pysips 0.0.0__tar.gz

pysips-0.0.0/LICENSE

@@ -0,0 +1,94 @@
+NASA OPEN SOURCE AGREEMENT VERSION 1.3
+
+THIS OPEN SOURCE AGREEMENT (“AGREEMENT”) DEFINES THE RIGHTS OF USE, REPRODUCTION, DISTRIBUTION, MODIFICATION AND REDISTRIBUTION OF CERTAIN COMPUTER SOFTWARE ORIGINALLY RELEASED BY THE UNITED STATES GOVERNMENT AS REPRESENTED BY THE GOVERNMENT AGENCY LISTED BELOW ("GOVERNMENT AGENCY"). THE UNITED STATES GOVERNMENT, AS REPRESENTED BY GOVERNMENT AGENCY, IS AN INTENDED THIRD-PARTY BENEFICIARY OF ALL SUBSEQUENT DISTRIBUTIONS OR REDISTRIBUTIONS OF THE SUBJECT SOFTWARE. ANYONE WHO USES, REPRODUCES, DISTRIBUTES, MODIFIES OR REDISTRIBUTES THE SUBJECT SOFTWARE, AS DEFINED HEREIN, OR ANY PART THEREOF, IS, BY THAT ACTION, ACCEPTING IN FULL THE RESPONSIBILITIES AND OBLIGATIONS CONTAINED IN THIS AGREEMENT.
+
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+Government Agency Original Software Designation: LAR-20644-1
+Government Agency Original Software Title: Sequential Monte Carlo-based Symbolic Regression (SMC-SR)
+Government Agency Point of Contact for Original Software: patrick.e.leser@nasa.gov
+
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+Copyright 2025 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. No copyright is claimed in the United States under Title 17, U.S. Code. All Other Rights Reserved.
+The NASA Software “Sequential Monte Carlo-based Symbolic Regression (SMC-SR)” (LAR-20644-1) calls the following third-party software, which is subject to the terms and conditions of its licensor, as applicable at the time of licensing. The third-party software is not bundled or included with this software but may be available from the licensor. License hyperlinks are provided here for information purposes only.
+
+NumPy
+https://numpy.org/devdocs/license.html
+Copyright (c) 2005-2025, NumPy Developers.
+All rights reserved.
+h5py
+https://github.com/h5py/h5py/blob/master/LICENSE
+Copyright (c) 2008 Andrew Collette and contributors
+All rights reserved.
+
+tqdm
+https://github.com/tqdm/tqdm/blob/master/LICENCE
+Copyright (c) 2013 noamraph
+
+SciPy
+https://github.com/scipy/scipy/blob/main/LICENSE.txt
+Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.
+All rights reserved.
+
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+  A. No Warranty: THE SUBJECT SOFTWARE IS PROVIDED “AS IS” WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE. FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE, AND DISTRIBUTES IT “AS IS.”
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+Email: larc-sra@mail.nasa.gov

