Barzilay, Regina

82 publications

FnTML 2025 Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Alex Strasser, Haiyang Yu, Yuqing Xie, Xiang Fu, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik J. Bekkers, Michael M. Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi S. Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess E. Smidt, Shuiwang Ji

ICLR 2025 Composing Unbalanced Flows for Flexible Docking and Relaxation Gabriele Corso, Vignesh Ram Somnath, Noah Getz, Regina Barzilay, Tommi Jaakkola, Andreas Krause

ICLRW 2025 Hierarchical Protein Backbone Generation with Latent and Structure Diffusion Jason Yim, Marouane Jaakik, Ge Liu, Jacob Gershon, Karsten Kreis, David Baker, Regina Barzilay, Tommi Jaakkola

ICML 2025 Identifying Biological Perturbation Targets Through Causal Differential Networks Menghua Wu, Umesh Padia, Sean H. Murphy, Regina Barzilay, Tommi Jaakkola

TMLR 2025 MiniFold: Simple, Fast, and Accurate Protein Structure Prediction Jeremy Wohlwend, Mateo Reveiz, Matt McPartlon, Axel Feldmann, Wengong Jin, Regina Barzilay

TMLR 2025 Predicting Sub-Population Specific Viral Evolution Wenxian Shi, Menghua Wu, Regina Barzilay

TMLR 2025 Sample, Estimate, Aggregate: A Recipe for Causal Discovery Foundation Models Menghua Wu, Yujia Bao, Regina Barzilay, Tommi Jaakkola

ICML 2024 CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes Peter Mikhael, Itamar Chinn, Regina Barzilay

ICLRW 2024 CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes Peter Mikhael, Itamar Chinn, Regina Barzilay

ICLR 2024 Conformal Language Modeling Victor Quach, Adam Fisch, Tal Schuster, Adam Yala, Jae Ho Sohn, Tommi S. Jaakkola, Regina Barzilay

ICLR 2024 Deep Confident Steps to New Pockets: Strategies for Docking Generalization Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi S. Jaakkola

ICML 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola

ICLRW 2024 Dirichlet Flow Matching with Applications to DNA Sequence Design Hannes Stark, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola

ICMLW 2024 Flexible Docking via Unbalanced Flow Matching Gabriele Corso, Vignesh Ram Somnath, Noah Getz, Regina Barzilay, Tommi Jaakkola, Andreas Krause

ICML 2024 Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi Jaakkola

ICLRW 2024 Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi Jaakkola

ICLRW 2024 Graph-Based Forward Synthesis Prediction of Biocatalyzed Reactions Peter Mikhael, Itamar Chinn, Regina Barzilay

ICML 2024 Harmonic Self-Conditioned Flow Matching for Joint Multi-Ligand Docking and Binding Site Design Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola

TMLR 2024 Improved Motif-Scaffolding with SE(3) Flow Matching Jason Yim, Andrew Campbell, Emile Mathieu, Andrew Y. K. Foong, Michael Gastegger, Jose Jimenez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Frank Noe, Regina Barzilay, Tommi Jaakkola

ICLRW 2024 Improved Motif-Scaffolding with SE(3) Flow Matching Jason Yim, Andrew Campbell, Emile Mathieu, Andrew Y. K. Foong, Michael Gastegger, Jose Jimenez-Luna, Sarah Lewis, Victor Garcia Satorras, Bastiaan S. Veeling, Frank Noe, Regina Barzilay, Tommi Jaakkola

ICLR 2024 Improving Protein Optimization with Smoothed Fitness Landscapes Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R Fiete

ICLR 2024 Particle Guidance: Non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso, Yilun Xu, Valentin De Bortoli, Regina Barzilay, Tommi S. Jaakkola

TMLR 2024 Risk-Controlling Model Selection via Guided Bayesian Optimization Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi Jaakkola

ICLRW 2024 Sample, Estimate, Aggregate: A Recipe for Causal Discovery Foundation Models Menghua Wu, Yujia Bao, Regina Barzilay, Tommi Jaakkola

