A New Approach To Expert System Explanations. - Regina Barzilay; Daryl McCullough; Owen Rambow; Jonathan D. DeCristofaro; Tanya Korelsky; Benoit Lavoie (INLG, 1998)

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

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

Information Fusion in the Context of Multi-Document Summarization. - Regina Barzilay; Kathleen R. McKeown; Michael Elhadad (ACL, 1999)

The Rules Behind Roles: Identifying Speaker Role in Radio Broadcasts. - Regina Barzilay; Michael Collins 001; Julia Hirschberg; Steve Whittaker 001 (AAAI/IAAI, 2000)

Extracting Paraphrases from a Parallel Corpus. - Regina Barzilay; Kathleen R. McKeown (ACL, 2001)

Sentence Ordering in Multidocument Summarization. - Regina Barzilay; Noémie Elhadad; Kathleen R. McKeown (HLT, 2001)

Bootstrapping Lexical Choice via Multiple-Sequence Alignment. - Regina Barzilay; Lillian Lee (EMNLP, 2002)

Inferring Strategies for Sentence Ordering in Multidocument News Summarization. - Regina Barzilay; Noemie Elhadad; Kathleen R. McKeown (J. Artif. Intell. Res., 2002)

Sentence Alignment for Monolingual Comparable Corpora. - Regina Barzilay; Noemie Elhadad (EMNLP, 2003)

Learning to Paraphrase: An Unsupervised Approach Using Multiple-Sequence Alignment. - Regina Barzilay; Lillian Lee (HLT-NAACL, 2003)

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 (HLT-NAACL, 2003)

Catching the Drift: Probabilistic Content Models, with Applications to Generation and Summarization. - Regina Barzilay; Lillian Lee (HLT-NAACL, 2004)

Automatic Processing of Spoken Dialogue in the Home Hemodialysis Domain. - Ronilda Lacson; Regina Barzilay (AMIA, 2005)

Automatic Evaluation of Text Coherence: Models and Representations. - Mirella Lapata; Regina Barzilay (IJCAI, 2005)

Collective Content Selection for Concept-to-Text Generation. - Regina Barzilay; Mirella Lapata (HLT/EMNLP, 2005)

Sentence Fusion for Multidocument News Summarization. - Regina Barzilay; Kathleen R. McKeown (Comput. Linguistics, 2005)

Minimum Cut Model for Spoken Lecture Segmentation. - Igor Malioutov; Regina Barzilay (ACL, 2006)

Finding Temporal Order in Discharge Summaries. - Philip Bramsen; Pawan Deshpande; Yoong Keok Lee; Regina Barzilay (AMIA, 2006)

Inducing Temporal Graphs. - Philip Bramsen; Pawan Deshpande; Yoong Keok Lee; Regina Barzilay (EMNLP, 2006)

Aggregation via Set Partitioning for Natural Language Generation. - Regina Barzilay; Mirella Lapata (HLT-NAACL, 2006)

Paraphrasing for Automatic Evaluation. - David Kauchak; Regina Barzilay (HLT-NAACL, 2006)

Automatic analysis of medical dialogue in the home hemodialysis domain: Structure induction and summarization. - Ronilda C. Lacson; Regina Barzilay; William J. Long (J. Biomed. Informatics, 2006)

Turning Lectures into Comic Books Using Linguistically Salient Gestures. - Jacob Eisenstein; Regina Barzilay; Randall Davis (AAAI, 2007)

Generating a Table-of-Contents. - S. R. K. Branavan; Pawan Deshpande; Regina Barzilay (ACL, 2007)

Making Sense of Sound: Unsupervised Topic Segmentation over Acoustic Input. - Igor Malioutov; Alex Park 001; Regina Barzilay; James R. Glass (ACL, 2007)

Incremental Text Structuring with Online Hierarchical Ranking. - Erdong Chen; Benjamin Snyder; Regina Barzilay (EMNLP-CoNLL, 2007)

Database-Text Alignment via Structured Multilabel Classification. - Benjamin Snyder; Regina Barzilay (IJCAI, 2007)

Recent progress in the MIT spoken lecture processing project. - James R. Glass; Timothy J. Hazen; D. Scott Cyphers; Igor Malioutov; David Huynh; Regina Barzilay (INTERSPEECH, 2007)

Randomized Decoding for Selection-and-Ordering Problems. - Pawan Deshpande; Regina Barzilay; David R. Karger (HLT-NAACL, 2007)