pysips-0.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: pysips
+Version: 0.0.0
+Summary: A python package for symbolic inference via posterior sampling.
+Author-email: Geoffrey Bomarito <geoffrey.f.bomarito@nasa.gov>, Patrick Leser <patrick.e.leser@nasa.gov>
+License-Expression: NASA-1.3
+Project-URL: Documentation, https://nasa.github.io/pysips/
+Project-URL: Repository, https://github.com/nasa/pysips
+Keywords: symbolic regression
+Classifier: Development Status :: 3 - Alpha
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: bingo-nasa
+Requires-Dist: smcpy>=0.1.6
+Requires-Dist: scikit-learn
+Dynamic: license-file
+
+# PySIPS: Python package for Symbolic Inference via Posterior Sampling
+
+PySIPS is an open-source implementation of Bayesian symbolic regression via posterior sampling as described in the paper "Bayesian Symbolic Regression via Posterior Sampling" by G. F. Bomarito and P. E. Leser from NASA Langley Research Center.
+
+## Purpose
+
+PySIPS provides a robust framework for discovering interpretable symbolic expressions from data, with a particular focus on handling noisy datasets. Unlike traditional symbolic regression approaches, PySIPS uses a Bayesian framework with Sequential Monte Carlo (SMC) sampling to:
+
+1. Enhance robustness to noise
+2. Provide built-in uncertainty quantification
+3. Discover parsimonious expressions with improved generalization
+4. Reduce overfitting in symbolic regression tasks
+
+## Algorithm Overview
+
+PySIPS implements a Sequential Monte Carlo (SMC) framework for Bayesian symbolic regression that:
+
+- Approximates the posterior distribution over symbolic expressions
+- Uses probabilistic selection and adaptive annealing to explore the search space efficiently
+- Employs normalized marginal likelihood for model evaluation
+- Combines mutation and crossover operations as proposal mechanisms
+- Provides model selection criteria based on maximum normalized marginal likelihood or posterior mode
+
+## Installation
+
+(Coming Soon!)
+
+```bash
+pip install pysips
+```
+
+## Example Usage
+
+```python
+import numpy as np
+from pysips import PysipsRegressor
+from sklearn.model_selection import train_test_split
+from sklearn.metrics import r2_score
+
+# Generate synthetic data (y = x^2 + noise)
+np.random.seed(42)
+X = np.linspace(-3, 3, 100).reshape(-1, 1)
+y = X[:, 0]**2 + np.random.normal(0, 0.1, size=X.shape[0])
+
+# Split data
+X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
+
+# Initialize and fit the regressor
+regressor = PysipsRegressor(
+    operators=['+', '-', '*', '^2'],
+    max_complexity=12,
+    num_particles=100,
+    num_mcmc_samples=10,
+    random_state=42
+)
+
+regressor.fit(X_train, y_train)
+
+# Make predictions
+y_pred = regressor.predict(X_test)