ICLRW 2023 DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models Mohamed Amine Ketata, Cedrik Laue, Ruslan Mammadov, Hannes Stark, Menghua Wu, Gabriele Corso, Céline Marquet, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2023 DiffDock-Pocket: Diffusion for Pocket-Level Docking with Sidechain Flexibility Michael Plainer, Marcella Toth, Simon Dobers, Hannes Stark, Gabriele Corso, Céline Marquet, Regina Barzilay

ICLR 2023 DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

ICLR 2023 Diffusion Probabilistic Modeling of Protein Backbones in 3D for the Motif-Scaffolding Problem Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola

ICLR 2023 Efficiently Controlling Multiple Risks with Pareto Testing Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2023 Harmonic Prior Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design Hannes Stark, Bowen Jing, Regina Barzilay, Tommi Jaakkola

ICMLW 2023 Optimizing Protein Fitness Using Gibbs Sampling with Graph-Based Smoothing Andrew Kirjner, Jason Yim, Raman Samusevich, Tommi S. Jaakkola, Regina Barzilay, Ila R Fiete

NeurIPSW 2023 Particle Guidance: Non-I.I.D. Diverse Sampling with Diffusion Models Gabriele Corso, Yilun Xu, Valentin De Bortoli, Regina Barzilay, Tommi Jaakkola

ICML 2023 SE(3) Diffusion Model with Application to Protein Backbone Generation Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi Jaakkola

NeurIPSW 2023 The Discovery of Binding Modes Requires Rethinking Docking Generalization Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi Jaakkola

TMLR 2022 Calibrated Selective Classification Adam Fisch, Tommi S. Jaakkola, Regina Barzilay

ICLR 2022 Crystal Diffusion Variational Autoencoder for Periodic Material Generation Tian Xie, Xiang Fu, Octavian-Eugen Ganea, Regina Barzilay, Tommi S. Jaakkola

NeurIPSW 2022 DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola

ICLRW 2022 EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction Hannes Stärk, Octavian-Eugen Ganea, Lagnajit Pattanaik, Regina Barzilay, Tommi S. Jaakkola

ICLR 2022 Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause

ICLR 2022 Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-Design Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola

NeurIPS 2022 Torsional Diffusion for Molecular Conformer Generation Bowen Jing, Gabriele Corso, Jeffrey Chang, Regina Barzilay, Tommi Jaakkola

ICLRW 2022 Torsional Diffusion for Molecular Conformer Generation Bowen Jing, Gabriele Corso, Regina Barzilay, Tommi S. Jaakkola

ICLR 2021 Efficient Conformal Prediction via Cascaded Inference with Expanded Admission Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay

NeurIPSW 2021 Fragment-Based Sequential Translation for Molecular Optimization Benson Chen, Xiang Fu, Regina Barzilay, Tommi S. Jaakkola

NeurIPS 2021 GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles Octavian Ganea, Lagnajit Pattanaik, Connor Coley, Regina Barzilay, Klavs Jensen, William Green, Tommi Jaakkola

NeurIPS 2021 Learning Graph Models for Retrosynthesis Prediction Vignesh Ram Somnath, Charlotte Bunne, Connor Coley, Andreas Krause, Regina Barzilay

CVPR 2021 Mol2Image: Improved Conditional Flow Models for Molecule to Image Synthesis Karren Yang, Samuel Goldman, Wengong Jin, Alex X. Lu, Regina Barzilay, Tommi Jaakkola, Caroline Uhler

AAAI 2021 Nutri-Bullets: Summarizing Health Studies by Composing Segments Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay

ICML 2021 Predict Then Interpolate: A Simple Algorithm to Learn Stable Classifiers Yujia Bao, Shiyu Chang, Regina Barzilay

AAAI 2020 Automatic Fact-Guided Sentence Modification Darsh J. Shah, Tal Schuster, Regina Barzilay

AAAI 2020 Capturing Greater Context for Question Generation Luu Anh Tuan, Darsh J. Shah, Regina Barzilay

