Wengong Jin

53 papers A* 17A 1Journal 32Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Accelerating Scientific Discovery with Autonomous Goal-evolving Agents.
CoRR
Yuanqi Du, Botao Yu, Tianyu Liu, Tony Shen, Junwu Chen, Jan G. Rittig, Kunyang Sun, Yikun Zhang, Zhangde Song, Bo Zhou, Cassandra Masschelein, Yingze Wang, Haorui Wang, Haojun Jia, Chao Zhang, Hongyu Zhao, Martin Ester, Teresa Head-Gordon, Carla P. Gomes, Huan Sun, Chenru Duan, Philippe Schwaller, Wengong Jin
2025 J jnl
BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design.
CoRR
Divya Nori, Anisha Parsan, Caroline Uhler, Wengong Jin
2025 A* conf
Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions.
ICLR
Xiaoran Jiao, Weian Mao, Wengong Jin, Peiyuan Yang, Hao Chen, Chunhua Shen
2025 J jnl
MiniFold: Simple, Fast, and Accurate Protein Structure Prediction.
Trans. Mach. Learn. Res.
Jeremy Wohlwend, Mateo Reveiz, Matt McPartlon, Axel Feldmann, Wengong Jin, Regina Barzilay
2025 J jnl
STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.
npj Digit. Medicine
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Rex Ying, Wengong Jin
2025 A* conf
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching.
ICML
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying
2025 J jnl
Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching.
CoRR
Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying
2024 J jnl
Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions.
CoRR
Xiaoran Jiao, Weian Mao, Wengong Jin, Peiyuan Yang, Hao Cheng, Chunhua Shen
2024 J jnl
Deep generative design of RNA aptamers using structural predictions.
Nat. Comput. Sci.
Felix Wong, Dongchen He, Aarti Krishnan, Liang Hong, Alexander Z. Wang, Jiuming Wang, Zhihang Hu, Satotaka Omori, Alicia Li, Jiahua Rao, Qinze Yu, Wengong Jin, Tianqing Zhang, Katherine Ilia, Jack X. Chen, Shuangjia Zheng, Irwin King, Yu Li, James J. Collins
2024 J jnl
Discovery of a structural class of antibiotics with explainable deep learning.
Nat.
Felix Wong, Erica J. Zheng, Jacqueline A. Valeri, Nina M. Donghia, Melis N. Anahtar, Satotaka Omori, Alicia Li, Andres Cubillos-Ruiz, Aarti Krishnan, Wengong Jin, Abigail L. Manson, Jens Friedrichs, Ralf Helbig, Behnoush Hajian, Dawid K. Fiejtek, Florence F. Wagner, Holly H. Soutter, Ashlee M. Earl, Jonathan M. Stokes, Lars D. Renner, James J. Collins
2024 A* conf
Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates.
ICML
Zhenqiao Song, Yunlong Zhao, Wenxian Shi, Wengong Jin, Yang Yang, Lei Li
2024 J jnl
Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates.
CoRR
Zhenqiao Song, Yunlong Zhao, Wenxian Shi, Wengong Jin, Yang Yang, Lei Li
2024 A* conf
Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer.
NeurIPS
Tinglin Huang, Zhenqiao Song, Rex Ying, Wengong Jin
2024 A* conf
RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching.
ICML
Divya Nori, Wengong Jin
2024 J jnl
RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching.
CoRR
Divya Nori, Wengong Jin
2024 J jnl
Reaction-conditioned De Novo Enzyme Design with GENzyme.
CoRR
Chenqing Hua, Jiarui Lu, Yong Liu, Odin Zhang, Jian Tang, Rex Ying, Wengong Jin, Guy Wolf, Doina Precup, Shuangjia Zheng
2024 A* conf
SurfPro: Functional Protein Design Based on Continuous Surface.
ICML
Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin
2024 J jnl
SurfPro: Functional Protein Design Based on Continuous Surface.
CoRR
Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin
2023 A* conf
Graph and Geometry Generative Modeling for Drug Discovery.
KDD
Minkai Xu, Meng Liu, Wengong Jin, Shuiwang Ji, Jure Leskovec, Stefano Ermon
2023 A* conf
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation.
NeurIPS
Wengong Jin, Siranush Sarkizova, Xun Chen, Nir Hacohen, Caroline Uhler
2023 J jnl
Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation.
