| 2025 | ICLR | Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions. | Xiaoran Jiao, Weian Mao, Wengong Jin, Peiyuan Yang, Hao Chen, Chunhua Shen |
| 2025 | ICML | Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching. | Tinglin Huang, Tianyu Liu, Mehrtash Babadi, Wengong Jin, Rex Ying |
| 2024 | ICML | RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching. | Divya Nori, Wengong Jin |
| 2024 | ICML | SurfPro: Functional Protein Design Based on Continuous Surface. | Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin |
| 2024 | ICML | Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates. | Zhenqiao Song, Yunlong Zhao, Wenxian Shi, Wengong Jin, Yang Yang, Lei Li |
| 2023 | KDD | Graph and Geometry Generative Modeling for Drug Discovery. | Minkai Xu, Meng Liu, Wengong Jin, Shuiwang Ji, Jure Leskovec, Stefano Ermon |
| 2022 | ICLR | Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design. | Wengong Jin, Jeremy Wohlwend, Regina Barzilay, Tommi S. Jaakkola |
| 2022 | ICML | Antibody-Antigen Docking and Design via Hierarchical Structure Refinement. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 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 |
| 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 | Improving Molecular Design by Stochastic Iterative Target Augmentation. | Kevin Yang, Wengong Jin, Kyle Swanson, 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 | ICML | Functional Transparency for Structured Data: a Game-Theoretic Approach. | Guang-He Lee, Wengong Jin, David Alvarez-Melis, Tommi S. Jaakkola |
| 2018 | ICML | Junction Tree Variational Autoencoder for Molecular Graph Generation. | Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2017 | ICML | Deriving Neural Architectures from Sequence and Graph Kernels. | Tao Lei, Wengong Jin, Regina Barzilay, Tommi S. Jaakkola |
| 2015 | Interspeech | Paragraph vector based topic model for language model adaptation. | Wengong Jin, Tianxing He, Yanmin Qian, Kai Yu |