Multiple Aspect Ranking Using the Good Grief Algorithm. - Benjamin Snyder; Regina Barzilay (HLT-NAACL, 2007)

Discourse Topic and Gestural Form. - Jacob Eisenstein; Regina Barzilay; Randall Davis (AAAI, 2008)

Cross-lingual Propagation for Morphological Analysis. - Benjamin Snyder; Regina Barzilay (AAAI, 2008)

Gestural Cohesion for Topic Segmentation. - Jacob Eisenstein; Regina Barzilay; Randall Davis (ACL, 2008)

Unsupervised Multilingual Learning for Morphological Segmentation. - Benjamin Snyder; Regina Barzilay (ACL, 2008)

Bayesian Unsupervised Topic Segmentation. - Jacob Eisenstein; Regina Barzilay (EMNLP, 2008)

Unsupervised Multilingual Learning for POS Tagging. - Benjamin Snyder; Tahira Naseem; Jacob Eisenstein; Regina Barzilay (EMNLP, 2008)

Modeling Local Coherence: An Entity-Based Approach. - Regina Barzilay; Mirella Lapata (Comput. Linguistics, 2008)

Gesture Salience as a Hidden Variable for Coreference Resolution and Keyframe Extraction. - Jacob Eisenstein; Regina Barzilay; Randall Davis (J. Artif. Intell. Res., 2008)

Reinforcement Learning for Mapping Instructions to Actions. - S. R. K. Branavan; Harr Chen; Luke Zettlemoyer; Regina Barzilay (ACL/IJCNLP, 2009)

Automatically Generating Wikipedia Articles: A Structure-Aware Approach. - Christina Sauper; Regina Barzilay (ACL/IJCNLP, 2009)

Unsupervised Multilingual Grammar Induction. - Benjamin Snyder; Tahira Naseem; Regina Barzilay (ACL/IJCNLP, 2009)

Probabilistic Approaches for Modeling Text Structure and their Application to Text-to-Text Generation (Invited Talk). - Regina Barzilay (ENLG, 2009)

WikiDo. - Nate Kushman; Micah Z. Brodsky; S. R. K. Branavan; Dina Katabi; Regina Barzilay; Martin C. Rinard (HotNets, 2009)

Global Models of Document Structure using Latent Permutations. - Harr Chen; S. R. K. Branavan; Regina Barzilay; David R. Karger (HLT-NAACL, 2009)

Adding More Languages Improves Unsupervised Multilingual Part-of-Speech Tagging: a Bayesian Non-Parametric Approach. - Benjamin Snyder; Tahira Naseem; Jacob Eisenstein; Regina Barzilay (HLT-NAACL, 2009)

Learning Document-Level Semantic Properties from Free-Text Annotations. - S. R. K. Branavan; Harr Chen; Jacob Eisenstein; Regina Barzilay (J. Artif. Intell. Res., 2009)

Content Modeling Using Latent Permutations. - Harr Chen; S. R. K. Branavan; Regina Barzilay; David R. Karger (J. Artif. Intell. Res., 2009)

Multilingual Part-of-Speech Tagging: Two Unsupervised Approaches. - Tahira Naseem; Benjamin Snyder; Jacob Eisenstein; Regina Barzilay (J. Artif. Intell. Res., 2009)

Reading between the Lines: Learning to Map High-Level Instructions to Commands. - S. R. K. Branavan; Luke Zettlemoyer; Regina Barzilay (ACL, 2010)

A Statistical Model for Lost Language Decipherment. - Benjamin Snyder; Regina Barzilay; Kevin Knight (ACL, 2010)

Probabilistic Approaches for Modeling Text Structure and Their Application to Text-to-Text Generation. - Regina Barzilay (Empirical Methods in Natural Language Generation, 2010)

Simple Type-Level Unsupervised POS Tagging. - Yoong Keok Lee; Aria Haghighi; Regina Barzilay (EMNLP, 2010)

Using Universal Linguistic Knowledge to Guide Grammar Induction. - Tahira Naseem; Harr Chen; Regina Barzilay; Mark Johnson (EMNLP, 2010)

Incorporating Content Structure into Text Analysis Applications. - Christina Sauper; Aria Haghighi; Regina Barzilay (EMNLP, 2010)

Climbing the Tower of Babel: Unsupervised Multilingual Learning. - Benjamin Snyder; Regina Barzilay (ICML, 2010)

Good grief, i can speak it! preliminary experiments in audio restaurant reviews. - Joseph Polifroni; Stephanie Seneff; S. R. K. Branavan; Chao Wang 018; Regina Barzilay (SLT, 2010)

