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VicentePerezSoloviev · Sep 29, 2023 · 451f992 · 451f992
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diff --git a/EDAspy.egg-info/PKG-INFO b/EDAspy.egg-info/PKG-INFO
@@ -1,17 +1,17 @@
 Metadata-Version: 2.1
 Name: EDAspy
-Version: 1.1.1
+Version: 1.1.2
 Summary: EDAspy is a Python package that implements Estimation of Distribution Algorithms. EDAspy allows toeither use already existing implementations or customize the EDAs baseline easily building it bymodules so new research can be easily developed. It also has several benchmarks for comparisons.
 Home-page: https://github.com/VicentePerezSoloviev/EDAspy
 Author: Vicente P. Soloviev
 Author-email: [email protected]
 License: MIT
-Download-URL: https://github.com/VicentePerezSoloviev/EDAspy/archive/1.1.1.tar.gz
+Download-URL: https://github.com/VicentePerezSoloviev/EDAspy/archive/1.1.2.tar.gz
 Description: # <img src='https://raw.githubusercontent.com/VicentePerezSoloviev/EDAspy/master/Logo%20EDAspy.png' align="right" height="150"/>
 
         [![PyPI](https://img.shields.io/pypi/v/edaspy)](https://pypi.python.org/pypi/EDAspy/)
         [![PyPI license](https://img.shields.io/pypi/l/EDAspy.svg)](https://pypi.python.org/pypi/EDAspy/)
-        [![Downloads](https://static.pepy.tech/personalized-badge/edaspy?period=total&units=none&left_color=grey&right_color=blue&left_text=downloads)](https://pepy.tech/project/edaspy)
+        [![Downloads](https://static.pepy.tech/badge/edaspy)](https://pepy.tech/project/edaspy)
         [![Documentation Status](https://readthedocs.org/projects/edaspy/badge/?version=latest)](https://edaspy.readthedocs.io/en/latest/?badge=latest)
 
         # EDAspy
@@ -48,7 +48,10 @@ Description: # <img src='https://raw.githubusercontent.com/VicentePerezSoloviev/
         * UMDAc: Univariate Marginal Distribution Algorithm continuous [3]. In this EDA all the variables assume a Gaussian distribution and there are not dependencies considered between the variables. Some usages include hyperparameter optimization, for example.
 
 
-        * UnivariateKEDA: Univariate Kernel Estimation of Distribution Algorithm [4]. Each variables distribution is estimated using Kernel Density Estimation. 
+        * UnivariateKEDA: Univariate Kernel Estimation of Distribution Algorithm [4]. Each variables distribution is estimated using Kernel Density Estimation.
+
+
+        * UMDAcat: Univariate Marginal Distribution Algorithm categorical [2]. UMDA variant for categorical data, where more than two possible values per dimension are used (otherwise, use binary version).
 
 
         * EGNA: Estimation of Gaussian Distribution Algorithm [5][6]. This is a complex implementation in which dependencies between the variables are considered during the optimization. In each iteration, a Gaussian Bayesian network is learned and sampled. The variables in the model are assumed to be Gaussian and also de dependencies between them. This implementation is focused in continuous optimization.
@@ -63,7 +66,7 @@ Description: # <img src='https://raw.githubusercontent.com/VicentePerezSoloviev/
         * MultivariateKEDA: Special case of SPEDA approach in which all nodes are restricted to be estimated using KDE (Gaussian nodes are forbidden) [7]. It is also an archive-based approach.
 
 
-        * Categorical EDA. In this implementation we consider some independent categorical variables. Some usages include portfolio optimization, for exampled.
+        * EBNA: Estimation of Bayesian Network Algorithm [1]. This version of EDAs is used for categorical data. The probabilistic model used is a Categorical Bayesian network, where conditional dependencies between variables can be analyzed. 
 
