Distributed Evolutionary Algorithms in Python

Related tags

Machine Learningdeap
Overview

DEAP

Build status Download Join the chat at https://gitter.im/DEAP/deap Build Status Documentation Status

DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. It works in perfect harmony with parallelisation mechanisms such as multiprocessing and SCOOP.

DEAP includes the following features:

  • Genetic algorithm using any imaginable representation
    • List, Array, Set, Dictionary, Tree, Numpy Array, etc.
  • Genetic programing using prefix trees
    • Loosely typed, Strongly typed
    • Automatically defined functions
  • Evolution strategies (including CMA-ES)
  • Multi-objective optimisation (NSGA-II, NSGA-III, SPEA2, MO-CMA-ES)
  • Co-evolution (cooperative and competitive) of multiple populations
  • Parallelization of the evaluations (and more)
  • Hall of Fame of the best individuals that lived in the population
  • Checkpoints that take snapshots of a system regularly
  • Benchmarks module containing most common test functions
  • Genealogy of an evolution (that is compatible with NetworkX)
  • Examples of alternative algorithms : Particle Swarm Optimization, Differential Evolution, Estimation of Distribution Algorithm

Downloads

Following acceptance of PEP 438 by the Python community, we have moved DEAP's source releases on PyPI.

You can find the most recent releases at: https://pypi.python.org/pypi/deap/.

Documentation

See the DEAP User's Guide for DEAP documentation.

In order to get the tip documentation, change directory to the doc subfolder and type in make html, the documentation will be under _build/html. You will need Sphinx to build the documentation.

Notebooks

Also checkout our new notebook examples. Using Jupyter notebooks you'll be able to navigate and execute each block of code individually and tell what every line is doing. Either, look at the notebooks online using the notebook viewer links at the botom of the page or download the notebooks, navigate to the you download directory and run

jupyter notebook

Installation

We encourage you to use easy_install or pip to install DEAP on your system. Other installation procedure like apt-get, yum, etc. usually provide an outdated version.

pip install deap

The latest version can be installed with

pip install git+https://github.com/DEAP/[email protected]

If you wish to build from sources, download or clone the repository and type

python setup.py install

Build Status

DEAP build status is available on Travis-CI https://travis-ci.org/DEAP/deap.

Requirements

The most basic features of DEAP requires Python2.6. In order to combine the toolbox and the multiprocessing module Python2.7 is needed for its support to pickle partial functions. CMA-ES requires Numpy, and we recommend matplotlib for visualization of results as it is fully compatible with DEAP's API.

Since version 0.8, DEAP is compatible out of the box with Python 3. The installation procedure automatically translates the source to Python 3 with 2to3.

Example

The following code gives a quick overview how simple it is to implement the Onemax problem optimization with genetic algorithm using DEAP. More examples are provided here.

import random
from deap import creator, base, tools, algorithms

creator.create("FitnessMax", base.Fitness, weights=(1.0,))
creator.create("Individual", list, fitness=creator.FitnessMax)

toolbox = base.Toolbox()

toolbox.register("attr_bool", random.randint, 0, 1)
toolbox.register("individual", tools.initRepeat, creator.Individual, toolbox.attr_bool, n=100)
toolbox.register("population", tools.initRepeat, list, toolbox.individual)

def evalOneMax(individual):
    return sum(individual),

toolbox.register("evaluate", evalOneMax)
toolbox.register("mate", tools.cxTwoPoint)
toolbox.register("mutate", tools.mutFlipBit, indpb=0.05)
toolbox.register("select", tools.selTournament, tournsize=3)

population = toolbox.population(n=300)

NGEN=40
for gen in range(NGEN):
    offspring = algorithms.varAnd(population, toolbox, cxpb=0.5, mutpb=0.1)
    fits = toolbox.map(toolbox.evaluate, offspring)
    for fit, ind in zip(fits, offspring):
        ind.fitness.values = fit
    population = toolbox.select(offspring, k=len(population))
top10 = tools.selBest(population, k=10)

How to cite DEAP

Authors of scientific papers including results generated using DEAP are encouraged to cite the following paper.

