pyensemblefs 0.3.13__tar.gz

pyensemblefs-0.3.13/LICENSE

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+MIT License
+
+Copyright (c) 2025 
+
+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.

pyensemblefs-0.3.13/PKG-INFO

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+Metadata-Version: 2.4
+Name: pyensemblefs
+Version: 0.3.13
+Summary: Ensemble feature selection with bootstrapping, heterogeneous selectors, and stability analysis.
+Author: David Chushig-Muzo, Bryan Peralta-Arboleda, Eva Milara, Cristina Soguero-Ruiz
+License: MIT License
+        
+        Copyright (c) 2025 
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/cdchushig/pyensemblefs.git
+Project-URL: Issues, https://github.com/cdchushig
+Keywords: feature selection,ensemble,stability,machine learning
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.23
+Requires-Dist: pandas>=2.0
+Requires-Dist: scikit-learn>=1.3
+Requires-Dist: scipy>=1.10
+Requires-Dist: networkx>=3.0
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: seaborn>=0.13
+Requires-Dist: upsetplot>=0.8
+Requires-Dist: requests>=2.31
+Requires-Dist: abcvoting>=2.0
+Requires-Dist: coloredlogs>=15.0
+Requires-Dist: tqdm>=4.66
+Requires-Dist: joblib>=1.3
+Requires-Dist: skrebate>=0.62
+Provides-Extra: viz
+Requires-Dist: matplotlib>=3.7; extra == "viz"
+Requires-Dist: seaborn>=0.13; extra == "viz"
+Requires-Dist: upsetplot>=0.8; extra == "viz"
+Provides-Extra: relief
+Requires-Dist: skrebate>=0.62; extra == "relief"
+Provides-Extra: dev
+Requires-Dist: pytest>=7; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: mypy>=1.8; extra == "dev"
+Requires-Dist: build>=1.2.1; extra == "dev"
+Requires-Dist: twine>=5; extra == "dev"
+Dynamic: license-file
+
+pyensemblefs: a multi-threading Python library for ensemble feature selection. 
+====
+
+This repository hosts **pyensemblefs**, a Python library for *ensemble feature selection*. Supports heterogeneous ensembles, bootstrapped evaluation, and stability analysis across feature selectors.<br> 
+It assists researchers in feature selection tasks without requiring significant programming effort.
+
+---
+
+## Installation and setup
+
+```bash
+pip install pyensemblefs
+```
+
+To download the source code, you can clone it from the GitHub repository:
+
+```bash
+git clone git@github.com:cdchushig/pyensemblefs.git
+```
+
+Requirements: Python ≥ 3.9, scikit-learn ≥ 1.2
+
+---
+
+## Library Highlights
+
+**pyensemblefs** automatically extracts relevant features in datasets using bootstrapping and ensemble aggregation.
+
+* **Intuitive, reproducible workflows:** compatible with scikit-learn pipelines.  
+* **Comprehensive documentation:** each feature selection and aggregation method is fully described.  
+* **Extensible architecture:** easily add custom selection or aggregation strategies.
+
+---
+
+## Main Features
+
+* **Bootstrap-based ensemble selection:** assess variability across resamples.
+
+* **Heterogeneous ensembles:** combine different feature selectors (e.g., ANOVA, MI, Chi²).
+
+* **Unified aggregator API:** aggregate results from scores, ranks, or binary supports.
+
+* **Visualization tools:** plot selection frequency, consensus ranks, and stability matrices.
+
+* **Stability metrics:** compute indices such as Kuncheva, Jaccard, or Spearman correlation.
+
+* **Extensible design:** register custom selectors and aggregators via a single factory call.
+
+---
+
+## Get started
+
+Example using a built-in dataset and a simple configuration:
+
+```python
+import pyensemblefs
+from pyensemblefs.datasets import load_pima_dataset
+
+# Load dataset
+df = load_pima_dataset()
+
+# Retrieve a pre-defined configuration (e.g., Relief filter)
+cfg = pyensemblefs.get_config('relief', n_bootrap=100, fnc_aggregation='voting')
+
+# Compute feature scores
+df_feature_scores = pyensemblefs.compute_scores(cfg, df)
+
+# Extract the most relevant features
+df_filtered = pyensemblefs.extract_features(n_max_features=10)
+```
+
+---
+
+## Heterogeneous ensemble feature selection
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, f_classif, mutual_info_classif, chi2
+from pyensemblefs.ensemble.metabootstrapper import MetaBootstrapper
