I’m currently a first year Ph.D student advised by Prof. Ming of EECS-Ling Lab from School of Integrated Circuits, Southeast University.
I received my B.S. and M.S. degrees from Central China Normal University (CCNU) and Nanjing University of Posts and Telecommunications (NJUPT), separately.
My research 
I was an research intern at Microsoft Research Asia (MSRA), AI for Science group from 2022 to 2023, during which I obtained the Stars of Tomorrow Internship Program Award.
🔥 News
- 2024.09: 🎉🎉 Vina-GPU 2.1: towards further optimizing docking speed and precision of AutoDock Vina and its derivatives has been accepted in IEEE/ACM Transactions on Computational Biology and Bioinformatics.
- 2024.06: 🎉🎉 Modeling equivariant neural networks for hardware acceleration, a case study on the molecular docking tool DiffDock has been accepted in IEEE PACRIM’2024.
- 2024.05: 🎉🎉 DiG has been accepted (as a co-author) in Nature Machine Intelligence. Much appreciated to MSRA AI4Science.
- 2024.04: 🎉🎉 Vina-FPGA-Cluster has been accepted (as a co-author) in IEEE Transactions on Biomedical Circuits and Systems
📝 Publications
Shidi Tang, Ji Ding, Xiangyu Zhu, Zheng Wang, Haitao Zhao, Jiansheng Wu
IEEE/ACM Transactions on Computational Biology and Bioinformatics (Early Access).
- This work presents Vina-GPU 2.1
, aimed at enhancing the docking speed and precision of AutoDock Vina and its derivatives through the integration of novel algorithms to facil-itate improved docking and virtual screening outcomes.
Shidi Tang, Xingxing Zhou, Ming Ling.
PACRIM’2024.
- This work proposes first SystemC model for equivariant neural networks, specifically targeting Diffdock, with the aim of accelerating its performance using customized hardware such as the FPGA..
Predicting equilibrium distributions for molecular systems with deep learning
Shuxin Zheng, Jiyan He, Chang Liu, Yu Shi, Ziheng Lu, Weitao Feng, Fusong Ju, Jiaxi Wang, Jianwei Zhu, Yaosen Min, He Zhang, Shidi Tang, Hongxia Hao, Peiran Jin, Chi Chen, Frank Noé, Haiguang Liu, Tie-Yan Liu.
Nature Machine Intelligence (2024): 1-10.
- This work proposes Distributional Graphormer (DiG) in an attempt to predict the equilibrium distribution of molecular systems.
Ming Ling, Zhihao Feng, Ruiqi Chen, Yi Shao, Shidi Tang, Yanxiang Zhu
IEEE Transactions on Biomedical Circuits and Systems (TBCAS) (2024).
- This work presents Vina-FPGA-cluster, a multi-FPGA-based molecular docking tool enabling high-accuracy and multi-level parallel Vina acceleration.
Vina-GPU 2.0: further accelerating AutoDock Vina and its derivatives with graphics processing units
Ji Ding, Shidi Tang, Zheming Mei, Lingyue Wang, Qinqin Huang, Haifeng Hu, Ming Ling, Jiansheng Wu
Journal of Chemical Information and Modeling (JCIM) 63 (7), 1982-1998
- This work presents Vina-GPU 2.0
to further accelerate AutoDock Vina and its derivatives with graphics processing units.
Xingxing Zhou, Ming Ling, Qingde Lin, Shidi Tang, Jiansheng Wu, Haifeng Hu
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2023
- This work presents a probabilistic model for the effectiveness of multiple initial states parallel SA (MISPSA) that is adapted in Vina-GPU.
Accelerate autodock vina with GPUs
Shidi Tang, Ruiqi Chen, Mengru Lin, Qingde Lin, Yanxiang Zhu, Ji Ding, Haifeng Hu, Ming Ling, Jiansheng Wu
Molecules, 2022, 27(9): 3041
- This work presents a parallel algorithm called Vina-GPU
and the OpenCL implementation on GPUs.
A fast approximate check polytope projection algorithm for ADMM decoding of LDPC codes
Qiaoqiao Xia, Yan Lin, Shidi Tang, Qinglin Zhang
IEEE Communications Letters, 2019, 23(9): 1520-1523.
- This work presents a fast projection algorithm for ADMM decoding of LDPC codes
🎖 Honors and Awards
- 2023.8 Stars of Tomorrow Internship Program Award at Microsoft Research Asia.
📖 Educations
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B.S. in Communication Engineering, 2016-2019
Central China Normal University (CCNU), Wuhan, China
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M.S. in Biomedical Engineering, 2020-2023
Nanjing University of Posts and Telecommunications (NJUPT), Nanjing, China
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Ph.D student, 2023-present
Southeast University, Nanjing, China
💻 Internships
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Research Intern, 2022-2023
Microsoft Research Asia (MSRA), AI for Science group, Beijing, China