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54 results for Jaakkola,+Tommi+S

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ArticlesPeer ReviewedFull Text
An Introduction to Variational Methods for Graphical Models
Author / Creator:Jordan, Michael I ; Ghahramani, Zoubin ; Jaakkola, Tommi S ; Saul, Lawrence K
Publisher:Dordrecht: Springer Nature B.V
Journal title:Machine learning, 1999-11, Vol.37 (2), p.183-233
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Computational discovery of gene modules and regulatory networks
Author / Creator:Bar-Joseph, Ziv ; Gerber, Georg K ; Lee, Tong Ihn ; Rinaldi, Nicola J ; Yoo, Jane Y ; Robert, François ; Gordon, D Benjamin ; Fraenkel, Ernest ; Jaakkola, Tommi S ; Young, Richard A ; Gifford, David K
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2003-11, Vol.21 (11), p.1337-1342
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ArticlesPeer ReviewedFull Text
Word Embeddings as Metric Recovery in Semantic Spaces
Author / Creator:Hashimoto, Tatsunori B. ; Alvarez-Melis, David ; Jaakkola, Tommi S.
Publisher:One Rogers Street, Cambridge, MA 02142-1209, USA: MIT Press
Journal title:Transactions of the Association for Computational Linguistics, 2021-03, Vol.4, p.273-286
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De novo design of protein structure and function with RFdiffusion
Author / Creator:Watson, Joseph L. ; Juergens, David ; Bennett, Nathaniel R. ; Trippe, Brian L. ; Yim, Jason ; Eisenach, Helen E. ; Ahern, Woody ; Borst, Andrew J. ; Ragotte, Robert J. ; Milles, Lukas F. ; Wicky, Basile I. M. ; Hanikel, Nikita ; Pellock, Samuel J. ; Courbet, Alexis ; Sheffler, William ; Wang, Jue ; Venkatesh, Preetham ; Sappington, Isaac ; Torres, Susana Vázquez ; Lauko, Anna ; De Bortoli, Valentin ; Mathieu, Emile ; Ovchinnikov, Sergey ; Barzilay, Regina ; Jaakkola, Tommi S. ; DiMaio, Frank ; Baek, Minkyung ; Baker, David
Publisher:London: Nature Publishing Group UK
Journal title:Nature (London), 2023-08, Vol.620 (7976), p.1089-1100
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Deep learning identifies synergistic drug combinations for treating COVID-19
Author / Creator:Jin, Wengong ; Stokes, Jonathan M. ; Eastman, Richard T. ; Itkin, Zina ; Zakharov, Alexey V. ; Collins, James J. ; Jaakkola, Tommi S. ; Barzilay, Regina
Publisher:Washington: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2021-09, Vol.118 (39), p.1-7
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ArticlesPeer ReviewedFull Text
Comparing the Continuous Representation of Time-Series Expression Profiles to Identify Differentially Expressed Genes
Author / Creator:Bar-Joseph, Ziv ; Gerber, Georg ; Simon, Itamar ; Gifford, David K. ; Jaakkola, Tommi S.
Publisher:United States: National Academy of Sciences
Journal title:Proceedings of the National Academy of Sciences - PNAS, 2003-09, Vol.100 (18), p.10146-10151
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ArticlesPeer ReviewedFull Text
Automated Discovery of Functional Generality of Human Gene Expression Programs
Author / Creator:Gerber, Georg K ; Dowell, Robin D ; Jaakkola, Tommi S ; Gifford, David K
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2007-08, Vol.3 (8), p.e148-e148
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High-resolution computational models of genome binding events
Author / Creator:Qi, Yuan ; Rolfe, Alex ; MacIsaac, Kenzie D ; Gerber, Georg K ; Pokholok, Dmitry ; Zeitlinger, Julia ; Danford, Timothy ; Dowell, Robin D ; Fraenkel, Ernest ; Jaakkola, Tommi S ; Young, Richard A ; Gifford, David K
Publisher:London: Nature Publishing Group UK
Journal title:Nature biotechnology, 2006-08, Vol.24 (8), p.963-970
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Variational Probabilistic Inference and the QMR-DT Network
Author / Creator:Jaakkola, T. S. ; Jordan, M. I.
Publisher:San Francisco: AI Access Foundation
Journal title:The Journal of artificial intelligence research, 1999-01, Vol.10, p.291-322
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Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models
Author / Creator:Watson, Joseph L ; Juergens, David ; Bennett, Nathaniel R ; Trippe, Brian L ; Yim, Jason ; Eisenach, Helen E ; Ahern, Woody ; Borst, Andrew J ; Ragotte, Robert J ; Milles, Lukas F ; Wicky, Basile I M ; Hanikel, Nikita ; Pellock, Samuel J ; Courbet, Alexis ; Sheffler, William ; Wang, Jue ; Venkatesh, Preetham ; Sappington, Isaac ; Susana Vázquez Torres ; Lauko, Anna ; De Bortoli, Valentin ; Mathieu, Emile ; Barzilay, Regina ; Jaakkola, Tommi S ; Dimaio, Frank ; Baek, Minkyung ; Baker, David
Publisher:Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Journal title:bioRxiv, 2022-12
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Conformal Language Modeling
Author / Creator:Quach, Victor ; Fisch, Adam ; Schuster, Tal ; Yala, Adam ; Jae Ho Sohn ; Jaakkola, Tommi S ; Barzilay, Regina
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2024-06
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Erratum: High-resolution computational models of genome binding events