+
+X, y = load_breast_cancer(return_X_y=True)
+
+fs_methods = [
+    SelectKBest(score_func=f_classif, k=10),
+    SelectKBest(score_func=mutual_info_classif, k=10),
+    SelectKBest(score_func=chi2, k=10),
+]
+
+# Assign higher weight to ANOVA
+weights = {"SelectKBest": 2.0}
+
+boot = MetaBootstrapper(
+    fs_methods,
+    n_bootstraps=20,
+    n_jobs=4,
+    random_state=42,
+    strategy="random",
+    normalize_scores=True,
+    method_weights=weights,
+    verbose=True
+)
+
+boot.fit(X, y)
+
+print("First bootstrap method:", boot.results_[0]["method"])
+print("Normalized + weighted scores:", boot.results_[0]["scores"][:10])
+```
+
+---
+
+## Visualization of frequency, top-k, and stability
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, mutual_info_classif
+from pyensemblefs.ensemble.bootstrapper import Bootstrapper
+from pyensemblefs.aggregators.rank import MeanRankAggregator
+from pyensemblefs.aggregators.score import MeanAggregator
+from pyensemblefs.viz.visualizer import Visualizer
+
+X, y = load_breast_cancer(return_X_y=True)
+fs = SelectKBest(score_func=mutual_info_classif, k=10)
+boot = Bootstrapper(fs, n_bootstraps=25, n_jobs=2)
+boot.fit(X, y)
+
+# Aggregators
+rank_agg = MeanRankAggregator(top_k=10).fit(boot.results_)
+mean_agg = MeanAggregator(top_k=10).fit(boot.results_)
+
+# Visualizations
+Visualizer.feature_frequency(boot.results_, n_features=X.shape[1], top_k=15)
+Visualizer.consensus_ranking(rank_agg.final_ranking_, top_k=10)
+Visualizer.stability_heatmap(boot.results_, n_features=X.shape[1])
+Visualizer.compare_aggregators({
+    "RankAggregator": rank_agg.final_ranking_,
+    "MeanAggregator": mean_agg.final_ranking_,
+}, top_k=10)
+```
+
+All figures are automatically saved under ./images/.
+
+---
+
+## Stability Metrics
+
+Stability analysis quantifies how consistent the selected features remain across bootstrap samples.
+
+```python
+from pyensemblefs.stats.stability import StabilityEvaluator
+
+stab = StabilityEvaluator(metric="kuncheva")
+stability_score = stab.compute(boot.results_binary_)
+print("Stability (Kuncheva):", stability_score)
+```
+
+Available metrics include Jaccard,Dice, Ochiai, Hamming, Novovicova, Davis, Lustgartn, Phi, Kappa, Nogueira, Yu, and Zucknick.
+They can be directly compared between homogeneous and heterogeneous ensembles.
+
+
+---
+
+## Usage examples (scikit-learn compatible)
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, f_classif
+from src.ensemble.bootstrapper import Bootstrapper
+from src.aggregators.score import MeanAggregator
+from src.aggregators.rank import MeanRankAggregator
+
+X, y = load_breast_cancer(return_X_y=True)
+
+fs = SelectKBest(score_func=f_classif, k=10)
+boot = Bootstrapper(fs, n_bootstraps=30, n_jobs=4, random_state=42)
+boot.fit(X, y)
+
+# Aggregate scores and ranks
+mean_agg = MeanAggregator().fit(boot.results_)
+rank_agg = MeanRankAggregator().fit(boot.results_)
+
+print("Consensus scores:", mean_agg.scores_[:10])
+print("Consensus ranks:", rank_agg.rank_[:10])
+```
+
+```python
+from sklearn.feature_selection import SelectKBest, chi2
+from src.ensemble.bootstrapper import Bootstrapper
+from src.aggregators.score import MeanAggregator
+
+fs = SelectKBest(score_func=chi2, k=5)
+boot = Bootstrapper(fs, n_bootstraps=15, n_jobs=2)
+boot.fit(X, y)
+
+mean_agg = MeanAggregator().fit(boot.results_)
+print("Consensus Scores (Chi2):", mean_agg.scores_)
+```
+
+---
+
+## How It Fits Together
+
+Data → Bootstrapper / MetaBootstrapper<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;↓<br>
+Aggregators (Score / Rank / Subset)<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;↓<br>
+Visualizer / StabilityEvaluator → Reports
+
+---
+
+## Citation
+
+If you use pyensemblefs in academic work, please cite:
+
+@software{pyensemblefs2025,<br>
+  author = {Chushig-Muzo, C.D. and collaborators},<br>
+  title  = {pyensemblefs: Ensemble Feature Selection Library},<br>
+  year   = {2025},<br>
+  url    = {https://github.com/cdchushig/pyensemblefs}
+}
+
+
+---
+
+## License
+
+This project is licensed under the MIT License – see the [LICENSE](LICENSE) file for details.
+

