Discriminating the single-cell gene regulatory networks of human pancreatic islets: A novel deep learning application

Abstract

Analysis of single-cell pancreatic data can play an important role in understanding various metabolic diseases and health conditions. Due to the sparsity and noise present in such single-cell gene expression data, inference of single-cell gene regulatory networks remains a challenge. Since recent studies have reported the reliable inference of single-cell gene regulatory networks (SCGRNs), the current study focused on discriminating the SCGRNs of T2D patients from those of healthy controls. By accurately distinguishing SCGRNs of healthy pancreas from those of T2D pancreas, it would be possible to annotate, organize, visualize, and identify common patterns of SCGRNs in metabolic diseases. Such annotated SCGRNs could play an important role in accelerating the process of building large data repositories. This study aimed to contribute to the development of a novel deep learning (DL) application. First, we generated a dataset consisting of 224 SCGRNs belonging to both T2D and healthy pancreas and made it freely available. Next, we chose seven DL architectures, including VGG16, VGG19, Xception, ResNet50, ResNet101, DenseNet121, and DenseNet169, trained each of them on the dataset, and checked their prediction based on a test set. Of note, we evaluated the DL architectures on a single NVIDIA GeForce RTX 2080Ti GPU. Experimental results on the whole dataset, using several performance measures, demonstrated the superiority of VGG19 DL model in the automatic classification of SCGRNs, derived from the single-cell pancreatic data.

Keywords: Applications in biology and medicine; Cell biological processes; Deep learning; Gene regulatory networks; Pancreatic islets; Single-cell analysis.