Scalable Algorithms for String Kernels with Inexact Matching

  title={Scalable Algorithms for String Kernels with Inexact Matching},
  author={Pavel P. Kuksa and Pai-Hsi Huang and Vladimir Pavlovic},
We present a new family of linear time algorithms for string comparison with mismatches under the string kernels framework. Based on sufficient statistics, our algorithms improve theoretical complexity bounds of existing approaches while scaling well in sequence alphabet size, the number of allowed mismatches and the size of the dataset. In particular, on large alphabets and under loose mismatch constraints our algorithms are several orders of magnitude faster than the existing algorithms for… CONTINUE READING
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and Inna Dubchak . Multi - class protein fold recognition using support vector machines and neural networks

  • Chris H. Q. Ding
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