Protein Sequence Classification Using Feature Hashing

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Article on protein sequence classification using feature hashing.

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8 p.: ill.

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Caragea, Cornelia; Silvescu, Adrian & Mitra, Prasenjit June 21, 2012.


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Article on protein sequence classification using feature hashing.

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8 p.: ill.


This article is part of the supplement: Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2011: Proteome Science.

Abstract: Recent advances in next-generation sequencing technologies have resulted in an exponential increase in the rate at which protein sequence data are being acquired. The k-gram feature representation, commonly used for protein sequence classification, usually results in prohibitively high dimensional input spaces, for large values of k. Applying data mining algorithms to these input spaces may be intractable due to the large number of dimensions. Hence, using dimensionality reduction techniques can be crucial for the performance and the complexity of the learning algorithms. In this paper, we study the applicability of a recently introduced feature hashing technique to protein sequence classification, where the original high-dimensional space is "reduced" by hashing the features, using a hash function, into a lower-dimensional space, i.e., mapping features to hash keys, where multiple features can be mapped (at random) to the same hash key, and "aggregating" their counts. We compare feature hashing with the "bag of k-grams" and feature selection approaches. Our results show that feature hashing is an effective approach to reducing dimensionality on protein sequence classification tasks.


  • Proteome Science, 2012, London: BioMed Central Ltd.


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  • Publication Title: Proteome Science
  • Volume: 10
  • Issue: Suppl 1
  • Pages: 8
  • Peer Reviewed: Yes


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Materials from the UNT community's research, creative, and scholarly activities and UNT's Open Access Repository. Access to some items in this collection may be restricted.

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  • June 21, 2012

Added to The UNT Digital Library

  • Sept. 20, 2013, 3:37 p.m.

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  • March 27, 2014, 12:49 p.m.

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Caragea, Cornelia; Silvescu, Adrian & Mitra, Prasenjit. Protein Sequence Classification Using Feature Hashing, article, June 21, 2012; [London, United Kingdom]. ( accessed December 12, 2018), University of North Texas Libraries, Digital Library,; crediting UNT College of Engineering.