Using Semantic Cues to Learn Syntax. - Tahira Naseem; Regina Barzilay (AAAI, 2011)

Event Discovery in Social Media Feeds. - Edward Benson; Aria Haghighi; Regina Barzilay (ACL, 2011)

In-domain Relation Discovery with Meta-constraints via Posterior Regularization. - Harr Chen; Edward Benson; Tahira Naseem; Regina Barzilay (ACL, 2011)

Content Models with Attitude. - Christina Sauper; Aria Haghighi; Regina Barzilay (ACL, 2011)

Modeling Syntactic Context Improves Morphological Segmentation. - Yoong Keok Lee; Aria Haghighi; Regina Barzilay (CoNLL, 2011)

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

Inferring Strategies for Sentence Ordering in Multidocument News Summarization - Regina Barzilay; Noemie Elhadad (CoRR, 2011)

Learning High-Level Planning from Text. - S. R. K. Branavan; Nate Kushman; Tao Lei 001; Regina Barzilay (ACL (1), 2012)

Selective Sharing for Multilingual Dependency Parsing. - Tahira Naseem; Regina Barzilay; Amir Globerson (ACL (1), 2012)

Unsupervised Morphology Rivals Supervised Morphology for Arabic MT. - David Stallard; Jacob Devlin; Michael Kayser; Yoong Keok Lee; Regina Barzilay (ACL (2), 2012)

Learning to Behave by Reading. - Regina Barzilay (EACL, 2012)

Learning to Map into a Universal POS Tagset. - Yuan Zhang 001; Roi Reichart; Regina Barzilay; Amir Globerson (EMNLP-CoNLL, 2012)

Multi-Event Extraction Guided by Global Constraints. - Roi Reichart; Regina Barzilay (HLT-NAACL, 2012)

Learning to Win by Reading Manuals in a Monte-Carlo Framework. - S. R. K. Branavan; David Silver; Regina Barzilay (J. Artif. Intell. Res., 2012)

From Natural Language Specifications to Program Input Parsers. - Tao Lei 001; Fan Long; Regina Barzilay; Martin C. Rinard (ACL (1), 2013)

Transfer Learning for Constituency-Based Grammars. - Yuan Zhang 001; Regina Barzilay; Amir Globerson (ACL (1), 2013)

Using Semantic Unification to Generate Regular Expressions from Natural Language. - Nate Kushman; Regina Barzilay (HLT-NAACL, 2013)

Automatic Aggregation by Joint Modeling of Aspects and Values. - Christina Sauper; Regina Barzilay (J. Artif. Intell. Res., 2013)

Learning to Automatically Solve Algebra Word Problems. - Nate Kushman; Luke Zettlemoyer; Regina Barzilay; Yoav Artzi (ACL (1), 2014)

Low-Rank Tensors for Scoring Dependency Structures. - Tao Lei 001; Yu Xin; Yuan Zhang 001; Regina Barzilay; Tommi S. Jaakkola (ACL (1), 2014)

Steps to Excellence: Simple Inference with Refined Scoring of Dependency Trees. - Yuan Zhang 001; Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola; Amir Globerson (ACL (1), 2014)

Morphological Segmentation for Keyword Spotting. - Karthik Narasimhan; Damianos G. Karakos; Richard M. Schwartz; Stavros Tsakalidis; Regina Barzilay (EMNLP, 2014)

Greed is Good if Randomized: New Inference for Dependency Parsing. - Yuan Zhang 001; Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola (EMNLP, 2014)

Exploring Compositional Architectures and Word Vector Representations for Prepositional Phrase Attachment. - Yonatan Belinkov; Tao Lei 001; Regina Barzilay; Amir Globerson (Trans. Assoc. Comput. Linguistics, 2014)

Machine Comprehension with Discourse Relations. - Karthik Narasimhan; Regina Barzilay (ACL (1), 2015)

Molding CNNs for text: non-linear, non-consecutive convolutions. - Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola (EMNLP, 2015)

Language Understanding for Text-based Games using Deep Reinforcement Learning. - Karthik Narasimhan; Tejas D. Kulkarni; Regina Barzilay (EMNLP, 2015)

Hierarchical Low-Rank Tensors for Multilingual Transfer Parsing. - Yuan Zhang 001; Regina Barzilay (EMNLP, 2015)

