| 2025 | ICLR | Composing Unbalanced Flows for Flexible Docking and Relaxation. | Gabriele Corso, Vignesh Ram Somnath, Noah Getz, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause |
| 2025 | ICML | Identifying biological perturbation targets through causal differential networks. | Menghua Wu, Umesh Padia, Sean H. Murphy, Regina Barzilay, Tommi S. Jaakkola |
| 2024 | ICLR | Deep Confident Steps to New Pockets: Strategies for Docking Generalization. | Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi S. Jaakkola |
| 2024 | ICLR | Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models. | Gabriele Corso, Yilun Xu, Valentin De Bortoli, Regina Barzilay, Tommi S. Jaakkola |
| 2024 | ICLR | Improving protein optimization with smoothed fitness landscapes. | Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R. Fiete |
| 2024 | ICLR | Conformal Language Modeling. | Victor Quach, Adam Fisch, Tal Schuster, Adam Yala, Jae Ho Sohn, Tommi S. Jaakkola, Regina Barzilay |
| 2024 | ICML | Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design. | Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola |
| 2024 | ICML | CLIPZyme: Reaction-Conditioned Virtual Screening of Enzymes. | Peter Mikhael, Itamar Chinn, Regina Barzilay |
| 2024 | ICML | Harmonic Self-Conditioned Flow Matching for joint Multi-Ligand Docking and Binding Site Design. | Hannes Strk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola |
| 2024 | ICML | Dirichlet Flow Matching with Applications to DNA Sequence Design. | Hannes Strk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola |
| 2023 | EMNLP | Predictive Chemistry Augmented with Text Retrieval. | Yujie Qian, Zhening Li, Zhengkai Tu, Connor W. Coley, Regina Barzilay |
| 2023 | ICASSP | InfoShape: Task-Based Neural Data Shaping via Mutual Information. | Homa Esfahanizadeh, William Wu, Manya Ghobadi, Regina Barzilay, Muriel Mdard |
| 2023 | ICLR | DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. | Gabriele Corso, Hannes Strk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola |
| 2023 | ICLR | Efficiently Controlling Multiple Risks with Pareto Testing. | Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi S. Jaakkola |
| 2023 | ICLR | 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 |
| 2023 | ICML | 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 S. Jaakkola |
| 2022 | ICLR | 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 |
| 2022 | ICLR | Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design. | Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola |
| 2022 | ICLR | Crystal Diffusion Variational Autoencoder for Periodic Material Generation. | Tian Xie, Xiang Fu, Octavian-Eugen Ganea, Regina Barzilay, Tommi S. Jaakkola |
| 2022 | ICML | Learning Stable Classifiers by Transferring Unstable Features. | Yujia Bao, Shiyu Chang, Regina Barzilay |
| 2022 | ICML | Conformal Prediction Sets with Limited False Positives. | Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay |
| 2022 | ICML | Antibody-Antigen Docking and Design via Hierarchical Structure Refinement. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2022 | ICML | EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction. | Hannes Strk, Octavian Ganea, Lagnajit Pattanaik, Regina Barzilay, Tommi S. Jaakkola |
| 2021 | AAAI | Nutri-bullets: Summarizing Health Studies by Composing Segments. | Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay |
| 2021 | CVPR | Mol2Image: Improved Conditional Flow Models for Molecule to Image Synthesis. | Karren D. Yang, Samuel Goldman, Wengong Jin, Alex X. Lu, Regina Barzilay, Tommi S. Jaakkola, Caroline Uhler |
| 2021 | EMNLP | Consistent Accelerated Inference via Confident Adaptive Transformers. | Tal Schuster, Adam Fisch, Tommi S. Jaakkola, Regina Barzilay |
