String kernel

Recognizing the different functional parts of genes, such as promoters, translation initiation sites, donors, acceptors and stop codons, is a fundamental task of many current studies in Bioinformatics. Currently, the most successful methods use powerful classifiers, such as support vector machines with various string kernels.

16p vioklahoma2711 19-11-2020 12 2   Download

Molecular structures can be represented as strings of special characters using SMILES. Since each molecule is represented as a string, the similarity between compounds can be computed using SMILES-based string similarity functions. Most previous studies on drug-target interaction prediction use 2D-based compound similarity kernels such as SIMCOMP.

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The amino acid sequence of a protein is the blueprint from which its structure and ultimately function can be derived. Therefore, sequence comparison methods remain essential for the determination of similarity between proteins.

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Alignment-free methods for comparing protein sequences have proved to be viable alternatives to approaches that first rely on an alignment of the sequences to be compared. Much work however need to be done before those methods provide reliable fold recognition for proteins whose sequences share little similarity.

14p viflorida2711 30-10-2020 13 1   Download

We present a new approach for mapping natural language sentences to their formal meaning representations using stringkernel-based classifiers. Our system learns these classifiers for every production in the formal language grammar. Meaning representations for novel natural language sentences are obtained by finding the most probable semantic parse using these string classifiers. Our experiments on two realworld data sets show that this approach compares favorably to other existing systems and is particularly robust to noise. ...

8p hongvang_1 16-04-2013 51 2   Download

Learning for sentence re-writing is a fundamental task in natural language processing and information retrieval. In this paper, we propose a new class of kernel functions, referred to as string re-writing kernel, to address the problem. A string re-writing kernel measures the similarity between two pairs of strings, each pair representing re-writing of a string. It can capture the lexical and structural similarity between two pairs of sentences without the need of constructing syntactic trees.

10p nghetay_1 07-04-2013 46 1   Download

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học 'Respiratory Research cung cấp cho các bạn kiến thức về ngành y đề tài: "HIV-1 coreceptor usage prediction without multiple alignments: an application of string kernels...

14p toshiba15 25-10-2011 24 2   Download