Sensitivity analysis of boosting PSI-BLAST with case study on subcellular localization

F. Mai, M. W. Mak, Y. S. Hung, Sun-Yuan Kung

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

Abstract

This paper studies the sensitivity of PSI-BLAST with respect to the 'h' parameter. Observing that the standard PSI-BLAST is sensitive to parameter 'h' in the high-value region, we propose a new technique, called Boosting PSI-BLAST, to reduce the sensitivity, By constraining 'h' to a small value first so as to reduce the chance of early corruption and then relaxing it gradually to increase divergence, the boosting PSI-BLAST not only can reduce the sensitivity to h-value, but also may strike a good balance between corruption and divergence in profiles. Tests on Reinhardt and Hubbard's eukaryotic protein dataset verify that our method is better in reducing the sensitivity of profile alignment scores to h-value than the standard PSI-BLAST.

Original languageEnglish (US)
Title of host publicationMachine Learning for Signal Processing 17 - Proceedings of the 2007 IEEE Signal Processing Society Workshop, MLSP
Pages39-44
Number of pages6
DOIs
StatePublished - Dec 1 2007
Event17th IEEE International Workshop on Machine Learning for Signal Processing, MLSP-2007 - Thessaloniki, Greece
Duration: Aug 27 2007Aug 29 2007

Publication series

NameMachine Learning for Signal Processing 17 - Proceedings of the 2007 IEEE Signal Processing Society Workshop, MLSP

Other

Other17th IEEE International Workshop on Machine Learning for Signal Processing, MLSP-2007
CountryGreece
CityThessaloniki
Period8/27/078/29/07

All Science Journal Classification (ASJC) codes

  • Computer Science(all)
  • Signal Processing

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