ICLR 2020 Few-Shot Text Classification with Distributional Signatures Yujia Bao, Menghua Wu, Shiyu Chang, Regina Barzilay

NeurIPS 2019 Generative Models for Graph-Based Protein Design John Ingraham, Vikas Garg, Regina Barzilay, Tommi Jaakkola

ICLRW 2019 Generative Models for Graph-Based Protein Design John Ingraham, Vikas K. Garg, Regina Barzilay, Tommi Jaakkola

ICLR 2019 Learning Multimodal Graph-to-Graph Translation for Molecule Optimization Wengong Jin, Kevin Yang, Regina Barzilay, Tommi Jaakkola

JAIR 2018 Grounding Language for Transfer in Deep Reinforcement Learning Karthik Narasimhan, Regina Barzilay, Tommi S. Jaakkola

ICML 2018 Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin, Regina Barzilay, Tommi Jaakkola

ICML 2017 Deriving Neural Architectures from Sequence and Graph Kernels Tao Lei, Wengong Jin, Regina Barzilay, Tommi Jaakkola

NeurIPS 2017 Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network Wengong Jin, Connor Coley, Regina Barzilay, Tommi Jaakkola

NeurIPS 2017 Style Transfer from Non-Parallel Text by Cross-Alignment Tianxiao Shen, Tao Lei, Regina Barzilay, Tommi Jaakkola

JAIR 2013 Automatic Aggregation by Joint Modeling of Aspects and Values Christina Sauper, Regina Barzilay

JAIR 2012 Learning to Win by Reading Manuals in a Monte-Carlo Framework S. R. K. Branavan, David Silver, Regina Barzilay

IJCAI 2011 Non-Linear Monte-Carlo Search in Civilization II S. R. K. Branavan, David Silver, Regina Barzilay

AAAI 2011 Using Semantic Cues to Learn Syntax Tahira Naseem, Regina Barzilay

ICML 2010 Climbing the Tower of Babel: Unsupervised Multilingual Learning Benjamin Snyder, Regina Barzilay

JAIR 2009 Content Modeling Using Latent Permutations Harr Chen, S. R. K. Branavan, Regina Barzilay, David R. Karger

JAIR 2009 Learning Document-Level Semantic Properties from Free-Text Annotations S. R. K. Branavan, Harr Chen, Jacob Eisenstein, Regina Barzilay

JAIR 2009 Multilingual Part-of-Speech Tagging: Two Unsupervised Approaches Tahira Naseem, Benjamin Snyder, Jacob Eisenstein, Regina Barzilay

AAAI 2008 Cross-Lingual Propagation for Morphological Analysis Benjamin Snyder, Regina Barzilay

AAAI 2008 Discourse Topic and Gestural Form Jacob Eisenstein, Regina Barzilay, Randall Davis

JAIR 2008 Gesture Salience as a Hidden Variable for Coreference Resolution and Keyframe Extraction Jacob Eisenstein, Regina Barzilay, Randall Davis

IJCAI 2007 Database-Text Alignment via Structured Multilabel Classification Benjamin Snyder, Regina Barzilay

AAAI 2007 Turning Lectures into Comic Books Using Linguistically Salient Gestures Jacob Eisenstein, Regina Barzilay, Randall Davis

IJCAI 2005 Automatic Evaluation of Text Coherence: Models and Representations Mirella Lapata, Regina Barzilay

JAIR 2002 Inferring Strategies for Sentence Ordering in Multidocument News Summarization Regina Barzilay, Noemie Elhadad, Kathleen R. McKeown

AAAI 2000 The Rules Behind Roles: Identifying Speaker Role in Radio Broadcasts Regina Barzilay, Michael Collins, Julia Hirschberg, Steve Whittaker

AAAI 1999 Towards Multidocument Summarization by Reformulation: Progress and Prospects Kathleen R. McKeown, Judith Klavans, Vasileios Hatzivassiloglou, Regina Barzilay, Eleazar Eskin

AAAI 1999 Verbalization of High-Level Formal Proofs Amanda M. Holland-Minkley, Regina Barzilay, Robert L. Constable