+
+# Get the discovered expression
+expression = regressor.get_expression()
+print(f"Discovered expression: {expression}")
+print(f"R² score: {r2_score(y_test, y_pred):.4f}")
+
+# Get model posterior and their likelihoods
+models, likelihoods = regressor.get_models()
+```
+
+### Example Output
+
+```
+Discovered expression: x_0^2
+R² score: 0.9987
+Number of unique models sampled: 32
+```
+
+## Advanced Features
+
+- Control over operators and expression complexity
+- Multiple model selection strategies
+- Access to the full posterior distribution over expressions
+- Compatible with scikit-learn's API for easy integration into ML pipelines
+- Uncertainty quantification for symbolic regression results
+
+## Citation
+
+If you use PySIPS, please cite the following paper:
+
+```bibtex
+@article{bomarito2024bayesian,
+  title={Bayesian Symbolic Regression via Posterior Sampling},
+  author={Bomarito, Geoffrey F. and Leser, Patrick E.},
+  journal={Philosophical Transactions of the Royal Society A},
+  year={2025},
+  publisher={Royal Society}
+}
+```
+
+## License
+
+Notices:
+Copyright 2025 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. No copyright is claimed in the United States under Title 17, U.S. Code. All Other Rights Reserved.
+ 
+The NASA Software “PySIPS” (LAR-20644-1) calls the following third-party software, which is subject to the terms and conditions of its licensor, as applicable at the time of licensing.  The third-party software is not bundled or included with this software but may be available from the licensor.  License hyperlinks are provided here for information purposes only.
+ 
+NumPy  
+https://numpy.org/devdocs/license.html  
+Copyright (c) 2005-2025, NumPy Developers.  
+All rights reserved.
+ 
+h5py  
+https://github.com/h5py/h5py/blob/master/LICENSE  
+Copyright (c) 2008 Andrew Collette and contributors  
+All rights reserved.
+ 
+tqdm  
+https://github.com/tqdm/tqdm/blob/master/LICENCE  
+Copyright (c) 2013 noamraph
+ 
+SciPy  
+https://github.com/scipy/scipy/blob/main/LICENSE.txt  
+Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.  
+All rights reserved.
+ 
+Disclaimers
+No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.  FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE, AND DISTRIBUTES IT "AS IS."
+ 
+Waiver and Indemnity:  RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT.  IF RECIPIENT'S USE OF THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED STATES GOVERNMENT, ITS CONTRACTORS, AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT, TO THE EXTENT PERMITTED BY LAW.  RECIPIENT'S SOLE REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL TERMINATION OF THIS AGREEMENT.
+
+
+## Acknowledgements
+
+This work was developed at NASA Langley Research Center.

