Sequence kernels for predicting protein essentiality

Cyril Allauzen, Mehryar Mohri, Ameet Talwalkar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The problem of identifying the minimal gene set required to sustain life is of crucial importance in understanding cellular mechanisms and designing therapeutic drugs. This work describes several kernel-based solutions for predicting essential genes that outperform existing models while using less training data. Our first solution is based on a semi-manually designed kernel derived from the Pfam database, which includes several Pfam domains. We then present novel and general domain-based sequence kernels that capture sequence similarity with respect to several domains made of large sets of protein sequences. We show how to deal with the large size of the problem - several thousands of domains with individual domains sometimes containing thousands of sequences - by representing and efficiently computing these kernels using automata. We report results of extensive experiments demonstrating that they compare favorably with the Pfam kernel in predicting protein essentiality, while requiring no manual tuning.

Original languageEnglish (US)
Title of host publicationProceedings of the 25th International Conference on Machine Learning
Pages9-16
Number of pages8
StatePublished - 2008
Event25th International Conference on Machine Learning - Helsinki, Finland
Duration: Jul 5 2008Jul 9 2008

Other

Other25th International Conference on Machine Learning
CountryFinland
CityHelsinki
Period7/5/087/9/08

Fingerprint

Genes
Proteins
Tuning
Experiments

ASJC Scopus subject areas

  • Artificial Intelligence
  • Human-Computer Interaction
  • Software

Cite this

Allauzen, C., Mohri, M., & Talwalkar, A. (2008). Sequence kernels for predicting protein essentiality. In Proceedings of the 25th International Conference on Machine Learning (pp. 9-16)

Sequence kernels for predicting protein essentiality. / Allauzen, Cyril; Mohri, Mehryar; Talwalkar, Ameet.

Proceedings of the 25th International Conference on Machine Learning. 2008. p. 9-16.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Allauzen, C, Mohri, M & Talwalkar, A 2008, Sequence kernels for predicting protein essentiality. in Proceedings of the 25th International Conference on Machine Learning. pp. 9-16, 25th International Conference on Machine Learning, Helsinki, Finland, 7/5/08.
Allauzen C, Mohri M, Talwalkar A. Sequence kernels for predicting protein essentiality. In Proceedings of the 25th International Conference on Machine Learning. 2008. p. 9-16
Allauzen, Cyril ; Mohri, Mehryar ; Talwalkar, Ameet. / Sequence kernels for predicting protein essentiality. Proceedings of the 25th International Conference on Machine Learning. 2008. pp. 9-16
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