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Tommi S. Jaakkola - Publications

Affiliations: 
Massachusetts Institute of Technology, Cambridge, MA, United States 
Website:
http://people.csail.mit.edu/tommi/
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52 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Yang K, Swanson K, Jin W, Coley CW, Eiden P, Gao H, Guzman-Perez A, Hopper T, Kelley B, Mathea M, Palmer A, Settels V, Jaakkola TS, Jensen KF, Barzilay R. Analyzing Learned Molecular Representations for Property Prediction. Journal of Chemical Information and Modeling. PMID 31361484 DOI: 10.1021/Acs.Jcim.9B00237  0.38
2019 Coley CW, Jin W, Rogers L, Jamison TF, Jaakkola TS, Green WH, Barzilay R, Jensen KF. A graph-convolutional neural network model for the prediction of chemical reactivity. Chemical Science. 10: 370-377. PMID 30746086 DOI: 10.1039/C8Sc04228D  0.315
2019 Hazan T, Orabona F, Sarwate AD, Maji S, Jaakkola TS. High Dimensional Inference With Random Maximum A-Posteriori Perturbations Ieee Transactions On Information Theory. 65: 6539-6560. DOI: 10.1109/Tit.2019.2916805  0.32
2018 Mueller J, Jaakkola T, Gifford D. Modeling Persistent Trends in Distributions. Journal of the American Statistical Association. 113: 1296-1310. PMID 30906084 DOI: 10.1080/01621459.2017.1341412  0.601
2017 Coley CW, Barzilay R, Green WH, Jaakkola TS, Jensen KF. Convolutional embedding of attributed molecular graphs for physical property prediction. Journal of Chemical Information and Modeling. PMID 28696688 DOI: 10.1021/Acs.Jcim.6B00601  0.327
2016 Hashimoto TB, Sherwood R, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford D. A synergistic DNA logic predicts genome-wide chromatin accessibility. Genome Research. PMID 27456004 DOI: 10.1101/Gr.199778.115  0.748
2016 Hashimoto TB, Alvarez-Melis D, Jaakkola TS. Word Embeddings as Metric Recovery in Semantic Spaces Transactions of the Association For Computational Linguistics. 4: 273-286. DOI: 10.1162/tacl_a_00098  0.726
2014 Sherwood RI, Hashimoto T, O'Donnell CW, Lewis S, Barkal AA, van Hoff JP, Karun V, Jaakkola T, Gifford DK. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nature Biotechnology. 32: 171-8. PMID 24441470 DOI: 10.1038/Nbt.2798  0.754
2012 Hashimoto T, Jaakkola T, Sherwood R, Mazzoni EO, Wichterle H, Gifford D. Lineage-based identification of cellular states and expression programs. Bioinformatics (Oxford, England). 28: i250-7. PMID 22689769 DOI: 10.1093/Bioinformatics/Bts204  0.767
2010 Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics (Oxford, England). 26: 3028-34. PMID 20966006 DOI: 10.1093/Bioinformatics/Btq590  0.564
2010 Jaakkola T, Sontag D, Globerson A, Meila M. Learning Bayesian network structure using LP relaxations Journal of Machine Learning Research. 9: 358-365.  0.587
2010 Sontag D, Meshi O, Jaakkola T, Globerson A. More data means less inference: A pseudo-max approach to structured learning Advances in Neural Information Processing Systems 23: 24th Annual Conference On Neural Information Processing Systems 2010, Nips 2010.  0.59
2009 Sontag D, Jaakkola T. Tree block coordinate descent for MAP in graphical models Journal of Machine Learning Research. 5: 544-551.  0.587
2009 Sontag D, Jaakkola T. New outer bounds on the marginal polytope Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference.  0.571
2008 Sontag D, Meltzer T, Globerson A, Jaakkola T, Weiss Y. Tightening LP relaxations for MAP using message passing Proceedings of the 24th Conference On Uncertainty in Artificial Intelligence, Uai 2008. 503-510.  0.365
2007 Gerber GK, Dowell RD, Jaakkola TS, Gifford DK. Automated discovery of functional generality of human gene expression programs. Plos Computational Biology. 3: e148. PMID 17696603 DOI: 10.1371/journal.pcbi.0030148  0.578
