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Improving cell type identification with Gaussian noise-augmented single-cell RNA-seq contrastive learning.

Ibrahim AlsaggafDaniel BuchanCen Wan
Published in: Briefings in functional genomics (2024)
Cell type identification is an important task for single-cell RNA-sequencing (scRNA-seq) data analysis. Many prediction methods have recently been proposed, but the predictive accuracy of difficult cell type identification tasks is still low. In this work, we proposed a novel Gaussian noise augmentation-based scRNA-seq contrastive learning method (GsRCL) to learn a type of discriminative feature representations for cell type identification tasks. A large-scale computational evaluation suggests that GsRCL successfully outperformed other state-of-the-art predictive methods on difficult cell type identification tasks, while the conventional random genes masking augmentation-based contrastive learning method also improved the accuracy of easy cell type identification tasks in general.
Keyphrases
  • single cell
  • rna seq
  • bioinformatics analysis
  • working memory
  • data analysis
  • high throughput
  • genome wide
  • air pollution
  • dna methylation
  • deep learning
  • soft tissue