Zhang, Zuobai

23 publications

ICLR 2025 Proteina: Scaling Flow-Based Protein Structure Generative Models Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Kucukbenli, Arash Vahdat, Karsten Kreis

ICMLW 2024 Augmenting Evolutionary Models with Structure-Based Retrieval Yining Huang, Zuobai Zhang, Jian Tang, Debora Susan Marks, Pascal Notin

NeurIPS 2024 Cell Ontology Guided Transcriptome Foundation Model Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang

NeurIPSW 2024 Cell Ontology Guided Transcriptome Foundation Model Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang

NeurIPSW 2024 Cell Ontology Guided Transcriptome Foundation Model Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang

NeurIPSW 2024 Cell Ontology Guided Transcriptome Foundation Model Xinyu Yuan, Zhihao Zhan, Zuobai Zhang, Manqi Zhou, Jianan Zhao, Boyu Han, Yue Li, Jian Tang

ICLR 2024 Evaluating Representation Learning on the Protein Structure Universe Arian Rokkum Jamasb, Alex Morehead, Chaitanya K. Joshi, Zuobai Zhang, Kieran Didi, Simon V Mathis, Charles Harris, Jian Tang, Jianlin Cheng, Pietro Lio, Tom Leon Blundell

ICLRW 2024 Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations Jiarui Lu, Zuobai Zhang, Bozitao Zhong, Chence Shi, Jian Tang

NeurIPS 2024 Multi-Scale Representation Learning for Protein Fitness Prediction Zuobai Zhang, Pascal Notin, Yining Huang, Aurélie Lozano, Vijil Chenthamarakshan, Debora Marks, Payel Das, Jian Tang

ICLR 2024 Str2Str: A Score-Based Framework for Zero-Shot Protein Conformation Sampling Jiarui Lu, Bozitao Zhong, Zuobai Zhang, Jian Tang

ICLRW 2024 Structure-Informed Protein Language Model Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang

NeurIPS 2023 DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang

ICLRW 2023 Enhancing Protein Language Model with Structure-Based Encoder and Pre-Training Zuobai Zhang, Minghao Xu, Aurelie Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang

ICML 2023 FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning Songtao Liu, Zhengkai Tu, Minkai Xu, Zuobai Zhang, Lu Lin, Rex Ying, Jian Tang, Peilin Zhao, Dinghao Wu

NeurIPSW 2023 PDB-Struct: A Comprehensive Benchmark for Structure-Based Protein Design Chuanrui Wang, Bozitao Zhong, Zuobai Zhang, Narendra Chaudhary, Sanchit Misra, Jian Tang

NeurIPS 2023 Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction Zuobai Zhang, Minghao Xu, Aurelie C. Lozano, Vijil Chenthamarakshan, Payel Das, Jian Tang

ICLR 2023 Protein Representation Learning by Geometric Structure Pretraining Zuobai Zhang, Minghao Xu, Arian Rokkum Jamasb, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang

AISTATS 2022 Structured Multi-Task Learning for Molecular Property Prediction Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang

ICML 2022 Neural-Symbolic Models for Logical Queries on Knowledge Graphs Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang, Jian Tang

NeurIPS 2022 PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Ma Chang, Runcheng Liu, Jian Tang

ICMLW 2022 Protein Representation Learning by Geometric Structure Pretraining Zuobai Zhang, Minghao Xu, Arian Rokkum Jamasb, Vijil Chenthamarakshan, Aurelie Lozano, Payel Das, Jian Tang

NeurIPSW 2021 Multi-Task Learning with Domain Knowledge for Molecular Property Prediction Shengchao Liu, Meng Qu, Zuobai Zhang, Huiyu Cai, Jian Tang

NeurIPS 2021 Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux, Jian Tang