High-Order Low-Rank Tensors for Semantic Role Labeling. - Tao Lei 001; Yuan Zhang 001; Lluís Màrquez i Villodre; Alessandro Moschitti; Regina Barzilay (HLT-NAACL, 2015)

Randomized Greedy Inference for Joint Segmentation, POS Tagging and Dependency Parsing. - Yuan Zhang 001; Chengtao Li; Regina Barzilay; Kareem Darwish (HLT-NAACL, 2015)

Denoising Bodies to Titles: Retrieving Similar Questions with Recurrent Convolutional Models. - Tao Lei 001; Hrishikesh Joshi; Regina Barzilay; Tommi S. Jaakkola; Kateryna Tymoshenko; Alessandro Moschitti; Lluís Màrquez i Villodre (CoRR, 2015)

Erratum: "Exploring Compositional Architectures and Word Vector Representations for Prepositional Phrase Attachment". - Yonatan Belinkov; Tao Lei 001; Regina Barzilay; Amir Globerson (Trans. Assoc. Comput. Linguistics, 2015)

An Unsupervised Method for Uncovering Morphological Chains. - Karthik Narasimhan; Regina Barzilay; Tommi S. Jaakkola (Trans. Assoc. Comput. Linguistics, 2015)

Learning to refine text based recommendations. - Youyang Gu; Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola (EMNLP, 2016)

Rationalizing Neural Predictions. - Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola (EMNLP, 2016)

Neural Generation of Regular Expressions from Natural Language with Minimal Domain Knowledge. - Nicholas Locascio; Karthik Narasimhan; Eduardo DeLeon; Nate Kushman; Regina Barzilay (EMNLP, 2016)

Improving Information Extraction by Acquiring External Evidence with Reinforcement Learning. - Karthik Narasimhan; Adam Yala; Regina Barzilay (EMNLP, 2016)

Semi-supervised Question Retrieval with Gated Convolutions. - Tao Lei 001; Hrishikesh Joshi; Regina Barzilay; Tommi S. Jaakkola; Kateryna Tymoshenko; Alessandro Moschitti; Lluís Màrquez (HLT-NAACL, 2016)

Making Dependency Labeling Simple, Fast and Accurate. - Tianxiao Shen; Tao Lei 001; Regina Barzilay (HLT-NAACL, 2016)

Ten Pairs to Tag - Multilingual POS Tagging via Coarse Mapping between Embeddings. - Yuan Zhang 001; David Gaddy; Regina Barzilay; Tommi S. Jaakkola (HLT-NAACL, 2016)

sk_p: a neural program corrector for MOOCs. - Yewen Pu; Karthik Narasimhan; Armando Solar-Lezama; Regina Barzilay (SPLASH (Companion Volume), 2016)

Deriving Neural Architectures from Sequence and Graph Kernels. - Tao Lei 001; Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (ICML, 2017)

Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network. - Wengong Jin; Connor W. Coley; Regina Barzilay; Tommi S. Jaakkola (NIPS, 2017)

Style Transfer from Non-Parallel Text by Cross-Alignment. - Tianxiao Shen; Tao Lei 001; Regina Barzilay; Tommi S. Jaakkola (NIPS, 2017)

Deep Transfer in Reinforcement Learning by Language Grounding. - Karthik Narasimhan; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2017)

Unsupervised Learning of Morphological Forests. - Jiaming Luo; Karthik Narasimhan; Regina Barzilay (Trans. Assoc. Comput. Linguistics, 2017)

Aspect-augmented Adversarial Networks for Domain Adaptation. - Yuan Zhang 001; Regina Barzilay; Tommi S. Jaakkola (Trans. Assoc. Comput. Linguistics, 2017)

Convolutional Embedding of Attributed Molecular Graphs for Physical Property Prediction. - Connor W. Coley; Regina Barzilay; William H. Green Jr.; Tommi S. Jaakkola; Klavs F. Jensen (J. Chem. Inf. Model., 2017)

Deriving Machine Attention from Human Rationales. - Yujia Bao; Shiyu Chang; Mo Yu; Regina Barzilay (EMNLP, 2018)

Multi-Source Domain Adaptation with Mixture of Experts. - Jiang Guo; Darsh J. Shah; Regina Barzilay (EMNLP, 2018)

Junction Tree Variational Autoencoder for Molecular Graph Generation. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (ICML, 2018)

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 (MAPL@PLDI, 2018)

The Three Pillars of Machine-Based Programming. - Justin Gottschlich; Armando Solar-Lezama; Nesime Tatbul; Michael Carbin; Martin C. Rinard; Regina Barzilay; Saman P. Amarasinghe; Joshua B. Tenenbaum; Tim Mattson (CoRR, 2018)

