Nonparametric clustering of RNA-sequencing data

TL;DR

This paper introduces a nonparametric clustering method for RNA-sequencing data that avoids specifying explicit distributions, simplifies analysis, and produces biologically meaningful clusters, outperforming traditional mixture-model approaches.

Contribution

It applies a nonparametric Maximum Smoothed Likelihood algorithm to transcriptomics data, bypassing the need for distributional assumptions in clustering RNA-seq data.

Findings

Produces biologically meaningful clusters

Outperforms traditional mixture-model algorithms

Eases the practitioner's task by avoiding explicit distribution specification

Abstract

Identification of clusters of co-expressed genes in transcriptomic data is a difficult task. Most algorithms used for this purpose can be classified into two broad categories: distance-based or model-based approaches. Distance-based approaches typically utilize a distance function between pairs of data objects and group similar objects together into clusters. Model-based approaches are based on using the mixture-modeling framework. Compared to distance-based approaches, model-based approaches offer better interpretability because each cluster can be explicitly characterized in terms of the proposed model. However, these models present a particular difficulty in identifying a correct multivariate distribution that a mixture can be based upon. In this manuscript, we review some of the approaches used to select a distribution for the needed mixture model first. Then, we propose avoiding this problem altogether by using a nonparametric MSL (Maximum Smoothed Likelihood) algorithm. This algorithm was proposed earlier in statistical literature but has not been, to the best of our knowledge, applied to transcriptomics data. The salient feature of this approach is that it avoids explicit specification of distributions of individual biological samples altogether, thus making the task of a practitioner easier. When used on a real dataset, the algorithm produces a large number of biologically meaningful clusters and compares favorably to the two other mixture-based algorithms commonly used for RNA-seq data clustering. Our code is publicly available in Github at https://github.com/Matematikoi/non_parametric_clustering.