Tommi S. Jaakkola received M.Sc. in theoretical physics from Helsinki University of Technology, 1992, and Ph.D. from MIT in computational neuroscience, 1997. Following a postdoctoral position in computational molecular biology (DOE/Sloan fellow, UCSC) he joined the MIT EECS faculty 1998. His research interests include many aspects of machine learning, statistical inference and estimation, and analysis and development of algorithms for various modern estimation problems such as those involving predominantly incomplete data sources. His applied research focuses on problems in computational functional genomics such as transcriptional regulation.
- D. Sontag and T. Jaakkola. New Outer Bounds on the Marginal Polytope, Advances in Neural Information Processing Systems 20, 2007
- A. Globerson and T. Jaakkola. Convergent propagation algorithms via oriented trees, Proceedings of the 23rd Conference on Uncertainty in Artificial Intelligence, 2007.
- G. Gerber, R. Dowell, T. Jaakkola, and D. Gifford. Automated discovery of functional generality of human gene expression programs, PloS Computational Biology 3(8): 148, 2007.
- L. Perez-Breva, L. Ortiz, C-H. Yeang, and T. Jaakkola. Game theoretic algorithms for protein-DNA binding, Advances in Neural Information Processing Systems 19, 2006.
- Y. Qi, A. Rolfe, K. MacIsaac, G. Gerber, D. Pokholok, J. Zeitlinger, T. Danford, R. Dowell, E. Fraenkel, T. Jaakkola, R. Young, and D. Gifford. High-resolution computational models of genome binding events, Nature Biotechnology, 24:963-970, 2006.
- Conference on Uncertainty in Artificial Intelligence: Best paper award (2007)
- Conference on Uncertainty in Artificial Intelligence: Best paper award (2003)
- Sloan Foundation: Research Fellowship (2002)
- Conference on Uncertainty in Artificial Intelligence: Best paper award (2002)
- International Conference on Intelligent Systems for Molecular Biology: Outstanding paper (1997)
- Conference on Uncertainty in Artificial Intelligence: Outstanding paper (1996)