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization. - Wengong Jin; Kevin Yang; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2018)

Grounding Language for Transfer in Deep Reinforcement Learning. - Karthik Narasimhan; Regina Barzilay; Tommi S. Jaakkola (J. Artif. Intell. Res., 2018)

Representation Learning for Grounded Spatial Reasoning. - Michaela Jänner; Karthik Narasimhan; Regina Barzilay (Trans. Assoc. Comput. Linguistics, 2018)

Neural Decipherment via Minimum-Cost Flow: From Ugaritic to Linear B. - Jiaming Luo; Yuan Cao; Regina Barzilay (ACL (1), 2019)

Working Hard or Hardly Working: Challenges of Integrating Typology into Neural Dependency Parsers. - Adam Fisch; Jiang Guo; Regina Barzilay (EMNLP/IJCNLP (1), 2019)

Towards Debiasing Fact Verification Models. - Tal Schuster; Darsh J. Shah; Yun Jie Serene Yeo; Daniel Filizzola; Enrico Santus; Regina Barzilay (EMNLP/IJCNLP (1), 2019)

Learning Multimodal Graph-to-Graph Translation for Molecule Optimization. - Wengong Jin; Kevin Yang; Regina Barzilay; Tommi S. Jaakkola (ICLR (Poster), 2019)

Inferring Which Medical Treatments Work from Reports of Clinical Trials. - Eric Lehman; Jay DeYoung; Regina Barzilay; Byron C. Wallace (NAACL-HLT (1), 2019)

GraphIE: A Graph-Based Framework for Information Extraction. - Yujie Qian; Enrico Santus; Zhijing Jin 001; Jiang Guo; Regina Barzilay (NAACL-HLT (1), 2019)

Cross-Lingual Alignment of Contextual Word Embeddings, with Applications to Zero-shot Dependency Parsing. - Tal Schuster; Ori Ram; Regina Barzilay; Amir Globerson (NAACL-HLT (1), 2019)

Generative Models for Graph-Based Protein Design. - John Ingraham; Vikas K. Garg 001; Regina Barzilay; Tommi S. Jaakkola (NeurIPS, 2019)

Are Learned Molecular Representations Ready For Prime Time? - Kevin Yang; Kyle Swanson; Wengong Jin; Connor W. Coley; Philipp Eiden; Hua Gao; Angel Guzman-Perez; Timothy Hopper; Brian Kelley; Miriam Mathea; Andrew Palmer; Volker Settels; et al. (CoRR, 2019)

Using Machine Learning and Natural Language Processing to Review and Classify the Medical Literature on Cancer Susceptibility Genes. - Yujia Bao; Zhengyi Deng; Yan Wang; Heeyoon Kim; Victor Diego Armengol; Francisco Acevedo; Nofal Ouardaoui; Cathy Wang; Giovanni Parmigiani; Regina Barzilay; Danielle Braun; Kevin S. Hughes (CoRR, 2019)

Path-Augmented Graph Transformer Network. - Benson Chen; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2019)

Latent Space Secrets of Denoising Text-Autoencoders. - Tianxiao Shen; Jonas Mueller 001; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2019)

Multi-resolution Autoregressive Graph-to-Graph Translation for Molecules. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2019)

Are We Safe Yet? The Limitations of Distributional Features for Fake News Detection. - Tal Schuster; Roei Schuster; Darsh J. Shah; Regina Barzilay (CoRR, 2019)

Learning to Make Generalizable and Diverse Predictions for Retrosynthesis. - Benson Chen; Tianxiao Shen; Tommi S. Jaakkola; Regina Barzilay (CoRR, 2019)

Analyzing Learned Molecular Representations for Property Prediction. - Kevin Yang; Kyle Swanson; Wengong Jin; Connor W. Coley; Philipp Eiden; Hua Gao; Angel Guzman-Perez; Timothy Hopper; Brian Kelley; Miriam Mathea; Andrew Palmer; Volker Settels; et al. (J. Chem. Inf. Model., 2019)

Correction to Analyzing Learned Molecular Representations for Property Prediction. - Kevin Yang; Kyle Swanson; Wengong Jin; Connor W. Coley; Philipp Eiden; Hua Gao; Angel Guzman-Perez; Timothy Hopper; Brian Kelley; Miriam Mathea; Andrew Palmer; Volker Settels; et al. (J. Chem. Inf. Model., 2019)

