Department of Food Science
Faculty of Science
University of Copenhagen
Joint Data Analysis for Enhanced Knowledge Discovery in Metabolomics

Recent technological advances enable us to collect huge amounts of data from multiple sources; however, extracting meaningful information remains to be the main challenge. In complex problems, the structure we are looking for is often buried in the data. In those cases, in particular, looking at the data from different aspects; in other words, jointly analyzing data from multiple sources, i.e., data fusion (also called multiblock, multiview or multiset data analysis), increases the chances of capturing the hidden dynamics. For instance, in metabolomics, biological fluids are measured using a variety of analytical techniques such as Liquid ChromatographyMass Spectrometry (LCMS), Gas ChromatographyMass Spectrometry (GCMS) and Nuclear Magnetic Resonance (NMR) Spectroscopy with an ultimate goal of identifying chemicals related to certain conditions such as diseases. Data measured using different analytical methods are often complementary and their fusion enhances knowledge discovery.
This project focuses on developing mathematical models/algorithms for data fusion. We apply the developed methods in different domains including metabolomics and social network analysis.
PI: Evrim Acar, Faculty of Science, University of Copenhagen, Denmark
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RELATED PUBLICATIONS:
Conferences/Workshops C7. A Flexible Modeling Framework for Coupled Matrix and Tensor Factorizations (E. Acar, M. Nilsson, M. Saunders), EUSIPCO, 2014. C6. Incorporating Higher Dimensionality in Joint Decomposition of EEG and fMRI (W. Swinnen, B. Hunyadi, E. Acar, S. Van Huffel, M. De Vos), EUSIPCO, 2014. C5. Optimal Weight Learning for Coupled Tensor Factorization with Mixed Divergences (U. Simsekli, B. Ermis, A. T. Cemgil, E. Acar), EUSIPCO, 2013. C4. Structure Revealing Data Fusion Model with Applications in Metabolomics (E. Acar, A. J. Lawaetz, M. A. Rasmussen, R. Bro), IEEE EMBC, pp. 60236026, 2013. C3. Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics (E. Acar, G. Gurdeniz, M. Rasmussen, D. Rago, L. Dragsted, R. Bro), ICDM Workshop on Biological Data Mining and its Applications in Healthcare, pp. 18, 2012. C2. Link Prediction via Generalized Coupled Tensor Factorisation (B. Ermis, E. Acar, A. T. Cemgil), ECML/PKDD Workshop on Collective Learning and Inference on Structured Data, 2012. C1. Allatonce Optimization for Coupled Matrix and Tensor Factorizations (E. Acar, T.G.Kolda and D.M. Dunlavy), KDD Workshop on Mining and Learning with Graphs, 2011.
Journals J7. Common and Distinct Components in Data Fusion (A. K. Smilde, I. Mage, T. Naes, T. Hankemeier, M. A. Lips, H. A. L. Kiers, E. Acar and R. Bro), arXiv:1607.02328v1, Submitted for Publication, 2016. J6. Data Fusion in Metabolomics using Coupled Matrix and Tensor Factorizations (E. Acar, R. Bro and A. K. Smilde), Proceedings of the IEEE, 103: 16021620, 2015. J5. Link Prediction in Heterogeneous Data via Generalized Coupled Tensor Factorization (B. Ermis, E. Acar, A. T. Cemgil), Data Mining and Knowledge Discovery, 29(1): 203236, 2015. J4. StructureRevealing Data Fusion (E. Acar, E. E. Papalexakis, G. Gurdeniz, M. A. Rasmussen, A. J. Lawaetz, M. Nilsson, R. Bro), BMC Bioinformatics, 15: 239, 2014. J3. Understanding Data Fusion Within the Framework of Coupled Matrix and Tensor Factorizations (E. Acar, M. A. Rasmussen, F. Savorani, T. Naes, R. Bro), Chemometrics and Intelligent Laboratory Systems, 129: 5363, 2013. J2. Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics (E. Acar, G. Gurdeniz, M. Rasmussen, D. Rago, L. Dragsted, R. Bro), International Journal of Knowledge Discovery in Bioinformatics, 3:2243, 2012. J1. Coupled Analysis of in Vitro and Histology Tissue Samples to Quantify StructureFunction Relationship (E. Acar, G. E. Plopper, B. Yener), PLoS One , 7(3): e32227, 2012.
