Tommi S. Jaakkola
Affiliations:- MIT, Computer Science and Artificial Intelligence Laboratory
According to our database1,
Tommi S. Jaakkola
authored at least 265 papers
between 1994 and 2024.
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Bibliography
2024
Nat. Comput. Sci., July, 2024
CoRR, 2024
CoRR, 2024
Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design.
CoRR, 2024
Structural Constraint Integration in Generative Model for Discovery of Quantum Material Candidates.
CoRR, 2024
CoRR, 2024
CoRR, 2024
CoRR, 2024
CoRR, 2024
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Harmonic Self-Conditioned Flow Matching for joint Multi-Ligand Docking and Binding Site Design.
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design.
Proceedings of the Forty-first International Conference on Machine Learning, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Proceedings of the Twelfth International Conference on Learning Representations, 2024
Revisiting Who's Harry Potter: Towards Targeted Unlearning from a Causal Intervention Perspective.
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing, 2024
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2024
2023
Simulate Time-integrated Coarse-grained Molecular Dynamics with Multi-scale Graph Networks.
Trans. Mach. Learn. Res., 2023
Forces are not Enough: Benchmark and Critical Evaluation for Machine Learning Force Fields with Molecular Simulations.
Trans. Mach. Learn. Res., 2023
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design.
CoRR, 2023
CoRR, 2023
CoRR, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Proceedings of the International Conference on Machine Learning, 2023
Proceedings of the International Conference on Machine Learning, 2023
Proceedings of the International Conference on Machine Learning, 2023
Proceedings of the Eleventh International Conference on Learning Representations, 2023
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem.
Proceedings of the Eleventh International Conference on Learning Representations, 2023
Proceedings of the Eleventh International Conference on Learning Representations, 2023
Proceedings of the Eleventh International Conference on Learning Representations, 2023
Proceedings of the Eleventh International Conference on Learning Representations, 2023
2022
J. Mach. Learn. Res., 2022
CoRR, 2022
Simulate Time-integrated Coarse-grained Molecular Dynamics with Geometric Machine Learning.
CoRR, 2022
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022
Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022
Proceedings of the International Conference on Machine Learning, 2022
Proceedings of the International Conference on Machine Learning, 2022
Proceedings of the International Conference on Machine Learning, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
Proceedings of the Tenth International Conference on Learning Representations, 2022
Proceedings of the Computer Vision - ECCV 2022, 2022
2021
Proc. Natl. Acad. Sci. USA, 2021
NeuraCrypt: Hiding Private Health Data via Random Neural Networks for Public Training.
CoRR, 2021
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021
Proceedings of the 38th International Conference on Machine Learning, 2021
Proceedings of the 38th International Conference on Machine Learning, 2021
Proceedings of the 38th International Conference on Machine Learning, 2021
Proceedings of the 9th International Conference on Learning Representations, 2021
Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing, 2021
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, 2021
2020
Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models.
CoRR, 2020
CoRR, 2020
CoRR, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 37th International Conference on Machine Learning, 2020
Proceedings of the 8th International Conference on Learning Representations, 2020
Proceedings of the 8th International Conference on Learning Representations, 2020
Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing, 2020
Proceedings of the 23rd International Conference on Artificial Intelligence and Statistics, 2020
2019
IEEE Trans. Inf. Theory, 2019
J. Chem. Inf. Model., 2019
J. Chem. Inf. Model., 2019
CoRR, 2019
Alignment Based Matching Networks for One-Shot Classification and Open-Set Recognition.
CoRR, 2019
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Proceedings of the 36th International Conference on Machine Learning, 2019
Proceedings of the 7th International Conference on Learning Representations, 2019
Proceedings of the 7th International Conference on Learning Representations, 2019
Rethinking Cooperative Rationalization: Introspective Extraction and Complement Control.
Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing, 2019
Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics, 2019
Bidirectional Inference Networks: A Class of Deep Bayesian Networks for Health Profiling.
Proceedings of the Thirty-Third AAAI Conference on Artificial Intelligence, 2019
2018
J. Artif. Intell. Res., 2018
CoRR, 2018
The Variational Homoencoder: Learning to learn high capacity generative models from few examples.
