Tommi S. Jaakkola, Ph.D.
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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 Papers

You can view papers in reverse chronological order or in (partially overlapping) categories:

  • Computational biology
  • Machine learning theory
  • Information retrieval
  • Reinforcement learning
    •  More information about research areas is available in research descriptions.

    Recent papers

  • 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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