README.md

AlpineGP

AlpineGP is a Python library for symbolic regression via Genetic Programming. It provides a high-level interface to the DEAP library, including distributed computing functionalities.

Besides solving classical symbolic regression problems involving algebraic equations (see, for example, the benchmark problems contained in the SRBench repository), AlpineGP is specifically designed to help identifying symbolic models of physical systems governed by field equations. To this aim, it allows to exploit the discrete calculus framework defined and implemented in the library dctkit as a natural and effective language to express physical models (i.e., conservation laws).

AlpineGP has been introduced in the paper Discovering interpretable physical models with symbolic regression and discrete exterior calculus, along with several benchmark problems (heat transfer, linear elasticity, Euler's elastica). Scripts to reproduce these benchmarks can be found here.

Features:

• distributed computing provided by the ray library;
• scikit-learn compatible interface;
• hyperparameter configuration via YAML files;
• support for custom operators (with/without strong-typing);
• benchmark suite (Nguyen and SRBench)

Installation

Dependencies should be installed within a conda environment. We recommend using mamba since it is much faster than conda at solving the environment and downloading the dependencies. To create a suitable environment based on the provided .yaml file, use the command

$ mamba env create -f environment.yaml

Otherwise, you can update an existing environment using the same .yaml file.

After activating the environment, clone the git repository and launch the following command

$ pip install -e .

to install a development version of the library.

Running the tests:

$ tox

Generating the docs:

$ tox -e docs

Benchmarks

To run the benchmarks, cd into the bench folder and execute:

$ ./bench.sh

Then process the results using the process_results notebook.

Usage

Setting up a symbolic regression problem in AlpineGP involves several key steps:

1. Define the function that computes the prediction associated to an individual (model expression tree). Its arguments may be a function obtained by parsing the individual tree and possibly other parameters, such as the features (X) needed to evaluate the model. It returns both the error between the predictions and the labels (y) and the predictions themselves.

def eval_MSE_sol(individual, X, y):

    # ...
    return MSE, prediction

2. Define the functions that return the prediction and the fitness associated to an individual. These functions must have at least the following arguments in the first three positions:
   • the list of trees to be evaluated by the current worker;
   • the toolbox object used to compile the individual trees into callable functions;
   • the dataset features needed for the evaluation of the individuals. The name of the argument must be X.

Additionally, the fourth argument of the fitness function must be the dataset labels, called y. For unsupervised problems, None can be passed for the labels to the fit method of the regressor. Both functions must be decorated with ray.remote to support distributed evaluation (multiprocessing). Any additional arguments can be set using the common_data argument of the GPSymbolicRegressor object (see below).

@ray.remote
def predict(trees, toolbox, X):

    callables = compile_individuals(toolbox, trees)

    preds = [None]*len(trees)

    for i, ind in enumerate(callables):
        _, preds[i] = eval_MSE_sol(ind, X, None)

    return preds

@ray.remote
def fitness(trees, toolbox, X, y):
    callables = compile_individuals(toolbox, trees)

    fitnesses = [None]*len(trees)

    for i, ind in enumerate(callables):
        MSE, _ = eval_MSE_sol(ind, X, y)
        
        # each fitness MUST be a tuple (required by DEAP)
        fitnesses[i] = (MSE,)

    return fitnesses

3. Set up and solve the symbolic regression problem. The configuration of the GPSymbolicRegressor object can be specified via the arguments of its constructor (see the API docs), or loaded from a YAML file.

# read config parameters from YAML file
yamlfile = "ex1.yaml"
filename = os.path.join(os.path.dirname(__file__), yamlfile)

regressor_params, config_file_data = util.load_config_data(filename)

# ...
# ...

# load datasets...

# define the primitive set (input/output types)
pset = gp.PrimitiveSetTyped(...)

# rename arguments of the tree function
pset.renameArguments(ARG0="u")

# define extra common arguments of fitness and predict functions
common_params = {'penalty': penalty}

# create the Symbolic Regression Problem object
gpsr = gps.GPSymbolicRegressor(pset=pset, fitness=fitness.remote,
                               predict_func=predict.remote, common_data=common_params,
                               print_log=True, 
                               **regressor_params)

# solve the symbolic regression problem
gpsr.fit(X_train, y_train)

# compute the prediction on the test dataset given by the best model found during the SR
pred_test = gpsr.predict(X_test)

A complete example notebook can be found in the examples directory. Also check the simple_sr.py script for an introductory example (use it as a template/skeleton for defining your symbolic regression problem).

Citing

@article{Manti_2024,
    doi = {10.1088/2632-2153/ad1af2},
    url = {https://dx.doi.org/10.1088/2632-2153/ad1af2},
    year = {2024},
    publisher = {IOP Publishing},
    volume = {5},
    number = {1},
    pages = {015005},
    author = {Simone Manti and Alessandro Lucantonio},
    title = {Discovering interpretable physical models using symbolic regression and discrete exterior calculus},
    journal = {Machine Learning: Science and Technology}
}