scCompressSA: dual-channel self-attention based deep autoencoder model for single-cell clustering by compressing gene-gene interactions.
BMC Genomics
; 25(1): 423, 2024 Apr 29.
Article
em En
| MEDLINE
| ID: mdl-38684946
ABSTRACT
BACKGROUND:
Single-cell clustering has played an important role in exploring the molecular mechanisms about cell differentiation and human diseases. Due to highly-stochastic transcriptomics data, accurate detection of cell types is still challenged, especially for RNA-sequencing data from human beings. In this case, deep neural networks have been increasingly employed to mine cell type specific patterns and have outperformed statistic approaches in cell clustering.RESULTS:
Using cross-correlation to capture gene-gene interactions, this study proposes the scCompressSA method to integrate topological patterns from scRNA-seq data, with support of self-attention (SA) based coefficient compression (CC) block. This SA-based CC block is able to extract and employ static gene-gene interactions from scRNA-seq data. This proposed scCompressSA method has enhanced clustering accuracy in multiple benchmark scRNA-seq datasets by integrating topological and temporal features.CONCLUSION:
Static gene-gene interactions have been extracted as temporal features to boost clustering performance in single-cell clustering For the scCompressSA method, dual-channel SA based CC block is able to integrate topological features and has exhibited extraordinary detection accuracy compared with previous clustering approaches that only employ temporal patterns.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Análise de Célula Única
Limite:
Humans
Idioma:
En
Revista:
BMC Genomics
Ano de publicação:
2024
Tipo de documento:
Article