| 2021 | ICLR | Efficient Conformal Prediction via Cascaded Inference with Expanded Admission. | Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay |
| 2021 | ICML | Predict then Interpolate: A Simple Algorithm to Learn Stable Classifiers. | Yujia Bao, Shiyu Chang, Regina Barzilay |
| 2021 | ICML | Few-Shot Conformal Prediction with Auxiliary Tasks. | Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay |
| 2021 | NAACL | Get Your Vitamin C! Robust Fact Verification with Contrastive Evidence. | Tal Schuster, Adam Fisch, Regina Barzilay |
| 2021 | NAACL | Nutri-bullets Hybrid: Consensual Multi-document Summarization. | Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay |
| 2020 | AAAI | Automatic Fact-Guided Sentence Modification. | Darsh J. Shah, Tal Schuster, Regina Barzilay |
| 2020 | AAAI | Capturing Greater Context for Question Generation. | Luu Anh Tuan, Darsh J. Shah, Regina Barzilay |
| 2020 | EMNLP | CapWAP: Image Captioning with a Purpose. | Adam Fisch, Kenton Lee, Ming-Wei Chang, Jonathan H. Clark, Regina Barzilay |
| 2020 | EMNLP | Blank Language Models. | Tianxiao Shen, Victor Quach, Regina Barzilay, Tommi S. Jaakkola |
| 2020 | ICLR | Few-shot Text Classification with Distributional Signatures. | Yujia Bao, Menghua Wu, Shiyu Chang, Regina Barzilay |
| 2020 | ICML | Hierarchical Generation of Molecular Graphs using Structural Motifs. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2020 | ICML | Multi-Objective Molecule Generation using Interpretable Substructures. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2020 | ICML | Educating Text Autoencoders: Latent Representation Guidance via Denoising. | Tianxiao Shen, Jonas Mueller, Regina Barzilay, Tommi S. Jaakkola |
| 2020 | ICML | Improving Molecular Design by Stochastic Iterative Target Augmentation. | Kevin Yang, Wengong Jin, Kyle Swanson, Regina Barzilay, Tommi S. Jaakkola |
| 2019 | ACL | Neural Decipherment via Minimum-Cost Flow: From Ugaritic to Linear B. | Jiaming Luo, Yuan Cao, Regina Barzilay |
| 2019 | EMNLP | Working Hard or Hardly Working: Challenges of Integrating Typology into Neural Dependency Parsers. | Adam Fisch, Jiang Guo, Regina Barzilay |
| 2019 | EMNLP | Towards Debiasing Fact Verification Models. | Tal Schuster, Darsh J. Shah, Yun Jie Serene Yeo, Daniel Filizzola, Enrico Santus, Regina Barzilay |
| 2019 | ICLR | Generative Models for Graph-Based Protein Design. | John Ingraham, Vikas K. Garg, Regina Barzilay, Tommi S. Jaakkola |
| 2019 | ICLR | Learning Multimodal Graph-to-Graph Translation for Molecule Optimization. | Wengong Jin, Kevin Yang, Regina Barzilay, Tommi S. Jaakkola |
| 2019 | NAACL | Inferring Which Medical Treatments Work from Reports of Clinical Trials. | Eric P. Lehman, Jay DeYoung, Regina Barzilay, Byron C. Wallace |
| 2019 | NAACL | GraphIE: A Graph-Based Framework for Information Extraction. | Yujie Qian, Enrico Santus, Zhijing Jin, Jiang Guo, Regina Barzilay |
| 2019 | NAACL | Cross-Lingual Alignment of Contextual Word Embeddings, with Applications to Zero-shot Dependency Parsing. | Tal Schuster, Ori Ram, Regina Barzilay, Amir Globerson |
| 2018 | EMNLP | Deriving Machine Attention from Human Rationales. | Yujia Bao, Shiyu Chang, Mo Yu, Regina Barzilay |
| 2018 | EMNLP | Multi-Source Domain Adaptation with Mixture of Experts. | Jiang Guo, Darsh J. Shah, Regina Barzilay |
| 2018 | ICML | Junction Tree Variational Autoencoder for Molecular Graph Generation. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2018 | PLDI | The three pillars of machine programming. | Justin Gottschlich, Armando Solar-Lezama, Nesime Tatbul, Michael Carbin, Martin C. Rinard, Regina Barzilay, Saman P. Amarasinghe, Joshua B. Tenenbaum, Tim Mattson |