pyensemblefs-0.3.13/README.md

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+pyensemblefs: a multi-threading Python library for ensemble feature selection. 
+====
+
+This repository hosts **pyensemblefs**, a Python library for *ensemble feature selection*. Supports heterogeneous ensembles, bootstrapped evaluation, and stability analysis across feature selectors.<br> 
+It assists researchers in feature selection tasks without requiring significant programming effort.
+
+---
+
+## Installation and setup
+
+```bash
+pip install pyensemblefs
+```
+
+To download the source code, you can clone it from the GitHub repository:
+
+```bash
+git clone git@github.com:cdchushig/pyensemblefs.git
+```
+
+Requirements: Python ≥ 3.9, scikit-learn ≥ 1.2
+
+---
+
+## Library Highlights
+
+**pyensemblefs** automatically extracts relevant features in datasets using bootstrapping and ensemble aggregation.
+
+* **Intuitive, reproducible workflows:** compatible with scikit-learn pipelines.  
+* **Comprehensive documentation:** each feature selection and aggregation method is fully described.  
+* **Extensible architecture:** easily add custom selection or aggregation strategies.
+
+---
+
+## Main Features
+
+* **Bootstrap-based ensemble selection:** assess variability across resamples.
+
+* **Heterogeneous ensembles:** combine different feature selectors (e.g., ANOVA, MI, Chi²).
+
+* **Unified aggregator API:** aggregate results from scores, ranks, or binary supports.
+
+* **Visualization tools:** plot selection frequency, consensus ranks, and stability matrices.
+
+* **Stability metrics:** compute indices such as Kuncheva, Jaccard, or Spearman correlation.
+
+* **Extensible design:** register custom selectors and aggregators via a single factory call.
+
+---
+
+## Get started
+
+Example using a built-in dataset and a simple configuration:
+
+```python
+import pyensemblefs
+from pyensemblefs.datasets import load_pima_dataset
+
+# Load dataset
+df = load_pima_dataset()
+
+# Retrieve a pre-defined configuration (e.g., Relief filter)
+cfg = pyensemblefs.get_config('relief', n_bootrap=100, fnc_aggregation='voting')
+
+# Compute feature scores
+df_feature_scores = pyensemblefs.compute_scores(cfg, df)
+
+# Extract the most relevant features
+df_filtered = pyensemblefs.extract_features(n_max_features=10)
+```
+
+---
+
+## Heterogeneous ensemble feature selection
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, f_classif, mutual_info_classif, chi2
+from pyensemblefs.ensemble.metabootstrapper import MetaBootstrapper
+
+X, y = load_breast_cancer(return_X_y=True)
+
+fs_methods = [
+    SelectKBest(score_func=f_classif, k=10),
+    SelectKBest(score_func=mutual_info_classif, k=10),
+    SelectKBest(score_func=chi2, k=10),
+]
+
+# Assign higher weight to ANOVA
+weights = {"SelectKBest": 2.0}
+
+boot = MetaBootstrapper(
+    fs_methods,
+    n_bootstraps=20,
+    n_jobs=4,
+    random_state=42,
+    strategy="random",
+    normalize_scores=True,
+    method_weights=weights,
+    verbose=True
+)
+
+boot.fit(X, y)
+
+print("First bootstrap method:", boot.results_[0]["method"])
+print("Normalized + weighted scores:", boot.results_[0]["scores"][:10])
+```
+
+---
+
+## Visualization of frequency, top-k, and stability
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, mutual_info_classif
+from pyensemblefs.ensemble.bootstrapper import Bootstrapper
