Shuangjia Zheng

72 papers A* 11Journal 56Unranked 5

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	CACHE Challenge #3: Targeting the Nsp3 Macrodomain of SARS-CoV-2. J. Chem. Inf. Model. Oleksandra Herasymenko, Madhushika Silva, Galen J. Correy, Abd Al-Aziz A. Abu-Saleh, Suzanne Ackloo, Cheryl H. Arrowsmith, Alan Ashworth, Fuqiang Ban, Hartmut Beck, Kevin P. Bishop, Hugo J. Bohórquez, Albina Bolotokova, Marko Breznik, Irene Chau, Yu Chen, Artem Cherkasov, Wim Dehaen, Dennis Della Corte, Katrin Denzinger, Niklas Piet Doering, Kristina Edfeldt, Aled M. Edwards, Darren Fayne, Francesco Gentile, Elisa Gibson, Ozan Gökdemir, Anders Gunnarsson, Judith Guenther, John J. Irwin, Jan Halborg Jensen, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Ashley Hutchinson, Shubhangi Kandwal, Andrea Karlova, Kushal Koirala, Sergei Kotelnikov, Dima Kozakov, Juyong Lee, Soowon Lee, Uta F. Lessel, Sijie Liu, Xuefeng Liu, Peter Loppnau, Jens Meiler, Rocco Moretti, Yurii S. Moroz, Charuvaka Muvva, Tudor I. Oprea, Brooks Paige, Amit Pandit, Keunwan Park, Gennady Poda, Mykola V. Protopopov, Vera Pütter, Rahul Ravichandran, Didier Rognan, Edina Rosta, Yogesh Sabnis, Thomas Scott, Almagul Seitova, Purshotam Sharma, François Sindt, Minghu Song, Casper Steinmann, Rick Stevens, Valerij Talagayev, Valentyna V. Tararina, Olga O. Tarkhanova, Damon Tingey, John F. Trant, Dakota Treleaven, Alexander Tropsha, W. Patrick Walters, Jude Wells, Yvonne Westermaier, Gerhard Wolber, Lars Wortmann, Shuangjia Zheng, James S. Fraser, Matthieu Schapira
2026	A*	`conf`	Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics. AAAI Jiahao Wang, Shuangjia Zheng
2026	J	`jnl`	Efficient Protein Optimization via Structure-aware Hamiltonian Dynamics. CoRR Jiahao Wang, Shuangjia Zheng
2025	J	`jnl`	A 3D pocket-aware and affinity-guided diffusion model for lead optimization. CoRR Anjie Qiao, Junjie Xie, Weifeng Huang, Hao Zhang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang, Zhen Wang, Guo-Bo Li, Jinping Lei
2025	J	`jnl`	A 3D pocket-aware lead optimization model with knowledge guidance and its application for discovery of new glutaminyl cyclase inhibitors. Briefings Bioinform. 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
2025	J	`jnl`	CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. J. Chem. Inf. Model. 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
2025	J	`jnl`	ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design. Nat. Comput. Sci. Odin Zhang, Jieyu Jin, Zhenxing Wu, Jintu Zhang, Po Yuan, Yuntao Yu, Haitao Lin, Haiyang Zhong, Xujun Zhang, Chenqing Hua, Weibo Zhao, Zhengshuo Zhang, Kejun Ying, Yufei Huang, Huifeng Zhao, Yu Kang, Peichen Pan, Jike Wang, Dong Guo, Shuangjia Zheng, Chang-Yu Hsieh, Tingjun Hou
2025	J	`jnl`	EnerBridge-DPO: Energy-Guided Protein Inverse Folding with Markov Bridges and Direct Preference Optimization. CoRR Dingyi Rong, Haotian Lu, Wenzhuo Zheng, Fan Zhang, Shuangjia Zheng, Ning Liu
2025	J	`jnl`	Fitness aligned structural modeling enables scalable virtual screening with AuroBind. CoRR 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
2025	J	`jnl`	From AI for Science to Agentic Science: A Survey on Autonomous Scientific Discovery. CoRR 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
2025	—	`conf`	GeoMHCII: Pan-Specific MHCII Peptide Interaction Prediction with Evolutionary-Guided Geometric Deep Learning. BIBM Yaokun Ji, Runze Ma, Shuangjia Zheng