| 2017 | ICML | Deriving Neural Architectures from Sequence and Graph Kernels. | Tao Lei, Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2016 | EMNLP | Learning to refine text based recommendations. | Youyang Gu, Tao Lei, Regina Barzilay, Tommi S. Jaakkola |
| 2016 | EMNLP | Rationalizing Neural Predictions. | Tao Lei, Regina Barzilay, Tommi S. Jaakkola |
| 2016 | EMNLP | Neural Generation of Regular Expressions from Natural Language with Minimal Domain Knowledge. | Nicholas Locascio, Karthik Narasimhan, Eduardo DeLeon, Nate Kushman, Regina Barzilay |
| 2016 | EMNLP | Improving Information Extraction by Acquiring External Evidence with Reinforcement Learning. | Karthik Narasimhan, Adam Yala, Regina Barzilay |
| 2016 | NAACL | Semi-supervised Question Retrieval with Gated Convolutions. | Tao Lei, Hrishikesh Joshi, Regina Barzilay, Tommi S. Jaakkola, Kateryna Tymoshenko, Alessandro Moschitti, Llus Mrquez |
| 2016 | NAACL | Making Dependency Labeling Simple, Fast and Accurate. | Tianxiao Shen, Tao Lei, Regina Barzilay |
| 2016 | NAACL | Ten Pairs to Tag - Multilingual POS Tagging via Coarse Mapping between Embeddings. | Yuan Zhang, David Gaddy, Regina Barzilay, Tommi S. Jaakkola |
| 2016 | OOPSLA | sk_p: a neural program corrector for MOOCs. | Yewen Pu, Karthik Narasimhan, Armando Solar-Lezama, Regina Barzilay |
| 2015 | ACL | Machine Comprehension with Discourse Relations. | Karthik Narasimhan, Regina Barzilay |
| 2015 | EMNLP | Molding CNNs for text: non-linear, non-consecutive convolutions. | Tao Lei, Regina Barzilay, Tommi S. Jaakkola |
| 2015 | EMNLP | Language Understanding for Text-based Games using Deep Reinforcement Learning. | Karthik Narasimhan, Tejas D. Kulkarni, Regina Barzilay |
| 2015 | EMNLP | Hierarchical Low-Rank Tensors for Multilingual Transfer Parsing. | Yuan Zhang, Regina Barzilay |
| 2015 | NAACL | High-Order Low-Rank Tensors for Semantic Role Labeling. | Tao Lei, Yuan Zhang, Llus Mrquez i Villodre, Alessandro Moschitti, Regina Barzilay |
| 2015 | NAACL | Randomized Greedy Inference for Joint Segmentation, POS Tagging and Dependency Parsing. | Yuan Zhang, Chengtao Li, Regina Barzilay, Kareem Darwish |
| 2014 | ACL | Learning to Automatically Solve Algebra Word Problems. | Nate Kushman, Luke Zettlemoyer, Regina Barzilay, Yoav Artzi |
| 2014 | ACL | Low-Rank Tensors for Scoring Dependency Structures. | Tao Lei, Yu Xin, Yuan Zhang, Regina Barzilay, Tommi S. Jaakkola |
| 2014 | ACL | Steps to Excellence: Simple Inference with Refined Scoring of Dependency Trees. | Yuan Zhang, Tao Lei, Regina Barzilay, Tommi S. Jaakkola, Amir Globerson |
| 2014 | EMNLP | Morphological Segmentation for Keyword Spotting. | Karthik Narasimhan, Damianos Karakos, Richard M. Schwartz, Stavros Tsakalidis, Regina Barzilay |
| 2014 | EMNLP | Greed is Good if Randomized: New Inference for Dependency Parsing. | Yuan Zhang, Tao Lei, Regina Barzilay, Tommi S. Jaakkola |
| 2013 | ACL | From Natural Language Specifications to Program Input Parsers. | Tao Lei, Fan Long, Regina Barzilay, Martin C. Rinard |
| 2013 | ACL | Transfer Learning for Constituency-Based Grammars. | Yuan Zhang, Regina Barzilay, Amir Globerson |
| 2013 | NAACL | Using Semantic Unification to Generate Regular Expressions from Natural Language. | Nate Kushman, Regina Barzilay |
| 2012 | ACL | Learning High-Level Planning from Text. | S. R. K. Branavan, Nate Kushman, Tao Lei, Regina Barzilay |
| 2012 | ACL | Selective Sharing for Multilingual Dependency Parsing. | Tahira Naseem, Regina Barzilay, Amir Globerson |
| 2012 | ACL | Unsupervised Morphology Rivals Supervised Morphology for Arabic MT. | David Stallard, Jacob Devlin, Michael Kayser, Yoong Keok Lee, Regina Barzilay |
| 2012 | EACL | Learning to Behave by Reading. | Regina Barzilay |