@article{DEAP_JMLR2012, 
    author    = " F\'elix-Antoine Fortin and Fran\c{c}ois-Michel {De Rainville} and Marc-Andr\'e Gardner and Marc Parizeau and Christian Gagn\'e ",
    title     = { {DEAP}: Evolutionary Algorithms Made Easy },
    pages    = { 2171--2175 },
    volume    = { 13 },
    month     = { jul },
    year      = { 2012 },
    journal   = { Journal of Machine Learning Research }
}

Publications on DEAP

  • François-Michel De Rainville, Félix-Antoine Fortin, Marc-André Gardner, Marc Parizeau and Christian Gagné, "DEAP -- Enabling Nimbler Evolutions", SIGEVOlution, vol. 6, no 2, pp. 17-26, February 2014. Paper
  • Félix-Antoine Fortin, François-Michel De Rainville, Marc-André Gardner, Marc Parizeau and Christian Gagné, "DEAP: Evolutionary Algorithms Made Easy", Journal of Machine Learning Research, vol. 13, pp. 2171-2175, jul 2012. Paper
  • François-Michel De Rainville, Félix-Antoine Fortin, Marc-André Gardner, Marc Parizeau and Christian Gagné, "DEAP: A Python Framework for Evolutionary Algorithms", in !EvoSoft Workshop, Companion proc. of the Genetic and Evolutionary Computation Conference (GECCO 2012), July 07-11 2012. Paper