2006 Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. High-resolution computational models of genome binding events. Nature Biotechnology. 24: 963-70. PMID 16900145 DOI: 10.1038/Nbt1233  0.58
2006 Qi Y, Missiuro PE, Kapoor A, Hunter CP, Jaakkola TS, Gifford DK, Ge H. Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics (Oxford, England). 22: e417-23. PMID 16873502 DOI: 10.1093/bioinformatics/btl256  0.599
2006 Yeang CH, Jaakkola T. Modeling the combinatorial functions of multiple transcription factors Journal of Computational Biology. 13: 463-480. PMID 16597252 DOI: 10.1089/cmb.2006.13.463  0.366
2006 Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Erratum: High-resolution computational models of genome binding events Nature Biotechnology. 24: 1293-1293. DOI: 10.1038/Nbt1006-1293A  0.526
2005 Yeang CH, Mak HC, McCuine S, Workman C, Jaakkola T, Ideker T. Validation and refinement of gene-regulatory pathways on a network of physical interactions. Genome Biology. 6: R62. PMID 15998451 DOI: 10.1186/Gb-2005-6-7-R62  0.348
2005 Yeang CH, Jaakkola T. Time series analysis of gene expression and location data International Journal On Artificial Intelligence Tools. 14: 755-769. DOI: 10.1142/S0218213005002375  0.35
2005 Wainwright MJ, Jaakkola TS, Willsky AS. MAP estimation via agreement on trees: Message-passing and linear programming Ieee Transactions On Information Theory. 51: 3697-3717. DOI: 10.1109/TIT.2005.856938  0.689
2005 Wainwright MJ, Jaakkola TS, Willsky AS. A new class of upper bounds on the log partition function Ieee Transactions On Information Theory. 51: 2313-2335. DOI: 10.1109/TIT.2005.850091  0.684
2004 Yeang CH, Ideker T, Jaakkola T. Physical network models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 11: 243-62. PMID 15285891 DOI: 10.1089/1066527041410382  0.382
2004 Wainwright M, Jaakkola T, Willsky A. Tree consistency and bounds on the performance of the max-product algorithm and its generalizations Statistics and Computing. 14: 143-166. DOI: 10.1023/B:STCO.0000021412.33763.d5  0.691
2004 Sachs K, Perez OD, Pe'er D, Nolan GP, Gifford DK, Jaakkola TS, Lauffenburger DA. Analysis of signaling pathways in human T-cells using Bayesian network modeling of single cell data Proceedings - 2004 Ieee Computational Systems Bioinformatics Conference, Csb 2004. 644.  0.496
2003 Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, Gifford DK. Computational discovery of gene modules and regulatory networks. Nature Biotechnology. 21: 1337-42. PMID 14555958 DOI: 10.1038/Nbt890  0.717
2003 Bar-Joseph Z, Gerber GK, Gifford DK, Jaakkola TS, Simon I. Continuous representations of time-series gene expression data. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 341-56. PMID 12935332 DOI: 10.1089/10665270360688057  0.719
2003 Bar-Joseph Z, Gerber G, Simon I, Gifford DK, Jaakkola TS. Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes. Proceedings of the National Academy of Sciences of the United States of America. 100: 10146-51. PMID 12934016 DOI: 10.1073/Pnas.1732547100  0.716
2003 Bar-Joseph Z, Demaine ED, Gifford DK, Srebro N, Hamel AM, Jaakkola TS. K-ary clustering with optimal leaf ordering for gene expression data. Bioinformatics (Oxford, England). 19: 1070-8. PMID 12801867 DOI: 10.1093/Bioinformatics/Btg030  0.735
2003 Wainwright MJ, Jaakkola TS, Willsky AS. Tree-based reparameterization framework for analysis of sum-product and related algorithms Ieee Transactions On Information Theory. 49: 1120-1146. DOI: 10.1109/TIT.2003.810642  0.7
2003 Wainwright MJ, Jaakkola TS, Willsky AS. Exact MAP estimates by (hyper)tree agreement Advances in Neural Information Processing Systems.  0.411
