2020
DOI: 10.1101/2020.04.21.053975
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FastSK: Fast Sequence Analysis with Gapped String Kernels

Abstract: AbstractGapped k-mer kernels with Support Vector Machines (gkm-SVMs) have achieved strong predictive performance on regulatory DNA sequences on modestly-sized training sets. However, existing gkm-SVM algorithms suffer from slow kernel computation time, as they depend exponentially on the sub-sequence feature-length, number of mismatch positions, and the task’s alphabet size. In this work, we introduce a fast and scalable algorithm for calculating gapp… Show more

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