REQUIRE(scoret == Catch::Approx(0.99f).epsilon(raw.epsilon));
|
||||
// //
|
||||
// // std::cout << "Number of nodes " << clf.getNumberOfNodes() << std::endl;
|
||||
// // std::cout << "Number of edges " << clf.getNumberOfEdges() << std::endl;
|
||||
// // std::cout << "Notes size " << clf.getNotes().size() << std::endl;
|
||||
// // for (auto note : clf.getNotes()) {
|
||||
// // std::cout << note << std::endl;
|
||||
// // }
|
||||
// // std::cout << "Score " << score << std::endl;
|
||||
// }
|
||||
@ -1,72 +0,0 @@
|
||||
// ***************************************************************
|
||||
// SPDX-FileCopyrightText: Copyright 2024 Ricardo Montañana Gómez
|
||||
// SPDX-FileType: SOURCE
|
||||
// SPDX-License-Identifier: MIT
|
||||
// ***************************************************************
|
||||
|
||||
#include <catch2/catch_test_macros.hpp>
|
||||
#include <catch2/catch_approx.hpp>
|
||||
#include <catch2/generators/catch_generators.hpp>
|
||||
#include <catch2/matchers/catch_matchers.hpp>
|
||||
#include <string>
|
||||
#include <vector>
|
||||
#include "TestUtils.h"
|
||||
#include "bayesnet/utils/Mst.h"
|
||||
|
||||
|
||||
TEST_CASE("MST::insertElement tests", "[MST]")
|
||||
{
|
||||
bayesnet::MST mst({}, torch::tensor({}), 0);
|
||||
SECTION("Insert into an empty list")
|
||||
{
|
||||
std::list<int> variables;
|
||||
mst.insertElement(variables, 5);
|
||||
REQUIRE(variables == std::list<int>{5});
|
||||
}
|
||||
SECTION("Insert a non-duplicate element")
|
||||
{
|
||||
std::list<int> variables = { 1, 2, 3 };
|
||||
mst.insertElement(variables, 4);
|
||||
REQUIRE(variables == std::list<int>{4, 1, 2, 3});
|
||||
}
|
||||
SECTION("Insert a duplicate element")
|
||||
{
|
||||
std::list<int> variables = { 1, 2, 3 };
|
||||
mst.insertElement(variables, 2);
|
||||
REQUIRE(variables == std::list<int>{1, 2, 3});
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("MST::reorder tests", "[MST]")
|
||||
{
|
||||
bayesnet::MST mst({}, torch::tensor({}), 0);
|
||||
SECTION("Reorder simple graph")
|
||||
{
|
||||
std::vector<std::pair<float, std::pair<int, int>>> T = { {2.0, {1, 2}}, {1.0, {0, 1}} };
|
||||
auto result = mst.reorder(T, 0);
|
||||
REQUIRE(result == std::vector<std::pair<int, int>>{{0, 1}, { 1, 2 }});
|
||||
}
|
||||
SECTION("Reorder with disconnected graph")
|
||||
{
|
||||
std::vector<std::pair<float, std::pair<int, int>>> T = { {2.0, {2, 3}}, {1.0, {0, 1}} };
|
||||
auto result = mst.reorder(T, 0);
|
||||
REQUIRE(result == std::vector<std::pair<int, int>>{{0, 1}, { 2, 3 }});
|
||||
}
|
||||
}
|
||||
|
||||
TEST_CASE("MST::maximumSpanningTree tests", "[MST]")
|
||||
{
|
||||
std::vector<std::string> features = { "A", "B", "C" };
|
||||
auto weights = torch::tensor({
|
||||
{0.0, 1.0, 2.0},
|
||||
{1.0, 0.0, 3.0},
|
||||
{2.0, 3.0, 0.0}
|
||||
});
|
||||
bayesnet::MST mst(features, weights, 0);
|
||||
|
||||
SECTION("MST of a complete graph")
|
||||
{
|
||||
auto result = mst.maximumSpanningTree();
|
||||
REQUIRE(result.size() == 2); // Un MST para 3 nodos tiene 2 aristas
|
||||
}
|
||||
}
|
||||
@ -16,7 +16,7 @@
|
||||
#include "TestUtils.h"
|
||||
|
||||
std::map<std::string, std::string> modules = {
|
||||
{ "mdlp", "2.0.1" },
|
||||
{ "mdlp", "2.0.0" },
|
||||
{ "Folding", "1.1.0" },
|
||||
{ "json", "3.11" },
|
||||
{ "ArffFiles", "1.1.0" }
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -1 +1 @@
|
||||
Subproject commit a4329f5f9dfdb18ee3faa63bd5b665f2f253b8d2
|
||||
Subproject commit a5316928d408266aa425f64131ab0f592b010a8d
|
||||
@ -1 +1 @@
|
||||
Subproject commit 506276c59217429c93abd2fe9507c7f45eb81072
|
||||
Subproject commit 4e8d92bf02f7d1c8006a0e7a5ecabd8e62d98502
|
||||
Loading…
Reference in New Issue
Block a user