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 multi-block, multi-view or multi-set 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 Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS) 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, neuroscience and social network analysis.

PI: Evrim Acar, Faculty of Science, University of Copenhagen, Denmark

COLLABORATORS:

Rasmus Bro, Faculty of Science, University of Copenhagen, Denmark
Mathias Nilsson, School of Chemistry, The University of Manchester, UK
Lars Ove Dragsted, Faculty of Science, University of Copenhagen, Denmark
Gozde Gurdeniz, Faculty of Science, University of Copenhagen, Denmark
Michael Saunders, Stanford University, Stanford, CA
Anne Tjønneland, Danish Cancer Society, Denmark
Tormod Næs, Nofima, Norway
Tamara G. Kolda, Sandia National Labs, Livermore, CA
A. Taylan Cemgil, Bogazici University, Istanbul, Turkey
Beyza Ermis, Bogazici University, Istanbul, Turkey
Bulent Yener, Rensselaer Polytechnic Institute, Troy, NY
Vagelis Papalexakis, University of California Riverside, CA
Age K. Smilde, University of Amsterdam, Netherlands
Tulay Adali, University of Maryland Baltimore County, MD

SOFTWARE:

The MATLAB CMTF Toolbox:
- Version 1.1 (Dec. 2014)
- Version 1.0 (April 2013)

DATA:

Prototypical Experimental Coupled Data Sets

RELATED PUBLICATIONS:

Coupled Matrix/Tensor Factorizations (Methodology)

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), Journal of Chemometrics (In Press), 2017.
Structure-Revealing Data Fusion (E. Acar, E. E. Papalexakis, G. Gurdeniz, M. A. Rasmussen, A. J. Lawaetz, M. Nilsson, and R. Bro), BMC Bioinformatics, 15: 239, 2014.
A Flexible Modeling Framework for Coupled Matrix and Tensor Factorizations (E. Acar, M. Nilsson, and M. Saunders), EUSIPCO, 2014.
Understanding Data Fusion Within the Framework of Coupled Matrix and Tensor Factorizations (E. Acar, M. A. Rasmussen, F. Savorani, T. Naes, and R. Bro), Chemometrics and Intelligent Laboratory Systems, 129: 53-63, 2013.
Optimal Weight Learning for Coupled Tensor Factorization with Mixed Divergences (U. Simsekli, B. Ermis, A. T. Cemgil, and E. Acar), EUSIPCO, 2013.
All-at-once 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.

Metabolomics

Forecasting Chronic Diseases using Data Fusion (E. Acar, G. Gurdeniz, F. Savorani, L. Hansen, A. Olsen, A. Tjønneland, L. O. Dragsted, and R. Bro), Journal of Proteome Research, 2017.
New Nordic diet versus average Danish diet: a randomized controlled trial revealed healthy long-term effects of the new Nordic diet by GC-MS blood plasma metabolomics, (B. Khakimov, S.K. Poulsen, F. Savorani, E. Acar , G. Gürdeniz, T.M. Larsen, A. Astrup, L.O. Dragsted, and S.B. Engelsen), Journal of Proteome Research, 15(6): 1939-1954, 2016.
Data Fusion in Metabolomics using Coupled Matrix and Tensor Factorizations (E. Acar, R. Bro, and A. K. Smilde), Proceedings of the IEEE, 103: 1602-1620, 2015.
Structure Revealing Data Fusion Model with Applications in Metabolomics (E. Acar, A. J. Lawaetz, M. A. Rasmussen, and R. Bro), IEEE EMBC, pp. 6023-6026, 2013.
Patterns of time since last meal revealed by sparse PCA in an observational LC-MS based metabolomics study, (G. Gurdeniz, L. Hansen, M. Rasmussen, E. Acar, A. Olsen, J. Christensen, T. Barri, A. Tjønneland, and L.O. Dragsted), Metabolomics, 9(5): 1073-1081, 2013.
Coupled Matrix Factorization with Sparse Factors to Identify Potential Biomarkers in Metabolomics (E. Acar, G. Gurdeniz, M. Rasmussen, D. Rago, L. Dragsted, and R. Bro), International Journal of Knowledge Discovery in Bioinformatics, 3:22-43, 2012.
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. 1-8, 2012.

