Regina Barzilay

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 169

Top Venues

CoRR

ICML

ICLR

EMNLP

Publications

Andrew Kirjner, Jason Yim, Raman Samusevich, Shahar Bracha, Tommi S. Jaakkola, Regina Barzilay, Ila R. Fiete
Improving protein optimization with smoothed fitness landscapes. ICLR (2024)
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
Improved motif-scaffolding with SE(3) flow matching. Trans. Mach. Learn. Res. 2024 (2024)
Gabriele Corso, Arthur Deng, Nicholas Polizzi, Regina Barzilay, Tommi S. Jaakkola
Deep Confident Steps to New Pockets: Strategies for Docking Generalization. ICLR (2024)
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
Improved motif-scaffolding with SE(3) flow matching. CoRR (2024)
Victor Quach, Adam Fisch, Tal Schuster, Adam Yala, Jae Ho Sohn, Tommi S. Jaakkola, Regina Barzilay
Conformal Language Modeling. ICLR (2024)
Menghua Wu, Yujia Bao, Regina Barzilay, Tommi S. Jaakkola
Sample, estimate, aggregate: A recipe for causal discovery foundation models. CoRR (2024)
Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay
OpenChemIE: An Information Extraction Toolkit For Chemistry Literature. CoRR (2024)
Vincent Fan, Yujie Qian, Alex Wang, Amber Wang, Connor W. Coley, Regina Barzilay
OpenChemIE: An Information Extraction Toolkit for Chemistry Literature. J. Chem. Inf. Model. 64 (14) (2024)
Gabriele Corso, Yilun Xu, Valentin De Bortoli, Regina Barzilay, Tommi S. Jaakkola
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models. ICLR (2024)
Gabriele Corso, Arthur Deng, Benjamin Fry, Nicholas Polizzi, Regina Barzilay, Tommi S. Jaakkola
Deep Confident Steps to New Pockets: Strategies for Docking Generalization. CoRR (2024)
Andrew Campbell, Jason Yim, Regina Barzilay, Tom Rainforth, Tommi S. Jaakkola
Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design. CoRR (2024)
Hannes Stärk, Bowen Jing, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi S. Jaakkola
Dirichlet Flow Matching with Applications to DNA Sequence Design. CoRR (2024)
Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi S. Jaakkola
Risk-Controlling Model Selection via Guided Bayesian Optimization. CoRR (2023)
Yujie Qian, Jiang Guo, Zhengkai Tu, Connor W. Coley, Regina Barzilay
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. CoRR (2023)
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi S. Jaakkola
Diffusion Probabilistic Modeling of Protein Backbones in 3D for the motif-scaffolding problem. ICLR (2023)
Yujie Qian, Jiang Guo, Zhengkai Tu, Connor W. Coley, Regina Barzilay
RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing. J. Chem. Inf. Model. 63 (13) (2023)
Andrew Kirjner, Jason Yim, Raman Samusevich, Tommi S. Jaakkola, Regina Barzilay, Ila Fiete
Optimizing protein fitness using Gibbs sampling with Graph-based Smoothing. CoRR (2023)
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, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, 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 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
Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems. CoRR (2023)
Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola
SE(3) diffusion model with application to protein backbone generation. ICML (2023)
Yujie Qian, Zhening Li, Zhengkai Tu, Connor W. Coley, Regina Barzilay
Predictive Chemistry Augmented with Text Retrieval. CoRR (2023)
Yujie Qian, Jiang Guo, Zhengkai Tu, Zhening Li, Connor W. Coley, Regina Barzilay
MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation. J. Chem. Inf. Model. 63 (7) (2023)
Victor Quach, Adam Fisch, Tal Schuster, Adam Yala, Jae Ho Sohn, Tommi S. Jaakkola, Regina Barzilay
Conformal Language Modeling. CoRR (2023)
Yujie Qian, Zhening Li, Zhengkai Tu, Connor W. Coley, Regina Barzilay
Predictive Chemistry Augmented with Text Retrieval. EMNLP (2023)
Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola
Harmonic Self-Conditioned Flow Matching for Multi-Ligand Docking and Binding Site Design. CoRR (2023)
Mohamed Amine Ketata, Cedrik Laue, Ruslan Mammadov, Hannes Stärk, Menghua Wu, Gabriele Corso, Céline Marquet, Regina Barzilay, Tommi S. Jaakkola
DiffDock-PP: Rigid Protein-Protein Docking with Diffusion Models. CoRR (2023)
Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi S. Jaakkola
Efficiently Controlling Multiple Risks with Pareto Testing. ICLR (2023)
Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi S. Jaakkola
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. ICLR (2023)
Gabriele Corso, Yilun Xu, Valentin De Bortoli, Regina Barzilay, Tommi S. Jaakkola
Particle Guidance: non-I.I.D. Diverse Sampling with Diffusion Models. CoRR (2023)
Jason Yim, Brian L. Trippe, Valentin De Bortoli, Emile Mathieu, Arnaud Doucet, Regina Barzilay, Tommi S. Jaakkola
SE(3) diffusion model with application to protein backbone generation. CoRR (2023)
Homa Esfahanizadeh, William Wu, Manya Ghobadi, Regina Barzilay, Muriel Médard
InfoShape: Task-Based Neural Data Shaping via Mutual Information. ICASSP (2023)
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
PEOPL: Characterizing Privately Encoded Open Datasets with Public Labels. CoRR (2023)
Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen, Regina Barzilay
Automated Chemical Reaction Extraction from Scientific Literature. J. Chem. Inf. Model. 62 (9) (2022)
Gabriele Corso, Hannes Stärk, Bowen Jing, Regina Barzilay, Tommi Jaakkola
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking. CoRR (2022)
Homa Esfahanizadeh, William Wu, Manya Ghobadi, Regina Barzilay, Muriel Médard
InfoShape: Task-Based Neural Data Shaping via Mutual Information. CoRR (2022)
Yujie Qian, Zhengkai Tu, Jiang Guo, Connor W. Coley, Regina Barzilay
Robust Molecular Image Recognition: A Graph Generation Approach. CoRR (2022)
Yujia Bao, Shiyu Chang, Regina Barzilay
Learning Stable Classifiers by Transferring Unstable Features. ICML (2022)
Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design. ICLR (2022)
Yujia Bao, Regina Barzilay
Learning to Split for Automatic Bias Detection. CoRR (2022)
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi S. Jaakkola, Andreas Krause
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking. ICLR (2022)
Adam Fisch, Tal Schuster, Tommi Jaakkola, Regina Barzilay
Conformal Prediction Sets with Limited False Positives. ICML (2022)
Adam Fisch, Tommi Jaakkola, Regina Barzilay
Calibrated Selective Classification. CoRR (2022)
Hannes Stärk, Octavian-Eugen Ganea, Lagnajit Pattanaik, Regina Barzilay, Tommi Jaakkola
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction. CoRR (2022)
Brian L. Trippe, Jason Yim, Doug Tischer, David Baker, Tamara Broderick, Regina Barzilay, Tommi Jaakkola
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem. CoRR (2022)
Hannes Stärk, Octavian Ganea, Lagnajit Pattanaik, Regina Barzilay, Tommi Jaakkola
EquiBind: Geometric Deep Learning for Drug Binding Structure Prediction. ICML (2022)
Wengong Jin, Regina Barzilay, Tommi Jaakkola
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement. CoRR (2022)
Adam Yala, Victor Quach, Homa Esfahanizadeh, Rafael G. L. D'Oliveira, Ken R. Duffy, Muriel Médard, Tommi S. Jaakkola, Regina Barzilay
Syfer: Neural Obfuscation for Private Data Release. CoRR (2022)
Bracha Laufer-Goldshtein, Adam Fisch, Regina Barzilay, Tommi Jaakkola
Efficiently Controlling Multiple Risks with Pareto Testing. CoRR (2022)
Adam Fisch, Tommi S. Jaakkola, Regina Barzilay
Calibrated Selective Classification. Trans. Mach. Learn. Res. 2022 (2022)
Bowen Jing, Gabriele Corso, Jeffrey Chang, Regina Barzilay, Tommi S. Jaakkola
Torsional Diffusion for Molecular Conformer Generation. NeurIPS (2022)
Wengong Jin, Regina Barzilay, Tommi Jaakkola