CoRR
Wengong Jin, Siranush Sarkizova, Xun Chen, Nir Hacohen, Caroline Uhler
2022 J jnl
Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2022 A* conf
Antibody-Antigen Docking and Design via Hierarchical Structure Refinement.
ICML
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2022 A* conf
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design.
ICLR
Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola
2021 J jnl
Deep learning identifies synergistic drug combinations for treating COVID-19.
Proc. Natl. Acad. Sci. USA
Wengong Jin, Jonathan M. Stokes, Richard T. Eastman, Zina Itkin, Alexey V. Zakharov, James J. Collins, Tommi S. Jaakkola, Regina Barzilay
2021 — —
Graph Representation Learning for Drug Discovery.
Wengong Jin
2021 J jnl
Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design.
CoRR
Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola
2021 A* conf
Mol2Image: Improved Conditional Flow Models for Molecule to Image Synthesis.
CVPR
Karren D. Yang, Samuel Goldman, Wengong Jin, Alex X. Lu, Regina Barzilay, Tommi S. Jaakkola, Caroline Uhler
2020 J jnl
Adaptive Invariance for Molecule Property Prediction.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Composing Molecules with Multiple Property Constraints.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Domain Extrapolation via Regret Minimization.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 A* conf
Hierarchical Generation of Molecular Graphs using Structural Motifs.
ICML
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Hierarchical Generation of Molecular Graphs using Structural Motifs.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Improved Conditional Flow Models for Molecule to Image Synthesis.
CoRR
Karren D. Yang, Samuel Goldman, Wengong Jin, Alex Lu, Regina Barzilay, Tommi S. Jaakkola, Caroline Uhler
2020 A* conf
Improving Molecular Design by Stochastic Iterative Target Augmentation.
ICML
Kevin Yang, Wengong Jin, Kyle Swanson, Regina Barzilay, Tommi S. Jaakkola
2020 J jnl
Improving Molecular Design by Stochastic Iterative Target Augmentation.
CoRR
Kevin Yang, Wengong Jin, Kyle Swanson, Regina Barzilay, Tommi S. Jaakkola
2020 A* conf
Multi-Objective Molecule Generation using Interpretable Substructures.
ICML
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2019 J jnl
Analyzing Learned Molecular Representations for Property Prediction.
J. Chem. Inf. Model.
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, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
2019 J jnl
Are Learned Molecular Representations Ready For Prime Time?
CoRR
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, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
2019 J jnl
Correction to Analyzing Learned Molecular Representations for Property Prediction.
J. Chem. Inf. Model.
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, Tommi S. Jaakkola, Klavs F. Jensen, Regina Barzilay
2019 A* conf
Functional Transparency for Structured Data: a Game-Theoretic Approach.
ICML
Guang-He Lee, Wengong Jin, David Alvarez-Melis, Tommi S. Jaakkola
2019 J jnl
Functional Transparency for Structured Data: a Game-Theoretic Approach.
CoRR
Guang-He Lee, Wengong Jin, David Alvarez-Melis, Tommi S. Jaakkola
2019 — conf
Learning Multimodal Graph-to-Graph Translation for Molecule Optimization.
ICLR (Poster)
Wengong Jin, Kevin Yang, Regina Barzilay, Tommi S. Jaakkola
2019 J jnl
Multi-resolution Autoregressive Graph-to-Graph Translation for Molecules.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2018 A* conf
Junction Tree Variational Autoencoder for Molecular Graph Generation.
ICML
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2018 J jnl
Junction Tree Variational Autoencoder for Molecular Graph Generation.
CoRR
Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2018 J jnl
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization.
CoRR
Wengong Jin, Kevin Yang, Regina Barzilay, Tommi S. Jaakkola
2017 A* conf
Deriving Neural Architectures from Sequence and Graph Kernels.
ICML
Tao Lei, Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2017 J jnl
Deriving Neural Architectures from Sequence and Graph Kernels.
CoRR
Tao Lei, Wengong Jin, Regina Barzilay, Tommi S. Jaakkola
2017 — conf
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network.
NIPS
Wengong Jin, Connor W. Coley, Regina Barzilay, Tommi S. Jaakkola
2017 J jnl
Predicting Organic Reaction Outcomes with Weisfeiler-Lehman Network.
CoRR
Wengong Jin, Connor W. Coley, Regina Barzilay, Tommi S. Jaakkola
2015 A conf
Paragraph vector based topic model for language model adaptation.
INTERSPEECH
Wengong Jin, Tianxing He, Yanmin Qian, Kai Yu