Shuangjia Zheng

According to our database, Shuangjia Zheng authored at least 56 papers between 2019 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery.

Jiaqi Wei, Yuejin Yang, Xiang Zhang, Yuhan Chen, Xiang Zhuang, Zhangyang Gao, Dongzhan Zhou, Guangshuai Wang, Zhiqiang Gao, Juntai Cao, Zijie Qiu, Xuming He, Qiang Zhang, Chenyu You, Shuangjia Zheng, Ning Ding, Wanli Ouyang, Nanqing Dong, Yu Cheng, Siqi Sun, Lei Bai, Bowen Zhou

CoRR, August, 2025

Fitness aligned structural modeling enables scalable virtual screening with AuroBind.

Zhongyue Zhang, Jiahua Rao, Jie Zhong, Weiqiang Bai, Dongxue Wang, Shaobo Ning, Lifeng Qiao, Sheng Xu, Runze Ma, Will Hua, Jack Xiaoyu Chen, Odin Zhang, Wei Lu, Hanyi Feng, He Yang, Xinchao Shi, Rui Li, Wanli Ouyang, Xinzhu Ma, Jiahao Wang, Jixian Zhang, Jia Duan, Siqi Sun, Jian Zhang, Shuangjia Zheng

CoRR, August, 2025

MolPIF: A Parameter Interpolation Flow Model for Molecule Generation.

Yaowei Jin, Junjie Wang, Wenkai Xiang, Duanhua Cao, Dan Teng, Zhehuan Fan, Jiacheng Xiong, Xia Sheng, Chuanlong Zeng, Duo An, Mingyue Zheng, Shuangjia Zheng, Qian Shi

CoRR, July, 2025

EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization.

Dingyi Rong, Haotian Lu, Wenzhuo Zheng, Fan Zhang, Shuangjia Zheng, Ning Liu

CoRR, June, 2025

A 3D pocket-aware and affinity-guided diffusion model for lead optimization.

Anjie Qiao, Junjie Xie, Weifeng Huang, Hao Zhang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang, Zhen Wang, Guo-Bo Li, Jinping Lei

CoRR, April, 2025

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.

Oleksandra Herasymenko, Madhushika Silva, Abd Al-Aziz A. Abu-Saleh, Ayaz Ahmad, Jesus Alvarado-Huayhuaz, Oscar Emilio Arrúa Arce, Roly J. Armstrong, Cheryl H. Arrowsmith, Kelly E. Bachta, Hartmut Beck, Dénes Berta, Mateusz K. Bieniek, Vincent Blay, Albina Bolotokova, Philip E. Bourne, Marko Breznik, Peter J. Brown, Aaron D. G. Campbell, Emanuele Carosati, Irene Chau, Daniel J. Cole, Ben Cree, Wim Dehaen, Katrin Denzinger, Karina dos Santos Machado, Ian Dunn, Prasannavenkatesh Durai, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Daniel Felfoldi, Kallie Friston, Pegah Ghiabi, Elisa Gibson, Judith Guenther, Anders Gunnarsson, Alexander Hillisch, Douglas R. Houston, Jan Halborg Jensen, Rachel J. Harding, Kate S. Harris, Laurent Hoffer, Anders Hogner, Joshua T. Horton, Scott Houliston, Judd F. Hultquist, Ashley Hutchinson, John J. Irwin, Marko Jukic, Shubhangi Kandwal, Andrea Karlova, Vittorio L. Katis, Ryan P. Kich, Dmitri Kireev, David Koes, Nicole L. Inniss, Uta F. Lessel, Sijie Liu, Peter Loppnau, Wei Lu, Sam Alexander Martino, Miles McGibbon, Jens Meiler, Akhila Mettu, Sam Money-Kyrle, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Joseph A. Newman, Leon Obendorf, Brooks Paige, Amit Pandit, Keunwan Park, Sumera Perveen, Rachael Pirie, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Federico Ricci, Natalie J. Roper, Edina Rosta, Margarita Rzhetskaya, Yogesh Sabnis, Karla J. F. Satchell, Frederico Schmitt Kremer, Thomas Scott, Almagul Seitova, Casper Steinmann, Valerij Talagayev, Olga O. Tarkhanova, Natalie J. Tatum, Dakota Treleaven, Adriano Velasque Werhli, W. Patrick Walters, Xiaowen Wang, Jude Wells, Geoffrey Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Jixian Zhang, Zheng Zhao, Shuangjia Zheng, Matthieu Schapira

J. Chem. Inf. Model., 2025

A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors.

Anjie Qiao, Yuting Chen, Junjie Xie, Weifeng Huang, Hao Zhang, Qirui Deng, Jiahua Rao, Ji Deng, Fanbo Meng, Zhen Wang, Mingyuan Xu, Hongming Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang, Guo-Bo Li, Jinping Lei

Briefings Bioinform., 2025

Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization.

Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng

Proceedings of the Thirteenth International Conference on Learning Representations, 2025

Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery.

Jiahua Rao, Hanjing Lin, Leyu Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang

Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2025

2024

Deep generative design of RNA aptamers using structural predictions.

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

Nat. Comput. Sci., November, 2024

Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph.

Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang

J. Chem. Inf. Model., 2024

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein.

Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, Jan Beránek, Francois Berenger, Albina Bolotokova, Guillaume Bret, Marko Breznik, Emanuele Carosati, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira

J. Chem. Inf. Model., 2024

Reaction-conditioned De Novo Enzyme Design with GENzyme.

