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Multitask matrix completion for learning protein interactions across diseases
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Kshirsagar, Meghana, Carbonell, Jaime G., Klein-Seetharaman, Judith and Murugesan, Keerthiram (2016) Multitask matrix completion for learning protein interactions across diseases. In: Singh, Mona, (ed.) Research in Computational Molecular Biology : 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Lecture Notes in Computer Science, 9649 . Springer International Publishing, pp. 53-64. ISBN 9783319319575
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Official URL: http://dx.doi.org/10.1007/978-3-319-31957-5_4
Abstract
Disease causing pathogens such as viruses, introduce their proteins into the host cells where they interact with the host’s proteins enabling the virus to replicate inside the host. These interactions between pathogen and host proteins are key to understanding infectious diseases. Often multiple diseases involve phylogenetically related or biologically similar pathogens. Here we present a multitask learning method to jointly model interactions between human proteins and three different, but related viruses: Hepatitis C, Ebola virus and Influenza A. Our multitask matrix completion based model uses a shared low-rank structure in addition to a task-specific sparse structure to incorporate the various interactions. We obtain upto a 39% improvement in predictive performance over prior state-of-the-art models. We show how our model’s parameters can be interpreted to reveal both general and specific interactionrelevant characteristics of the viruses. Our code and data is available at: http://www.cs.cmu.edu/~mkshirsa/bsl_mtl.tgz
| Item Type: | Book Item | ||||
|---|---|---|---|---|---|
| Divisions: | Faculty of Medicine > Warwick Medical School > Biomedical Sciences Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine > Metabolic and Vascular Health (- until July 2016) Faculty of Medicine > Warwick Medical School > Biomedical Sciences > Translational & Experimental Medicine Faculty of Medicine > Warwick Medical School |
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| Series Name: | Lecture Notes in Computer Science | ||||
| Journal or Publication Title: | Research in Computational Molecular Biology : 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings | ||||
| Publisher: | Springer International Publishing | ||||
| ISBN: | 9783319319575 | ||||
| ISSN: | 0302-9743 | ||||
| Book Title: | Research in Computational Molecular Biology : 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings | ||||
| Editor: | Singh, Mona | ||||
| Official Date: | 8 April 2016 | ||||
| Dates: |
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| Volume: | 9649 | ||||
| Page Range: | pp. 53-64 | ||||
| DOI: | 10.1007/978-3-319-31957-5 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access |
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