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 (AAAI, 2020)

CapWAP: Image Captioning with a Purpose. - Adam Fisch; Kenton Lee; Ming-Wei Chang; Jonathan H. Clark; Regina Barzilay (EMNLP (1), 2020)

Blank Language Models. - Tianxiao Shen; Victor Quach; Regina Barzilay; Tommi S. Jaakkola (EMNLP (1), 2020)

Few-shot Text Classification with Distributional Signatures. - Yujia Bao; Menghua Wu; Shiyu Chang; Regina Barzilay (ICLR, 2020)

Hierarchical Generation of Molecular Graphs using Structural Motifs. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (ICML, 2020)

Multi-Objective Molecule Generation using Interpretable Substructures. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (ICML, 2020)

Educating Text Autoencoders: Latent Representation Guidance via Denoising. - Tianxiao Shen; Jonas Mueller 001; Regina Barzilay; Tommi S. Jaakkola (ICML, 2020)

Improving Molecular Design by Stochastic Iterative Target Augmentation. - Kevin Yang; Wengong Jin; Kyle Swanson; Regina Barzilay; Tommi S. Jaakkola (ICML, 2020)

The Limitations of Stylometry for Detecting Machine-Generated Fake News. - Tal Schuster; Roei Schuster; Darsh J. Shah; Regina Barzilay (Comput. Linguistics, 2020)

Composing Molecules with Multiple Property Constraints. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2020)

Adaptive Invariance for Molecule Property Prediction. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2020)

Domain Extrapolation via Regret Minimization. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2020)

Optimal Transport Graph Neural Networks. - Gary Bécigneul; Octavian-Eugen Ganea; Benson Chen; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2020)

Learning Graph Models for Template-Free Retrosynthesis. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (CoRR, 2020)

Improved Conditional Flow Models for Molecule to Image Synthesis. - Karren D. Yang; Samuel Goldman; Wengong Jin; Alex Lu 002; Regina Barzilay; Tommi S. Jaakkola; Caroline Uhler (CoRR, 2020)

Relaxed Conformal Prediction Cascades for Efficient Inference Over Many Labels. - Adam Fisch; Tal Schuster; Tommi S. Jaakkola; Regina Barzilay (CoRR, 2020)

CapWAP: Captioning with a Purpose. - Adam Fisch; Kenton Lee; Ming-Wei Chang; Jonathan H. Clark; Regina Barzilay (CoRR, 2020)

Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2020)

Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. - Lior Hirschfeld; Kyle Swanson; Kevin Yang; Regina Barzilay; Connor W. Coley (J. Chem. Inf. Model., 2020)

Nutri-bullets: Summarizing Health Studies by Composing Segments. - Darsh J. Shah; Lili Yu; Tao Lei 001; Regina Barzilay (AAAI, 2021)

COVID-19 classification using thermal images: thermal images capability for identifying COVID-19 using traditional machine learning classifiers. - Martha Rebeca Canales-Fiscal; Rocío Ortiz López; Regina Barzilay; Victor Treviño; Servando Cardona-Huerta; Luis Javier Ramírez-Treviño; Adam Yala; José G. Tamez-Peña (BCB, 2021)

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 (CVPR, 2021)

Consistent Accelerated Inference via Confident Adaptive Transformers. - Tal Schuster; Adam Fisch; Tommi S. Jaakkola; Regina Barzilay (EMNLP (1), 2021)

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

Predict then Interpolate: A Simple Algorithm to Learn Stable Classifiers. - Yujia Bao; Shiyu Chang; Regina Barzilay (ICML, 2021)

Few-Shot Conformal Prediction with Auxiliary Tasks. - Adam Fisch; Tal Schuster; Tommi S. Jaakkola; Regina Barzilay (ICML, 2021)

Get Your Vitamin C! Robust Fact Verification with Contrastive Evidence. - Tal Schuster; Adam Fisch; Regina Barzilay (NAACL-HLT, 2021)

Nutri-bullets Hybrid: Consensual Multi-document Summarization. - Darsh J. Shah; Lili Yu; Tao Lei 001; Regina Barzilay (NAACL-HLT, 2021)

GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. - Octavian Ganea; Lagnajit Pattanaik; Connor W. Coley; Regina Barzilay; Klavs F. Jensen; William H. Green Jr.; Tommi S. Jaakkola (NeurIPS, 2021)

