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Kernel based methods for sequence comparison.

Yeung, Hau Man. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2011. / Includes bibliographical references (p. 59-63). / Abstracts in English and Chinese. / Chapter 1 --- Introduction --- p.7 / Chapter 2 --- Work Flows and Kernel Methods --- p.9 / Chapter 2.1 --- Work Flows --- p.9 / Chapter 2.2 --- Frequency Vector --- p.11 / Chapter 2.3 --- Motivation for Kernel Based Distance --- p.12 / Chapter 2.3.1 --- Similarity between sequences --- p.13 / Chapter 2.3.2 --- Distance between sequences --- p.14 / Chapter 2.4 --- Kernels for DNA Sequence --- p.15 / Chapter 2.4.1 --- Kernels based on evolution model --- p.15 / Chapter 2.4.2 --- Kernels based on empirical data --- p.17 / Chapter 2.5 --- Kernels for Peptide Sequence --- p.18 / Chapter 3 --- Dataset for DNA Sequence and Results --- p.25 / Chapter 3.1 --- Dataset and Goal --- p.25 / Chapter 3.1.1 --- Mitochondrial DNA dataset --- p.26 / Chapter 3.1.2 --- 18S ribosomal RNA --- p.28 / Chapter 3.2 --- Results --- p.28 / Chapter 4 --- Dataset for Peptide Sequence and Results --- p.35 / Chapter 4.1 --- Dataset and Goal --- p.36 / Chapter 4.2 --- Classification and Evaluation Methods --- p.39 / Chapter 4.2.1 --- Partition of training and testing datasets --- p.39 / Chapter 4.2.2 --- Classification methods --- p.40 / Chapter 4.3 --- Results --- p.45 / Chapter 4.3.1 --- KNN performs better than the FDSM --- p.45 / Chapter 4.3.2 --- BLOSUM62 performs best and window length not important --- p.46 / Chapter 4.3.3 --- Distance formula (2.4) performs better --- p.49 / Chapter 5 --- Discussion --- p.51 / Chapter 5.1 --- Sequence Length and Window Length --- p.51 / Chapter 5.2 --- Possible Kernels --- p.52 / Chapter 5.3 --- Distance Formulae --- p.53 / Chapter 5.4 --- Protein Structural Problem --- p.54 / Chapter 6 --- Appendix --- p.55 / Chapter 6.1 --- Kernel for Peptide Sequences --- p.55 / Bibliography --- p.59

Identiferoai:union.ndltd.org:cuhk.edu.hk/oai:cuhk-dr:cuhk_327578
Date January 2011
ContributorsYeung, Hau Man., Chinese University of Hong Kong Graduate School. Division of Mathematics.
Source SetsThe Chinese University of Hong Kong
LanguageEnglish, Chinese
Detected LanguageEnglish
TypeText, bibliography
Formatprint, 63 p. : ill. ; 30 cm.
RightsUse of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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