+from pyensemblefs.aggregators.rank import MeanRankAggregator
+from pyensemblefs.aggregators.score import MeanAggregator
+from pyensemblefs.viz.visualizer import Visualizer
+
+X, y = load_breast_cancer(return_X_y=True)
+fs = SelectKBest(score_func=mutual_info_classif, k=10)
+boot = Bootstrapper(fs, n_bootstraps=25, n_jobs=2)
+boot.fit(X, y)
+
+# Aggregators
+rank_agg = MeanRankAggregator(top_k=10).fit(boot.results_)
+mean_agg = MeanAggregator(top_k=10).fit(boot.results_)
+
+# Visualizations
+Visualizer.feature_frequency(boot.results_, n_features=X.shape[1], top_k=15)
+Visualizer.consensus_ranking(rank_agg.final_ranking_, top_k=10)
+Visualizer.stability_heatmap(boot.results_, n_features=X.shape[1])
+Visualizer.compare_aggregators({
+    "RankAggregator": rank_agg.final_ranking_,
+    "MeanAggregator": mean_agg.final_ranking_,
+}, top_k=10)
+```
+
+All figures are automatically saved under ./images/.
+
+---
+
+## Stability Metrics
+
+Stability analysis quantifies how consistent the selected features remain across bootstrap samples.
+
+```python
+from pyensemblefs.stats.stability import StabilityEvaluator
+
+stab = StabilityEvaluator(metric="kuncheva")
+stability_score = stab.compute(boot.results_binary_)
+print("Stability (Kuncheva):", stability_score)
+```
+
+Available metrics include Jaccard,Dice, Ochiai, Hamming, Novovicova, Davis, Lustgartn, Phi, Kappa, Nogueira, Yu, and Zucknick.
+They can be directly compared between homogeneous and heterogeneous ensembles.
+
+
+---
+
+## Usage examples (scikit-learn compatible)
+
+```python
+from sklearn.datasets import load_breast_cancer
+from sklearn.feature_selection import SelectKBest, f_classif
+from src.ensemble.bootstrapper import Bootstrapper
+from src.aggregators.score import MeanAggregator
+from src.aggregators.rank import MeanRankAggregator
+
+X, y = load_breast_cancer(return_X_y=True)
+
+fs = SelectKBest(score_func=f_classif, k=10)
+boot = Bootstrapper(fs, n_bootstraps=30, n_jobs=4, random_state=42)
+boot.fit(X, y)
+
+# Aggregate scores and ranks
+mean_agg = MeanAggregator().fit(boot.results_)
+rank_agg = MeanRankAggregator().fit(boot.results_)
+
+print("Consensus scores:", mean_agg.scores_[:10])
+print("Consensus ranks:", rank_agg.rank_[:10])
+```
+
+```python
+from sklearn.feature_selection import SelectKBest, chi2
+from src.ensemble.bootstrapper import Bootstrapper
+from src.aggregators.score import MeanAggregator
+
+fs = SelectKBest(score_func=chi2, k=5)
+boot = Bootstrapper(fs, n_bootstraps=15, n_jobs=2)
+boot.fit(X, y)
+
+mean_agg = MeanAggregator().fit(boot.results_)
+print("Consensus Scores (Chi2):", mean_agg.scores_)
+```
+
+---
+
+## How It Fits Together
+
+Data → Bootstrapper / MetaBootstrapper<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;↓<br>
+Aggregators (Score / Rank / Subset)<br>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;↓<br>
+Visualizer / StabilityEvaluator → Reports
+
+---
+
+## Citation
+
+If you use pyensemblefs in academic work, please cite:
+
+@software{pyensemblefs2025,<br>
+  author = {Chushig-Muzo, C.D. and collaborators},<br>
+  title  = {pyensemblefs: Ensemble Feature Selection Library},<br>
+  year   = {2025},<br>
+  url    = {https://github.com/cdchushig/pyensemblefs}
+}
+
+
+---
+
+## License
+
+This project is licensed under the MIT License – see the [LICENSE](LICENSE) file for details.
+

