Frequency Fitness Assignment for Untangling Proteins in 2D

Koutstaal, Jonathan; Kommandeur, Jesse; Timmer, Rik; Horn, Ruben; Thomson, Sarah L.; van den Berg, Daan

Abstract

At the time of writing, there is no known deterministic-time algorithm to sample valid initial solutions with uniform random distribution for the HP protein folding model, because guaranteed uniform random sampling produces collisions (i.e. constraint violations). The expected number of collisions increases so fast with problem instance size that resampling is also infeasible. Maybe we can try uniform random sampling, and then hillclimb our way out of the violations? Here, we report results on a regular hillClimbers and an FFA-hillClimber, which traverses the search space following rare objective values instead of good objective values, applied to the task.

Citation

Koutstaal, J., Kommandeur, J., Timmer, R., Horn, R., Thomson, S. L., & van den Berg, D. (2024, April). Frequency Fitness Assignment for Untangling Proteins in 2D. Presented at EvoStar 2024, Aberyswyth, UK

• Presentation Conference Type: Conference Abstract
• Conference Name: EvoStar 2024
• Start Date: Apr 3, 2024
• End Date: Apr 5, 2024
• Acceptance Date: Mar 22, 2024
• Online Publication Date: Apr 3, 2024
• Publication Date: Apr 3, 2024
• Deposit Date: May 14, 2024
• Publicly Available Date: Apr 4, 2026
• Peer Reviewed: Not Peer Reviewed