Fast String Kernels using Inexact Matching for Protein Sequences

@article{Leslie2004FastSK,
  title={Fast String Kernels using Inexact Matching for Protein Sequences},
  author={Christina S. Leslie and Rui Kuang},
  journal={Journal of Machine Learning Research},
  year={2004},
  volume={5},
  pages={1435-1455}
}
We describe several families of k-mer based string kernels related to the recently presented mismatch kernel and designed for use with support vector machines (SVMs) for classification of protein sequence data. These new kernels – restricted gappy kernels, substitution kernels, and wildcard kernels – are based on feature spaces indexed by k-length subsequences (“k-mers”) from the string alphabet Σ. However, for all kernels we define here, the kernel value K(x,y) can be computed in O(cK(|x|+ |y… CONTINUE READING
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