scTPC: a novel semi-supervised deep clustering model for scRNA-seq data.

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Abstract

Continuous advancements in single-cell RNA sequencing technology (scRNA-seq) 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.This study investigates a semi-supervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint and cross-entropy constraint based on deep learning. Specifically, the model begins by pre-training a denoising autoencoder based on a zero-inflated negative binomial (ZINB) 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 5 simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework.scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.Supplementary data are available at Bioinformatics online.© The Author(s) 2024. Published by Oxford University Press.