Unsupervisedly Prompting AlphaFold2 for Few-Shot Learning of Accurate Folding Landscape and Protein Structure Prediction

2 code implementations • 20 Aug 2022 • Jun Zhang, Sirui Liu, Mengyun Chen, Haotian Chu, Min Wang, Zidong Wang, Jialiang Yu, Ningxi Ni, Fan Yu, Diqing Chen, Yi Isaac Yang, Boxin Xue, Lijiang Yang, YuAn Liu, Yi Qin Gao

Data-driven predictive methods which can efficiently and accurately transform protein sequences into biologically active structures are highly valuable for scientific research and medical development.

Denoising Few-Shot Learning +2

PSP: Million-level Protein Sequence Dataset for Protein Structure Prediction

2 code implementations • 24 Jun 2022 • Sirui Liu, Jun Zhang, Haotian Chu, Min Wang, Boxin Xue, Ningxi Ni, Jialiang Yu, Yuhao Xie, Zhenyu Chen, Mengyun Chen, YuAn Liu, Piya Patra, Fan Xu, Jie Chen, Zidong Wang, Lijiang Yang, Fan Yu, Lei Chen, Yi Qin Gao

We provide in addition the benchmark training procedure for SOTA protein structure prediction model on this dataset.

Protein Structure Prediction

THOR, Trace-based Hardware-adaptive layer-ORiented Natural Gradient Descent Computation

no code implementations • AAAI Technical Track on Machine Learning 2021 • Mengyun Chen, Kaixin Gao, Xiaolei Liu, Zidong Wang, Ningxi Ni, Qian Zhang, Lei Chen, Chao Ding, ZhengHai Huang, Min Wang, Shuangling Wang, Fan Yu, Xinyuan Zhao, Dachuan Xu

It is well-known that second-order optimizer can accelerate the training of deep neural networks, however, the huge computation cost of second-order optimization makes it impractical to apply in real practice.