2025	—	`conf`	Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Molecular Graph Learning. KDD (2) Jiahua Rao, Hanjing Lin, Jiancong Xie, Zhen Wang, Shuangjia Zheng, Yuedong Yang
2025	J	`jnl`	MolPIF: A Parameter Interpolation Flow Model for Molecule Generation. CoRR 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
2025	A*	`conf`	Multi-modal Contrastive Learning with Negative Sampling Calibration for Phenotypic Drug Discovery. CVPR Jiahua Rao, Hanjing Lin, Leyu Chen, Jiancong Xie, Shuangjia Zheng, Yuedong Yang
2025	J	`jnl`	NABench: Large-Scale Benchmarks of Nucleotide Foundation Models for Fitness Prediction. CoRR Zhongmin Li, Runze Ma, Jiahao Tan, Chengzi Tan, Shuangjia Zheng
2025	A*	`conf`	Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization. ICLR Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng
2025	J	`jnl`	VCWorld: A Biological World Model for Virtual Cell Simulation. CoRR Zhijian Wei, Runze Ma, Zichen Wang, Zhongmin Li, Shuotong Song, Shuangjia Zheng
2024	J	`jnl`	CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. J. Chem. Inf. Model. 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
2024	A*	`conf`	Causal Subgraph Learning for Generalizable Inductive Relation Prediction. KDD Mei Li, Xiaoguang Liu, Hua Ji, Shuangjia Zheng
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`	Effective Protein-Protein Interaction Exploration with PPIretrieval. CoRR Chenqing Hua, Connor W. Coley, Guy Wolf, Doina Precup, Shuangjia Zheng
2024	J	`jnl`	EnzymeFlow: Generating Reaction-specific Enzyme Catalytic Pockets through Flow Matching and Co-Evolutionary Dynamics. CoRR Chenqing Hua, Yong Liu, Dinghuai Zhang, Odin Zhang, Sitao Luan, Kevin K. Yang, Guy Wolf, Doina Precup, Shuangjia Zheng
2024	—	`conf`	GP-nano: a geometric graph network for nanobody polyreactivity prediction. BIBM Xiaolong Zhou, Qianmu Yuan, Shuangjia Zheng, Yu Wang, Yuedong Yang
2024	J	`jnl`	Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks. CoRR Jiahua Rao, Jiancong Xie, Hanjing Lin, Shuangjia Zheng, Zhen Wang, Yuedong Yang
2024	A*	`conf`	ReactZyme: A Benchmark for Enzyme-Reaction Prediction. NeurIPS Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, Shuangjia Zheng
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	J	`jnl`	Reactzyme: A Benchmark for Enzyme-Reaction Prediction. CoRR Chenqing Hua, Bozitao Zhong, Sitao Luan, Liang Hong, Guy Wolf, Doina Precup, Shuangjia Zheng
2024	J	`jnl`	Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimization. CoRR Zichen Wang, Yaokun Ji, Jianing Tian, Shuangjia Zheng
2024	J	`jnl`	RetroCaptioner: beyond attention in end-to-end retrosynthesis transformer via contrastively captioned learnable graph representation. Bioinform. Xiaoyi Liu, Chengwei Ai, Hongpeng Yang, Ruihan Dong, Jijun Tang, Shuangjia Zheng, Fei Guo
2024	J	`jnl`	Self-Supervised Contrastive Molecular Representation Learning with a Chemical Synthesis Knowledge Graph. J. Chem. Inf. Model. Jiancong Xie, Yi Wang, Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2023	J	`jnl`	Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis. IEEE Trans. Affect. Comput. Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu
2023	J	`jnl`	Mixup-Augmented Meta-Learning for Sample-Efficient Fine-Tuning of Protein Simulators. CoRR Jingbang Chen, Yian Wang, Xingwei Qu, Shuangjia Zheng, Yaodong Yang, Hao Dong, Jie Fu
