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Abstract

Chinwe Ekenna, Shawna Thomas, Nancy Amato, "Adaptive Local Learning in Sampling Based Motion Planning for Protein Folding," In The IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 61-68, Washington DC, USA, Nov 2015.
Proceedings(pdf, abstract)

Motivation: Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms such as Probabilistic Roadmap Methods (PRMs) have been successful in modeling the protein folding landscape. PRMs and variants contain several phases (i.e., sampling, connection, and path extraction). Global machine learning has been applied to the connection phase but is inefficient in situations with varying topology, such as those typical of folding landscapes. Results: We present a local learning algorithm that considers the past performance near the current connection attempt as a basis for learning. It is sensitive not only to different types of landscapes but also to differing regions in the landscape itself, removing the need to explicitly partition the landscape. We perform experiments on 23 proteins of varying secondary structure makeup with 52–114 residues. Our method models the landscape with better quality and comparable time to the best performing individual method and to global learning.