NDLI: Multi-biomarker panel selection on a GPU

Content Provider	IEEE Xplore Digital Library
Author	Johnson, D. Shafer, B. Lee, J.J. Chen, J.Y.
Copyright Year	2012
Description	Author affiliation: Indiana Center for Systems Biology and Personalized Medicine, Indiana University School of Informatics, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA (Chen, J.Y.) \|\| Department of Electrical and Computer Engineering, Purdue University School of Engineering and Technology, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA (Johnson, D.; Shafer, B.; Lee, J.J.)
Abstract	Liquid chromatography-based tandem mass spectrometry (LC-MS) technique allows for identification and quantification of thousands of proteins in parallel. This technique coupled with a feed-forward artificial neural network provides a technique to analyze and select protein panels for use in multi-biomarker panel discovery applications. In this study, we enhance this technique by utilizing massively parallel computation enabled by a high-end Graphics Processing Unit (GPU). We utilize a GPU-based back-propagation feed-forward artificial neural network to help select an optimal panel of protein biomarkers for breast cancer diagnosis. By exploiting the GPU particularly for accelerating optimal biomarker panel discovery, we achieved a computation speedup of 32.2X over a comparable sequential program implemented on a CPU. GPUs have become a cost-effective alternative, offering end-user high-performance computing alternative to computer cluster or cloud computing. We showed how to achieve substantial improvement in computation using domain-specific parallel computing on a GPU. This approach can be generalized to other bioinformatics problems.
Starting Page	1
Ending Page	6
File Size	643679
Page Count	6
File Format	PDF
ISBN	9781467308199
ISSN	21540373
e-ISBN	9781467308182
DOI	10.1109/EIT.2012.6220762
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-05-06
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Graphics processing unit Neural networks Instruction sets Training Proteins Educational institutions Kernel back-propagation biomarker panel discovery GPU CUDA neural network
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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