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TRAFICA: An Open Chromatin Language Model to Improve Transcription Factor Binding Affinity Prediction
An open chromatin language model for transcription factor-DNA binding affinity prediction by integrating ATAC-seq data and in vitro binding profiles, achieving state-of-the-art performance.
Yu Xu 许煜, Lu Zhang, et al
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TRAFICA: An Open Chromatin Language Model to Improve Transcription Factor Binding Affinity Prediction
Causal Transformer for Learning Embeddings from Structured Medical History Records and Multi-Source Data Integration for Complex Disease Risk Prediction
A multi-source integration framework for disease risk prediction that uses causal Transformer to learn embeddings from medical history records combined with genetic, lifestyle, and physical data.
Zeming Li, Yu Xu 许煜, Debajyoti Chowdhury, Hip Fung Yip, Chonghao Wang, Lu Zhang
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Mitigation of Multi-scale Biases in Cell-type Deconvolution for Spatially Resolved Transcriptomics Using HarmoDecon
A semi-supervised deep learning model for spatial cell-type deconvolution that mitigates multi-scale biases in spatially resolved transcriptomics.
Zirui Wang, Ke Xu, Yang Liu, Yu Xu 许煜, Lu Zhang
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stDyer enables spatial domain clustering with dynamic graph embedding
An end-to-end deep learning framework for spatial domain clustering in spatially resolved transcriptomics data using dynamic graph embedding and Gaussian Mixture Variational AutoEncoder.
Ke Xu, Yu Xu 许煜, Zirui Wang, Xin Maizie Zhou, Lu Zhang
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stDyer enables spatial domain clustering with dynamic graph embedding
dynDeepDRIM: a dynamic deep learning model to infer direct regulatory interactions using time-course single-cell gene expression data
Time-course single-cell RNA sequencing (scRNA-seq) data have been widely used to explore dynamic changes in gene expression of …
Yu Xu 许煜, JiaxingCheng, Aiping Lyu, William K. Cheung, Lu Zhang
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