WJ

Wengong Jin

0000-0002-0555-3056

cs.LGq-bio.BMstat.MLcs.AIDeep Learningcs.CVcs.NEdrug discoveryphysics.chem-phq-bio.QM

On Valency

published · living versions

ProTEUS: A mutation-resolved world model for closed-loop protein evolution

with Yikun Zhang, Minghao Guo, Guangxue Xu, Peter Yichen Chen +3

1 version

W_46sn8wbzv1 · current

MoLRSI: A Recursive Self-Improving AI agent for Molecular Discovery

W_ka3rjr2vv1

Preprints & journals

52 papers in the corpus · 2017–2026

From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

Siyuan Chen, Cai Zhou, Jinrui Zhang et al.

0 citations

2609.36277v12026arXiv

Where Should Physics Enter a Molecular Crystal Generator?

Haocheng Tang, Junmei Wang, Wengong Jin

0 citations

2609.36398v12026arXiv

LabAgent: Customize Any Research Hubs for Scientific Discoveries Using AI Agents

Lei Liu, Yikun Zhang, Jialin Chen et al.

0 citations

2609.13437v12026arXiv

Predicting Immune Biomarkers with MultiModal Mixture-of-Expert Pathology Foundation Models Empowers Precision Oncology

Tianyu Liu, Ziqing Wang, Zhaokang Liang et al.

0 citations

2606.18123v22026arXiv

Benchmarking AI Agents for Addressing Scientific Challenges Across Scales

Tianyu Liu, Allen Xin Wang, Antonia Panescu et al.

1 citation

2606.12736v12026arXiv

DrugSAGE:Self-evolving Agent Experience for Efficient State-of-the-Art Drug Discovery

Yikun Zhang, Xiwei Cheng, Tianyu Liu et al.

0 citations

2605.15461v12026arXiv

spRefine denoises and imputes spatial transcriptomic data with a reference-free framework powered by genomic language model.

Liu, Tianyu, Huang, Tinglin, Jin, Wengong et al.

0 citations

416337672026Genome research. 2026;36(4):754-768

Generative Artificial Intelligence for Biology: Toward Unifying Models, Algorithms, and Modalities

Xiner Li, Xingyu Su, Yuchao Lin et al.

1 citation

10.26434/chemrxiv.10002066/v32026ChemRxiv

FlashBind: Towards Accurate and Efficient Structure-based Virtual Screening

Jiang, S., Chen, Y., Krishnan, A. et al.

0 citations

10.64898/2025.12.22.695983v32025bioRxiv

Accelerating Scientific Discovery with Autonomous Goal-evolving Agents

Yuanqi Du, Botao Yu, Tianyu Liu et al.

1 citation

2512.21782v22025arXiv

STPath: a generative foundation model for integrating spatial transcriptomics and whole-slide images.

Huang, Tinglin, Liu, Tianyu, Babadi, Mehrtash et al.

27 citations

412387842025NPJ digital medicine. 2025;8(1):659

Redefining druggable targets with artificial intelligence.

Akinsanya, Karen, AlQuraishi, Mohammed, Boija, Ann et al.

4 citations

408302622026Nature biotechnology. 2025;43(9):1416-1418

A generative deep learning approach to de novo antibiotic design.

Krishnan, Aarti, Anahtar, Melis N, Valeri, Jacqueline A et al.

102 citations

408162672025Cell. 2025;188(21):5962-5979.e22

spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model.

Liu, Tianyu, Huang, Tinglin, Jin, Wengong et al.

0 citations

406312302026bioRxiv : the preprint server for biology. 2025

BindEnergyCraft: Casting Protein Structure Predictors as Energy-Based Models for Binder Design

Divya Nori, Anisha Parsan, Caroline Uhler et al.

1 citation

2505.21241v12025arXiv

Scalable Generation of Spatial Transcriptomics from Histology Images via Whole-Slide Flow Matching

Tinglin Huang, Tianyu Liu, Mehrtash Babadi et al.

0 citations

2506.05361v12025arXiv

AI-driven discovery of synergistic drug combinations against pancreatic cancer.

Pourmousa, Mohsen, Jain, Sankalp, Barnaeva, Elena et al.

38 citations

403013002025Nature communications. 2025;16(1):4020

Reaction-conditioned De Novo Enzyme Design with GENzyme

Chenqing Hua, Jiarui Lu, Yong Liu et al.

6 citations

2411.16694v12024arXiv

Deep generative design of RNA aptamers using structural predictions.

Wong, Felix, He, Dongchen, Krishnan, Aarti et al.

86 citations

395060802024Nature computational science. 2024;4(11):829-839

Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions

Xiaoran Jiao, Weian Mao, Wengong Jin et al.

1 citation

2410.09543v12024arXiv

Protein-Nucleic Acid Complex Modeling with Frame Averaging Transformer

Tinglin Huang, Zhenqiao Song, Rex Ying et al.

4 citations

2406.09586v32024arXiv

RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching

Divya Nori, Wengong Jin

6 citations

2405.18768v22024arXiv

Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates

Zhenqiao Song, Yunlong Zhao, Wenxian Shi et al.

2 citations

2405.08205v42024arXiv

SurfPro: Functional Protein Design Based on Continuous Surface

Zhenqiao Song, Tinglin Huang, Lei Li et al.

