Journal
COMPUTERS IN BIOLOGY AND MEDICINE
Volume 132, Issue -, Pages -Publisher
PERGAMON-ELSEVIER SCIENCE LTD
DOI: 10.1016/j.compbiomed.2021.104257
Keywords
Single-cell analysis; Gene regulatory networks; Cell biological processes; Pancreatic islets; Deep learning; Applications in biology and medicine
Categories
Funding
- Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah [D-152-611-1440]
Ask authors/readers for more resources
Analysis of single-cell pancreatic data is crucial for understanding metabolic diseases and health conditions, but inferring single-cell gene regulatory networks remains challenging due to data sparsity and noise. This study focused on discriminating SCGRNs of T2D patients from healthy controls to accelerate data repository construction, comparing various DL architectures and demonstrating the superior performance of the VGG19 model in automatic classification of SCGRNs from single-cell pancreatic data.
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available