scTPC: a novel semisupervised deep clustering model for scRNA-seq data

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 5
• Main Authors: Qiu, Yushan, Yang, Lingfei, Jiang, Hao, Zou, Quan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 02.05.2024; Oxford Publishing Limited (England)
• Subjects: Algorithms; Availability; Binomial distribution; Biological effects; Cluster Analysis; Clustering; Constraints; Data analysis; Datasets; Deep Learning; Entropy; Entropy (Information theory); Gene sequencing; Heterogeneity; Humans; Machine learning; Neurology; Original Paper; RNA-Seq - methods; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Single-Cell Gene Expression Analysis; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae293

Motivation Continuous advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled researchers to further explore the study of cell heterogeneity, trajectory inference, identification of rare cell types, and neurology. Accurate scRNA-seq data clustering is crucial in single-cell sequencing data analysis. However, the high dimensionality, sparsity, and presence of “false” zero values in the data can pose challenges to clustering. Furthermore, current unsupervised clustering algorithms have not effectively leveraged prior biological knowledge, making cell clustering even more challenging. Results This study investigates a semisupervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint, and cross-entropy constraint based on deep learning. Specifically, the model begins by pretraining a denoising autoencoder based on a zero-inflated negative binomial distribution. Deep clustering is then performed in the learned latent feature space using triplet constraints and pairwise constraints generated from partial labeled cells. Finally, to address imbalanced cell-type datasets, a weighted cross-entropy loss is introduced to optimize the model. A series of experimental results on 10 real scRNA-seq datasets and five simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework. Availability and implementation scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.