dorsal/arxiv
View SchemaA covariance kernel for proteins
| Authors | Marco Cuturi, Jean-Philippe Vert |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0310022 |
| URL | https://arxiv.org/abs/q-bio/0310022 |
| DOI | 10.1109/IJCNN.2004.1380902 |
Abstract
We propose a new kernel for biological sequences which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for protein classification. By incorporating prior biological assumptions on the properties of amino-acid sequences and using a Bayesian averaging framework, we compute the value of this kernel in linear time and space, benefiting from previous achievements proposed in the field of universal coding. Encouraging classification results are reported on a standard protein homology detection experiment.
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"abstract": "We propose a new kernel for biological sequences which borrows ideas and\ntechniques from information theory and data compression. This kernel can be\nused in combination with any kernel method, in particular Support Vector\nMachines for protein classification. By incorporating prior biological\nassumptions on the properties of amino-acid sequences and using a Bayesian\naveraging framework, we compute the value of this kernel in linear time and\nspace, benefiting from previous achievements proposed in the field of universal\ncoding. Encouraging classification results are reported on a standard protein\nhomology detection experiment.",
"arxiv_id": "q-bio/0310022",
"authors": [
"Marco Cuturi",
"Jean-Philippe Vert"
],
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"q-bio.GN"
],
"doi": "10.1109/IJCNN.2004.1380902",
"title": "A covariance kernel for proteins",
"url": "https://arxiv.org/abs/q-bio/0310022"
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