Structure-revealing data fusion model with applications in metabolomics

Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS

Volumn , Issue , 2013, Pages 6023-6026

  Acar, Evrim ^a   Lawaetz, Anders J ^a   Rasmussen, Morten A ^a   Bro, Rasmus ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL METHOD; BIOLOGICAL FLUIDS; COLORECTAL CANCER; COMPLEMENTARY DATA; HIGHER-ORDER TENSOR; INDIVIDUAL COMPONENTS; LIQUID CHROMATOGRAPHY - MASS SPECTROMETRIES; MULTIPLE DATA SETS;

BIOINFORMATICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SIGNAL PROCESSING; SOCIAL NETWORKING (ONLINE); TENSORS;

DATA FUSION;

ALGORITHM; BIOLOGY; BLOOD; COLORECTAL TUMOR; COMPUTER SIMULATION; HUMAN; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; METABOLOME; METABOLOMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SIGNAL PROCESSING; THEORETICAL MODEL;

ALGORITHMS; CHROMATOGRAPHY, LIQUID; COLORECTAL NEOPLASMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MASS SPECTROMETRY; METABOLOME; METABOLOMICS; MODELS, THEORETICAL; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 84886503159     PISSN: 1557170X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/EMBC.2013.6610925     Document Type: Conference Paper

References (25)

1. O. Alter, P. O Brown, and D. Botstein, "Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms", PNAS, 100:3351-3356, 2003.
2. L. Badea, "Extracting gene expression profiles common to colon and pancreatic adenocarcinoma using simultaneous nonnegative matrix factorization", In Pacific Symposium on Biocomputing, pp. 279-290, 2008.
3. E. Acar, G. E. Plopper, and B. Yener, "Coupled analysis of in vitro and histology tissue samples to quantify structure-function relationship", PLoS One, 7(3): E32227, 2012.
4. S. E. Richards, M. E. Dumas, J. M. Fonville et al., "Intra- and interomic fusion of metabolic profiling data in a systems biology framework", Chemometr. Intell., 104(1), 121-131, 2010.
5. A. P. Singh and G. J. Gordon, "Relational Learning via collective matrix factorization ", In KDD'08, pp. 650-658, 2008.
6. A. K. Smilde, J. A. Westerhuis, and R. Boque, "Multiway multiblock component and covariates regression models", Journal of Chemometrics, 14:301-331, 2000.
7. A. Banerjee, S. Basu and S. Merugu, "Multi-way clustering on relation graphs", In SDM'07, pp. 145-156, 2007.
8. Y. R. Lin, J. Sun, P. Castro, R. Konuru, H. Sundaram, and A. Kelliher, " Metafac: Community discovery via relational hypergraph factorization", In KDD'09, pp. 527-536, 2009.
9. B. Ermis, E. Acar, and T. Cemgil, "Link Prediction via Generalized Coupled Tensor Factorisation", In ECML/PKDD Workshop on Collective Learning and Inference on Structured Data, 2012.
10. K. Van Deun, I. Van Mechelen, L. Thorrez, M. Schouteden, B. De Moor, M. J. Van Der Werf, et al., "DISCO-SCA and Properly Applied GSVD as Swinging Methods to Find Common and Distinctive Processes", PLoS One, 7(5): E37840, 2012.
11. S. K. Gupta, D. Phung, B. Adams, T. Tran and S. Venkatesh, "Nonnegative Shared Subspace Learning and Its Application to Social Media Retrieval", In KDD'10, pp. 1169-1178, 2010.
12. J. A. Westerhuis, T. Kourti, and J. F. Macgregor, "Analysis of multiblock and hierarchical pca and pls models", Journal of Chemometrics., 12: 301-321, 1998.
13. R. A. Harshman, "Foundations of the PARAFAC procedure: Models and conditions for an explanatory multi-model factor analysis", UCLA Working Papers in Phonetics, 16:1-84, 1970.
14. J. D. Carroll and J. J. Chang, "Analysis of individual differences in multidimensional scaling via an N-way generalization of Eckart- Young decomposition", Psychometrika, 35: 283-319, 1970.
15. R. A. Harshman and M. E. Lundy, "Parafac: Parallel factor analysis", Computational Statistics and Data Analysis, 18: 39-72, 1994.
16. T. F. Wilderjans, E. Ceulemans, H. A. L. Kiers, and K. Meers, "The LMPCA program: A graphical user interface for fitting the linkedmode parafac-pca model to coupled real-valued data", Behavior Research Methods, 41: 1073-1082, 2009.
17. E. Acar, T. G. Kolda, and D. M. Dunlavy, "All-at-once optimization for coupled matrix and tensor factorizations", In KDD Workshop on Mining and Learning with Graphs, 2011.
18. J. Nocedal, and S.J. Wright, Numerical Optimization, Springer, 2006.
19. S. Lee, H. Lee, P. Abbeel, and A. Y. Ng, " Efficient l1 regularized logistic regression", In AAAI'06, pp. 401-408, 2006.
20. E. Acar and B. Yener, "Unsupervised Multiway Data Analysis: A Literature Survey", IEEE Transactions on Knowledge and Data Engineering, 21(1): 1-15, 2009.
21. T. G. Kolda and B. Bader, "Tensor Decompositions and Applications", SIAM Review, 51(3): 455-500, 2009.
22. D. M. Dunlavy, T. G. Kolda and E. Acar, "Poblano v1.0:A Matlab toolbox for gradient-based optimization", Sandia National Labs, Tech. Rep. SAND2010-1422, 2010.
23. The MATLAB CMTF Toolbox, http://www.models.life.ku.dk/joda/CMTF-Toolbox [April 10, 2013].
24. R. Bro, H. J. Nielsen, F. Savorani, K. Kjeldahl et al., "Data Fusion in Metabolomic Cancer Diagnostics", Metabolomics, 9(1):3-8, 2013.
25. I. Georgakoudi, B. C. Jacobson, M. G. Muller, E. E. Sheets, K. Badizadegan et al., "NAD(P)H and Collagen as in Vivo Quantitative Fluorescent Biomarkers of Epithelial Precancerous Changes", Cancer Research, 62(3), 682-7, 2002.