 
         Some tools are also available in EDAspy such as the Bayesian network structure plotting, for visualizing the graph learnt in some of the implementations, if needed.
@@ -99,7 +102,7 @@ Description: # <img src='https://raw.githubusercontent.com/VicentePerezSoloviev/
         ```bash
             git clone https://github.com/VicentePerezSoloviev/EDAspy.git
             cd EDAspy
-            git checkout v1.0.0 # You can checkout a specific version if you want
+            git checkout v1.1.2 # You can checkout a specific version if you want
             python setup.py install
         ```
         ## Testing 
@@ -133,12 +136,11 @@ Description: # <img src='https://raw.githubusercontent.com/VicentePerezSoloviev/
 
         [7] Soloviev, Vicente P.& Bielza, Concha & LarraÃ±aga, Pedro (2023). Semiparametric Estimation of Distribution Algorithms for continuous optimization. IEEE Transactions on Evolutionary Computation.
 
-
 Keywords: EDA,estimation,bayesian,evolutionary,algorithm,optimization,time_series,feature,selection,semiparametric,Gaussian
 Platform: UNKNOWN
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.0
+Requires-Python: >=3.8
 Description-Content-Type: text/markdown
diff --git a/EDAspy.egg-info/SOURCES.txt b/EDAspy.egg-info/SOURCES.txt
@@ -18,42 +18,53 @@ EDAspy/optimization/custom/__init__.py
 EDAspy/optimization/custom/eda_custom.py
 EDAspy/optimization/custom/initialization_models/__init__.py
 EDAspy/optimization/custom/initialization_models/_generation_init.py
+EDAspy/optimization/custom/initialization_models/categorical_geninit.py
+EDAspy/optimization/custom/initialization_models/latin_hypercube_sampling_geninit.py
 EDAspy/optimization/custom/initialization_models/multi_gauss_geninit.py
 EDAspy/optimization/custom/initialization_models/uni_bin_geninit.py
 EDAspy/optimization/custom/initialization_models/uni_gauss_geninit.py
 EDAspy/optimization/custom/initialization_models/uniform_geninit.py
 EDAspy/optimization/custom/probabilistic_models/__init__.py
 EDAspy/optimization/custom/probabilistic_models/_probabilistic_model.py
+EDAspy/optimization/custom/probabilistic_models/discrete_bayesian_network.py
 EDAspy/optimization/custom/probabilistic_models/gaussian_bayesian_network.py
 EDAspy/optimization/custom/probabilistic_models/kde_bayesian_network.py
 EDAspy/optimization/custom/probabilistic_models/multivariate_gaussian.py
 EDAspy/optimization/custom/probabilistic_models/semiparametric_bayesian_network.py
 EDAspy/optimization/custom/probabilistic_models/univariate_binary.py
+EDAspy/optimization/custom/probabilistic_models/univariate_categorical.py
 EDAspy/optimization/custom/probabilistic_models/univariate_gaussian.py
 EDAspy/optimization/custom/probabilistic_models/univariate_kde.py
 EDAspy/optimization/multivariate/__init__.py
+EDAspy/optimization/multivariate/ebna.py
 EDAspy/optimization/multivariate/egna.py
 EDAspy/optimization/multivariate/emna.py
 EDAspy/optimization/multivariate/keda.py
 EDAspy/optimization/multivariate/speda.py
 EDAspy/optimization/univariate/__init__.py
 EDAspy/optimization/univariate/keda.py
 EDAspy/optimization/univariate/umda_binary.py
+EDAspy/optimization/univariate/umda_categorical.py
 EDAspy/optimization/univariate/umda_continuous.py
-EDAspy/timeseries/TS_transformations.py
-EDAspy/timeseries/TransformationsFeatureSelection.py
-EDAspy/timeseries/__init__.py
 tests/__init__.py
-tests/test_egna.py
-tests/test_emna.py
-tests/test_gbn.py
-tests/test_geninit.py
-tests/test_kdebn.py
-tests/test_keda.py
-tests/test_multivariate_keda.py
-tests/test_pm.py
-tests/test_spbn.py
-tests/test_speda.py
-tests/test_umdac.py
-tests/test_umdad.py
-tests/test_univariate_keda.py
+tests/edas_multivariate/__init__.py
+tests/edas_multivariate/test_ebna.py
+tests/edas_multivariate/test_egna.py
+tests/edas_multivariate/test_emna.py
+tests/edas_multivariate/test_multivariate_keda.py
+tests/edas_multivariate/test_speda.py
+tests/edas_univariate/__init__.py
+tests/edas_univariate/test_umdac.py
+tests/edas_univariate/test_umdacat.py
+tests/edas_univariate/test_umdad.py
+tests/edas_univariate/test_univariate_keda.py
+tests/inits/__init__.py
+tests/inits/test_geninit.py
+tests/pms/__init__.py
+tests/pms/test_discrete_bn.py
+tests/pms/test_gbn.py
+tests/pms/test_kdebn.py
+tests/pms/test_spbn.py
+tests/pms/test_uni_bin_pm.py
+tests/pms/test_uni_cat_pm.py
+tests/pms/test_uni_gauss_pm.py
diff --git a/EDAspy/optimization/custom/probabilistic_models/discrete_bayesian_network.py b/EDAspy/optimization/custom/probabilistic_models/discrete_bayesian_network.py
@@ -4,7 +4,7 @@
 import numpy as np
 import pandas as pd
 from pgmpy.models import BayesianNetwork
-from pgmpy.estimators import BicScore, ExhaustiveSearch, MaximumLikelihoodEstimator
+from pgmpy.estimators import HillClimbSearch, MaximumLikelihoodEstimator
 
