NDLI: Transfer Learning across Cancers on DNA Copy Number Variation Analysis

Content Provider	IEEE Xplore Digital Library
Author	Huanan Zhang Ze Tian Rui Kuang
Copyright Year	2013
Description	Author affiliation: Microsoft Corp., Redmond, WA, USA (Ze Tian) \|\| Dept. of Comput. Sci. & Eng., Univ. of Minnesota Twin Cities, Minneapolis, MN, USA (Huanan Zhang; Rui Kuang)
Abstract	DNA copy number variations (CNVs) are prevalent in all types of tumors. It is still a challenge to study how CNVs play a role in driving tumorgenic mechanisms that are either universal or specific in different cancer types. To address the problem, we introduce a transfer learning framework to discover common CNVs shared across different tumor types as well as CNVs specific to each tumor type from genome-wide CNV data measured by array CGH and SNP genotyping array. The proposed model, namely Transfer Learning with Fused LASSO (TLFL), detects latent CNV components from multiple CNV datasets of different tumor types to distinguish the CNVs that are common across the datasets and those that are specific in each dataset. Both the common and type-specific CNVs are detected as latent components in matrix factorization coupled with fused LASSO on adjacent CNV probe features. TLFL considers the common latent components underlying the multiple datasets to transfer knowledge across different tumor types. In simulations and experiments on real cancer CNV datasets, TLFL detected better latent components that can be used as features to improve classification of patient samples in each individual dataset compared with the model without the knowledge transfer. In cross-dataset analysis on bladder cancer and cross-domain analysis on breast cancer and ovarian cancer, TLFL also learned latent CNV components that are both predictive of tumor stages and correlate with known cancer genes.
Sponsorship	Toshiba
Starting Page	1283
Ending Page	1288
File Size	288978
Page Count	6
File Format	PDF
ISBN	9780769551081
ISSN	15504786
DOI	10.1109/ICDM.2013.58
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2013-12-07
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Cancer Probes Biological cells Hidden Markov models Arrays Tumors Genomics Fused LASSO Components Transfer Learning DNA Copy Number Cancer Genomics
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	Mr. Siddhartha Mukherjee siddhartha@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	ndl-support@iitkgp.ac.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Libarray 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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