Chenqing Hua, Jiarui Lu, Yong Liu, Odin Zhang, Jian Tang, Rex Ying, Wengong Jin, Guy Wolf, Doina Precup, Shuangjia Zheng

CoRR, 2024

EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics.

Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K. Yang, Guy Wolf, Doina Precup, Shuangjia Zheng

CoRR, 2024

Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks.

Jiahua Rao, Jiancong Xie, Hanjing Lin, Shuangjia Zheng, Zhen Wang, Yuedong Yang

CoRR, 2024

Effective Protein-Protein Interaction Exploration with PPIretrieval.

Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng

CoRR, 2024

ReactZyme: A Benchmark for Enzyme-Reaction Prediction.

Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, Shuangjia Zheng

Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024

Causal Subgraph Learning for Generalizable Inductive Relation Prediction.

Mei Li, Xiaoguang Liu, Hua Ji, Shuangjia Zheng

Proceedings of the 30th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, 2024

GP-nano: a geometric graph network for nanobody polyreactivity prediction.

Xiaolong Zhou, Qianmu Yuan, Shuangjia Zheng, Yu Wang, Yuedong Yang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2024

2023

Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning.

Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang

IEEE Trans. Knowl. Data Eng., June, 2023

Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis.

Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu

IEEE Trans. Affect. Comput., 2023

Mixup-Augmented Meta-Learning for Sample-Efficient Fine-Tuning of Protein Simulators.

Jingbang Chen, Yian Wang, Xingwei Qu, Shuangjia Zheng, Yaodong Yang, Hao Dong, Jie Fu

CoRR, 2023

SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation.

Deqin Liu, Sheng Chen, Shuangjia Zheng, Sen Zhang, Yuedong Yang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

Accelerated rational PROTAC design via deep learning and molecular simulations.

Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang

Nat. Mac. Intell., September, 2022

To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks.

Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Integrating supercomputing and artificial intelligence for life science.

Jiahua Rao, Shuangjia Zheng, Yuedong Yang

Patterns, 2022

Quantitative evaluation of explainable graph neural networks for molecular property prediction.

Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang

Patterns, 2022

Dynamic graph dropout for subgraph-based relation prediction.

Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu

Knowl. Based Syst., 2022

Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction.

Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang

J. Chem. Inf. Model., 2022

DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design.

Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang

J. Chem. Inf. Model., 2022

AlphaFold2-aware protein-DNA binding site prediction using graph transformer.

Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang

Briefings Bioinform., 2022

TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction.

Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng

Proceedings of the Advances in Neural Information Processing Systems 35: Annual Conference on Neural Information Processing Systems 2022, 2022

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction.

Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang

Proceedings of the Thirty-First International Joint Conference on Artificial Intelligence, 2022

2021

PharmKG: a dedicated knowledge graph benchmark for bomedical data mining.

Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu

Briefings Bioinform., July, 2021

Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images.

Ying Song, Shuangjia Zheng, Liang Li, Xiang Zhang, Xiaodong Zhang, Ziwang Huang, Jianwen Chen, Ruixuan Wang, Huiying Zhao, Yutian Chong, Jun Shen, Yunfei Zha, Yuedong Yang

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Meta Learning for Low-Resource Molecular Optimization.

Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang

J. Chem. Inf. Model., 2021

Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches.

Lizhao Hu, Yuyao Yang, Shuangjia Zheng, Jun Xu, Ting Ran, Hongming Chen

J. Chem. Inf. Model., 2021

Deep scaffold hopping with multimodal transformer neural networks.

Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang

J. Cheminformatics, 2021

Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map.

Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang

J. Cheminformatics, 2021

Molecular Attributes Transfer from Non-Parallel Data.

Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang

CoRR, 2021

Learning Attributed Graph Representations with Communicative Message Passing Transformer.

Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang

CoRR, 2021

Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction.

Jiahua Rao, Shuangjia Zheng, Yuedong Yang

CoRR, 2021

BioNavi-NP: Biosynthesis Navigator for Natural Products.

Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu

CoRR, 2021

Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method.

Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu

Bioinform., 2021

Learning Attributed Graph Representation with Communicative Message Passing Transformer.

Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang

Proceedings of the Thirtieth International Joint Conference on Artificial Intelligence, 2021

DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks.

Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

Communicative Message Passing for Inductive Relation Reasoning.

Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu

Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021

2020

Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system.

Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang

Nat. Mach. Intell., 2020

Predicting drug-protein interaction using quasi-visual question answering system.

Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang

Nat. Mach. Intell., 2020

Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks.

Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang

J. Chem. Inf. Model., 2020

Predicting the Feasibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reactions Using a Recurrent Neural Network with a Self-Attention Mechanism.

Shimin Su, Yuyao Yang, Hanlin Gan, Shuangjia Zheng, Fenglong Gu, Chao Zhao, Jun Xu

J. Chem. Inf. Model., 2020

RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist.

Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang

Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020

Communicative Representation Learning on Attributed Molecular Graphs.

Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang

Proceedings of the Twenty-Ninth International Joint Conference on Artificial Intelligence, 2020

2019

Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism.

Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu

J. Chem. Inf. Model., 2019

QBMG: quasi-biogenic molecule generator with deep recurrent neural network.

Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu

J. Cheminformatics, 2019

Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks.

Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang

CoRR, 2019