2002 Sachs K, Gifford D, Jaakkola T, Sorger P, Lauffenburger DA. Bayesian network approach to cell signaling pathway modeling. Science's Stke : Signal Transduction Knowledge Environment. 2002: pe38. PMID 12209052 DOI: 10.1126/Stke.2002.148.Pe38  0.568
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Combining location and expression data for principled discovery of genetic regulatory network models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 437-49. PMID 11928497  0.569
2002 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Bayesian methods for elucidating genetic regulatory networks Ieee Intelligent Systems and Their Applications. 17: 37-43. DOI: 10.1109/5254.999218  0.56
2002 Wainwright M, Jaakkola T, Willsky A. Tree-based reparameterization analysis of belief propagation and related algorithms for approximate inference on graphs with cycles Ieee International Symposium On Information Theory - Proceedings. 113.  0.572
2002 Wainwright. MJ, Jaakkola T, Willsky AS. Tree-based reparameterization for approximate inference on loopy graphs Advances in Neural Information Processing Systems.  0.442
2002 Bar-Joseph Z, Gerber G, Gifford DK, Jaakkola TS, Simon I. A new approach to analyzing gene expression time series data Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 39-48.  0.52
2001 Simon I, Barnett J, Hannett N, Harbison CT, Rinaldi NJ, Volkert TL, Wyrick JJ, Zeitlinger J, Gifford DK, Jaakkola TS, Young RA. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell. 106: 697-708. PMID 11572776 DOI: 10.1016/S0092-8674(01)00494-9  0.556
2001 Bar-Joseph Z, Gifford DK, Jaakkola TS. Fast optimal leaf ordering for hierarchical clustering. Bioinformatics (Oxford, England). 17: S22-9. PMID 11472989 DOI: 10.1093/Bioinformatics/17.Suppl_1.S22  0.692
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 422-33. PMID 11262961  0.573
2001 Hartemink AJ, Gifford DK, Jaakkola TS, Young RA. Maximum likelihood estimation of optimal scaling factors for expression array normalization Proceedings of Spie - the International Society For Optical Engineering. 4266: 132-140. DOI: 10.1117/12.427981  0.483
2000 Jaakkola TS, Jordan MI. Bayesian parameter estimation via variational methods Statistics and Computing. 10: 25-37. DOI: 10.1023/A:1008932416310  0.616
2000 Singh S, Jaakkola T, Littman ML, Szepesvári C. Convergence results for single-step on-policy reinforcement-learning algorithms Machine Learning. 38: 287-308. DOI: 10.1023/A:1007678930559  0.317
2000 Jaakkola T, Meila M, Jebara T. Maximum entropy discrimination Advances in Neural Information Processing Systems. 470-476.  0.544
1999 Jaakkola TS, Jordan MI. Variational probabilistic inference and the QMR-DT network Journal of Artificial Intelligence Research. 10: 291-322. DOI: 10.1613/Jair.583  0.655
1999 Jordan MI, Ghahramani Z, Jaakkola TS, Saul LK. Introduction to variational methods for graphical models Machine Learning. 37: 183-233. DOI: 10.1023/A:1007665907178  0.779
1998 Bishop CM, Lawrence N, Jaakkola T, Jordan MI. Approximating posterior distributions in belief networks using mixtures Advances in Neural Information Processing Systems. 416-422.  0.556
1997 Jaakkola TS, Jordan MI. Recursive algorithms for approximating probabilities in graphical models Advances in Neural Information Processing Systems. 487-493.  0.604
1996 Saul LK, Jaakkola T, Jordan MI. Mean field theory for sigmoid belief networks Journal of Artificial Intelligence Research. 4: 61-76. DOI: 10.1613/Jair.251  0.713
1994 Jaakkola T, Jordan MI, Singh SP. On the Convergence of Stochastic Iterative Dynamic Programming Algorithms Neural Computation. 6: 1185-1201. DOI: 10.1162/neco.1994.6.6.1185  0.599
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