A Novel EA-based Memetic Approach for Efficiently Mapping Complex Fitness Landscapes

An evolutionary algorithm to model structural excursions of a protein

“…e EA presented here evolves a population of paths directly, exploits experimentally-known structures of a protein in its initialization, and makes use of novel selection and crossover operators. Key building blocks in the proposed path-evolving EA have been developed and analyzed in prior work [18][19][20]. ey include exploiting known structures of a protein (of healthy and diseased sequence variants) to extract a lower-dimensional variable space for exploration.…”

“…A recent roadmap-based approach, which is the subject of our comparative analysis in Section 3 rst reconstructs the energy landscape of a protein with a powerful memetic EA (making use of several building blocks developed over the years [4,5,19,20]) and then exploits a graph-based representation of the landscape to answer path queries corresponding to structural excursions of interest [18].…”

Evolutionary search for paths on protein energy landscapes

“…Key building blocks in the path-evolving EA have been developed and analyzed in prior work [3][4][5]. ey include exploiting known structures of a protein (of healthy and diseased sequence variants) to extract a lower-dimensional variable space for exploration.…”

“…Protein modeling research aims to uncover the functionally-relevant structural excursions that a protein employs to tune its biological function. One direction of in-silico work involves rst reconstructing energy landscapes (o en with powerful memetic EAs [4,5]) and then exploiting graph-based representations of such landscapes to answer path queries corresponding to structural excursions of interest. is direction has revealed key insights on many proteins [3] but has a large computational footprint due to the need to construct comprehensive and detailed representations of energy landscapes that are vast and high-dimensional [1,2].…”

Novel Approach for Parallelizing Pairwise Comparison Problems as Applied to Detecting Segments Identical By Decent in Whole-Genome Data

“…Situations where all pairs of observations in a dataset must be compared arise in many areas of science. For example, in protein studies, forming the graphs used in protein clustering relies on finding a protein's likeness to every other protein (Chapman and Kalyanaraman 2011;Sapin et al 2016), and in physics, calculating the total force each body has on every other body is required in order to predict the position and motion of all bodies in the n-body problem (Leimanis and Minorsky 1958). Such pairwise comparison problems are extremely computationally challenging with large datasets because they grow at the square of the sample size (are of order O(n 2 )).…”