pysips 0.0.0__py3-none-any.whl

pysips-0.0.0.dist-info/METADATA

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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.dist-info/RECORD

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+pysips-0.0.0.dist-info/top_level.txt,sha256=-JZT9y5QJV6SZnWdfFctDC_Qc_ulByTB0-qRuXZyGYY,13
+pysips-0.0.0.dist-info/RECORD,,

pysips-0.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

pysips-0.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,94 @@
+NASA OPEN SOURCE AGREEMENT VERSION 1.3
+
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+
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+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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+  A. Distribution or Redistribution of the Subject Software must be made under this Agreement except for additions covered under paragraph 3H.
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+This software may be used, reproduced, and provided to others only as permitted under the terms of the agreement under which it was acquired from the U.S. Government. Neither title to, nor ownership of, the software is hereby transferred. This notice shall remain on all copies of the software.
+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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+  B. 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.
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pysips-0.0.0.dist-info/top_level.txt

@@ -0,0 +1,2 @@
+pysips
+tests

tests/integration/test_log_likelihood.py

@@ -0,0 +1,18 @@
+import numpy as np
+
+from pysips.laplace_nmll import LaplaceNmll
+from pysips.metropolis import Metropolis
+from bingo.symbolic_regression.agraph.agraph import AGraph
+
+
+def test_log_likelihood_relative():
+    x = np.arange(0, 100)
+    model = lambda a, b: a * x + b
+    data = model(5, 5) + np.random.default_rng(34).normal(0, 0.1, 100)
+
+    models = np.c_[[AGraph(equation="1.0"), AGraph(equation="1.0 + 2.0*X_0")]]
+    likelihood = LaplaceNmll(np.c_[x], data)
+    mcmc = Metropolis(likelihood=likelihood, proposal=None, prior=None)
+
+    log_likes = mcmc.evaluate_log_likelihood(models).flatten()
+    assert log_likes[0] < log_likes[1]

tests/integration/test_prior_with_bingo.py

@@ -0,0 +1,45 @@
+import pytest
+from bingo.symbolic_regression import ComponentGenerator, AGraphGenerator
+
+
+from pysips.prior import Prior
+
+
+def get_generator(
+    X_dim,
+    operators,
+    terminal_probability=0.1,
+    constant_probability=0.5,
+    max_complexity=48,
+    **kwargs,
+):
+    USE_PYTHON = True
+    USE_SIMPLIFICATION = True
+    component_generator = ComponentGenerator(
+        input_x_dimension=X_dim,
+        terminal_probability=terminal_probability,
+        constant_probability=constant_probability,
+    )
+    for comp in operators:
+        component_generator.add_operator(comp)
+    generator = AGraphGenerator(
+        max_complexity,
+        component_generator,
+        use_python=USE_PYTHON,
+        use_simplification=USE_SIMPLIFICATION,
+    )
+
+    return generator
+
+
+@pytest.mark.parametrize("N", [10, 500])
+def test_prior_makes_initial_set_of_unique_expressions(N):
+    """Test rvs with different values of N"""
+    generator = get_generator(1, ["+", "-", "*"])
+    prior = Prior(generator)
+
+    result = prior.rvs(N)
+
+    assert result.shape == (N, 1)
+    unique_models = set(result.flatten())
+    assert len(unique_models) == N

tests/regression/test_basic_end_to_end.py

@@ -0,0 +1,131 @@
+import argparse
+from pathlib import Path
+import numpy as np
+import h5py
+
+from pysips.laplace_nmll import LaplaceNmll
+from pysips.mutation_proposal import MutationProposal
+from pysips.crossover_proposal import CrossoverProposal
+from pysips.random_choice_proposal import RandomChoiceProposal
+from pysips.sampler import sample
+
+from bingo.symbolic_regression import ComponentGenerator, AGraphGenerator
+
+
+def get_proposal(
+    X_dim,
+    operators,
+    terminal_probability=0.1,
+    constant_probability=None,
+    command_probability=0.2,
+    node_probability=0.2,
+    parameter_probability=0.2,
+    prune_probability=0.2,
+    fork_probability=0.2,
+    repeat_mutation_probability=0.0,
+    crossover_pool_size=500,
+    mutation_prob=0.5,
+    crossover_prob=0.5,
+    exclusuive=True,
+    max_complexity=48,
+    **kwargs,
+):
+    generator = get_generator(
+        X_dim, operators, terminal_probability, constant_probability, max_complexity
+    )
+
+    mutation = MutationProposal(
+        X_dim,
+        operators=operators,
+        terminal_probability=terminal_probability,
+        constant_probability=constant_probability,
+        command_probability=command_probability,
+        node_probability=node_probability,
+        parameter_probability=parameter_probability,
+        prune_probability=prune_probability,
+        fork_probability=fork_probability,
+        repeat_mutation_probability=repeat_mutation_probability,
+    )
+
+    pool = set()
+    while len(pool) < crossover_pool_size:
+        pool.add(generator())
+    crossover = CrossoverProposal(list(pool))
+
+    proposal = RandomChoiceProposal(
+        [mutation, crossover], [mutation_prob, crossover_prob], exclusuive
+    )
+
+    return proposal
+
+
+def get_generator(
+    X_dim,
+    operators,
+    terminal_probability=0.1,
+    constant_probability=None,
+    max_complexity=48,
+    **kwargs,
+):
+    USE_PYTHON = True
+    USE_SIMPLIFICATION = True
+    component_generator = ComponentGenerator(
+        input_x_dimension=X_dim,
+        terminal_probability=terminal_probability,
+        constant_probability=constant_probability,
+    )
+    for comp in operators:
+        component_generator.add_operator(comp)
+    generator = AGraphGenerator(
+        max_complexity,
+        component_generator,
+        use_python=USE_PYTHON,
+        use_simplification=USE_SIMPLIFICATION,
+    )
+
+    return generator
+
+
+def test_basic_end_to_end():
+
+    n_pts = 21
+    X = np.c_[np.linspace(0, 2 * np.pi, n_pts)]
+    y = (np.sin(X) * 2 + 4).flatten() + np.random.default_rng(34).normal(0, 0.5, n_pts)
+
+    config = {
+        "X_dim": X.shape[1],
+        "constant_probability": 1 / (X.shape[1] + 1),
+        "operators": ["+", "*"],
+        "param_init_bounds": [-5, 5],
+        "opt_restarts": 1,
+        "terminal_probability": 0.1,
+        "command_probability": 0.2,
+        "node_probability": 0.2,
+        "parameter_probability": 0.2,
+        "prune_probability": 0.2,
+        "fork_probability": 0.2,
+        "repeat_mutation_probability": 0.05,
+        "crossover_pool_size": 50,
+        "mutation_prob": 0.75,
+        "crossover_prob": 0.25,
+        "exclusuive": True,
+        "max_complexity": 24,
+        "num_particles": 50,
+        "num_mcmc_samples": 5,
+        "target_ess": 0.8,
+    }
+
+    likelihood = LaplaceNmll(X, y)
+    generator = get_generator(**config)
+    proposal = get_proposal(**config)
+    models, likelihoods = sample(
+        likelihood,
+        proposal,
+        generator,
+        seed=34,
+        kwargs={
+            "num_particles": config["num_particles"],
+            "num_mcmc_samples": config["num_mcmc_samples"],
+            "target_ess": config["target_ess"],
+        },
+    )