4 citations

2405.06693v22024arXiv

Autonomous, multiproperty-driven molecular discovery: From predictions to measurements and back.

Koscher, Brent A, Canty, Richard B, McDonald, Matthew A et al.

173 citations

381277342023Science (New York, N.Y.). 2023;382(6677):eadi1407

Discovery of a structural class of antibiotics with explainable deep learning.

Wong, Felix, Zheng, Erica J, Valeri, Jacqueline A et al.

461 citations

381236862024Nature. 2024;626(7997):177-185

Unsupervised Protein-Ligand Binding Energy Prediction via Neural Euler's Rotation Equation.

Jin, Wengong, Sarkizova, Siranush, Chen, Xun et al.

5 citations

381684562024ArXiv. 2023

DSMBind: SE(3) denoising score matching for unsupervised binding energy prediction and nanobody design

Jin, W., Chen, X., Vetticaden, A. et al.

15 citations

10.1101/2023.12.10.570461v12023bioRxiv

Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii.

Liu, Gary, Catacutan, Denise B, Rathod, Khushi et al.

360 citations

372312672023Nature chemical biology. 2023;19(11):1342-1350

Antibody-Antigen Docking and Design via Hierarchical Equivariant Refinement

Wengong Jin, Regina Barzilay, Tommi Jaakkola

12 citations

2207.06616v12022arXiv

Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design

Wengong Jin, Jeremy Wohlwend, Regina Barzilay et al.

69 citations

2110.04624v32021arXiv

Deep learning identifies synergistic drug combinations for treating COVID-19.

Jin, Wengong, Stokes, Jonathan M, Eastman, Richard T et al.

169 citations

345263882021Proceedings of the National Academy of Sciences of the United States of America. 2021;118(39)

Discovering Synergistic Drug Combinations for COVID with Biological Bottleneck Models

Wengong Jin, Regina Barzilay, Tommi Jaakkola

3 citations

2011.04651v22020arXiv

Improved Conditional Flow Models for Molecule to Image Synthesis

Karren Yang, Samuel Goldman, Wengong Jin et al.

5 citations

2006.08532v12020arXiv

Enforcing Predictive Invariance across Structured Biomedical Domains

Wengong Jin, Regina Barzilay, Tommi Jaakkola

8 citations

2006.03908v32020arXiv

Adaptive Invariance for Molecule Property Prediction

Wengong Jin, Regina Barzilay, Tommi Jaakkola

4 citations

2005.03004v12020arXiv

A Deep Learning Approach to Antibiotic Discovery.

Stokes, Jonathan M, Yang, Kevin, Swanson, Kyle et al.

298 citations

323025742020Cell. 2020;181(2):475-483

A Deep Learning Approach to Antibiotic Discovery.

Stokes, Jonathan M, Yang, Kevin, Swanson, Kyle et al.

2,435 citations

320843402020Cell. 2020;180(4):688-702.e13

Improving Molecular Design by Stochastic Iterative Target Augmentation

Kevin Yang, Wengong Jin, Kyle Swanson et al.

3 citations

10.26434/chemrxiv.11839230.v12020ChemRxiv

Improving Molecular Design by Stochastic Iterative Target Augmentation

Kevin Yang, Wengong Jin, Kyle Swanson et al.

14 citations

2002.04720v32020PMLR 119:10716-10726, 2020

Hierarchical Generation of Molecular Graphs using Structural Motifs

Wengong Jin, Regina Barzilay, Tommi Jaakkola

112 citations

2002.03230v22020arXiv

Multi-Objective Molecule Generation using Interpretable Substructures

Wengong Jin, Regina Barzilay, Tommi Jaakkola

110 citations

2002.03244v32020arXiv

Correction to Analyzing Learned Molecular Representations for Property Prediction.

Yang, Kevin, Swanson, Kyle, Jin, Wengong et al.

40 citations

318144002021Journal of chemical information and modeling. 2019;59(12):5304-5305

Analyzing Learned Molecular Representations for Property Prediction.

Yang, Kevin, Swanson, Kyle, Jin, Wengong et al.

2,002 citations

313614842020Journal of chemical information and modeling. 2019;59(8):3370-3388

Multi-Resolution Autoregressive Graph-to-Graph Translation for Molecules

Wengong Jin, Regina Barzilay, Tommi S Jaakkola

10 citations

10.26434/chemrxiv.8266745.v12019ChemRxiv

Hierarchical Graph-to-Graph Translation for Molecules

Wengong Jin, Regina Barzilay, Tommi Jaakkola

21 citations

1907.11223v22019arXiv

Functional Transparency for Structured Data: a Game-Theoretic Approach

Guang-He Lee, Wengong Jin, David Alvarez-Melis et al.

9 citations

1902.09737v12019arXiv

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization

Wengong Jin, Kevin Yang, Regina Barzilay et al.

129 citations

1812.01070v32018arXiv

A graph-convolutional neural network model for the prediction of chemical reactivity.

Coley, Connor W, Jin, Wengong, Rogers, Luke et al.

707 citations

307460862024Chemical science. 2019;10(2):370-377

Junction Tree Variational Autoencoder for Molecular Graph Generation

Wengong Jin, Regina Barzilay, Tommi Jaakkola

844 citations

1802.04364v42018arXiv

Career total: 81 works. 52 are in this corpus.Showing the 50 most recent.

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