Can HP-protein Folding Be Solved with Genetic Algorithms? Maybe not

Reitze Jansen, Ruben Horn, Ruben Horn, Okke van Eck, Kristian Verduin, Sarah Thomson, Daan van den Berg

2023

Abstract

Genetic algorithms might not be able to solve the HP-protein folding problem because creating random individuals for an initial population is very hard, if not impossible. The reason for this, is that the expected number of constraint violations increases with instance size when randomly sampling individuals, as we will show in an experiment. Thereby, the probability of randomly sampling a valid individual decreases exponentially with instance size. This immediately prohibits resampling, and repair mechanisms might also be non-applicable. Backtracking could generate a valid random individual, but it runs in exponential time, and is therefore also unsuitable. No wonder that previous approaches do not report how (often) random samples are created, and only address small instances. We contrast our findings with TSP, which is also NP-hard, but does not have these problems.

Paper Citation

in Harvard Style

Jansen R., Horn R., van Eck O., Verduin K., Thomson S. and van den Berg D. (2023). Can HP-protein Folding Be Solved with Genetic Algorithms? Maybe not. In Proceedings of the 15th International Joint Conference on Computational Intelligence - Volume 1: ECTA; ISBN 978-989-758-674-3, SciTePress, pages 131-140. DOI: 10.5220/0012248500003595

in Bibtex Style

@conference{ecta23,
author={Reitze Jansen and Ruben Horn and Okke van Eck and Kristian Verduin and Sarah Thomson and Daan van den Berg},
title={Can HP-protein Folding Be Solved with Genetic Algorithms? Maybe not},
booktitle={Proceedings of the 15th International Joint Conference on Computational Intelligence - Volume 1: ECTA},
year={2023},
pages={131-140},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0012248500003595},
isbn={978-989-758-674-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 15th International Joint Conference on Computational Intelligence - Volume 1: ECTA
TI - Can HP-protein Folding Be Solved with Genetic Algorithms? Maybe not
SN - 978-989-758-674-3
AU - Jansen R.
AU - Horn R.
AU - van Eck O.
AU - Verduin K.
AU - Thomson S.
AU - van den Berg D.
PY - 2023
SP - 131
EP - 140
DO - 10.5220/0012248500003595
PB - SciTePress