tests/regression/test_regressor_end_to_end.py

@@ -0,0 +1,95 @@
+import numpy as np
+import pytest
+from sklearn.model_selection import train_test_split, GridSearchCV
+from sklearn.metrics import mean_squared_error
+from pysips.regressor import PysipsRegressor
+
+
+@pytest.fixture
+def synthetic_data():
+    """Fixture to create synthetic sin wave data."""
+    n_pts = 21
+    X = np.c_[np.linspace(0, 2 * np.pi, n_pts)]
+    # Use seed 34 for consistent test data
+    y = (np.sin(X) * 2 + 4).flatten() + np.random.default_rng(34).normal(0, 0.5, n_pts)
+    return X, y
+
+
+@pytest.fixture
+def train_test_data(synthetic_data):
+    """Fixture to split data into train and test sets."""
+    X, y = synthetic_data
+    return train_test_split(X, y, test_size=0.2, random_state=42)
+
+
+@pytest.fixture
+def base_regressor():
+    """Fixture for basic regressor with default settings."""
+    return PysipsRegressor(
+        operators=["+", "*", "sin"],
+        max_complexity=24,
+        num_particles=20,
+        random_state=42,
+    )
+
+
+def test_basic_end_to_end(train_test_data, base_regressor):
+    """Test basic end-to-end workflow for PysipsRegressor."""
+    X_train, X_test, y_train, y_test = train_test_data
+
+    model = base_regressor
+    model.fit(X_train, y_train)
+    y_pred = model.predict(X_test)
+    mse = mean_squared_error(y_test, y_pred)
+
+    # print(f"Best expression: {model.get_expression()}")
+    # print(f"Test MSE: {mse:.4f}")
+    # print(f"R² score: {model.score(X_test, y_test):.4f}")
+
+
+def test_hyperparameter_optimization(synthetic_data):
+    """Test compatibility with scikit-learn's hyperparameter optimization."""
+    X, y = synthetic_data
+
+    # Create the regressor with reduced computation for faster testing
+    base_model = PysipsRegressor(
+        operators=["+", "*", "sin"],
+        max_complexity=20,
+        num_particles=10,
+        num_mcmc_samples=50,
+        random_state=42,
+    )
+
+    # Define hyperparameter grid
+    param_grid = {
+        "max_complexity": [15, 20],
+        "terminal_probability": [0.1, 0.2],
+        "mutation_prob": [0.6, 0.7],
+    }
+
+    # Set up GridSearchCV
+    grid_search = GridSearchCV(
+        estimator=base_model,
+        param_grid=param_grid,
+        cv=3,
+        scoring="neg_mean_squared_error",
+        verbose=1,
+        n_jobs=1,  # Use single job for testing
+    )
+
+    # Perform grid search
+    grid_search.fit(X, y)
+
+    # Check that grid search completed successfully
+    assert hasattr(grid_search, "best_params_")
+
+    # Check that the best estimator is fitted
+    assert hasattr(grid_search.best_estimator_, "best_model_")
+
+    # Verify it can make predictions
+    y_pred = grid_search.predict(X)
+    assert y_pred.shape == y.shape
+
+    # print(f"Best parameters: {grid_search.best_params_}")
+    # print(f"Best CV score: {-grid_search.best_score_:.4f}")  # Convert back to MSE
+    # print(f"Best model expression: {grid_search.best_estimator_.get_expression()}")