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 usually provide an outdated version.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
Uplift modeling and causal inference with machine learning algorithms

Disclaimer This project is stable and being incubated for long-term support. It may contain new experimental code, for which APIs are subject to chang

Uber Open Source 3.7k Jan 07, 2023
High performance implementation of Extreme Learning Machines (fast randomized neural networks).

High Performance toolbox for Extreme Learning Machines. Extreme learning machines (ELM) are a particular kind of Artificial Neural Networks, which sol

Anton Akusok 174 Dec 07, 2022
Bodywork deploys machine learning projects developed in Python, to Kubernetes.

Bodywork deploys machine learning projects developed in Python, to Kubernetes. It helps you to: serve models as microservices execute batch jobs run r

Bodywork Machine Learning 409 Jan 01, 2023
Open source time series library for Python

PyFlux PyFlux is an open source time series library for Python. The library has a good array of modern time series models, as well as a flexible array

Ross Taylor 2k Jan 02, 2023
BudouX is the successor to Budou, the machine learning powered line break organizer tool.

BudouX Standalone. Small. Language-neutral. BudouX is the successor to Budou, the machine learning powered line break organizer tool. It is standalone

Google 868 Jan 05, 2023
Greykite: A flexible, intuitive and fast forecasting library

The Greykite library provides flexible, intuitive and fast forecasts through its flagship algorithm, Silverkite.

LinkedIn 1.7k Jan 04, 2023
Flask app to predict daily radiation from the time series of Solcast from Islamabad, Pakistan

Solar-radiation-ISB-MLOps - Flask app to predict daily radiation from the time series of Solcast from Islamabad, Pakistan.

Abid Ali Awan 1 Dec 31, 2021
LiuAlgoTrader is a scalable, multi-process ML-ready framework for effective algorithmic trading

LiuAlgoTrader is a scalable, multi-process ML-ready framework for effective algorithmic trading. The framework simplify development, testing, deployment, analysis and training algo trading strategies

Amichay Oren 458 Dec 24, 2022
李航《统计学习方法》复现

本项目复现李航《统计学习方法》每一章节的算法 特点: 笔记摘要:在每个文件开头都会有一些核心的摘要 pythonic:这里会用尽可能规范的方式来实现,包括编程风格几乎严格按照PEP8 循序渐进:前期的算法会更list的方式来做计算,可读性比较强,后期几乎完全为numpy.array的计算,并且辅助详

58 Oct 22, 2021
Predicting job salaries from ads - a Kaggle competition

Predicting job salaries from ads - a Kaggle competition

Zygmunt Zając 57 Oct 23, 2020
Databricks Certified Associate Spark Developer preparation toolkit to setup single node Standalone Spark Cluster along with material in the form of Jupyter Notebooks.

Databricks Certification Spark Databricks Certified Associate Spark Developer preparation toolkit to setup single node Standalone Spark Cluster along

19 Dec 13, 2022
Skoot is a lightweight python library of machine learning transformer classes that interact with scikit-learn and pandas.

Skoot is a lightweight python library of machine learning transformer classes that interact with scikit-learn and pandas. Its objective is to ex

Taylor G Smith 54 Aug 20, 2022
AutoOED: Automated Optimal Experiment Design Platform

AutoOED is an optimal experiment design platform powered with automated machine learning to accelerate the discovery of optimal solutions. Our platform solves multi-objective optimization problems an

Yunsheng Tian 107 Jan 03, 2023
Firebase + Cloudrun + Machine learning

A simple end to end consumer lending decision engine powered by Google Cloud Platform (firebase hosting and cloudrun)

Emmanuel Ogunwede 8 Aug 16, 2022
Drug prediction

I have collected data about a set of patients, all of whom suffered from the same illness. During their course of treatment, each patient responded to one of 5 medications, Drug A, Drug B, Drug c, Dr

Khazar 1 Jan 28, 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
[HELP REQUESTED] Generalized Additive Models in Python

pyGAM Generalized Additive Models in Python. Documentation Official pyGAM Documentation: Read the Docs Building interpretable models with Generalized

daniel servén 747 Jan 05, 2023
Feature-engine is a Python library with multiple transformers to engineer and select features for use in machine learning models.

Feature-engine is a Python library with multiple transformers to engineer and select features for use in machine learning models. Feature-engine's transformers follow scikit-learn's functionality wit

Soledad Galli 33 Dec 27, 2022
Send rockets to Mars with artificial intelligence(Genetic algorithm) in python.

Send Rockets To Mars With AI Send rockets to Mars with artificial intelligence(Genetic algorithm) in python. Tools Python 3 EasyDraw How to Play Insta

Mohammad Dori 3 Jul 15, 2022
Timeseries analysis for neuroscience data

=================================================== Nitime: timeseries analysis for neuroscience data ===============================================

NIPY developers 212 Dec 09, 2022