Tommi S. Jaakkola, Ph.D.
Associate Professor of Electrical Engineering and Computer Science

MIT Computer Science and Artificial Intelligence Laboratory
Stata Center, Bldg 32-G498
Cambridge, MA 02139

E-mail: tommi at csail.mit.edu

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Research

 Research synopsis (more...)

On the theoretical side, our research focuses on statistical inference and estimation, development of principled approximation methods for problems with limited computational resources, analysis and development of algorithms for various modern estimation problems such as those involving predominantly incomplete data. The applied side of our work involves primarily functional genomics (transcriptional regulation), large scale inference problems, and information retrieval.

Students/postdocs (more...)

John Barnett, Amir Globerson, Luis Perez-Breva, Alan Qi, Jason Rennie, David Sontag

Recent papers (more...)

  • D. Sontag, T. Meltzer, A. Globerson, T. Jaakkola, and Y. Weiss.
    Tightening lp relaxations for map using message passing.
    In Proceedings of the 24rd Conference on Uncertainty in Artificial Intelligence, 2008. To appear.
    [pdf]

  • D. Sontag and T. Jaakkola.
    New outer bounds on the marginal polytope.
    In Advances in Neural Information Processing Systems 21, 2007.
    [pdf]

  • A. Globerson and T. Jaakkola.
    Fixing max-product: Convergent message passing algorithms for map lp-relaxations.
    In Advances in Neural Information Processing Systems 21, 2007.
    [pdf]

  • G. Gerber, R. Dowell, T. Jaakkola, and D. Gifford.
    Automated discovery of functional generality of human gene expression programs.
    PloS Computational biology, 2007. To appear.
    [link to paper]

  • A. Globerson and T. Jaakkola.
    Convergent propagation algorithms via oriented trees.
    In Proceedings of the 23rd Conference on Uncertainty in Artificial Intelligence, 2007. To appear.
    [pdf]

  • D. Sontag and T. Jaakkola.
    On iteratively constraining the marginal polytope for approximate inference and map.
    Technical report, 2007.
    [pdf]

  • A. Globerson and T. Jaakkola.
    Approximate inference using conditional entropy decompositions.
    In Proceedings of the 11th International Conference on Artificial Intelligence and Statistics, 2007. To appear.
    [pdf]

  • H. Steck and T. Jaakkola.
    Predictive discretization during model selection.
    In Proceedings of the 11th International Conference on Artificial Intelligence and Statistics, 2007.
    [pdf]

  • A. Globerson and T. Jaakkola.
    Approximate inference using planar graph decomposition.
    In Advances in Neural Information Processing Systems 20, 2006.
    [pdf]

  • L. Perez-Breva, L. Ortiz, C-H. Yeang, and T. Jaakkola.
    Game theoretic algorithms for protein-dna binding.
    In Advances in Neural Information Processing Systems 20, 2006. To appear.
    [pdf]

  • A. Qi and T. Jaakkola.
    Parameter expanded variational bayesian methods.
    In Advances in Neural Information Processing Systems 20, 2006.
    [pdf]

  • 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.
    [pdf], [pdf]

  • Y. Qi, P. Missiuro, A. Kapoor, C. Hunter, T. Jaakkola, D. Gifford, and H. Ge.
    Semi-supervised analysis of gene expression profiles for lineage-specific development in the caenorhabditis elegans embryo.
    Bioinformatics, 22(14):417--423, 2006.
    [pdf]

  • L. Perez-Breva, L. Ortiz, C-H. Yeang, and T. Jaakkola.
    Dna binding and games.
    MIT CSAIL Technical Report TR-2006-018, 2006.
    [pdf]

  • A. Corduneanu and T. Jaakkola.
    Data dependent regularization.
    In Semi-supervised learning. MIT Press, 2006.
    [pdf]

  • M. Wainwright, T. Jaakkola, and A. Willsky.
    Map estimation via agreement on (hyper)trees: Message-passing and linear-programming approaches.
    IEEE Transactions on Information Theory, 51(11):3697--3717, 2005.
    [pdf]

  • J. Rennie and T. Jaakkola.
    Using term informativeness for named entity detection.
    In Proceedings of the 28th Annual Conference on Research and Development in Information Retrieval (SIGIR), 2005.
    [pdf]

  • C-H. Yeang and T. Jaakkola.
    Modeling the combinatorial functions of multiple transcription factors.
    In The Ninth Annual International Conference on Research in Computational Molecular Biology, 2005.
    [pdf]

  • C-H. Yeang, H. Mak, S. McCuine, C. Workman, T. Jaakkola, and T. Ideker.
    Validation and refinement of gene-regulatory pathways on a network of physical interactions.
    Genome Biology, 6(7):R62, 2005.
    [pdf], [link to paper]

  • M. Wainwright, T. Jaakkola, and A. Willsky.
    A new class of upper bounds on the log partition function.
    IEEE Transactions on Information Theory, 51:2313--2335, 2005.
    [pdf]

  • R. Rosales and T. Jaakkola.
    Focused inference.
    In Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, 2005.
    [pdf]

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