title: Exact learning of RNA energy parameters from structure.
abstract: We consider the problem of exact learning of parameters of a linear RNA energy model from secondary structure data. A necessary and sufficient condition for learnability of parameters is derived, which is based on computing the convex hull of union of translated Newton polytopes of input sequences. The set of learned energy parameters is characterized as the convex cone generated by the normal vectors to those facets of the resulting polytope that are incident to the origin. In practice, the sufficient condition may not be satisfied by the entire training data set; hence, computing a maximal subset of training data for which the sufficient condition is satisfied is often desired. We show that the problem is NP-hard in general for an arbitrary dimensional feature space. Using a randomized greedy algorithm, we select a subset of RNA STRAND v2.0 database that satisfies the sufficient condition for separate A-U, C-G, G-U base pair counting model. The set of learned energy parameters includes experimentally measured energies of A-U, C-G, and G-U pairs; hence, our parameter set is in agreement with the Turner parameters.
authors.affiliation: 1Department of Computer Science, Colorado State University, Fort Collins, Colorado.
authors.forename: Hamidreza
authors.initials: H
authors.lastname: Chitsaz
authors.affiliation: 2Department of Computer Science, Wayne State University, Detroit, Michigan.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Aminisharifabad
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D030561:Databases, Nucleic Acid; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012313:RNA
keywords: RNA; genomics; next generation sequencing; sequence analysis; statistical mechanics