Messenger RNA Design via Expected Partition Function and Continuous Optimization

arXiv:2401.00037v2 Announce Type: replace-cross
Abstract: The tasks of designing RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a generalization of classical partition function which we call "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from …

abstract arxiv continuous cs.ai cs.lg design designing framework function general messenger np-hard optimization q-bio.bm rna search tasks type versions via