pyensemblefs-0.3.13/pyproject.toml

@@ -0,0 +1,63 @@
+[build-system]
+requires = ["setuptools>=69", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "pyensemblefs"
+version = "0.3.13"
+description = "Ensemble feature selection with bootstrapping, heterogeneous selectors, and stability analysis."
+readme = { file = "README.md", content-type = "text/markdown" }
+requires-python = ">=3.9"
+license = { file = "LICENSE" }
+authors = [{ name = "David Chushig-Muzo" },
+  { name = "Bryan Peralta-Arboleda" },
+  { name = "Eva Milara" },
+  { name = "Cristina Soguero-Ruiz" }]
+keywords = ["feature selection", "ensemble", "stability", "machine learning"]
+classifiers = [
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "License :: OSI Approved :: MIT License",
+  "Operating System :: OS Independent",
+  "Topic :: Scientific/Engineering :: Artificial Intelligence",
+]
+
+dependencies = [
+  "numpy>=1.23",
+  "pandas>=2.0",
+  "scikit-learn>=1.3",
+  "scipy>=1.10",
+  "networkx>=3.0",
+  "matplotlib>=3.7",
+  "seaborn>=0.13",
+  "upsetplot>=0.8",
+  "requests>=2.31",
+  "abcvoting>=2.0",
+  "coloredlogs>=15.0",
+  "tqdm>=4.66",
+  "joblib>=1.3",
+  "skrebate>=0.62"   
+]
+
+[project.optional-dependencies]
+viz = ["matplotlib>=3.7", "seaborn>=0.13", "upsetplot>=0.8"]
+relief = ["skrebate>=0.62"]
+dev = ["pytest>=7", "ruff>=0.4", "mypy>=1.8", "build>=1.2.1", "twine>=5"]
+
+[project.urls]
+Homepage = "https://github.com/cdchushig/pyensemblefs.git"
+Issues = "https://github.com/cdchushig"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+include = ["pyensemblefs*"]
+
+[tool.setuptools.package-data]
+pyensemblefs = ["py.typed"]
+
+[project.scripts]
+pyefs = "pyensemblefs.cli:main"
+pyefs-stab = "pyensemblefs.main_stab:main"
+pyefs-pipeline = "pyensemblefs.pipeline:main"
+pyefs-gen = "pyensemblefs.tools.generate_feature_sets:main"
+pyefs-sim = "pyensemblefs.tools.sim_matrix:main"

pyensemblefs-0.3.13/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

pyensemblefs-0.3.13/src/pyensemblefs/__init__.py

@@ -0,0 +1,17 @@
+from __future__ import annotations
+from importlib.metadata import version, PackageNotFoundError
+
+from . import datasets
+from .api import get_config, compute_scores, extract_features
+
+__all__ = [
+  "aggregators","ensemble","estimators","fsmethods","selectors",
+  "stability","tools","utils","viz",
+  "datasets","get_config","compute_scores","extract_features"
+]
+
+def _get_version() -> str:
+    try: return version("pyensemblefs")
+    except PackageNotFoundError: return "0.0.0"
+
+__version__ = _get_version()