Subgraph extraction and graph representation learning for single cell Hi-C imputation and clustering
Jiahao Zheng, Yuedong Yang, Zhiming Dai
Abstract
Single-cell Hi-C (scHi-C) technology enables the investigation of 3D chromatin structure variability across individual cells. However, the analysis of scHi-C data is challenged by a large number of missing values. Here, we present a scHi-C data imputation model HiC-SGL, based on Subgraph extraction and graph representation learning. HiC-SGL can also learn informative low-dimensional embeddings of cells. We demonstrate that our method surpasses existing methods in terms of imputation accuracy and clustering performance by various metrics.
Topics & Concepts
Imputation (statistics)Cluster analysisComputer scienceGraphArtificial intelligenceMachine learningTheoretical computer scienceMissing dataGenomics and Chromatin DynamicsGene expression and cancer classificationSingle-cell and spatial transcriptomics