Novel visualization methods for protein data

Mumtaz, Shahzad, Nabney, Ian and Flower, Darren (2012). Novel visualization methods for protein data. IN: 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). USA: IEEE.

Abstract

Visualization of high-dimensional data has always been a challenging task. Here we discuss and propose variants of non-linear data projection methods (Generative Topographic Mapping (GTM) and GTM with simultaneous feature saliency (GTM-FS)) that are adapted to be effective on very high-dimensional data. The adaptations use log space values at certain steps of the Expectation Maximization (EM) algorithm and during the visualization process. We have tested the proposed algorithms by visualizing electrostatic potential data for Major Histocompatibility Complex (MHC) class-I proteins. The experiments show that the variation in the original version of GTM and GTM-FS worked successfully with data of more than 2000 dimensions and we compare the results with other linear/nonlinear projection methods: Principal Component Analysis (PCA), Neuroscale (NSC) and Gaussian Process Latent Variable Model (GPLVM).

Divisions: Engineering & Applied Sciences > Computer Science
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Life & Health Sciences > Pharmacy
Life & Health Sciences
Life & Health Sciences > Chronic and Communicable Conditions
Additional Information: © 2012 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Event Title: 2012 IEEE symposium on computational intelligence in bioinformatics and computational biology
Event Type: Other
Event Dates: 2012-05-09 - 2012-05-12
Uncontrolled Keywords: Electrical and Electronic Engineering
Full Text Link:
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
Published Date: 2012
Authors: Mumtaz, Shahzad
Nabney, Ian ( 0000-0003-1513-993X)
Flower, Darren ( 0000-0002-8542-7067)

Download

[img]

Version: Accepted Version


Export / Share Citation


Statistics

Additional statistics for this record