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Tutorial: "Multi-objective optimization with metaheuristics. Applications to multiple sequence alignment and other bioinformatics problems"

This site contains stuff to be used in the tutorial I will give in the Omics Data Analysis Master of the University of Vic on 7th February 2018.

In this tutorial we will learn:

  • What are metaheuristic techniques and why they are useful.
  • Issues related to optimizing problems having more tan one objective function (multi-objective optimization problems).
  • How to use the jMetal optimization framework to solve both single and multi-objective optimization problems.
  • To apply the M2Align metaheuristic to deal with multi-objective formulations of the multiple sequence alignment problem.

Recommended readings

  • Metaheuristics in combinatorial optimization: Overview and conceptual comparison. C. Blum, A. Roli. ACM Computing Surveys Volume 35 Issue 3, September 2003. DOI.

  • An Introduction to Evolutionary Algorithms. Shahim Rostami. Video.

  • Multiobjective optimization in bioinformatics and computational biology. J. Handl, DB Kell, J Knowles. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2), 279-292. 2007. DOI

  • Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns. F.M. Ortuño et al. Bioinformatics, Volume 29, Issue 17, 1 September 2013, Pages 2112–2121. DOI.

  • M2Align: parallel multiple sequence alignment with a multi-objective metaheuristic. C. Zambrano-Vega, A.J. Nebro, J. García-Nieto, J.F. Aldana-Montes. Bioinformatics, Volume 33, Issue 19, 1 October 2017, Pages 3011–3017. DOI.

Software requirements