While standard evolutionary algorithms employ a static, absolute fitness metric, coevolutionary algorithms assess individuals by their performance relative to populations of opponents that are themselves evolving. Although this arrangement offers the possibility of avoiding long-standing difficulties such as premature convergence, it suffers from its own unique problems, cycling, over-focusing and disengagement. Here, we introduce a novel technique for dealing with the third and least explored of these problems. Inspired by studies of natural host-parasite systems, we show that disengagement can be avoided by selecting for individuals that exhibit reduced levels of "virulence", rather than maximum ability to defeat coevolutionary adversaries. Experiments in both simple and complex domains are used to explain how this counterintuitive approach may be used to improve the success of coevolutionary algorithms.
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http://dx.doi.org/10.1162/106365604773955148 | DOI Listing |
Heliyon
October 2024
Department of Computers and Information Technologies, College of Sciences and Arts Turaif, Northern Border University, Arar 91431, Saudi Arabia.
The Environmental Economic Power Dispatch (EEPD) problem, a widely studied bi-objective nonlinear optimization challenge in power systems, traditionally focuses on the economic dispatch of thermal generators without considering network security constraints. However, environmental sustainability necessitates reducing emissions and increasing the penetration of renewable energy sources (RES) into the electrical grid. The integration of high levels of RES, such as wind and solar PV, introduces stability issues due to their uncertain and intermittent nature.
View Article and Find Full Text PDFMethods Mol Biol
September 2024
Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL Research University, ESPCI Paris, Paris, France.
RNA ribozyme (Walter Engelke, Biologist (London, England) 49:199-203, 2002) datasets typically contain from a few hundred to a few thousand naturally occurring sequences. However, the potential sequence space of RNA is huge. For example, the number of possible RNA sequences of length 150 nucleotides is approximately , a figure that far surpasses the estimated number of atoms in the known universe, which is around .
View Article and Find Full Text PDFNat Commun
August 2024
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
Recent work suggests that AlphaFold (AF)-a deep learning-based model that can accurately infer protein structure from sequence-may discern important features of folded protein energy landscapes, defined by the diversity and frequency of different conformations in the folded state. Here, we test the limits of its predictive power on fold-switching proteins, which assume two structures with regions of distinct secondary and/or tertiary structure. We find that (1) AF is a weak predictor of fold switching and (2) some of its successes result from memorization of training-set structures rather than learned protein energetics.
View Article and Find Full Text PDFProtein Sci
September 2024
Zelixir Biotech Company Ltd, Shanghai, China.
Disulfide bonds, covalently formed by sulfur atoms in cysteine residues, play a crucial role in protein folding and structure stability. Considering their significance, artificial disulfide bonds are often introduced to enhance protein thermostability. Although an increasing number of tools can assist with this task, significant amounts of time and resources are often wasted owing to inadequate consideration.
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