Visualization of protein structure relationships using Twin Kernel Embedding

Yi Guo; Junbin Gao; Paul W. Kwan; Kevin X. Hou

doi:10.1109/ICBBE.2007.4

Visualization of protein structure relationships using Twin Kernel Embedding

Yi Guo, Junbin Gao, Paul W. Kwan, Kevin X. Hou

Research output: Chapter in Book / Conference Paper › Conference Paper › peer-review

Abstract

In this paper, a recently proposed dimensionality reduction method called Twin Kernel Embedding (TKE) is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Protein (SCOP) database confirmed the effectiveness of TKE in preserving the original relationships among protein structures in the lower dimensional embedding according to their similarities. This result is expected to benefit subsequent analyses of protein structures and their functions.

Original language	English
Title of host publication	2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE
Pages	1-4
Number of pages	4
DOIs	https://doi.org/10.1109/ICBBE.2007.4
Publication status	Published - 2007
Externally published	Yes
Event	2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE - Wuhan, China Duration: 6 Jul 2007 → 8 Jul 2007

Publication series

Name	2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE

Conference

Conference	2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE
Country/Territory	China
City	Wuhan
Period	6/07/07 → 8/07/07

Keywords

Dimensionality reduction
Protein
TKE

Access to Document

10.1109/ICBBE.2007.4

Cite this

Guo, Y., Gao, J., Kwan, P. W., & Hou, K. X. (2007). Visualization of protein structure relationships using Twin Kernel Embedding. In 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE (pp. 1-4). Article 4272488 (2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE). https://doi.org/10.1109/ICBBE.2007.4

@inproceedings{53348d3129054d95af5dd91cc9308dfa,

title = "Visualization of protein structure relationships using Twin Kernel Embedding",

abstract = "In this paper, a recently proposed dimensionality reduction method called Twin Kernel Embedding (TKE) is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Protein (SCOP) database confirmed the effectiveness of TKE in preserving the original relationships among protein structures in the lower dimensional embedding according to their similarities. This result is expected to benefit subsequent analyses of protein structures and their functions.",

keywords = "Dimensionality reduction, Protein, TKE",

author = "Yi Guo and Junbin Gao and Kwan, {Paul W.} and Hou, {Kevin X.}",

year = "2007",

doi = "10.1109/ICBBE.2007.4",

language = "English",

isbn = "1424411203",

series = "2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE",

pages = "1--4",

booktitle = "2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE",

note = "2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE ; Conference date: 06-07-2007 Through 08-07-2007",

}

Guo, Y, Gao, J, Kwan, PW & Hou, KX 2007, Visualization of protein structure relationships using Twin Kernel Embedding. in 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE., 4272488, 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE, pp. 1-4, 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE, Wuhan, China, 6/07/07. https://doi.org/10.1109/ICBBE.2007.4

Visualization of protein structure relationships using Twin Kernel Embedding. / Guo, Yi; Gao, Junbin; Kwan, Paul W. et al.
2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE. 2007. p. 1-4 4272488 (2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE).

Research output: Chapter in Book / Conference Paper › Conference Paper › peer-review

TY - GEN

T1 - Visualization of protein structure relationships using Twin Kernel Embedding

AU - Guo, Yi

AU - Gao, Junbin

AU - Kwan, Paul W.

AU - Hou, Kevin X.

PY - 2007

Y1 - 2007

N2 - In this paper, a recently proposed dimensionality reduction method called Twin Kernel Embedding (TKE) is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Protein (SCOP) database confirmed the effectiveness of TKE in preserving the original relationships among protein structures in the lower dimensional embedding according to their similarities. This result is expected to benefit subsequent analyses of protein structures and their functions.

AB - In this paper, a recently proposed dimensionality reduction method called Twin Kernel Embedding (TKE) is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted on a subset of the Structural Classification Of Protein (SCOP) database confirmed the effectiveness of TKE in preserving the original relationships among protein structures in the lower dimensional embedding according to their similarities. This result is expected to benefit subsequent analyses of protein structures and their functions.

KW - Dimensionality reduction

KW - Protein

KW - TKE

UR - http://www.scopus.com/inward/record.url?scp=35348917296&partnerID=8YFLogxK

U2 - 10.1109/ICBBE.2007.4

DO - 10.1109/ICBBE.2007.4

M3 - Conference Paper

AN - SCOPUS:35348917296

SN - 1424411203

SN - 9781424411207

T3 - 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE

SP - 1

EP - 4

BT - 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE

T2 - 2007 1st International Conference on Bioinformatics and Biomedical Engineering, ICBBE

Y2 - 6 July 2007 through 8 July 2007

ER -

Visualization of protein structure relationships using Twin Kernel Embedding

Abstract

Publication series

Conference

Keywords

Access to Document

Other files and links

Fingerprint

Cite this