Learning Graph Models for Retrosynthesis Prediction. - Vignesh Ram Somnath; Charlotte Bunne; Connor W. Coley; Andreas Krause 001; Regina Barzilay (NeurIPS, 2021)

Nutribullets Hybrid: Multi-document Health Summarization. - Darsh J. Shah; Lili Yu; Tao Lei 001; Regina Barzilay (CoRR, 2021)

Generating Related Work. - Darsh J. Shah; Regina Barzilay (CoRR, 2021)

NeuraCrypt: Hiding Private Health Data via Random Neural Networks for Public Training. - Adam Yala; Homa Esfahanizadeh; Rafael G. L. D'Oliveira; Ken R. Duffy; Manya Ghobadi; Tommi S. Jaakkola; Vinod Vaikuntanathan; Regina Barzilay; Muriel Médard (CoRR, 2021)

Fragment-based Sequential Translation for Molecular Optimization. - Benson Chen; Xiang Fu 005; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2021)

Correction to Automated Chemical Reaction Extraction from Scientific Literature. - Jiang Guo; A. Santiago Ibanez-Lopez; Hanyu Gao; Victor Quach; Connor W. Coley; Klavs F. Jensen; Regina Barzilay (J. Chem. Inf. Model., 2021)

Deep learning identifies synergistic drug combinations for treating COVID-19. - Wengong Jin; Jonathan M. Stokes; Richard T. Eastman; Zina Itkin; Alexey V. Zakharov; James J. Collins; Tommi S. Jaakkola; Regina Barzilay (Proc. Natl. Acad. Sci. USA, 2021)

Deciphering Undersegmented Ancient Scripts Using Phonetic Prior. - Jiaming Luo; Frederik Hartmann; Enrico Santus; Yuan Cao; Regina Barzilay (Trans. Assoc. Comput. Linguistics, 2021)

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 001 (ICLR, 2022)

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

Crystal Diffusion Variational Autoencoder for Periodic Material Generation. - Tian Xie 002; Xiang Fu 005; Octavian-Eugen Ganea; Regina Barzilay; Tommi S. Jaakkola (ICLR, 2022)

Learning Stable Classifiers by Transferring Unstable Features. - Yujia Bao; Shiyu Chang; Regina Barzilay (ICML, 2022)

Conformal Prediction Sets with Limited False Positives. - Adam Fisch; Tal Schuster; Tommi S. Jaakkola; Regina Barzilay (ICML, 2022)

Antibody-Antigen Docking and Design via Hierarchical Structure Refinement. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (ICML, 2022)

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

Torsional Diffusion for Molecular Conformer Generation. - Bowen Jing; Gabriele Corso; Jeffrey Chang; Regina Barzilay; Tommi S. Jaakkola (NeurIPS, 2022)

Syfer: Neural Obfuscation for Private Data Release. - Adam Yala; Victor Quach; Homa Esfahanizadeh; Rafael G. L. D'Oliveira; Ken R. Duffy; Muriel Médard; Tommi S. Jaakkola; Regina Barzilay (CoRR, 2022)

Learning to Split for Automatic Bias Detection. - Yujia Bao; Regina Barzilay (CoRR, 2022)

Robust Molecular Image Recognition: A Graph Generation Approach. - Yujie Qian; Zhengkai Tu; Jiang Guo; Connor W. Coley; Regina Barzilay (CoRR, 2022)

Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement. - Wengong Jin; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2022)

Automated Chemical Reaction Extraction from Scientific Literature. - Jiang Guo; A. Santiago Ibanez-Lopez; Hanyu Gao; Victor Quach; Connor W. Coley; Klavs F. Jensen; Regina Barzilay (J. Chem. Inf. Model., 2022)

Calibrated Selective Classification. - Adam Fisch; Tommi S. Jaakkola; Regina Barzilay (Trans. Mach. Learn. Res., 2022)

Predictive Chemistry Augmented with Text Retrieval. - Yujie Qian; Zhening Li; Zhengkai Tu; Connor W. Coley; Regina Barzilay (EMNLP, 2023)

InfoShape: Task-Based Neural Data Shaping via Mutual Information. - Homa Esfahanizadeh; William Wu; Manya Ghobadi; Regina Barzilay; Muriel Médard (ICASSP, 2023)

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

Efficiently Controlling Multiple Risks with Pareto Testing. - Bracha Laufer-Goldshtein; Adam Fisch; 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 001; Tamara Broderick; Regina Barzilay; Tommi S. Jaakkola (ICLR, 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 S. Jaakkola (ICML, 2023)

