203-EpiAgent: Foundation Model for Single-Cell Epigenomics

Paper Talk · Nov 2, 2025 · 16m

This paper introduces EpiAgent, the first foundation model specifically designed for single-cell epigenomic data, focusing on single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) data. Developed by researchers primarily from Tsinghua University, EpiAgent is a transformer-based model pretrained on a massive corpus of human scATAC-seq data to analyze chromatin accessibility patterns. The model overcomes challenges like data sparsity by encoding chromatin accessibility as concise "cell sentences" and utilizes a bidirectional attention mechanism to capture cellular…