Projects using DEAP

  • Ribaric, T., & Houghten, S. (2017, June). Genetic programming for improved cryptanalysis of elliptic curve cryptosystems. In 2017 IEEE Congress on Evolutionary Computation (CEC) (pp. 419-426). IEEE.
  • Ellefsen, Kai Olav, Herman Augusto Lepikson, and Jan C. Albiez. "Multiobjective coverage path planning: Enabling automated inspection of complex, real-world structures." Applied Soft Computing 61 (2017): 264-282.
  • S. Chardon, B. Brangeon, E. Bozonnet, C. Inard (2016), Construction cost and energy performance of single family houses : From integrated design to automated optimization, Automation in Construction, Volume 70, p.1-13.
  • B. Brangeon, E. Bozonnet, C. Inard (2016), Integrated refurbishment of collective housing and optimization process with real products databases, Building Simulation Optimization, pp. 531–538 Newcastle, England.
  • Randal S. Olson, Ryan J. Urbanowicz, Peter C. Andrews, Nicole A. Lavender, La Creis Kidd, and Jason H. Moore (2016). Automating biomedical data science through tree-based pipeline optimization. Applications of Evolutionary Computation, pages 123-137.
  • Randal S. Olson, Nathan Bartley, Ryan J. Urbanowicz, and Jason H. Moore (2016). Evaluation of a Tree-based Pipeline Optimization Tool for Automating Data Science. Proceedings of GECCO 2016, pages 485-492.
  • Van Geit W, Gevaert M, Chindemi G, Rössert C, Courcol J, Muller EB, Schürmann F, Segev I and Markram H (2016). BluePyOpt: Leveraging open source software and cloud infrastructure to optimise model parameters in neuroscience. Front. Neuroinform. 10:17. doi: 10.3389/fninf.2016.00017 https://github.com/BlueBrain/BluePyOpt
  • Lara-Cabrera, R., Cotta, C. and Fernández-Leiva, A.J. (2014). Geometrical vs topological measures for the evolution of aesthetic maps in a rts game, Entertainment Computing,
  • Macret, M. and Pasquier, P. (2013). Automatic Tuning of the OP-1 Synthesizer Using a Multi-objective Genetic Algorithm. In Proceedings of the 10th Sound and Music Computing Conference (SMC). (pp 614-621).
  • Fortin, F. A., Grenier, S., & Parizeau, M. (2013, July). Generalizing the improved run-time complexity algorithm for non-dominated sorting. In Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference (pp. 615-622). ACM.
  • Fortin, F. A., & Parizeau, M. (2013, July). Revisiting the NSGA-II crowding-distance computation. In Proceeding of the fifteenth annual conference on Genetic and evolutionary computation conference (pp. 623-630). ACM.
  • Marc-André Gardner, Christian Gagné, and Marc Parizeau. Estimation of Distribution Algorithm based on Hidden Markov Models for Combinatorial Optimization. in Comp. Proc. Genetic and Evolutionary Computation Conference (GECCO 2013), July 2013.
  • J. T. Zhai, M. A. Bamakhrama, and T. Stefanov. "Exploiting Just-enough Parallelism when Mapping Streaming Applications in Hard Real-time Systems". Design Automation Conference (DAC 2013), 2013.
  • V. Akbarzadeh, C. Gagné, M. Parizeau, M. Argany, M. A Mostafavi, "Probabilistic Sensing Model for Sensor Placement Optimization Based on Line-of-Sight Coverage", Accepted in IEEE Transactions on Instrumentation and Measurement, 2012.
  • M. Reif, F. Shafait, and A. Dengel. "Dataset Generation for Meta-Learning". Proceedings of the German Conference on Artificial Intelligence (KI'12). 2012.
  • M. T. Ribeiro, A. Lacerda, A. Veloso, and N. Ziviani. "Pareto-Efficient Hybridization for Multi-Objective Recommender Systems". Proceedings of the Conference on Recommanders Systems (!RecSys'12). 2012.
  • M. Pérez-Ortiz, A. Arauzo-Azofra, C. Hervás-Martínez, L. García-Hernández and L. Salas-Morera. "A system learning user preferences for multiobjective optimization of facility layouts". Pr,oceedings on the Int. Conference on Soft Computing Models in Industrial and Environmental Applications (SOCO'12). 2012.
  • Lévesque, J.C., Durand, A., Gagné, C., and Sabourin, R., Multi-Objective Evolutionary Optimization for Generating Ensembles of Classifiers in the ROC Space, Genetic and Evolutionary Computation Conference (GECCO 2012), 2012.
  • Marc-André Gardner, Christian Gagné, and Marc Parizeau, "Bloat Control in Genetic Programming with Histogram-based Accept-Reject Method", in Proc. Genetic and Evolutionary Computation Conference (GECCO 2011), 2011.
  • Vahab Akbarzadeh, Albert Ko, Christian Gagné, and Marc Parizeau, "Topography-Aware Sensor Deployment Optimization with CMA-ES", in Proc. of Parallel Problem Solving from Nature (PPSN 2010), Springer, 2010.
  • DEAP is used in TPOT, an open source tool that uses genetic programming to optimize machine learning pipelines.
  • DEAP is also used in ROS as an optimization package http://www.ros.org/wiki/deap.
  • DEAP is an optional dependency for PyXRD, a Python implementation of the matrix algorithm developed for the X-ray diffraction analysis of disordered lamellar structures.
  • DEAP is used in glyph, a library for symbolic regression with applications to MLC.

If you want your project listed here, send us a link and a brief description and we'll be glad to add it.

Owner
Distributed Evolutionary Algorithms in Python
Distributed Evolutionary Algorithms in Python
XGBoost-Ray is a distributed backend for XGBoost, built on top of distributed computing framework Ray.

XGBoost-Ray is a distributed backend for XGBoost, built on top of distributed computing framework Ray.