pysips-0.0.0/README.md

@@ -0,0 +1,135 @@
+# PySIPS: Python package for Symbolic Inference via Posterior Sampling
+
+PySIPS is an open-source implementation of Bayesian symbolic regression via posterior sampling as described in the paper "Bayesian Symbolic Regression via Posterior Sampling" by G. F. Bomarito and P. E. Leser from NASA Langley Research Center.
+
+## Purpose
+
+PySIPS provides a robust framework for discovering interpretable symbolic expressions from data, with a particular focus on handling noisy datasets. Unlike traditional symbolic regression approaches, PySIPS uses a Bayesian framework with Sequential Monte Carlo (SMC) sampling to:
+
+1. Enhance robustness to noise
+2. Provide built-in uncertainty quantification
+3. Discover parsimonious expressions with improved generalization
+4. Reduce overfitting in symbolic regression tasks
+
+## Algorithm Overview
+
+PySIPS implements a Sequential Monte Carlo (SMC) framework for Bayesian symbolic regression that:
+
+- Approximates the posterior distribution over symbolic expressions
+- Uses probabilistic selection and adaptive annealing to explore the search space efficiently
+- Employs normalized marginal likelihood for model evaluation
+- Combines mutation and crossover operations as proposal mechanisms
+- Provides model selection criteria based on maximum normalized marginal likelihood or posterior mode
+
+## Installation
+
+(Coming Soon!)
+
+```bash
+pip install pysips
+```
+
+## Example Usage
+
+```python
+import numpy as np
+from pysips import PysipsRegressor
+from sklearn.model_selection import train_test_split
+from sklearn.metrics import r2_score
+
+# Generate synthetic data (y = x^2 + noise)
+np.random.seed(42)
+X = np.linspace(-3, 3, 100).reshape(-1, 1)
+y = X[:, 0]**2 + np.random.normal(0, 0.1, size=X.shape[0])
+
+# Split data
+X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)
+
+# Initialize and fit the regressor
+regressor = PysipsRegressor(
+    operators=['+', '-', '*', '^2'],
+    max_complexity=12,
+    num_particles=100,
+    num_mcmc_samples=10,
+    random_state=42
+)
+
+regressor.fit(X_train, y_train)
+
+# Make predictions
+y_pred = regressor.predict(X_test)
+
+# Get the discovered expression
+expression = regressor.get_expression()
+print(f"Discovered expression: {expression}")
+print(f"R² score: {r2_score(y_test, y_pred):.4f}")
+
+# Get model posterior and their likelihoods
+models, likelihoods = regressor.get_models()
+```
+
+### Example Output
+
+```
+Discovered expression: x_0^2
+R² score: 0.9987
+Number of unique models sampled: 32
+```
+
+## Advanced Features
+
+- Control over operators and expression complexity
+- Multiple model selection strategies
+- Access to the full posterior distribution over expressions
+- Compatible with scikit-learn's API for easy integration into ML pipelines
+- Uncertainty quantification for symbolic regression results
+
+## Citation
+
+If you use PySIPS, please cite the following paper:
+
+```bibtex
+@article{bomarito2024bayesian,
+  title={Bayesian Symbolic Regression via Posterior Sampling},
+  author={Bomarito, Geoffrey F. and Leser, Patrick E.},
+  journal={Philosophical Transactions of the Royal Society A},
+  year={2025},
+  publisher={Royal Society}
+}
+```
+
+## License
+
+Notices:
+Copyright 2025 United States Government as represented by the Administrator of the National Aeronautics and Space Administration. No copyright is claimed in the United States under Title 17, U.S. Code. All Other Rights Reserved.
+ 
+The NASA Software “PySIPS” (LAR-20644-1) calls the following third-party software, which is subject to the terms and conditions of its licensor, as applicable at the time of licensing.  The third-party software is not bundled or included with this software but may be available from the licensor.  License hyperlinks are provided here for information purposes only.
+ 
+NumPy  
+https://numpy.org/devdocs/license.html  
+Copyright (c) 2005-2025, NumPy Developers.  
+All rights reserved.
+ 
+h5py  
+https://github.com/h5py/h5py/blob/master/LICENSE  
+Copyright (c) 2008 Andrew Collette and contributors  
+All rights reserved.
+ 
+tqdm  
+https://github.com/tqdm/tqdm/blob/master/LICENCE  
+Copyright (c) 2013 noamraph
+ 
+SciPy  
+https://github.com/scipy/scipy/blob/main/LICENSE.txt  
+Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.  
+All rights reserved.
+ 
+Disclaimers
+No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND, EITHER EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE ERROR FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE SUBJECT SOFTWARE. THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY PRIOR RECIPIENT OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.  FURTHER, GOVERNMENT AGENCY DISCLAIMS ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL SOFTWARE, AND DISTRIBUTES IT "AS IS."
+ 
+Waiver and Indemnity:  RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT.  IF RECIPIENT'S USE OF THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM, RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED STATES GOVERNMENT, ITS CONTRACTORS, AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT, TO THE EXTENT PERMITTED BY LAW.  RECIPIENT'S SOLE REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE, UNILATERAL TERMINATION OF THIS AGREEMENT.
+
+
+## Acknowledgements
+
+This work was developed at NASA Langley Research Center.

