Papers Daphne Koller Publications Research Areas Publication Type Years (all) BN Bayesian Networks    BM Biology and Medicine CGT Computational Game Theory    HM Hybrid Models LTW Language and Web    LGM Learning Graphical Models MN Markov Networks    RPM Richer Probabilistic Models RP Robotics and Perception    SL Supervised Learning TPM Temporal Probabilistic Models    J Journal Article C Conference Paper B Book Ch Book Chapter T Technical Report PhD PhD Disseration 1985 - 1989 1990 - 1994 1995 - 1999 2000 - 2004 2005 - 2009 2010 - 2014 Type Reference Download topics: BN BM CGT HM LTW LGM MN RPM RP SL TPM 2009 J   H. Wang, B. Kakaradov, S.R. Collins, L. Karotki, D. Fiedler, M. Shales, K.M. Shokat, T. Walther, N.J. Krogan, and D. Koller (2009). "A complex-based reconstruction of the S. cerevisiae interactome." Molecular Cell Proteomics, 8(6), 1361-81. bib topics:    BM                            J   D. Fiedler, H. Braberg, M. Mehta, G. Chechik, G. Cagney, P. Mukherjee, A.C. Silva, M. Shales, S.R. Collins, S. van Wageningen, P. Kemmeren, F.C.P. Holstege, J.S. Weissman, M. Christopher-Keogh, D. Koller, K.M. Shokat, and N.J. Krogan (2009). "Functional Organization of the S. cerevisiae Phosphorylation Network." Cell, 136(5), 952-63. bib topics:    BM                            J   G. Chechik and D. Koller (2009). "Timing of gene expression responses to environmental changes." Journal of Computational Biology, 16(2), 279-290. bib topics:    BM                            J   S.-I. Lee, A.M. Dudley, D. Drubin, P.A. Silver, N.J. Krogan, D. Pe’er, and D. Koller (2009). "Learning a Prior on Regulatory Potential from eQTL Data." PLOS Genetics, 5(1), e1000358. bib topics:    BM                            J   A.J. Gentles, A.A. Alizadeh, S.-I. Lee andJ.H. Myklebust, C.M. Shachaf, B. Shahbaba, R. Levy, D. Koller, and S.K. Plevritis (2009). "A pluripotency signature predicts histologic transformationand influences survival in follicular lymphoma patients." Blood, 114, 3158-66. bib topics:    BM                            J   G. Heitz, G. Elidan, B. Packer, and D. Koller (2009). "Shape-Based Object Localization for Descriptive Classification." International Journal of Computer Vision, 84(1), 40-62. [older version, 2008] bib topics:                         RP       C   S. Gould, T. Gao, and D. Koller (2009). "Region-based Segmentation and Object Detection." Advances in Neural Information Processing Systems (NIPS 2009). bib topics:                         RP       C   M.P. Kumar and D. Koller (2009). "Learning a Small Mixture of Trees." Advances in Neural Information Processing Systems (NIPS 2009). bib topics:                         RP       C   S. Gould, R. Fulton, and D. Koller (2009). "Decomposing a Scene into Geometric and Semantically Consistent Regions." Proceedings of the International Conference on Computer Vision (ICCV). bib topics:                         RP       C   M.P. Kumar and D. Koller (2009). "MAP Estimation of Semi-Metric MRFs via Hierarchical Graph Cuts." Proceedings of the Twenty-fifth Conference on Uncertainty in AI (UAI). bib topics:                   MN             C   S. Gould, F. Amat, and D. Koller (2009). "Alphabet SOUP: A Framework for Approximate Energy Minimization." Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR). bib topics:                   MN    RP       B   D. Koller and N. Friedman (2009). Probabilistic Graphical Models: Principles and Techniques. edited by . MIT Press. bib topics: BN             LGM MN             B   D. Koller, Y. Bengio, D. Schuurmans, and L. Bottou (2009). Proceedings Advances in Neural Information Processing Systems (NIPS-08). . bib topics:                LGM       RP SL    2008 J   G. Chechik, E. Oh, O. Rando, J. Weissman, A. Regev, and D. Koller (2008). "Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network." Nature Biotechnology, 26(11), 1251-1259. bib topics:    BM                            J   M. Boxem, Z. Maliga, N. Klitgord, N. Li, I. Lemmens, M. Mana, L. de Lichtervelde, J.D. Mul, D. van de Peut, M. Devos, N. Simonis, M.A. Yildirim, M. Cokol, H.