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Daphne Koller Publications
Research AreasPublication TypeYears (all)
BNBayesian Networks   BMBiology and Medicine
CGTComputational Game Theory   HMHybrid Models
LTWLanguage and Web   LGMLearning Graphical Models
MNMarkov Networks   RPMRicher Probabilistic Models
RPRobotics and Perception   SLSupervised Learning
TPMTemporal Probabilistic Models  
JJournal Article
CConference Paper
BBook
ChBook Chapter
TTechnical Report
PhDPhD Disseration
1985 - 1989
1990 - 1994
1995 - 1999
2000 - 2004
2005 - 2009
2010 - 2014

TypeReferenceDownload
topics: BNBMCGTHMLTWLGMMNRPMRPSLTPM

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 pdf html
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 pdf html
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 pdf
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 pdf ppt
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 pdf html
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf ppt
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 pdf
topics:                   MN    RP      

B   D. Koller and N. Friedman (2009). Probabilistic Graphical Models: Principles and Techniques. edited by . MIT Press.bib html
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 html
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 pdf html
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 html
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 html
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf ppt
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf ppt
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 pdf
topics:                                 

B   J.C. Platt, D. Koller, Y. Singer, and S. Roweis (2008). Proceedings Advances in Neural Information Processing Systems (NIPS-07). .bib html
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf
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 pdf ps.gz
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 pdf ps.gz
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 pdf ps.gz
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 pdf
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 pdf
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 pdf
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 pdf ps.gz
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 pdf
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 pdf
topics:    BM                RPM         

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