pysips-0.0.0/pyproject.toml

@@ -0,0 +1,36 @@
+[project]
+name = "pysips"
+keywords = ["symbolic regression"]
+description = "A python package for symbolic inference via posterior sampling."
+authors = [
+    {name = "Geoffrey Bomarito", email = "geoffrey.f.bomarito@nasa.gov" },
+    {name = "Patrick Leser", email = "patrick.e.leser@nasa.gov" },
+]
+requires-python = ">=3.12"
+readme = "README.md"
+license = "NASA-1.3"
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "bingo-nasa",
+    "smcpy>=0.1.6",
+    "scikit-learn"
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+]
+
+[project.urls]
+Documentation = "https://nasa.github.io/pysips/"
+Repository = "https://github.com/nasa/pysips"
+
+[tool.cibuildwheel]
+skip = "pp*"
+
+[tool.setuptools_scm]
+local_scheme = "no-local-version"
+
+[tool.setuptools.packages.find]
+    exclude = ['demos']

pysips-0.0.0/pysips/__init__.py

@@ -0,0 +1,53 @@
+"""
+Notices:
+Copyright 2025 United States Government as represented by the Administrator of the National
+Aeronautics and Space Administration. No copyright is claimed in the United States under Title 17,
+ U.S. Code. All Other Rights Reserved.
+
+The NASA Software “PySIPS” (LAR-20644-1) calls the following third-party software, which is
+subject to the terms and conditions of its licensor, as applicable at the time of licensing.  The
+third-party software is not bundled or included with this software but may be available from the
+licensor.  License hyperlinks are provided here for information purposes only.
+
+NumPy
+https://numpy.org/devdocs/license.html
+Copyright (c) 2005-2025, NumPy Developers.
+All rights reserved.
+
+h5py
+https://github.com/h5py/h5py/blob/master/LICENSE
+Copyright (c) 2008 Andrew Collette and contributors
+All rights reserved.
+
+tqdm
+https://github.com/tqdm/tqdm/blob/master/LICENCE
+Copyright (c) 2013 noamraph
+
+SciPy
+https://github.com/scipy/scipy/blob/main/LICENSE.txt
+Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.
+All rights reserved.
+
+Disclaimers
+No Warranty: THE SUBJECT SOFTWARE IS PROVIDED "AS IS" WITHOUT ANY WARRANTY OF ANY KIND, EITHER
+EXPRESSED, IMPLIED, OR STATUTORY, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTY THAT THE SUBJECT
+SOFTWARE WILL CONFORM TO SPECIFICATIONS, ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE, OR FREEDOM FROM INFRINGEMENT, ANY WARRANTY THAT THE SUBJECT SOFTWARE WILL BE
+ERROR FREE, OR ANY WARRANTY THAT DOCUMENTATION, IF PROVIDED, WILL CONFORM TO THE SUBJECT SOFTWARE.
+THIS AGREEMENT DOES NOT, IN ANY MANNER, CONSTITUTE AN ENDORSEMENT BY GOVERNMENT AGENCY OR ANY
+PRIOR RECIPIENT OF ANY RESULTS, RESULTING DESIGNS, HARDWARE, SOFTWARE PRODUCTS OR ANY OTHER
+APPLICATIONS RESULTING FROM USE OF THE SUBJECT SOFTWARE.  FURTHER, GOVERNMENT AGENCY DISCLAIMS
+ALL WARRANTIES AND LIABILITIES REGARDING THIRD-PARTY SOFTWARE, IF PRESENT IN THE ORIGINAL
+SOFTWARE, AND DISTRIBUTES IT "AS IS."
+
+Waiver and Indemnity:  RECIPIENT AGREES TO WAIVE ANY AND ALL CLAIMS AGAINST THE UNITED STATES
+GOVERNMENT, ITS CONTRACTORS AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT.  IF RECIPIENT'S
+USE OF THE SUBJECT SOFTWARE RESULTS IN ANY LIABILITIES, DEMANDS, DAMAGES, EXPENSES OR LOSSES
+ARISING FROM SUCH USE, INCLUDING ANY DAMAGES FROM PRODUCTS BASED ON, OR RESULTING FROM,
+RECIPIENT'S USE OF THE SUBJECT SOFTWARE, RECIPIENT SHALL INDEMNIFY AND HOLD HARMLESS THE UNITED
+STATES GOVERNMENT, ITS CONTRACTORS, AND SUBCONTRACTORS, AS WELL AS ANY PRIOR RECIPIENT, TO THE
+EXTENT PERMITTED BY LAW.  RECIPIENT'S SOLE REMEDY FOR ANY SUCH MATTER SHALL BE THE IMMEDIATE,
+UNILATERAL TERMINATION OF THIS AGREEMENT.
+"""
+
+from .regressor import PysipsRegressor

