Consensus Nature Inspired Clustering of Single-Cell RNA-Sequencing Data

Abstract

Single-cell RNA sequencing (scRNA-seq) uncovers the disparity of cellular heterogeneity giving insights about the expression profiles of distinct cells revealing cellular differentiation. The rapid advancements in scRNA-seq technologies enable researchers to exploit questions regarding cancer heterogeneity, tumor microenvironment, etc. The process of analyzing mainly clustering scRNA-seq data is computationally challenging due to its noisy high dimensionality nature. In this paper, a computational clustering approach is proposed to cluster scRNA-seq data based on consensus clustering using swarm intelligent optimization algorithms to accurately recognize cell subtypes. The proposed approach uses variational auto-encoders to handle the curse of dimensionality, as it operates to create a latent biologically relevant feature space representing the original data. The new latent space is then clustered using Particle Swarm Optimization Algorithm, Multi-Verse Optimization Algorithm and Grey Wolf Optimization Algorithm. A consensus solution is found using solutions returned by the swarm intelligent algorithms. The proposed approach automatically derives the number of clusters without any prior knowledge. To evaluate the performance of the proposed approach a total of four datasets have been used then a comparison against the existing methods in literature has been performed. Experimental results show that the proposed approach performs better achieving higher results in terms of adjusted rand index.