Evaluation of techniques for classifying biological sequences

Mukund Deshpande; George Karypis

doi:10.1007/3-540-47887-6_41

Evaluation of techniques for classifying biological sequences

Mukund Deshpande, George Karypis

Computer Science and Engineering

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

47 Scopus citations

Abstract

In recent years we have witnessed an exponential increase in the amount of biological information, either DNA or protein sequences, that has become available in public databases. This has been followed by an increased interest in developing computational techniques to automatically classify these large volumes of sequence data into various categories corresponding to either their role in the chromosomes, their structure, and/or their function. In this paper we evaluate some of the widely-used sequence classification algorithms and develop a framework for modeling sequences in a fashion so that traditional machine learning algorithms, such as support vector machines, can be applied easily. Our detailed experimental evaluation shows that the SVM-based approaches are able to achieve higher classification accuracy compared to the more traditional sequence classification algorithms such as Markov model based techniques and K-nearest neighbor based approaches.

Original language	English (US)
Title of host publication	Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings
Editors	Ming-Syan Chen, Philip S. Yu, Bing Liu
Publisher	Springer Verlag
Pages	417-431
Number of pages	15
ISBN (Print)	9783540437048
DOIs	https://doi.org/10.1007/3-540-47887-6_41
State	Published - 2002
Event	6th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2002 - Taipei, Taiwan, Province of China Duration: May 6 2002 → May 8 2002

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	2336
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Other

Other	6th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2002
Country/Territory	Taiwan, Province of China
City	Taipei
Period	5/6/02 → 5/8/02

Bibliographical note

Publisher Copyright:
© Springer-Verlag Berlin Heidelberg 2002.

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10.1007/3-540-47887-6_41

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Deshpande, M., & Karypis, G. (2002). Evaluation of techniques for classifying biological sequences. In M.-S. Chen, P. S. Yu, & B. Liu (Eds.), Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings (pp. 417-431). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2336). Springer Verlag. https://doi.org/10.1007/3-540-47887-6_41

Evaluation of techniques for classifying biological sequences. / Deshpande, Mukund; Karypis, George.
Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings. ed. / Ming-Syan Chen; Philip S. Yu; Bing Liu. Springer Verlag, 2002. p. 417-431 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 2336).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Deshpande, M & Karypis, G 2002, Evaluation of techniques for classifying biological sequences. in M-S Chen, PS Yu & B Liu (eds), Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 2336, Springer Verlag, pp. 417-431, 6th Pacific-Asia Conference on Knowledge Discovery and Data Mining, PAKDD 2002, Taipei, Taiwan, Province of China, 5/6/02. https://doi.org/10.1007/3-540-47887-6_41

Deshpande M, Karypis G. Evaluation of techniques for classifying biological sequences. In Chen MS, Yu PS, Liu B, editors, Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings. Springer Verlag. 2002. p. 417-431. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/3-540-47887-6_41

Deshpande, Mukund ; Karypis, George. / Evaluation of techniques for classifying biological sequences. Advances in Knowledge Discovery and Data Mining - 6th Pacific-Asia Conference, PAKDD 2002, Proceedings. editor / Ming-Syan Chen ; Philip S. Yu ; Bing Liu. Springer Verlag, 2002. pp. 417-431 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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Evaluation of techniques for classifying biological sequences

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