Antibody-Antigen Docking and Design via Hierarchical Structure Refinement. ICML (2022)
Bowen Jing, Gabriele Corso, Jeffrey Chang, Regina Barzilay, Tommi S. Jaakkola
Torsional Diffusion for Molecular Conformer Generation. CoRR (2022)
Adam Fisch, Tal Schuster, Tommi Jaakkola, Regina Barzilay
Conformal Prediction Sets with Limited False Positives. CoRR (2022)
Tian Xie, Xiang Fu, Octavian-Eugen Ganea, Regina Barzilay, Tommi S. Jaakkola
Crystal Diffusion Variational Autoencoder for Periodic Material Generation. ICLR (2022)
Tal Schuster, Adam Fisch, Tommi S. Jaakkola, Regina Barzilay
Consistent Accelerated Inference via Confident Adaptive Transformers. EMNLP (1) (2021)
Yujia Bao, Shiyu Chang, Regina Barzilay
Learning Stable Classifiers by Transferring Unstable Features. CoRR (2021)
Martha Rebeca Canales-Fiscal, Rocío Ortiz López, Regina Barzilay, Victor Treviño, Servando Cardona-Huerta, Luis Javier Ramírez-Treviño, Adam Yala, José G. Tamez-Peña
COVID-19 classification using thermal images: thermal images capability for identifying COVID-19 using traditional machine learning classifiers. BCB (2021)
Tal Schuster, Adam Fisch, Tommi S. Jaakkola, Regina Barzilay
Consistent Accelerated Inference via Confident Adaptive Transformers. CoRR (2021)
Octavian-Eugen Ganea, Lagnajit Pattanaik, Connor W. Coley, Regina Barzilay, Klavs F. Jensen, William H. Green Jr., Tommi S. Jaakkola
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. CoRR (2021)
Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay
Nutri-bullets: Summarizing Health Studies by Composing Segments. CoRR (2021)
Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay
Nutri-bullets: Summarizing Health Studies by Composing Segments. AAAI (2021)
Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay
Nutribullets Hybrid: Multi-document Health Summarization. CoRR (2021)
Tal Schuster, Adam Fisch, Regina Barzilay
Get Your Vitamin C! Robust Fact Verification with Contrastive Evidence. NAACL-HLT (2021)
Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design. CoRR (2021)
Adam Yala, Homa Esfahanizadeh, Rafael G. L. D'Oliveira, Ken R. Duffy, Manya Ghobadi, Tommi S. Jaakkola, Vinod Vaikuntanathan, Regina Barzilay, Muriel Médard
NeuraCrypt: Hiding Private Health Data via Random Neural Networks for Public Training. CoRR (2021)
Wengong Jin, Jonathan M. Stokes, Richard T. Eastman, Zina Itkin, Alexey V. Zakharov, James J. Collins, Tommi S. Jaakkola, Regina Barzilay
Deep learning identifies synergistic drug combinations for treating COVID-19. Proc. Natl. Acad. Sci. USA 118 (39) (2021)
Jiang Guo, A. Santiago Ibanez-Lopez, Hanyu Gao, Victor Quach, Connor W. Coley, Klavs F. Jensen, Regina Barzilay
Correction to Automated Chemical Reaction Extraction from Scientific Literature. J. Chem. Inf. Model. 61 (8) (2021)
Octavian-Eugen Ganea, Xinyuan Huang, Charlotte Bunne, Yatao Bian, Regina Barzilay, Tommi Jaakkola, Andreas Krause
Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking. CoRR (2021)
Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay
Efficient Conformal Prediction via Cascaded Inference with Expanded Admission. ICLR (2021)
Darsh J. Shah, Lili Yu, Tao Lei, Regina Barzilay
Nutri-bullets Hybrid: Consensual Multi-document Summarization. NAACL-HLT (2021)
Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay
Few-shot Conformal Prediction with Auxiliary Tasks. CoRR (2021)
Yujia Bao, Shiyu Chang, Regina Barzilay
Predict then Interpolate: A Simple Algorithm to Learn Stable Classifiers. ICML (2021)
Tian Xie, Xiang Fu, Octavian-Eugen Ganea, Regina Barzilay, Tommi S. Jaakkola
Crystal Diffusion Variational Autoencoder for Periodic Material Generation. CoRR (2021)
Darsh J. Shah, Regina Barzilay
Generating Related Work. CoRR (2021)
Octavian Ganea, Lagnajit Pattanaik, Connor W. Coley, Regina Barzilay, Klavs F. Jensen, William H. Green Jr., Tommi S. Jaakkola