Neuroscience

ACMTF for Fusion of Multi-modal Neuroimaging Data and Identification of Biomarkers (E. Acar, Y. Levin-Schwartz, V. D. Calhoun, and T. Adali), EUSIPCO (to appear), 2017.
Tensor-Based Fusion of EEG and FMRI to Understand Neurological Changes (E. Acar, Y. Levin-Schwartz, V. D. Calhoun, and T. Adali), IEEE ISCAS, pp. 314-317, 2017.
Incorporating Higher Dimensionality in Joint Decomposition of EEG and fMRI (W. Swinnen, B. Hunyadi, E. Acar, S. Van Huffel, and M. De Vos), EUSIPCO, 2014.

Social Network Analysis

Link Prediction in Heterogeneous Data via Generalized Coupled Tensor Factorization (B. Ermis, E. Acar, and A. T. Cemgil), Data Mining and Knowledge Discovery, 29(1): 203-236, 2015.
Link Prediction via Generalized Coupled Tensor Factorisation (B. Ermis, E. Acar, and A. T. Cemgil), ECML/PKDD Workshop on Collective Learning and Inference on Structured Data, 2012.

Bioinformatics

Coupled Analysis of in Vitro and Histology Tissue Samples to Quantify Structure-Function Relationship (E. Acar, G. E. Plopper, and B. Yener), PLoS One , 7(3): e32227, 2012.

TALKS AT CONFERENCES/WORKSHOPS & SEMINARS:

T33. Steno Diabetes Center, Copenhagen, Denmark, October 5, 2016.

T32. 13th NuGOweek: Phenotypes and Prevention - The Interplay of Genes, Life-style factors and Gut Environment (Copenhagen, Denmark), September 5-8, 2016 (Invited Talk).

T31. 20th Conference of the International Linear Algebra Society (ILAS), Leuven, Belgium, July 11-15, 2016 (Invited Minisymposium Talk)

T30. SIAM Conf. Parallel Processing for Scientific Computing, Paris, France, April 12-15, 2016 (Invited Minisymposium Talk)

T29. Dagstuhl Perspectives Workshop: Tensor Computing for Internet of Things, Schloss Dagstuhl, Germany, April 10-13, 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 19-22, 2014 (Invited Minisymposium Talk)

T17. KU Leuven, Belgium, June 2, 2014 (Invited Seminar)

T16. Arctic Analysis, Ilulissat, Greenland, March 10-14, 2014

T15. ERCIM 2013, University of London, UK, December 15, 2013 (Invited Minisymposium Talk)

T14. Gipsa-Lab, 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. 25-March 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 18-22, 2012 (Invited Minisymposium Talk)

T3. Three-way Methods in Chemistry and Psychology (TRICAP), Bruges, Belgium, June 2-7, 2012

T2. Linear Algebra/Optimization Seminar , Stanford University, CA, May 10, 2012

T1. Sandia National Labs, Livermore, CA, May 7, 2012

WORKSHOPS/MINISYMPOSIA:

Dagstuhl Perspectives Workshop: Tensor Computing for Internet of Things, Schloss Dagstuhl, Germany, April 10-13, 2016 (Organizers: Evrim Acar, Animashree Anandkumar, Lenore Mullin, Volker Tresp, Sebnem Rusitschka)
Mini-workshop on data fusion methods and applications, August 12, 2015, University of Copenhagen, Frederiksberg C, Denmark.
Two-part minisymposia on data fusion methods based on matrix and tensor factorizations at SIAM Conference on Computational Science and Engineering (CSE), Feb. 25-March 1, 2013, Boston, MA (Organizers: Evrim Acar, A. Taylan Cemgil, Rasmus Bro)

LITERATURE SURVEYS:

COURSES:

Copenhagen School of Chemometrics, May 25-26, 2016
ODIN Course on Data Fusion, November 25, 2015

This work is funded by the Danish Council for Independent Research | Technology and Production Sciences and Sapere Aude Program under the projects 11-116328 and 11-120947.