| 2012 | EMNLP | Learning to Map into a Universal POS Tagset. | Yuan Zhang, Roi Reichart, Regina Barzilay, Amir Globerson |
| 2012 | NAACL | Multi-Event Extraction Guided by Global Constraints. | Roi Reichart, Regina Barzilay |
| 2011 | AAAI | Using Semantic Cues to Learn Syntax. | Tahira Naseem, Regina Barzilay |
| 2011 | ACL | Event Discovery in Social Media Feeds. | Edward Benson, Aria Haghighi, Regina Barzilay |
| 2011 | ACL | Learning to Win by Reading Manuals in a Monte-Carlo Framework. | S. R. K. Branavan, David Silver, Regina Barzilay |
| 2011 | ACL | In-domain Relation Discovery with Meta-constraints via Posterior Regularization. | Harr Chen, Edward Benson, Tahira Naseem, Regina Barzilay |
| 2011 | ACL | Content Models with Attitude. | Christina Sauper, Aria Haghighi, Regina Barzilay |
| 2011 | CoNLL | Modeling Syntactic Context Improves Morphological Segmentation. | Yoong Keok Lee, Aria Haghighi, Regina Barzilay |
| 2011 | IJCAI | Non-Linear Monte-Carlo Search in Civilization II. | S. R. K. Branavan, David Silver, Regina Barzilay |
| 2010 | ACL | Reading between the Lines: Learning to Map High-Level Instructions to Commands. | S. R. K. Branavan, Luke Zettlemoyer, Regina Barzilay |
| 2010 | ACL | A Statistical Model for Lost Language Decipherment. | Benjamin Snyder, Regina Barzilay, Kevin Knight |
| 2010 | EACL | Probabilistic Approaches for Modeling Text Structure and Their Application to Text-to-Text Generation. | Regina Barzilay |
| 2010 | EMNLP | Simple Type-Level Unsupervised POS Tagging. | Yoong Keok Lee, Aria Haghighi, Regina Barzilay |
| 2010 | EMNLP | Using Universal Linguistic Knowledge to Guide Grammar Induction. | Tahira Naseem, Harr Chen, Regina Barzilay, Mark Johnson |
| 2010 | EMNLP | Incorporating Content Structure into Text Analysis Applications. | Christina Sauper, Aria Haghighi, Regina Barzilay |
| 2010 | ICML | Climbing the Tower of Babel: Unsupervised Multilingual Learning. | Benjamin Snyder, Regina Barzilay |
| 2009 | ACL | Reinforcement Learning for Mapping Instructions to Actions. | S. R. K. Branavan, Harr Chen, Luke Zettlemoyer, Regina Barzilay |
| 2009 | ACL | Automatically Generating Wikipedia Articles: A Structure-Aware Approach. | Christina Sauper, Regina Barzilay |
| 2009 | ACL | Unsupervised Multilingual Grammar Induction. | Benjamin Snyder, Tahira Naseem, Regina Barzilay |
| 2009 | HOTNETS | WikiDo. | Nate Kushman, Micah Z. Brodsky, S. R. K. Branavan, Dina Katabi, Regina Barzilay, Martin C. Rinard |
| 2009 | NAACL | Global Models of Document Structure using Latent Permutations. | Harr Chen, S. R. K. Branavan, Regina Barzilay, David R. Karger |
| 2009 | NAACL | Adding More Languages Improves Unsupervised Multilingual Part-of-Speech Tagging: a Bayesian Non-Parametric Approach. | Benjamin Snyder, Tahira Naseem, Jacob Eisenstein, Regina Barzilay |
| 2008 | AAAI | Discourse Topic and Gestural Form. | Jacob Eisenstein, Regina Barzilay, Randall Davis |
| 2008 | AAAI | Cross-lingual Propagation for Morphological Analysis. | Benjamin Snyder, Regina Barzilay |
| 2008 | ACL | Learning Document-Level Semantic Properties from Free-Text Annotations. | S. R. K. Branavan, Harr Chen, Jacob Eisenstein, Regina Barzilay |
| 2008 | ACL | Gestural Cohesion for Topic Segmentation. | Jacob Eisenstein, Regina Barzilay, Randall Davis |
| 2008 | ACL | Unsupervised Multilingual Learning for Morphological Segmentation. | Benjamin Snyder, Regina Barzilay |
| 2008 | EMNLP | Bayesian Unsupervised Topic Segmentation. | Jacob Eisenstein, Regina Barzilay |
| 2008 | EMNLP | Unsupervised Multilingual Learning for POS Tagging. | Benjamin Snyder, Tahira Naseem, Jacob Eisenstein, Regina Barzilay |
| 2007 | AAAI | Turning Lectures into Comic Books Using Linguistically Salient Gestures. | Jacob Eisenstein, Regina Barzilay, Randall Davis |