2023	—	`conf`	SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation. BIBM Deqin Liu, Sheng Chen, Shuangjia Zheng, Sen Zhang, Yuedong Yang
2023	J	`jnl`	Subgraph-Aware Few-Shot Inductive Link Prediction Via Meta-Learning. IEEE Trans. Knowl. Data Eng. Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
2022	J	`jnl`	Accelerated rational PROTAC design via deep learning and molecular simulations. Nat. Mac. Intell. Shuangjia Zheng, Youhai Tan, Zhenyu Wang, Chengtao Li, Zhiqing Zhang, Xu Sang, Hongming Chen, Yuedong Yang
2022	J	`jnl`	AlphaFold2-aware protein-DNA binding site prediction using graph transformer. Briefings Bioinform. Qianmu Yuan, Sheng Chen, Jiahua Rao, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
2022	A*	`conf`	Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. IJCAI Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
2022	J	`jnl`	Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction. CoRR Jiahua Rao, Shuangjia Zheng, Sijie Mai, Yuedong Yang
2022	J	`jnl`	DRlinker: Deep Reinforcement Learning for Optimization in Fragment Linking Design. J. Chem. Inf. Model. Youhai Tan, Lingxue Dai, Weifeng Huang, Yinfeng Guo, Shuangjia Zheng, Jinping Lei, Hongming Chen, Yuedong Yang
2022	J	`jnl`	Dynamic graph dropout for subgraph-based relation prediction. Knowl. Based Syst. Sijie Mai, Shuangjia Zheng, Ya Sun, Ying Zeng, Yuedong Yang, Haifeng Hu
2022	J	`jnl`	Integrating supercomputing and artificial intelligence for life science. Patterns Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2022	J	`jnl`	Quantitative evaluation of explainable graph neural networks for molecular property prediction. Patterns Jiahua Rao, Shuangjia Zheng, Yutong Lu, Yuedong Yang
2022	J	`jnl`	Structure-Aware Multimodal Deep Learning for Drug-Protein Interaction Prediction. J. Chem. Inf. Model. Penglei Wang, Shuangjia Zheng, Yize Jiang, Chengtao Li, Junhong Liu, Chang Wen, Atanas Patronov, Dahong Qian, Hongming Chen, Yuedong Yang
2022	A*	`conf`	TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction. NeurIPS Wei Lu, Qifeng Wu, Jixian Zhang, Jiahua Rao, Chengtao Li, Shuangjia Zheng
2022	J	`jnl`	To Improve Prediction of Binding Residues With DNA, RNA, Carbohydrate, and Peptide Via Multi-Task Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Zhe Sun, Shuangjia Zheng, Huiying Zhao, Zhangming Niu, Yutong Lu, Yi Pan, Yuedong Yang
2021	J	`jnl`	BioNavi-NP: Biosynthesis Navigator for Natural Products. CoRR Shuangjia Zheng, Tao Zeng, Chengtao Li, Binghong Chen, Connor W. Coley, Yuedong Yang, Ruibo Wu
2021	A*	`conf`	Communicative Message Passing for Inductive Relation Reasoning. AAAI Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
2021	J	`jnl`	Deep Learning Enables Accurate Diagnosis of Novel Coronavirus (COVID-19) With CT Images. IEEE ACM Trans. Comput. Biol. Bioinform. 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
2021	J	`jnl`	Deep scaffold hopping with multimodal transformer neural networks. J. Cheminformatics Shuangjia Zheng, Zengrong Lei, Haitao Ai, Hongming Chen, Daiguo Deng, Yuedong Yang
2021	—	`conf`	DeepANIS: Predicting antibody paratope from concatenated CDR sequences by integrating bidirectional long-short-term memory and transformer neural networks. BIBM Pan Zhang, Shuangjia Zheng, Jianwen Chen, Yaoqi Zhou, Yuedong Yang
2021	J	`jnl`	Hybrid Contrastive Learning of Tri-Modal Representation for Multimodal Sentiment Analysis. CoRR Sijie Mai, Ying Zeng, Shuangjia Zheng, Haifeng Hu