PEOPL: Characterizing Privately Encoded Open Datasets with Public Labels. - Homa Esfahanizadeh; Adam Yala; Rafael G. L. D'Oliveira; Andrea J. D. Jaba; Victor Quach; Ken R. Duffy; Tommi S. Jaakkola; Vinod Vaikuntanathan; Manya Ghobadi; Regina Barzilay; Muriel Médard (CoRR, 2023)

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

Optimizing protein fitness using Gibbs sampling with Graph-based Smoothing. - Andrew Kirjner; Jason Yim; Raman Samusevich; Tommi S. Jaakkola; Regina Barzilay; Ila Fiete (CoRR, 2023)

Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design. - Hannes Stärk; Bowen Jing; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2023)

MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. - Yujie Qian; Jiang Guo; Zhengkai Tu; Zhening Li; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2023)

RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. - Yujie Qian; Jiang Guo; Zhengkai Tu; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2023)

Deep Confident Steps to New Pockets: Strategies for Docking Generalization. - Gabriele Corso; Arthur Deng; Nicholas Polizzi; Regina Barzilay; Tommi S. Jaakkola (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 (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)

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

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

Harmonic Self-Conditioned Flow Matching for joint Multi-Ligand Docking and Binding Site Design. - Hannes Stärk; Bowen Jing; Regina Barzilay; Tommi S. Jaakkola (ICML, 2024)

Dirichlet Flow Matching with Applications to DNA Sequence Design. - Hannes Stärk; Bowen Jing; Chenyu Wang 003; Gabriele Corso; Bonnie Berger; Regina Barzilay; Tommi S. Jaakkola (ICML, 2024)

Deep Confident Steps to New Pockets: Strategies for Docking Generalization. - Gabriele Corso; Arthur Deng; Benjamin Fry; Nicholas Polizzi; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2024)

Predicting perturbation targets with causal differential networks. - Menghua Wu; Umesh Padia; Sean H. Murphy; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2024)

OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. - Vincent Fan; Yujie Qian; Alex Wang; Amber Wang; Connor W. Coley; Regina Barzilay (J. Chem. Inf. Model., 2024)

Risk-Controlling Model Selection via Guided Bayesian Optimization. - Bracha Laufer-Goldshtein; Adam Fisch; Regina Barzilay; Tommi S. Jaakkola (Trans. Mach. Learn. Res., 2024)

Improved motif-scaffolding with SE(3) flow matching. - Jason Yim; Andrew Campbell; Emile Mathieu; Andrew Y. K. Foong; Michael Gastegger; José Jiménez-Luna; Sarah Lewis; Victor Garcia Satorras; Bastiaan S. Veeling; Frank Noé; Regina Barzilay; Tommi S. Jaakkola (Trans. Mach. Learn. Res., 2024)

Composing Unbalanced Flows for Flexible Docking and Relaxation. - Gabriele Corso; Vignesh Ram Somnath; Noah Getz; Regina Barzilay; Tommi S. Jaakkola; Andreas Krause 001 (ICLR, 2025)

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. - Xuan Zhang; Limei Wang; Jacob Helwig; Youzhi Luo; Cong Fu 003; Yaochen Xie; Meng Liu 015; Yuchao Lin; Zhao Xu 005; Keqiang Yan; Keir Adams; Maurice Weiler; et al. (Found. Trends Mach. Learn., 2025)

Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens. - Jeremy Wohlwend; Anusha Nathan; Nitan Shalon; Charles R. Crain; Rhoda Tano-Menka; Benjamin Goldberg 004; Emma Richards; Gaurav D. Gaiha; Regina Barzilay (Nat. Mac. Intell., 2025)

Predicting sub-population specific viral evolution. - Wenxian Shi; Menghua Wu; Regina Barzilay (Trans. Mach. Learn. Res., 2025)

MiniFold: Simple, Fast, and Accurate Protein Structure Prediction. - Jeremy Wohlwend; Mateo Reveiz; Matt McPartlon; Axel Feldmann; Wengong Jin; Regina Barzilay (Trans. Mach. Learn. Res., 2025)

Sample, estimate, aggregate: A recipe for causal discovery foundation models. - Menghua Wu; Yujia Bao; Regina Barzilay; Tommi S. Jaakkola (Trans. Mach. Learn. Res., 2025)

ProxelGen: Generating Proteins as 3D Densities. - Felix Faltings; Hannes Stärk; Regina Barzilay; Tommi S. Jaakkola (CoRR, 2025)