Author / Creator:Qi, Yuan ; Rolfe, Alex ; MacIsaac, Kenzie D ; Gerber, Georg K ; Pokholok, Dmitry ; Zeitlinger, Julia ; Danford, Timothy ; Dowell, Robin D ; Fraenkel, Ernest ; Jaakkola, Tommi S ; Young, Richard A ; Gifford, David K
Publisher:New York: Nature Publishing Group US
Journal title:Nature biotechnology, 2006-10, Vol.24 (10), p.1293-1293
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Oblique Decision Trees from Derivatives of ReLU Networks
Author / Creator:Guang-He, Lee ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2020-05
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Understanding Interlocking Dynamics of Cooperative Rationalization
Author / Creator:Yu, Mo ; Zhang, Yang ; Chang, Shiyu ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2021-10
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Fundamental Limits and Tradeoffs in Invariant Representation Learning
Author / Creator:Zhao, Han ; Chen, Dan ; Aragam, Bryon ; Jaakkola, Tommi S ; Gordon, Geoffrey J ; Ravikumar, Pradeep
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2022-11
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Structural Constraint Integration in Generative Model for Discovery of Quantum Material Candidates
Author / Creator:Okabe, Ryotaro ; Cheng, Mouyang ; Chotrattanapituk, Abhijatmedhi ; Nguyen, Tuan Hung ; Fu, Xiang ; Bowen, Han ; Wang, Yao ; Xie, Weiwei ; Cava, Robert J ; Jaakkola, Tommi S ; Cheng, Yongqiang ; Li, Mingda
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2024-07
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Towards Robust Interpretability with Self-Explaining Neural Networks
Author / Creator:Alvarez-Melis, David ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2018-12
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DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models
Author / Creator:Ketata, Mohamed Amine ; Laue, Cedrik ; Mammadov, Ruslan ; Stärk, Hannes ; Wu, Menghua ; Corso, Gabriele ; Marquet, Céline ; Barzilay, Regina ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2023-04
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Gromov-Wasserstein Alignment of Word Embedding Spaces
Author / Creator:Alvarez-Melis, David ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2018-08
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Adversarial Support Alignment
Author / Creator:Tong, Shangyuan ; Garipov, Timur ; Zhang, Yang ; Chang, Shiyu ; Jaakkola, Tommi S
Publisher:Ithaca: Cornell University Library, arXiv.org
Journal title:arXiv.org, 2022-03
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Showing 1 to 20 of 54 results

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An Introduction to Variational Methods for Graphical Models

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Computational discovery of gene modules and regulatory networks

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Word Embeddings as Metric Recovery in Semantic Spaces

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De novo design of protein structure and function with RFdiffusion

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Deep learning identifies synergistic drug combinations for treating COVID-19

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Comparing the Continuous Representation of Time-Series Expression Profiles to Identify Differentially Expressed Genes

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Automated Discovery of Functional Generality of Human Gene Expression Programs

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High-resolution computational models of genome binding events

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Variational Probabilistic Inference and the QMR-DT Network

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Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

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Conformal Language Modeling

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Erratum: High-resolution computational models of genome binding events

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Oblique Decision Trees from Derivatives of ReLU Networks

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Understanding Interlocking Dynamics of Cooperative Rationalization

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Fundamental Limits and Tradeoffs in Invariant Representation Learning

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Structural Constraint Integration in Generative Model for Discovery of Quantum Material Candidates

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Towards Robust Interpretability with Self-Explaining Neural Networks

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DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models

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Gromov-Wasserstein Alignment of Word Embedding Spaces

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Adversarial Support Alignment

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