 from ._probabilistic_model import ProbabilisticModel
 
@@ -47,9 +47,8 @@ def learn(self, dataset: np.array, *args, **kwargs):
         self.pm.add_nodes_from(self.variables)
 
         # learn structure
-        bic = BicScore(data)
-        es = ExhaustiveSearch(data, scoring_method=bic)
-        best_structure = es.estimate()
+        es = HillClimbSearch(data)
+        best_structure = es.estimate(scoring_method='bicscore', max_iter=1000, show_progress=False)
 
         for edge in best_structure.edges():
             self.pm.add_edge(edge[0], edge[1])

diff --git a/docs/_build/doctrees/EDAspy.benchmarks.doctree b/docs/_build/doctrees/EDAspy.benchmarks.doctree
diff --git a/docs/_build/doctrees/EDAspy.doctree b/docs/_build/doctrees/EDAspy.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.custom.doctree b/docs/_build/doctrees/EDAspy.optimization.custom.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.custom.initialization_models.doctree b/docs/_build/doctrees/EDAspy.optimization.custom.initialization_models.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.custom.probabilistic_models.doctree b/docs/_build/doctrees/EDAspy.optimization.custom.probabilistic_models.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.doctree b/docs/_build/doctrees/EDAspy.optimization.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.multivariate.doctree b/docs/_build/doctrees/EDAspy.optimization.multivariate.doctree
diff --git a/docs/_build/doctrees/EDAspy.optimization.univariate.doctree b/docs/_build/doctrees/EDAspy.optimization.univariate.doctree
diff --git a/docs/_build/doctrees/categorical_optimization.doctree b/docs/_build/doctrees/categorical_optimization.doctree
diff --git a/docs/_build/doctrees/changelog.doctree b/docs/_build/doctrees/changelog.doctree
diff --git a/docs/_build/doctrees/eda_custom.doctree b/docs/_build/doctrees/eda_custom.doctree
diff --git a/docs/_build/doctrees/egna_opt.doctree b/docs/_build/doctrees/egna_opt.doctree
diff --git a/docs/_build/doctrees/emna_opt.doctree b/docs/_build/doctrees/emna_opt.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/examples.doctree b/docs/_build/doctrees/examples.doctree
diff --git a/docs/_build/doctrees/feature_selection_umdad.doctree b/docs/_build/doctrees/feature_selection_umdad.doctree
diff --git a/docs/_build/doctrees/hyperparameter_umdac.doctree b/docs/_build/doctrees/hyperparameter_umdac.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
diff --git a/docs/_build/doctrees/introduction.doctree b/docs/_build/doctrees/introduction.doctree
diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
diff --git a/docs/_build/doctrees/multivariate_keda_opt.doctree b/docs/_build/doctrees/multivariate_keda_opt.doctree
diff --git a/docs/_build/doctrees/speda_opt.doctree b/docs/_build/doctrees/speda_opt.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 548cc20651cbb788240a69431335e19f
+config: b17ce3ec747fb292f205046b405d7595
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/EDAspy.benchmarks.html b/docs/_build/html/EDAspy.benchmarks.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.benchmarks package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.benchmarks package &mdash; EDAspy 1.1.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.html b/docs/_build/html/EDAspy.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy package &mdash; EDAspy 1.1.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.optimization.custom.html b/docs/_build/html/EDAspy.optimization.custom.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom package &mdash; EDAspy 1.1.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.optimization.custom.initialization_models.html b/docs/_build/html/EDAspy.optimization.custom.initialization_models.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.initialization_models package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.initialization_models package &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/docs/_build/html/EDAspy.optimization.custom.probabilistic_models.html b/docs/_build/html/EDAspy.optimization.custom.probabilistic_models.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.probabilistic_models package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.probabilistic_models package &mdash; EDAspy 1.1.3 documentation</title>
