Lower-dimensional projections of cellular expression improves cell type classification from single-cell RNA sequencing

TL;DR

This paper introduces EnProCell, a reference-based method that combines ensemble dimensionality reduction and deep learning to improve cell type classification accuracy in single-cell RNA sequencing data.

Contribution

EnProCell is a novel approach that integrates PCA and discriminant analysis for feature extraction before deep learning classification, outperforming existing methods.

Findings

EnProCell achieves 98.91% accuracy on reference datasets.

EnProCell attains 99.52% accuracy on query datasets with unknown cell types.

The method is computationally efficient and easy to implement.

Abstract

Single-cell RNA sequencing (scRNA-seq) enables the study of cellular diversity at single cell level. It provides a global view of cell-type specification during the onset of biological mechanisms such as developmental processes and human organogenesis. Various statistical, machine and deep learning-based methods have been proposed for cell-type classification. Most of the methods utilizes unsupervised lower dimensional projections obtained from for a large reference data. In this work, we proposed a reference-based method for cell type classification, called EnProCell. The EnProCell, first, computes lower dimensional projections that capture both the high variance and class separability through an ensemble of principle component analysis and multiple discriminant analysis. In the second phase, EnProCell trains a deep neural network on the lower dimensional representation of data to classify cell types. The proposed method outperformed the existing state-of-the-art methods when tested on four different data sets produced from different single-cell sequencing technologies. The EnProCell showed higher accuracy (98.91) and F1 score (98.64) than other methods for predicting reference from reference datasets. Similarly, EnProCell also showed better performance than existing methods in predicting cell types for data with unknown cell types (query) from reference datasets (accuracy:99.52; F1 score: 99.07). In addition to improved performance, the proposed methodology is simple and does not require more computational resources and time. the EnProCell is available at https://github.com/umar1196/EnProCell.