The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
THE SPECTRUM KERNEL: A STRING KERNEL FOR SVM PROTEIN CLASSIFICATION
Abstract
We introduce a new sequence-similarity kernel, the spectrum kernel, for use with support vector machines (SVMs) in a discriminative approach to the protein classification problem. Our kernel is conceptually simple and efficient to compute and, in experiments on the SCOP database, performs well in comparison with state-of-the-art methods for homology detection. Moreover, our method produces an SVM classifier that allows linear time classification of test sequences. Our experiments provide evidence that string-based kernels, in conjunction with SVMs, could offer a viable and computationally efficient alternative to other methods of protein classification and homology detection.
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Cites
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Cited by
Machine learning applications in genetics and genomics
Libbrecht, M. W., & Noble, W. S. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3920 · Cited by 2,084
Self-citationA Geometric Framework for Unsupervised Anomaly Detection: Detecting Intrusions in Unlabeled Data
Eskin, E., Arnold, A., Prerau, M., Portnoy, L., & Stolfo, S. (2002) · Advances in Information Security · doi:10.1007/978-1-4615-0953-0_4 · Cited by 683
Self-citationKernel methods for predicting protein-protein interactions
Ben-Hur, A., & Noble, W. S. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1016 · Cited by 561
Self-citationMismatch string kernels for discriminative protein classification
Leslie, C. S., Eskin, E., Cohen, A., Weston, J., & Noble, W. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg431 · Cited by 561
Self-citationWord Spotting and Recognition with Embedded Attributes
Almazan, J., Gordo, A., Fornes, A., & Valveny, E. (2014) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2014.2339814 · Cited by 517
Metadata
- Authors
- LESLIE, C., ESKIN, E., & NOBLE, W. S.
- Venue
- Biocomputing 2002
- Publisher
- WORLD SCIENTIFIC
- Published
- 2001-12
- Pages
- 564-575
- OpenAlex
- W2020816856
- Cited by
- 927
- References
- 1
- FWCI
- 42.94
- Type
- conference paper
- Language
- en
- Open access
- closed
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- LESLIE, C., ESKIN, E., & NOBLE, W. S. (2001). THE SPECTRUM KERNEL: A STRING KERNEL FOR SVM PROTEIN CLASSIFICATION. Biocomputing 2002. https://doi.org/10.1142/9789812799623_0053
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