-L. Kao, A.-S. de Smet, H. Wang, A.-L. Schlaitz, T. Hao, S. Milstein, C. Fan andd M. Tipsword, K. Drew, M. Galli, K. Rhrissorrakrai, D. Drechsel, D. Koller, F.P. Roth, L.M. Iakoucheva, A.K. Dunker, R. Bonneau, K.C. Gunsalus, D.E. Hill, F. Piano andd J. Tavernier, S. van den Heuvel, A.A. Hyman, and M. Vidal (2008). "A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis." Cell, 134(3), 534-545. bib topics:    BM                            J   M.E. Hillenmeyer, E. Fung, J. Wildenhain, S.E. Pierce, S. Hoon, W. Lee, M. Proctor, R.P. St.Onge, M. Tyers, D. Koller, R.B. Altman, R.W. Davis, C. Nislow, and G. Giaever (2008). "The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes." Science, 18, 362-365. bib topics:    BM                            J   G. Chechik, G. Heitz, G. Elidan, P. Abbeel, and D. Koller (2008). "Max-margin Classification of Data with Absent Features." Journal of Machine Learning Research, 9, 1-21. bib topics:                            SL    J   S. Gould, J. Rodgers, D. Cohen, G. Elidan, and D. Koller (2008). "Multi-Class Segmentation with Relative Location Prior." International Journal of Computer Vision, 80(3), 300-316. bib topics:                         RP       C   D. Vickrey, A. Bronsan, W. Choi, A. Kumar, J. Turner-Maier, A. Wang, and D. Koller (2008). "Online Word Games for Semantic Data Collection." Conference on Empirical Methods in Natural Language Processing (EMNLP). bib topics:             LTW                   C   S. Gould, P. Baumstarck, M. Quigley, A.Y. Ng, and D. Koller (2008). "Integrating Visual and Range Data for Robotic Object Detection." Proc. ECCV-08 Workshop on Multi-camera and Multi-modal Sensor Fusion Algorithms and Applications. bib topics:                         RP       C   G. Heitz and D. Koller (2008). "Learning Spatial Context: Using Stuff to Find Things." Proc. 10th European Conference on Computer Vision. bib topics:                         RP       C   G. Heitz, S. Gould, A. Saxena, and D. Koller (2008). "Cascaded Classification Models: Combining Models for Holistic Scene Understanding." Advances in Neural Information Processing Systems (NIPS 2008). bib topics:                         RP SL    C   G. Heitz, G. Elidan, B. Packer, and D. Koller (2008). "Shape-Based Object Localization for Descriptive Classification." Advances in Neural Information Processing Systems (NIPS 2008). [newer version, 2009] bib topics:                   MN    RP       C   V. Ganapathi, D. Vickrey, J. Duchi, and D. Koller (2008). "Constrained Approximate Maximum Entropy Learning." Proceedings of the Twenty-fourth Conference on Uncertainty in AI (UAI). bib topics:                LGM MN             C   J. Duchi, S. Gould, and D. Koller (2008). "Projected Subgradient Methods for Learning Sparse Gaussians." Proceedings of the Twenty-fourth Conference on Uncertainty in AI (UAI). bib topics:          HM    LGM MN             C   G. Elidan, B. Packer, G. Heitz, and D. Koller (2008). "Convex Point Estimation using Undirected Bayesian Transfer Hierarchies." Proceedings of the Twenty-fourth Conference on Uncertainty in AI (UAI). bib topics:                LGM MN       SL    C   D. Vickrey and D. Koller (2008). "Sentence Simplification for Semantic Role Labeling." Proceedings of the 46th Meeting of the Association forComputational Linguistics: Human Language Technologies. bib topics:                                  B   J.C. Platt, D. Koller, Y. Singer, and S. Roweis (2008). Proceedings Advances in Neural Information Processing Systems (NIPS-07). . bib topics:                LGM       RP SL    2007 J   B.E. Stranger, A.C. Nica, M.S. Forrest, A. Dimas, C.P. Bird C. Beazley, C.E. Ingle, M. Dunning, P. Flicek, D. Koller, S. Montgomery, S. Tavaré, P. Deloukas, and E.T. Dermitzakis (2007). "Population genomics of human gene expression." Nature Genetics, 39(10), 1217-24. bib topics:    BM                            J   H. Wang, E. Segal, A. Ben-Hur, Q. Li, M. Vidal, and D. Koller (2007). "InSite: A computational method for identifying protein-protein interaction binding sites on a proteome-wide scale." Genome Biology, 8(9), R192.1-R192.18. bib topics:    BM                            C   S. Saria, U. Nodelman, and D. Koller (2007). "Reasoning at the Right Time Granularity." Proceedings of the Twenty-third Conference on Uncertainty in AI (UAI). Best student paper award. bib topics:                               TPM C   S.-I. Lee, V. Chatalbashev, D. Vickrey, and D. Koller (2007). "Learning a Meta-Level Prior for Feature Relevance from Multiple Related Tasks." Proceedings of International Conference on Machine Learning (ICML). bib topics:             LTW             SL    C   J. Duchi, D. Tarlow, G. Elidan, and D. Koller (2007). "Using Combinatorial Optimization within Max-Product Belief Propagation." Advances in Neural Information Processing Systems (NIPS 2006). bib topics:                   MN             C   A. Battle, G. Chechik, and D. Koller (2007). "Temporal and Cross-Subject Probabilistic Models for fMRI Prediction Task." Advances in Neural Information Processing Systems (NIPS 2006). bib topics:                   MN          TPM C   G. Chechik, G. Heitz, G. Elidan, P. Abbeel, and D. Koller (2007). "Max-margin classification of incomplete data." Advances in Neural Information Processing Systems (NIPS 2006). bib topics:                            SL    C   S.-I. Lee, V. Ganapathi, and D. Koller (2007). "Efficient Structure Learning of Markov Networks using L1-Regularization." Advances in Neural Information Processing Systems (NIPS 2006). bib topics:                LGM MN             Ch   D. Koller, N. Friedman, L. Getoor, and B. Taskar (2007). "Graphical Models in a Nutshell." In L. Getoor and B. Taskar, editors, Introduction to Statistical Relational Learning. bib topics: BN                MN             Ch   L. Getoor, N. Friedman, D. Koller, A. Pfeffer, and B. Taskar (2007). "Probabilistic Relational Models." In L. Getoor and B. Taskar, editors, Introduction to Statistical Relational Learning. bib topics:                LGM    RPM          Ch   D. Heckerman, C. Meek, and D. Koller (2007). "Probabilistic Entity-Relationship Models, PRMs, and Plate Models." In L. Getoor and B. Taskar, editors, Introduction to Statistical Relational Learning. bib topics:                LGM    RPM          Ch   B. Taskar, P. Abbeel, M.-F. Wong, and D. Koller (2007). "Relational Markov Networks." In L. Getoor and B. Taskar, editors, Introduction to Statistical Relational Learning. bib topics:                LGM MN RPM          2006 J   S.-I. Lee, D. Pe'er, A. Dudley, G. Church, and D. Koller (2006). "Identifying Regulatory Mechanisms using Individual Variation Reveals Key Role for Chromatin Modification." Proc. National Academy of Sciences, 103(38), 14062-14067. bib topics:    BM                            J   P. Abbeel, D. Koller, and A.Y. Ng (2006). "Learning Factor Graphs in Polynomial Time & Sample Complexity." Journal of Machine Learning Research, 7, 1743-1788. [older version, 2005] bib topics:                LGM MN             C   G. Elidan, I. McGraw, and D. Koller (2006). "Residual Belief Propagation: Informed Scheduling for Asynchronous Message Passing." Proceedings of the Twenty-second Conference on Uncertainty in AI (UAI). bib topics:                   MN             C   T. El-Hay, N. Friedman, D. Koller, and R. Kupferman (2006). "Continuous Time Markov Networks." Proceedings of the Twenty-second Conference on Uncertainty in AI (UAI). bib topics:                               TPM J   B. Blum, C.R. Shelton, and D. Koller (2006). "A Continuation Method for Nash Equilibria in Structured Games." Journal of Artificial Intelligence Resarch, 25, 457-502. [older version, 2003] bib topics:       CGT                         C   G. Elidan, G. Heitz, and D. Koller (2006). "Learning Object Shape: From Drawings to Images." Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR). bib topics:                   MN    RP       C   J. Rodgers, D. Anguelov, H.-C. Pang, and D. Koller (2006). "Object Pose Detection in Range Scan Data." Proceedings of the Conference on Computer Vision and Pattern Recognition (CVPR). bib topics:                   MN    RP       C   R. Raina, A.Y. Ng, and D. Koller (2006). "Constructing Informative Priors using Transfer Learning." Proc. Twenty-Third International Conference on Machine Learning. bib topics:             LTW             SL    2005 C   D. Vickrey, L. Biewald, M. Teyssier, and D. Koller (2005). "Word-Sense Disambiguation for Machine Translation." Conference on Empirical Methods in Natural Language Processing (EMNLP). bib/abs topics:             LTW                   C   D. Anguelov, P. Srinivasan, D. Koller, S. Thrun, J. Rodgers, and J. Davis (2005). "SCAPE: Shape Completion and Animation of People." Proceedings of the 32nd International Conference on Computer Graphics and Interactive Techniques (SIGGRAPH). bib/abs topics:                         RP       C   M. Teyssier and D. Koller (2005). "Ordering-based Search: A Simple and Effective Algorithm for Learning Bayesian Networks." Proceedings of the Twenty-first Conference on Uncertainty in AI (UAI) (pp. 584-590). bib/abs topics: BN             LGM                C   U. Nodelman, D. Koller, and C.R. Shelton (2005). "Expectation Propagation for Continuous Time Bayesian Networks." Proceedings of the Twenty-first Conference on Uncertainty in AI (UAI) (pp. 431-440). bib/abs topics:                               TPM C   U. Nodelman, C.R. Shelton, and D. Koller (2005). "Expectation Maximization and Complex Duration Distributions for Continuous Time Bayesian Networks." Proceedings of the Twenty-first Conference on Uncertainty in AI (UAI) (pp. 421-430). bib/abs topics:                               TPM C   P. Abbeel, D. Koller, and A.Y. Ng (2005). "Learning Factor Graphs in Polynomial Time & Sample Complexity." Proceedings of the Twenty-first Conference on Uncertainty in AI (UAI) (pp. 1-9). [newer version, 2006] bib/abs topics:                LGM MN             J   E. Segal, N. Friedman, N. Kaminski, A. Regev, and D. Koller (2005). "From signatures to models: Understanding cancer using microarrays." Nature Genetics, 37, S38-S45. By invitation. bib/abs topics:    BM                            C   D. Anguelov, B. Taskar, V. Chatalbashev, D. Koller, D. Gupta, G. Heitz, and A.Y. Ng (2005). "Discriminative Learning of Markov Random Fields for Segmentation of 3D Range Data." IEEE International Conference on Computer Vision and Pattern Recognition (CVPR). bib/abs topics:                   MN    RP       J   E. Segal, D. Pe'er, A. Regev, D. Koller, and N. Friedman (2005). "Learning Module Networks." Journal of Machine Learning Research, 6, 557-588. [older version, 2003] bib/abs topics:    BM          LGM    RPM          C   B. Taskar, V. Chatalbashev, D. Koller, and C. Guestrin (2005). "Learning Structured Prediction Models: A Large Margin Approach." Twenty-Second International Conference on Machine Learning (ICML). bib/abs topics:    BM          LGM    RPM    SL    C   D. Anguelov, D. Koller, P. Srinivasan, S. Thrun, H.-C. Pang, and J. Davis (2005). "The correlated correspondence algorithm for unsupervised registration of nonrigid surfaces." Advances in Neural Information Processing Systems (NIPS 2004). bib/abs topics:                   MN    RP       C   H. Wang, E. Segal, A. Ben-Hur, D. Koller, and D. Brutlag (2005). "Identifying protein-protein interaction sites on a genome-wide scale." Advances in Neural Information Processing Systems (NIPS 2004). bib/abs topics:    BM                RPM
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