Deep neural network models for cell type prediction based on single-cell Hi-C data

Abstract

Abstract Background Cell type prediction is crucial to cell type identification of genomics, cancer diagnosis and drug development, and it can solve the time-consuming and difficult problem of cell classification in biological experiments. Therefore, a computational method is urgently needed to classify and predict cell types using single-cell Hi-C data. In previous studies, there is a lack of convenient and accurate method to predict cell types based on single-cell Hi-C data. Deep neural networks can form complex representations of single-cell Hi-C data and make it possible to handle the multidimensional and sparse biological datasets. Results We compare the performance of SCANN with existing methods and analyze the model by using five different evaluation metrics. When using only ML1 and ML3 datasets, the ARI and NMI values of SCANN increase by 14% and 11% over those of scHiCluster respectively. However, when using all six libraries of data, the ARI and NMI values of SCANN increase by 63% and 88% over those of scHiCluster respectively. These findings show that SCANN is highly accurate in predicting the type of independent cell samples using single-cell Hi-C data. Conclusions SCANN enhances the training speed and requires fewer resources for predicting cell types. In addition, when the number of cells in different cell types was extremely unbalanced, SCANN has higher stability and flexibility in solving cell classification and cell type prediction using the single-cell Hi-C data. This predication method can assist biologists to study the differences in the chromosome structure of cells between different cell types.

Keywords

• Deep neural networks
• Single-cell Hi-C data
• Cell type prediction
• Cell classification