eckity 0.4.0

EC-KitY: Evolutionary Computation Tool Kit in Python.

EC-KitY is a Python tool kit for doing evolutionary computation, and it is scikit-learn compatible.

Currently we have implemented Genetic Algorithm (GA) and tree-based Genetic Programming (GP), but EC-KitY will grow!

EC-KitY is:

• A comprehensive toolkit for running evolutionary algorithms
• Written in Python
• Can work with or without scikit-learn, i.e., supports both sklearn and non-sklearn modes
• Designed with modern software engineering in mind
• Designed to support all popular EC paradigms (GA, GP, ES, coevolution, multi-objective, etc').

Dependencies

The minimal Python Version for EC-KitY is Python 3.8

The dependencies of our package are described in requirements.txt

For sklearn mode, EC-KitY additionally requires:

• scikit-learn (>=1.1)

User installation

pip install eckity

Documentation

API is available here

(Work in progress - some modules and functions are not documented yet.)

Tutorials

The tutorials are available here, walking you through running EC-KitY both in sklearn mode and in non-sklearn mode.

Examples

More examples are in the examples folder. All you need to do is define a fitness-evaluation method, through a SimpleIndividualEvaluator sub-class. You can run the examples with ease by opening this colab notebook.

Basic example (no sklearn)

You can run an EA with just 3 lines of code. The problem being solved herein is simple symbolic regression.

Additional information on this problem can be found in the Symbolic Regression Tutorial.

from eckity.subpopulation import Subpopulation
from eckity.algorithms import SimpleEvolution
from eckity.base.untyped_functions import f_add, f_sub, f_mul, f_div
from eckity.creators import FullCreator
from eckity.genetic_operators import SubtreeCrossover, SubtreeMutation
from examples.treegp.basic_mode.symbolic_regression import SymbolicRegressionEvaluator

algo = SimpleEvolution(
    Subpopulation(
        SymbolicRegressionEvaluator(),
        creator=FullCreator(
            terminal_set=['x', 'y', 'z'],
            function_set=[f_add, f_sub, f_mul, f_div]
        ),
        operators_sequence=[SubtreeCrossover(), SubtreeMutation()]
    )
)
algo.evolve()
print(f'algo.execute(x=2,y=3,z=4): {algo.execute(x=2, y=3, z=4)}')

Example with sklearn

The problem being solved herein is the same problem, but in this case we also involve sklearn compatability - a core feature of EC-KitY. Additional information for this example can be found in the Sklearn Symbolic Regression Tutorial.

A simple sklearn-compatible EA run:

from sklearn.datasets import make_regression
from sklearn.metrics import mean_absolute_error
from sklearn.model_selection import train_test_split

from eckity.algorithms.simple_evolution import SimpleEvolution
from eckity.creators.gp_creators.full import FullCreator
from eckity.genetic_encodings.gp.tree.utils import create_terminal_set
from eckity.sklearn_compatible.regression_evaluator import RegressionEvaluator
from eckity.sklearn_compatible.sk_regressor import SKRegressor
from eckity.subpopulation import Subpopulation

X, y = make_regression(n_samples=100, n_features=3)
terminal_set = create_terminal_set(X)

algo = SimpleEvolution(Subpopulation(creators=FullCreator(terminal_set=terminal_set),
                                     evaluator=RegressionEvaluator()))
regressor = SKRegressor(algo)

X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2)
regressor.fit(X_train, y_train)
print('MAE on test set:', mean_absolute_error(y_test, regressor.predict(X_test)))

Feature comparison

Here's a comparison table. The full paper is available here.

Authors

Moshe Sipper, Achiya Elyasaf, Itai Tzruia, Tomer Halperin

Citation

Citations are always appreciated 😊:

@article{eckity2023,
author = {Moshe Sipper and Tomer Halperin and Itai Tzruia and Achiya Elyasaf},
title = {{EC-KitY}: Evolutionary computation tool kit in {Python} with seamless machine learning integration},
journal = {SoftwareX},
volume = {22},
pages = {101381},
year = {2023},
url = {https://www.sciencedirect.com/science/article/pii/S2352711023000778},
}

@misc{eckity2022git,
    author = {Sipper, Moshe and Halperin, Tomer and Tzruia, Itai and  Elyasaf, Achiya},
    title = {{EC-KitY}: Evolutionary Computation Tool Kit in {Python}},
    year = {2022},
    publisher = {GitHub},
    journal = {GitHub repository},
    howpublished = {\url{https://www.eckity.org/} }
}

Sample repos using EC-KitY

• EC-KitY-Maze-Example
• EvolutionTSP
• Solving The 'Nurse Scheduling Problem' With EC-KitY