92 Dec 14, 2022
A Streamlit demo to interactively visualize Uber pickups in New York City

Streamlit Demo: Uber Pickups in New York City A Streamlit demo written in pure Python to interactively visualize Uber pickups in New York City. View t

Streamlit 230 Dec 28, 2022
hgboost - Hyperoptimized Gradient Boosting

hgboost is short for Hyperoptimized Gradient Boosting and is a python package for hyperparameter optimization for xgboost, catboost and lightboost using cross-validation, and evaluating the results o

Erdogan Taskesen 34 Jan 03, 2023
dirty_cat is a Python module for machine-learning on dirty categorical variables.

dirty_cat dirty_cat is a Python module for machine-learning on dirty categorical variables.

637 Dec 29, 2022
Using Logistic Regression and classifiers of the dataset to produce an accurate recall, f-1 and precision score

Using Logistic Regression and classifiers of the dataset to produce an accurate recall, f-1 and precision score

Thines Kumar 1 Jan 31, 2022
TorchDrug is a PyTorch-based machine learning toolbox designed for drug discovery

A powerful and flexible machine learning platform for drug discovery

MilaGraph 1.1k Jan 08, 2023
CobraML: Completely Customizable A python ML library designed to give the end user full control

CobraML: Completely Customizable What is it? CobraML is a python library built on both numpy and numba. Unlike other ML libraries CobraML gives the us

Sriram Govindan 14 Dec 19, 2021
Microsoft Machine Learning for Apache Spark

Microsoft Machine Learning for Apache Spark MMLSpark is an ecosystem of tools aimed towards expanding the distributed computing framework Apache Spark

Microsoft Azure 3.9k Dec 30, 2022
Basic Docker Compose for Machine Learning Purposes

Docker-compose for Machine Learning How to use: cd docker-ml-jupyterlab

Chris Chen 1 Oct 29, 2021
A Software Framework for Neuromorphic Computing

A Software Framework for Neuromorphic Computing

Lava 338 Dec 26, 2022
A Python implementation of the Robotics Toolbox for MATLAB

Robotics Toolbox for Python A Python implementation of the Robotics Toolbox for MATLAB® GitHub repository Documentation Wiki (examples and details) Sy

Peter Corke 1.2k Jan 07, 2023
A Python Module That Uses ANN To Predict A Stocks Price And Also Provides Accurate Technical Analysis With Many High Potential Implementations!

Stox A Module to predict the "close price" for the next day and give "technical analysis". It uses a Neural Network and the LSTM algorithm to predict

Stox 31 Dec 16, 2022
Pandas Machine Learning and Quant Finance Library Collection

Pandas Machine Learning and Quant Finance Library Collection

148 Dec 07, 2022
About Solve CTF offline disconnection problem - based on python3's small crawler

About Solve CTF offline disconnection problem - based on python3's small crawler, support keyword search and local map bed establishment, currently support Jianshu, xianzhi,anquanke,freebuf,seebug

天河 32 Oct 25, 2022
It is a forest of random projection trees

rpforest rpforest is a Python library for approximate nearest neighbours search: finding points in a high-dimensional space that are close to a given

Lyst 211 Dec 29, 2022
Kats is a toolkit to analyze time series data, a lightweight, easy-to-use, and generalizable framework to perform time series analysis.

Kats, a kit to analyze time series data, a lightweight, easy-to-use, generalizable, and extendable framework to perform time series analysis, from understanding the key statistics and characteristics

Facebook Research 4.1k Dec 29, 2022
A benchmark of data-centric tasks from across the machine learning lifecycle.

A benchmark of data-centric tasks from across the machine learning lifecycle.

61 Dec 28, 2022
MICOM is a Python package for metabolic modeling of microbial communities

Welcome MICOM is a Python package for metabolic modeling of microbial communities currently developed in the Gibbons Lab at the Institute for Systems

57 Dec 21, 2022
PyCaret is an open-source, low-code machine learning library in Python that automates machine learning workflows.

An open-source, low-code machine learning library in Python 🚀 Version 2.3.5 out now! Check out the release notes here. Official • Docs • Install • Tu

PyCaret 6.7k Jan 08, 2023