Fast non-negative dimensionality reduction for protein fold recognition

Authors:
Oleg Okun;Helen Priisalu;Alexessander Alves
Affiliations:
Infotech Oulu, 4500, Oulu, Finland;Infotech Oulu, 4500, Oulu, Finland;,LIACC, Porto, Portugal
Venue:
ECML'05 Proceedings of the 16th European conference on Machine Learning
Year:
2005

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Abstract

In this paper, dimensionality reduction via matrix factorization with nonnegativity constraints is studied. Because of these constraints, it stands apart from other linear dimensionality reduction methods. Here we explore nonnegative matrix factorization in combination with a classifier for protein fold recognition. Since typically matrix factorization is iteratively done, convergence can be slow. To alleviate this problem, a significantly faster (more than 11 times) algorithm is proposed.