Proceedings of the Thirty-Fourth Conference on Uncertainty in Artificial Intelligence, 2018
Proceedings of the Advances in Neural Information Processing Systems 31: Annual Conference on Neural Information Processing Systems 2018, 2018
Proceedings of the 35th International Conference on Machine Learning, 2018
Proceedings of the 2018 Conference on Empirical Methods in Natural Language Processing, Brussels, Belgium, October 31, 2018
Proceedings of the International Conference on Artificial Intelligence and Statistics, 2018
2017
Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction.
J. Chem. Inf. Model., August, 2017
Trans. Assoc. Comput. Linguistics, 2017
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
Proceedings of the 34th International Conference on Machine Learning, 2017
Proceedings of the 34th International Conference on Machine Learning, 2017
Proceedings of the 34th International Conference on Machine Learning, 2017
Proceedings of the 5th International Conference on Learning Representations, 2017
A causal framework for explaining the predictions of black-box sequence-to-sequence models.
Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing, 2017
Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 2017
2016
Trans. Assoc. Comput. Linguistics, 2016
Structured Prediction: From Gaussian Perturbations to Linear-Time Principled Algorithms.
Proceedings of the Thirty-Second Conference on Uncertainty in Artificial Intelligence, 2016
Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016
Proceedings of the NAACL HLT 2016, 2016
Proceedings of the NAACL HLT 2016, 2016
Proceedings of the 33nd International Conference on Machine Learning, 2016
Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing, 2016
Proceedings of the 2016 Conference on Empirical Methods in Natural Language Processing, 2016
Proceedings of the 19th International Conference on Artificial Intelligence and Statistics, 2016
2015
Trans. Assoc. Comput. Linguistics, 2015
Denoising Bodies to Titles: Retrieving Similar Questions with Recurrent Convolutional Models.
CoRR, 2015
Principal Differences Analysis: Interpretable Characterization of Differences between Distributions.
Proceedings of the Advances in Neural Information Processing Systems 28: Annual Conference on Neural Information Processing Systems 2015, 2015
Proceedings of the Advances in Neural Information Processing Systems 28: Annual Conference on Neural Information Processing Systems 2015, 2015
Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing, 2015
Proceedings of the Eighteenth International Conference on Artificial Intelligence and Statistics, 2015
2014
Proceedings of the Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, 2014
Proceedings of the 31th International Conference on Machine Learning, 2014
Proceedings of the 31th International Conference on Machine Learning, 2014
Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing, 2014
Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014
Tight Bounds for the Expected Risk of Linear Classifiers and PAC-Bayes Finite-Sample Guarantees.
Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014
Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, 2014
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics, 2014
Proceedings of the 52nd Annual Meeting of the Association for Computational Linguistics, 2014
2013
Inverse Covariance Estimation for High-Dimensional Data in Linear Time and Space: Spectral Methods for Riccati and Sparse Models.
Proceedings of the Twenty-Ninth Conference on Uncertainty in Artificial Intelligence, 2013
Learning Efficient Random Maximum A-Posteriori Predictors with Non-Decomposable Loss Functions.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
On Sampling from the Gibbs Distribution with Random Maximum A-Posteriori Perturbations.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
Proceedings of the 30th International Conference on Machine Learning, 2013
2012
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012
Approximate Inference in Additive Factorial HMMs with Application to Energy Disaggregation.
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012
Special Issue on the Fifth European Workshop on Probabilistic Graphical Models (PGM-2010).
Int. J. Approx. Reason., 2012
Proceedings of the Twenty-First Conference on Uncertainty in Artificial Intelligence (2005)
CoRR, 2012
Bioinform., 2012
Proceedings of the Advances in Neural Information Processing Systems 25: 26th Annual Conference on Neural Information Processing Systems 2012. Proceedings of a meeting held December 3-6, 2012
Proceedings of the 29th International Conference on Machine Learning, 2012
2010
Proceedings of the Thirteenth International Conference on Artificial Intelligence and Statistics, 2010
Proceedings of the Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010. Proceedings of a meeting held 6-9 December 2010, 2010
Proceedings of the 27th International Conference on Machine Learning (ICML-10), 2010
On Dual Decomposition and Linear Programming Relaxations for Natural Language Processing.
Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, 2010
Proceedings of the 2010 Conference on Empirical Methods in Natural Language Processing, 2010
Proceedings of the 19th ACM Conference on Information and Knowledge Management, 2010
2009
Proceedings of the Twelfth International Conference on Artificial Intelligence and Statistics, 2009
2008
Proceedings of the UAI 2008, 2008
Proceedings of the Advances in Neural Information Processing Systems 21, 2008
2007
PLoS Comput. Biol., 2007
Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics, 2007
Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics, 2007
Proceedings of the UAI 2007, 2007
Proceedings of the Advances in Neural Information Processing Systems 20, 2007
Proceedings of the Advances in Neural Information Processing Systems 20, 2007
2006
J. Comput. Biol., 2006
Proceedings of the Advances in Neural Information Processing Systems 19, 2006
Proceedings of the Advances in Neural Information Processing Systems 19, 2006
Proceedings of the Advances in Neural Information Processing Systems 19, 2006
Semi-supervised analysis of gene expression profiles for lineage-specific development in the <i>Caenorhabditis elegans</i> embryo.
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
2005
IEEE Trans. Inf. Theory, 2005
IEEE Trans. Inf. Theory, 2005
Int. J. Artif. Intell. Tools, 2005
CoRR, 2005
Proceedings of the SIGIR 2005: Proceedings of the 28th Annual International ACM SIGIR Conference on Research and Development in Information Retrieval, 2005
Proceedings of the Tenth International Workshop on Artificial Intelligence and Statistics, 2005
2004
Tree consistency and bounds on the performance of the max-product algorithm and its generalizations.
Stat. Comput., 2004
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data.
Proceedings of the 3rd International IEEE Computer Society Computational Systems Bioinformatics Conference, 2004
2003
Tree-based reparameterization framework for analysis of sum-product and related algorithms.
IEEE Trans. Inf. Theory, 2003
J. Comput. Biol., 2003
Bioinform., 2003
Proceedings of the Sventh Annual International Conference on Computational Biology, 2003
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003
Tree-reweighted belief propagation algorithms and approximate ML estimation by pseudo-moment matching.
Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, 2003
2002
IEEE Intell. Syst., 2002
Proceedings of the UAI '02, 2002
Proceedings of the Sixth Annual International Conference on Computational Biology, 2002
Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002
2001
Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001
Proceedings of the Advances in Neural Information Processing Systems 14 [Neural Information Processing Systems: Natural and Synthetic, 2001
Fast optimal leaf ordering for hierarchical clustering.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001
2000
Mach. Learn., 2000
J. Comput. Biol., 2000
Proceedings of the UAI '00: Proceedings of the 16th Conference in Uncertainty in Artificial Intelligence, Stanford University, Stanford, California, USA, June 30, 2000
Proceedings of the Advances in Neural Information Processing Systems 13, 2000
Proceedings of the Advances in Neural Information Processing Systems 13, 2000
1999
J. Artif. Intell. Res., 1999
Proceedings of the Advances in Neural Information Processing Systems 12, [NIPS Conference, Denver, Colorado, USA, November 29, 1999
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999
Proceedings of the Seventh International Workshop on Artificial Intelligence and Statistics, 1999
1998
Proceedings of the Advances in Neural Information Processing Systems 11, [NIPS Conference, Denver, Colorado, USA, November 30, 1998
Proceedings of the Learning in Graphical Models, 1998
Proceedings of the Learning in Graphical Models, 1998
1997
Proceedings of the Advances in Neural Information Processing Systems 10, 1997
Proceedings of the Sixth International Workshop on Artificial Intelligence and Statistics, 1997
1996
Proceedings of the UAI '96: Proceedings of the Twelfth Annual Conference on Uncertainty in Artificial Intelligence, 1996
Proceedings of the Advances in Neural Information Processing Systems 9, 1996
1995
Proceedings of the Advances in Neural Information Processing Systems 8, 1995
1994
Neural Comput., 1994
Proceedings of the Advances in Neural Information Processing Systems 7, 1994
Proceedings of the Advances in Neural Information Processing Systems 7, 1994
Learning Without State-Estimation in Partially Observable Markovian Decision Processes.
Proceedings of the Machine Learning, 1994