pysips-0.0.0/pysips/crossover_proposal.py

@@ -0,0 +1,138 @@
+"""
+Crossover-Based Proposal Generator for Symbolic Regression Models.
+
+This module provides a crossover-based proposal mechanism for symbolic regression
+that creates new candidate models by combining genetic material from existing
+models. It implements genetic programming crossover operations using bingo's
+AGraphCrossover functionality within an MCMC or evolutionary algorithm framework.
+
+The crossover operation mimics biological reproduction by exchanging subtrees
+between two parent expressions to create offspring that inherit characteristics
+from both parents. This approach can effectively explore the space of symbolic
+expressions by combining successful components from different models.
+
+Key Features
+------------
+- Random partner selection from a configurable gene pool
+- Stochastic child selection (50/50 probability between two crossover offspring)
+- Avoids self-crossover by ensuring different parent selection
+- Updateable gene pool for adaptive sampling strategies
+- Seeded random number generation for reproducible results
+
+Crossover Mechanism
+-------------------
+The crossover operation works by:
+1. Selecting a random crossover point in each parent expression tree
+2. Swapping the subtrees at those points between the two parents
+3. Producing two offspring that combine features from both parents
+4. Randomly selecting one of the two offspring as the proposal
+
+This process allows successful expression fragments to be preserved and
+recombined in novel ways, potentially discovering better solutions through
+the exploration of hybrid models.
+
+Usage Example
+-------------
+>>> # Assume you have a collection of symbolic models
+>>> gene_pool = [model1, model2, model3, model4]  # List of AGraph models
+>>>
+>>> # Create crossover proposal generator
+>>> crossover = CrossoverProposal(gene_pool, seed=42)
+>>>
+>>> # Use in MCMC or evolutionary sampling
+>>> current_model = model1
+>>> new_proposal = crossover(current_model)
+>>>
+>>> # Update gene pool as better models are discovered
+>>> updated_pool = [best_model1, best_model2, new_good_model]
+>>> crossover.update(updated_pool)
+
+Integration Notes
+-----------------
+The update() method allows for dynamic gene pool management, enabling
+adaptive strategies where successful models from the sampling process
+can be added to influence future proposals.
+"""
+
+import numpy as np
+from bingo.symbolic_regression import (
+    AGraphCrossover,
+)
+
+
+class CrossoverProposal:
+    """A proposal operator that performs crossover between AGraph models.
+
+    This class implements a callable object that creates new models by performing
+    crossover operations between an input model and randomly selected partners
+    from a gene pool. It utilizes bingo's AGraphCrossover mechanism and randomly
+    selects one of the two children produced by each crossover operation.
+
+    Parameters
+    ----------
+    gene_pool : list of AGraph
+        A collection of AGraph models that will be used as potential partners
+        during crossover operations
+    seed : int, optional
+        Random seed for the internal random number generator, used to control
+        repeatability of operations
+    """
+
+    def __init__(self, gene_pool, seed=None):
+        self._crossover = AGraphCrossover()
+        self._gene_pool = gene_pool
+        self._rng = np.random.default_rng(seed)
+
+    def _select_other_parent(self, model):
+        ind = self._rng.integers(0, len(self._gene_pool))
+        while self._gene_pool[ind] == model:
+            ind = self._rng.integers(0, len(self._gene_pool))
+        return self._gene_pool[ind]
+
+    def _do_crossover(self, model, other_parent):
+        child_1, child_2 = self._crossover(model, other_parent)
+        if self._rng.random() < 0.5:
+            return child_1
+        return child_2
+
+    def __call__(self, model):
+        """Perform crossover between the input model and a randomly selected one from the gene pool.
+
+        This method randomly selects a parent from the gene pool, performs crossover between
+        the input model and the selected parent, and returns one of the two resulting children
+        with equal probability.
+
+        Parameters
+        ----------
+        model : AGraph
+            The model to be used as the first parent in the crossover operation
+
+        Returns
+        -------
+        AGraph
+            A new model resulting from crossover between the input model and a
+            randomly selected model from the gene pool
+        """
+        other_parent = self._select_other_parent(model)
+        new_model = self._do_crossover(model, other_parent)
+        return new_model
+
+    def update(self, gene_pool, *_, **__):
+        """Update the gene pool used for selecting crossover partners.
+
+        Parameters
+        ----------
+        gene_pool : iterable of AGraph
+            The new collection of AGraph models to use as the gene pool
+        *_ : tuple
+            Additional positional arguments (ignored)
+        **__ : dict
+            Additional keyword arguments (ignored)
+
+        Notes
+        -----
+        This method allows for updating the gene pool while maintaining the same
+        crossover behavior. The additional parameters are included for compatibility
+        with other proposal update interfaces but are not used.
+        """
+        self._gene_pool = list(gene_pool)