Journal Article

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins

Yanjun Qi, Oznur Tastan, Jaime G. Carbonell, Judith Klein-Seetharaman and Jason Weston

in Bioinformatics

Volume 26, issue 18, pages i645-i652
Published in print September 2010 | ISSN: 1367-4803
Published online September 2010 | e-ISSN: 1460-2059 | DOI:

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Motivation: Protein–protein interactions (PPIs) are critical for virtually every biological function. Recently, researchers suggested to use supervised learning for the task of classifying pairs of proteins as interacting or not. However, its performance is largely restricted by the availability of truly interacting proteins (labeled). Meanwhile, there exists a considerable amount of protein pairs where an association appears between two partners, but not enough experimental evidence to support it as a direct interaction (partially labeled).

Results: We propose a semi-supervised multi-task framework for predicting PPIs from not only labeled, but also partially labeled reference sets. The basic idea is to perform multi-task learning on a supervised classification task and a semi-supervised auxiliary task. The supervised classifier trains a multi-layer perceptron network for PPI predictions from labeled examples. The semi-supervised auxiliary task shares network layers of the supervised classifier and trains with partially labeled examples. Semi-supervision could be utilized in multiple ways. We tried three approaches in this article, (i) classification (to distinguish partial positives with negatives); (ii) ranking (to rate partial positive more likely than negatives); (iii) embedding (to make data clusters get similar labels). We applied this framework to improve the identification of interacting pairs between HIV-1 and human proteins. Our method improved upon the state-of-the-art method for this task indicating the benefits of semi-supervised multi-task learning using auxiliary information.



Journal Article.  6262 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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