Artem Sokolov
ABSTRACT
The problem of predicting protein function using Gene Ontology terms is a hierarchical classification problem. There are a variety of genomic data that are relevant to a protein's function: its sequence, its interactions with other proteins, expression of its gene, etc. Some of these sources (interactions and expression) are species-specific, while protein sequence is comparable across species, which complicates the task of integrating labeled data from a target species with labeled data from other species. We address this problem using the methodology of structured output learning, present a framework based on multi-view learning that is naturally suited for combining both types of data, and demonstrate its effectiveness in making predictions for proteins in S. cerevisiae and M. musculus. The code for our framework is available at http://strut.sourceforge.net.
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Index Terms
- Multi-view prediction of protein function
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