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       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.optimization.html b/docs/_build/html/EDAspy.optimization.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization package &mdash; EDAspy 1.1.3 documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.optimization.multivariate.html b/docs/_build/html/EDAspy.optimization.multivariate.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.multivariate package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.multivariate package &mdash; EDAspy 1.1.3 documentation</title>
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       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/EDAspy.optimization.univariate.html b/docs/_build/html/EDAspy.optimization.univariate.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.17: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.univariate package &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.univariate package &mdash; EDAspy 1.1.3 documentation</title>
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       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
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diff --git a/docs/_build/html/_modules/EDAspy/benchmarks/binary.html b/docs/_build/html/_modules/EDAspy/benchmarks/binary.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.benchmarks.binary &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.benchmarks.binary &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/docs/_build/html/_modules/EDAspy/benchmarks/continuous.html b/docs/_build/html/_modules/EDAspy/benchmarks/continuous.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.benchmarks.continuous &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.benchmarks.continuous &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/docs/_build/html/_modules/EDAspy/optimization/custom/eda_custom.html b/docs/_build/html/_modules/EDAspy/optimization/custom/eda_custom.html
@@ -3,7 +3,7 @@
 <head>
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   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.eda_custom &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.eda_custom &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/...d/html/_modules/EDAspy/optimization/custom/initialization_models/categorical_geninit.html b/...d/html/_modules/EDAspy/optimization/custom/initialization_models/categorical_geninit.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.initialization_models.categorical_geninit &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.initialization_models.categorical_geninit &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/...es/EDAspy/optimization/custom/initialization_models/latin_hypercube_sampling_geninit.html b/...es/EDAspy/optimization/custom/initialization_models/latin_hypercube_sampling_geninit.html
@@ -3,7 +3,7 @@
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   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.initialization_models.latin_hypercube_sampling_geninit &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.initialization_models.latin_hypercube_sampling_geninit &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/...d/html/_modules/EDAspy/optimization/custom/initialization_models/multi_gauss_geninit.html b/...d/html/_modules/EDAspy/optimization/custom/initialization_models/multi_gauss_geninit.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.initialization_models.multi_gauss_geninit &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.initialization_models.multi_gauss_geninit &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/...build/html/_modules/EDAspy/optimization/custom/initialization_models/uni_bin_geninit.html b/...build/html/_modules/EDAspy/optimization/custom/initialization_models/uni_bin_geninit.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>EDAspy.optimization.custom.initialization_models.uni_bin_geninit &mdash; EDAspy 1.1.2 documentation</title>
+  <title>EDAspy.optimization.custom.initialization_models.uni_bin_geninit &mdash; EDAspy 1.1.3 documentation</title>
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diff --git a/...ild/html/_modules/EDAspy/optimization/custom/initialization_models/uni_gauss_geninit.html b/...ild/html/_modules/EDAspy/optimization/custom/initialization_models/uni_gauss_geninit.html
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-  <title>EDAspy.optimization.custom.initialization_models.uni_gauss_geninit &mdash; EDAspy 1.1.2 documentation</title>
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diff --git a/...build/html/_modules/EDAspy/optimization/custom/initialization_models/uniform_geninit.html b/...build/html/_modules/EDAspy/optimization/custom/initialization_models/uniform_geninit.html
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