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Kuang Lung Shing continuous relaxation of the mismatch kernel
Continuous Relaxation Of The Mismatch Kernel, supplied by Kuang Lung Shing, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/mismatch+kernel/profile+kernel/pm30753280-38-8-12
Average 90 stars, based on 1 article reviews
continuous relaxation of the mismatch kernel - by Bioz Stars, 2026-11
90/100 stars

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Article Title: Biological sequence modeling with convolutional kernel networks.
Article Snippet: CKN-seq relies on a continuous relaxation of the mismatch kernel (Leslie and Kuang, 2004).

Article Title: Phylogeny construction with rigid gapped motifs.
Article Snippet: Patterns with gaps have traditionally been used as signatures of protein families or as features in binary classification.. Current alignment-free algorithms construct phylogenies by comparing the repertoire and frequency of ungapped blocks in genomes and proteomes.. In this article, we measure the quality of phylogenies reconstructed by comparing suitably defined sets of gapped motifs that occur in mitochondrial proteomes.

Article Title: Biological sequence modeling with convolutional kernel networks.
Article Snippet: As observed by Morrow et al. (2017), the mismatch kernel (Leslie and Kuang, 2004) for modeling sequences may be written as Equation (2) when replacing K0 with a discrete function I0 that assesses whether the two k-mers are identical up to some mismatches.

Article Title: A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k -Mer Distances
Article Snippet: They have frequently been applied to biological sequence classification, as k -spectrum kernels (Leslie et al., 2002 ), mismatch k -spectrum kernels (Leslie et al., 2004 ), string alignment kernels (Saigo et al., 2004 ), and profile-based string kernels (Kuang et al., 2005 ) to cite a few examples.

Article Title: Protein remote homology detection by combining Chou's distance-pair pseudo amino acid composition and principal component analysis.
Article Snippet: pseudo amino acid composition (PseAAC) approach.. The predictive performance and computational cost are further improved by employing the principal component analysis strategy.. Various experiments are conducted on a benchmark dataset.

Article Title: Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
Article Snippet: For example, Top- n -grams ( Liu et al. , 2008 ) extracted the profile-based patterns by considering the most frequent elements in the profiles; profile kernel ( Kuang et al. , 2005 ) extracted the short substrings according to the profile-based ungapped alignment scores; some profile-based methods improved the predictive performance by developing more sensitive profiles.

Plasmid Preparation:

Article Title: LocTree2 predicts localization for all domains of life.
Article Snippet: .. The feature space was implicitly given by the profile kernel (Kuang et al., 2004) that maps such a tuple to a vector indexed by all possible subsequences of length k from the alphabet of amino acids. ..

Introduce:

Article Title: Biological sequence modeling with convolutional kernel networks.
Article Snippet: .. We introduce CKNs for sequences, and show their link with mismatch kernels (Leslie and Kuang, 2004). ..



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