2005 Special Issue: Learning protein secondary structure from sequential and relational data

Authors:
Alessio Ceroni;Paolo Frasconi;Gianluca Pollastri
Affiliations:
Dipartimento di Sistemi e Informatica, Universití degli Studi di Firenze Via Santa Marta, Firenze, Italy;Dipartimento di Sistemi e Informatica, Universití degli Studi di Firenze Via Santa Marta, Firenze, Italy;Department of Computer Science, University College Dublin Belfield, Dublin 4, Ireland
Venue:
Neural Networks - Special issue on neural networks and kernel methods for structured domains
Year:
2005

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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.