TALKS AT CONFERENCES/WORKSHOPS & SEMINARS: T32. 13th NuGOweek: Phenotypes and Prevention  The Interplay of Genes, Lifestyle factors and Gut Environment (Copenhagen, Denmark), September 58, 2016 (Invited Talk). T31. 20th Conference of the International Linear Algebra Society (ILAS), Leuven, Belgium, July 1115, 2016 (Invited Minisymposium Talk) T30. SIAM Conf. Parallel Processing for Scientific Computing, Paris, France, April 1215, 2016 (Invited Minisymposium Talk) T29. Dagstuhl Perspectives Workshop: Tensor Computing for Internet of Things, Schloss Dagstuhl, Germany, April 1013, 2016 (Organizer/Speaker) T28. Metabolomics Young Investigators Network Meeting, University of Copenhagen, March 30, 2016 (Invited Talk) T27. The University of Edinburgh, Edinburgh, UK, March 17, 2016 (Invited Seminar) T26. Workshop on Tensor Decompositions and Applications, Leuven, Belgium, January 21, 2016 T25. Ozyegin University, Istanbul, Turkey, December 29, 2015 T24. Nofima, Ås, Norway, November 5, 2015 T23. Yeditepe University, Istanbul, Turkey, September 8, 2015 T22. Bogazici University, Istanbul, Turkey, August 20, 2015 T21. JODA Workshop on data fusion methods and applications, Copenhagen, Denmark, August 12, 2015 (Organizer/Speaker) T20. SCIX, Reno Tahoe, Sept. 28 Oct.3, 2014 (Invited Minisymposium Talk) T19. EUSIPCO, Lisbon, Portugal, September 2, 2014 (Refereed Paper) T18. COMPSTAT, Geneva, Switzerland, August 1922, 2014 (Invited Minisymposium Talk) T17. KU Leuven, Belgium, June 2, 2014 (Invited Seminar) T16. Arctic Analysis, Ilulissat, Greenland, March 1014, 2014 T15. ERCIM 2013, University of London, UK, December 15, 2013 (Invited Minisymposium Talk) T14. GipsaLab, Grenoble, France, November 8, 2013 (Invited Seminar) T13. Xerox Research Centre Europe, Grenoble, France, November 7, 2013 (Invited Seminar) T12. Kadir Has University, Istanbul, Turkey, October 23, 2013 T11. Biomedical Engineering Society (BMES) Annual Meeting, Seattle, WA, September 28, 2013 (Invited Talk) T10. IEEE EMBC, Osaka, Japan, July 7, 2013 (Refereed Paper) T9. ICME Colloquium, Stanford University, CA, June 3, 2013 T8. SIAM Conference on Computational Science and Engineering (CSE), Boston, MA, Feb. 25March 1, 2013 (Minisymposium Organizer/Speaker) T7. SPIE Medical Imaging: Digital Pathology Conference, Orlando, FL, Feb. 10, 2013 (Refereed Paper) T6. SISTA Workshop on Tensors and Data Analysis, KU Leuven, Belgium, December 13, 2012 (Invited Talk) T5. ICDM Workshop on Biological Data Mining and its Applications in Healthcare, Brussels, Belgium, December 10, 2012 (Refereed Paper) T4. SIAM Conference on Applied Linear Algebra, Valencia, Spain, June 1822, 2012 (Invited Minisymposium Talk) T3. Threeway Methods in Chemistry and Psychology (TRICAP), Bruges, Belgium, June 27, 2012 T2. Linear Algebra/Optimization Seminar , Stanford University, CA, May 10, 2012 T1. Sandia National Labs, Livermore, CA, May 7, 2012
WORKSHOPS/MINISYMPOSIA:
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This work is funded by the Danish Council for Independent Research  Technology and Production Sciences and Sapere Aude Program under the projects 11116328 and 11120947.
Maintained by: Evrim Acar 
