Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
Reconstructing regulatory and signaling response networks is one of the major goals of systems biology. While several successful methods have been suggested for this task, some integrating large and diverse datasets, these methods have so far been applied to reconstruct a single response network at...
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2014
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| Online Access: | http://hdl.handle.net/1721.1/92474 https://orcid.org/0000-0002-5324-9833 |
| _version_ | 1826212786167873536 |
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| author | Jain, Siddhartha Gitter, Anthony Bar-Joseph, Ziv |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Jain, Siddhartha Gitter, Anthony Bar-Joseph, Ziv |
| author_sort | Jain, Siddhartha |
| collection | MIT |
| description | Reconstructing regulatory and signaling response networks is one of the major goals of systems biology. While several successful methods have been suggested for this task, some integrating large and diverse datasets, these methods have so far been applied to reconstruct a single response network at a time, even when studying and modeling related conditions. To improve network reconstruction we developed MT-SDREM, a multi-task learning method which jointly models networks for several related conditions. In MT-SDREM, parameters are jointly constrained across the networks while still allowing for condition-specific pathways and regulation. We formulate the multi-task learning problem and discuss methods for optimizing the joint target function. We applied MT-SDREM to reconstruct dynamic human response networks for three flu strains: H1N1, H5N1 and H3N2. Our multi-task learning method was able to identify known and novel factors and genes, improving upon prior methods that model each condition independently. The MT-SDREM networks were also better at identifying proteins whose removal affects viral load indicating that joint learning can still lead to accurate, condition-specific, networks. Supporting website with MT-SDREM implementation: http://sb.cs.cmu.edu/mtsdrem |
| first_indexed | 2024-09-23T15:37:53Z |
| format | Article |
| id | mit-1721.1/92474 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T15:37:53Z |
| publishDate | 2014 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/924742022-10-02T03:01:50Z Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu Jain, Siddhartha Gitter, Anthony Bar-Joseph, Ziv Massachusetts Institute of Technology. Department of Biological Engineering Gitter, Anthony Reconstructing regulatory and signaling response networks is one of the major goals of systems biology. While several successful methods have been suggested for this task, some integrating large and diverse datasets, these methods have so far been applied to reconstruct a single response network at a time, even when studying and modeling related conditions. To improve network reconstruction we developed MT-SDREM, a multi-task learning method which jointly models networks for several related conditions. In MT-SDREM, parameters are jointly constrained across the networks while still allowing for condition-specific pathways and regulation. We formulate the multi-task learning problem and discuss methods for optimizing the joint target function. We applied MT-SDREM to reconstruct dynamic human response networks for three flu strains: H1N1, H5N1 and H3N2. Our multi-task learning method was able to identify known and novel factors and genes, improving upon prior methods that model each condition independently. The MT-SDREM networks were also better at identifying proteins whose removal affects viral load indicating that joint learning can still lead to accurate, condition-specific, networks. Supporting website with MT-SDREM implementation: http://sb.cs.cmu.edu/mtsdrem Microsoft Research 2014-12-23T18:22:01Z 2014-12-23T18:22:01Z 2014-12 2014-06 Article http://purl.org/eprint/type/JournalArticle 1553-7358 1553-734X http://hdl.handle.net/1721.1/92474 Jain, Siddhartha, Anthony Gitter, and Ziv Bar-Joseph. “Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu.” Edited by Mona Singh. PLoS Comput Biol 10, no. 12 (December 18, 2014): e1003943. https://orcid.org/0000-0002-5324-9833 en_US http://dx.doi.org/10.1371/journal.pcbi.1003943 PLoS Computational Biology Creative Commons Attribution http://creativecommons.org/licenses/by/4.0/ application/pdf Public Library of Science Public Library of Science |
| spellingShingle | Jain, Siddhartha Gitter, Anthony Bar-Joseph, Ziv Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title | Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title_full | Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title_fullStr | Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title_full_unstemmed | Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title_short | Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu |
| title_sort | multitask learning of signaling and regulatory networks with application to studying human response to flu |
| url | http://hdl.handle.net/1721.1/92474 https://orcid.org/0000-0002-5324-9833 |
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