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Contents

• Home
  • Introduction
  • Installation
  • Example code
  • Bugs
  • Credits
• Basic Usage
  • A 1D example
  • A 2D example
• General advice for using pynmmso
  • Finding minima
  • Changing the number of fitness evaluations
  • Using uniform parameter ranges
  • Choosing the number of particles per swarm
  • Stepping through the iterations
• More advanced topics
  • Arguments to the NMMSO class
  • Methods of the NMMSO class
  • Attributes of the NMMSO and Swarm classes
• Using pynmmso with libRoadRunner & SBML
• Advanced: using pynmmso in a parallel environment
• Advanced: using the listener class
  • Tracing the algorithm's progress
  • Writing your own listener class

Introduction

pynmmso is a python implementation of the Niching Migratory Multi-Swarm Optimser, described in: “Running Up Those Hills: Multi-Modal Search with the Niching Migratory Multi-Swarm Optimiser” by Jonathan E. Fieldsend published in Proceedings of the IEEE Congress on Evolutionary Computation, pages 2593-2600, 2014 (http://hdl.handle.net/10871/15247)

Please reference this paper if you undertake work utilising this code.

The examples on this page can be obtained from: https://github.com/EPCCed/pynmmso-examples

Code to run benchmark problems using pynmmso can be found at: https://github.com/EPCCed/pynmmso-benchmarking

Install pynmmso

The Python implementation of NMMSO requires Python 3 and Numpy (https://www.numpy.org/).

You can install pynmmso using pip:

pip install pynmmso

Example code

The code for the examples in this documentation can be found at https://github.com/EPCCed/pynmmso-examples.

There are also examples showing how to use both the simple fitness caller and the multiprocess fitness caller in a Jupyter notebook.

Bugs

Bugs can be reported via Github. We'd also be keen for feedback on this documentation and the examples provided.

Credits

The following people have contributed to this project:

• Professor Jonathan Fieldsend, Computer Science, University of Exeter
• Dr Ozgur Akman, Mathematics, University of Exeter
• Dr Khulood Alyahya, Computer Science, University of Exeter
• Ally Hume, EPCC, University of Edinburgh
• Dr Chris Wood, EPCC, University of Edinburgh
• Dr Neelofer Banglawala, EPCC, University of Edinburgh
• Professor Andrew J Millar, Chair of Systems Biology, The University of Edinburgh
• Dr Kevin Doherty
• Benjamin J. Wareham

Thanks to the following people for feedback and suggested improvements:

• George De Ath

Thanks to the following tools used to produce the graphs on this documentation:

• Desmos (https://www.desmos.com)
• Academo (https://academo.org/demos/3d-surface-plotter)
• libRoadRunner (http://libroadrunner.org/)

This work was supported by the Engineering and Physical Sciences Research Council (grant number EP/N018125/1)