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles. NeurIPS (2021)
Jiaming Luo, Frederik Hartmann, Enrico Santus, Yuan Cao, Regina Barzilay
Deciphering Undersegmented Ancient Scripts Using Phonetic Prior. Trans. Assoc. Comput. Linguistics 9 (2021)
Karren D. Yang, Samuel Goldman, Wengong Jin, Alex X. Lu, Regina Barzilay, Tommi S. Jaakkola, Caroline Uhler
Mol2Image: Improved Conditional Flow Models for Molecule to Image Synthesis. CVPR (2021)
Tal Schuster, Adam Fisch, Regina Barzilay
Get Your Vitamin C! Robust Fact Verification with Contrastive Evidence. CoRR (2021)
Benson Chen, Xiang Fu, Regina Barzilay, Tommi S. Jaakkola
Fragment-based Sequential Translation for Molecular Optimization. CoRR (2021)
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Learning Graph Models for Retrosynthesis Prediction. NeurIPS (2021)
Yujia Bao, Shiyu Chang, Regina Barzilay
Predict then Interpolate: A Simple Algorithm to Learn Stable Classifiers. CoRR (2021)
Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay
Few-Shot Conformal Prediction with Auxiliary Tasks. ICML (2021)
Lior Hirschfeld, Kyle Swanson, Kevin Yang, Regina Barzilay, Connor W. Coley
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. J. Chem. Inf. Model. 60 (8) (2020)
Jiaming Luo, Frederik Hartmann, Enrico Santus, Yuan Cao, Regina Barzilay
Deciphering Undersegmented Ancient Scripts Using Phonetic Prior. CoRR (2020)
Vignesh Ram Somnath, Charlotte Bunne, Connor W. Coley, Andreas Krause, Regina Barzilay
Learning Graph Models for Template-Free Retrosynthesis. CoRR (2020)
Darsh J. Shah, Tal Schuster, Regina Barzilay
Automatic Fact-Guided Sentence Modification. AAAI (2020)
Karren D. Yang, Samuel Goldman, Wengong Jin, Alex Lu, Regina Barzilay, Tommi S. Jaakkola, Caroline Uhler
Improved Conditional Flow Models for Molecule to Image Synthesis. CoRR (2020)
Tal Schuster, Roei Schuster, Darsh J. Shah, Regina Barzilay
The Limitations of Stylometry for Detecting Machine-Generated Fake News. Comput. Linguistics 46 (2) (2020)
Tianxiao Shen, Jonas Mueller, Regina Barzilay, Tommi S. Jaakkola
Educating Text Autoencoders: Latent Representation Guidance via Denoising. ICML (2020)
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
Multi-Objective Molecule Generation using Interpretable Substructures. ICML (2020)
Kevin Yang, Wengong Jin, Kyle Swanson, Regina Barzilay, Tommi S. Jaakkola
Improving Molecular Design by Stochastic Iterative Target Augmentation. CoRR (2020)
Adam Fisch, Kenton Lee, Ming-Wei Chang, Jonathan H. Clark, Regina Barzilay
CapWAP: Image Captioning with a Purpose. EMNLP (1) (2020)
Adam Fisch, Tal Schuster, Tommi S. Jaakkola, Regina Barzilay
Relaxed Conformal Prediction Cascades for Efficient Inference Over Many Labels. CoRR (2020)
Luu Anh Tuan, Darsh J. Shah, Regina Barzilay
Capturing Greater Context for Question Generation. AAAI (2020)
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
Domain Extrapolation via Regret Minimization. CoRR (2020)
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
Adaptive Invariance for Molecule Property Prediction. CoRR (2020)
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
Composing Molecules with Multiple Property Constraints. CoRR (2020)
Yujia Bao, Menghua Wu, Shiyu Chang, Regina Barzilay
Few-shot Text Classification with Distributional Signatures. ICLR (2020)
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models. CoRR (2020)
Tianxiao Shen, Victor Quach, Regina Barzilay, Tommi S. Jaakkola
Blank Language Models. CoRR (2020)
Lior Hirschfeld, Kyle Swanson, Kevin Yang, Regina Barzilay, Connor W. Coley
Uncertainty Quantification Using Neural Networks for Molecular Property Prediction. CoRR (2020)

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Publication Activity (10 Years)

Top Topics

Top Venues

Regina Barzilay