| 2007 | ACL | Generating a Table-of-Contents. | S. R. K. Branavan, Pawan Deshpande, Regina Barzilay |
| 2007 | ACL | Making Sense of Sound: Unsupervised Topic Segmentation over Acoustic Input. | Igor Malioutov, Alex Park, Regina Barzilay, James R. Glass |
| 2007 | EMNLP | Incremental Text Structuring with Online Hierarchical Ranking. | Erdong Chen, Benjamin Snyder, Regina Barzilay |
| 2007 | IJCAI | Database-Text Alignment via Structured Multilabel Classification. | Benjamin Snyder, Regina Barzilay |
| 2007 | Interspeech | Recent progress in the MIT spoken lecture processing project. | James R. Glass, Timothy J. Hazen, D. Scott Cyphers, Igor Malioutov, David Huynh, Regina Barzilay |
| 2007 | NAACL | Randomized Decoding for Selection-and-Ordering Problems. | Pawan Deshpande, Regina Barzilay, David R. Karger |
| 2007 | NAACL | Multiple Aspect Ranking Using the Good Grief Algorithm. | Benjamin Snyder, Regina Barzilay |
| 2006 | ACL | Minimum Cut Model for Spoken Lecture Segmentation. | Igor Malioutov, Regina Barzilay |
| 2006 | AMIA | Finding Temporal Order in Discharge Summaries. | Philip Bramsen, Pawan Deshpande, Yoong Keok Lee, Regina Barzilay |
| 2006 | EMNLP | Inducing Temporal Graphs. | Philip Bramsen, Pawan Deshpande, Yoong Keok Lee, Regina Barzilay |
| 2006 | NAACL | Aggregation via Set Partitioning for Natural Language Generation. | Regina Barzilay, Mirella Lapata |
| 2006 | NAACL | Paraphrasing for Automatic Evaluation. | David Kauchak, Regina Barzilay |
| 2005 | ACL | Modeling Local Coherence: An Entity-Based Approach. | Regina Barzilay, Mirella Lapata |
| 2005 | AMIA | Automatic Processing of Spoken Dialogue in the Home Hemodialysis Domain. | Ronilda Lacson, Regina Barzilay |
| 2005 | IJCAI | Automatic Evaluation of Text Coherence: Models and Representations. | Mirella Lapata, Regina Barzilay |
| 2005 | NAACL | Collective Content Selection for Concept-to-Text Generation. | Regina Barzilay, Mirella Lapata |
| 2004 | NAACL | Catching the Drift: Probabilistic Content Models, with Applications to Generation and Summarization. | Regina Barzilay, Lillian Lee |
| 2003 | EMNLP | Sentence Alignment for Monolingual Comparable Corpora. | Regina Barzilay, Noemie Elhadad |
| 2003 | NAACL | Learning to Paraphrase: An Unsupervised Approach Using Multiple-Sequence Alignment. | Regina Barzilay, Lillian Lee |
| 2003 | NAACL | Columbia's Newsblaster: New Features and Future Directions. | Kathleen R. McKeown, Regina Barzilay, John Chen, David K. Elson, David Kirk Evans, Judith Klavans, Ani Nenkova, Barry Schiffman, Sergey Sigelman |
| 2002 | EMNLP | Bootstrapping Lexical Choice via Multiple-Sequence Alignment. | Regina Barzilay, Lillian Lee |
| 2001 | ACL | Extracting Paraphrases from a Parallel Corpus. | Regina Barzilay, Kathleen R. McKeown |
| 2001 | NAACL | Sentence Ordering in Multidocument Summarization. | Regina Barzilay, Nomie Elhadad, Kathleen R. McKeown |
| 2000 | AAAI | The Rules Behind Roles: Identifying Speaker Role in Radio Broadcasts. | Regina Barzilay, Michael Collins, Julia Hirschberg, Steve Whittaker |
| 1999 | AAAI | Verbalization of High-Level Formal Proofs. | Amanda M. Holland-Minkley, Regina Barzilay, Robert L. Constable |
| 1999 | AAAI | Towards Multidocument Summarization by Reformulation: Progress and Prospects. | Kathleen R. McKeown, Judith Klavans, Vasileios Hatzivassiloglou, Regina Barzilay, Eleazar Eskin |
| 1999 | ACL | Information Fusion in the Context of Multi-Document Summarization. | Regina Barzilay, Kathleen R. McKeown, Michael Elhadad |
| 1998 | INLG | A New Approach To Expert System Explanations. | Regina Barzilay, Daryl McCullough, Owen Rambow, Jonathan D. DeCristofaro, Tanya Korelsky, Benoit Lavoie |