Biological Factor Regulatory Neural Network

1 code implementation • 11 Apr 2023 • Xinnan Dai, Caihua Shan, Jie Zheng, Xiaoxiao Li, Dongsheng Li

BFReg-NN starts from gene expression data and is capable of merging most existing biological knowledge into the model, including the regulatory relations among genes or proteins (e. g., gene regulatory networks (GRN), protein-protein interaction networks (PPI)) and the hierarchical relations among genes, proteins and pathways (e. g., several genes/proteins are contained in a pathway).

Single Cells Are Spatial Tokens: Transformers for Spatial Transcriptomic Data Imputation

1 code implementation • 6 Feb 2023 • Hongzhi Wen, Wenzhuo Tang, Wei Jin, Jiayuan Ding, Renming Liu, Xinnan Dai, Feng Shi, Lulu Shang, Hui Liu, Yuying Xie

In particular, investigate the following two key questions: (1) $\textit{how to encode spatial information of cells in transformers}$, and (2) $\textit{ how to train a transformer for transcriptomic imputation}$.

Computational Efficiency Imputation