2021	J	`jnl`	Kinase Inhibitor Scaffold Hopping with Deep Learning Approaches. J. Chem. Inf. Model. Lizhao Hu, Yuyao Yang, Shuangjia Zheng, Jun Xu, Ting Ran, Hongming Chen
2021	A*	`conf`	Learning Attributed Graph Representation with Communicative Message Passing Transformer. IJCAI Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
2021	J	`jnl`	Learning Attributed Graph Representations with Communicative Message Passing Transformer. CoRR Jianwen Chen, Shuangjia Zheng, Ying Song, Jiahua Rao, Yuedong Yang
2021	J	`jnl`	Meta Learning for Low-Resource Molecular Optimization. J. Chem. Inf. Model. Jiahao Wang, Shuangjia Zheng, Jianwen Chen, Yuedong Yang
2021	J	`jnl`	Molecular Attributes Transfer from Non-Parallel Data. CoRR Shuangjia Zheng, Ying Song, Zhang Pan, Chengtao Li, Le Song, Yuedong Yang
2021	J	`jnl`	PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. Briefings Bioinform. Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu
2021	J	`jnl`	Precise estimation of residue relative solvent accessible area from Cα atom distance matrix using a deep learning method. Bioinform. Jianzhao Gao, Shuangjia Zheng, Mengting Yao, Peikun Wu
2021	J	`jnl`	Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction. CoRR Jiahua Rao, Shuangjia Zheng, Yuedong Yang
2021	J	`jnl`	Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J. Cheminformatics Jianwen Chen, Shuangjia Zheng, Huiying Zhao, Yuedong Yang
2021	J	`jnl`	Subgraph-aware Few-Shot Inductive Link Prediction via Meta-Learning. CoRR Shuangjia Zheng, Sijie Mai, Ya Sun, Haifeng Hu, Yuedong Yang
2020	J	`jnl`	Communicative Message Passing for Inductive Relation Reasoning. CoRR Sijie Mai, Shuangjia Zheng, Yuedong Yang, Haifeng Hu
2020	A*	`conf`	Communicative Representation Learning on Attributed Molecular Graphs. IJCAI Ying Song, Shuangjia Zheng, Zhangming Niu, Zhang-Hua Fu, Yutong Lu, Yuedong Yang
2020	J	`jnl`	Predicting Retrosynthetic Reactions Using Self-Corrected Transformer Neural Networks. J. Chem. Inf. Model. Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
2020	J	`jnl`	Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
2020	J	`jnl`	Predicting the Feasibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition Reactions Using a Recurrent Neural Network with a Self-Attention Mechanism. J. Chem. Inf. Model. Shimin Su, Yuyao Yang, Hanlin Gan, Shuangjia Zheng, Fenglong Gu, Chao Zhao, Jun Xu
2020	J	`jnl`	Publisher Correction: Predicting drug-protein interaction using quasi-visual question answering system. Nat. Mach. Intell. Shuangjia Zheng, Yongjian Li, Sheng Chen, Jun Xu, Yuedong Yang
2020	A*	`conf`	RetroXpert: Decompose Retrosynthesis Prediction Like A Chemist. NeurIPS Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang
2020	J	`jnl`	RetroXpert: Decompose Retrosynthesis Prediction like a Chemist. CoRR Chaochao Yan, Qianggang Ding, Peilin Zhao, Shuangjia Zheng, Jinyu Yang, Yang Yu, Junzhou Huang
2019	J	`jnl`	Identifying Structure-Property Relationships through SMILES Syntax Analysis with Self-Attention Mechanism. J. Chem. Inf. Model. Shuangjia Zheng, Xin Yan, Yuedong Yang, Jun Xu
2019	J	`jnl`	Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks. CoRR Shuangjia Zheng, Jiahua Rao, Zhongyue Zhang, Jun Xu, Yuedong Yang
2019	J	`jnl`	QBMG: quasi-biogenic molecule generator with deep recurrent neural network. J. Cheminformatics Shuangjia Zheng, Xin Yan, Qiong Gu, Yuedong Yang, Yunfei Du, Yutong Lu, Jun Xu