title: Learning protein secondary structure from sequential and relational data.
abstract: We propose a method for sequential supervised learning that exploits explicit knowledge of short- and long-range dependencies. The architecture consists of a recursive and bi-directional neural network that takes as input a sequence along with an associated interaction graph. The interaction graph models (partial) knowledge about long-range dependency relations. We tested the method on the prediction of protein secondary structure, a task in which relations due to beta-strand pairings and other spatial proximities are known to have a significant effect on the prediction accuracy. In this particular task, interactions can be derived from knowledge of protein contact maps at the residue level. Our results show that prediction accuracy can be significantly boosted by the integration of interaction graphs.
authors.affiliation: Dipartimento di Sistemi e Informatica, Università degli Studi di Firenze Via Santa Marta, Firenze, Italy.
authors.forename: Alessio
authors.initials: A
authors.lastname: Ceroni
authors.forename: Paolo
authors.initials: P
authors.lastname: Frasconi
authors.forename: Gianluca
authors.initials: G
authors.lastname: Pollastri
mesh_terms: D000818:Animals; D003198:Computer Simulation / Q000706:statistics & numerical data; D030562:Databases, Protein; D006801:Humans; D008956:Models, Chemical; D016571:Neural Networks, Computer; D011237:Predictive Value of Tests; D017510:Protein Folding; D025941:Protein Interaction Mapping / Q000379:methods; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis / Q000737:chemistry*
chemical_list: D011506:Proteins