ArticleBioinformatics (Oxford, England)2025
AcImpute: a constraint-enhancing smooth-based approach for imputing single-cell RNA sequencing data.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- scCADI: Cell-Aware Diffusion Model for Single-Cell RNA-seq Imputation.Interdisciplinary sciences, computational life sciences · 2026Article
- scTACL: a multitask topology-aware contrastive learning approach for single-cell transcriptomics analysis.Bioinformatics (Oxford, England) · 2026Article
- scZiva: imputation method for single-cell RNA-seq data with zero-inflated variational autoencoder.BMC bioinformatics · 2026Article
- scGACL: a generative adversarial network with multi-scale contrastive learning for accurate single-cell RNA sequencing imputation.Briefings in bioinformatics · 2026Article
- scVGAMF: a novel imputation method for scRNA-seq data by integrating linear and non-linear features.Briefings in bioinformatics · 2025Article
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Authors and funding
4 authors.
Funding
Abstract
motivationSingle-cell RNA sequencing (scRNA-seq) provides a powerful tool for studying cellular heterogeneity and complexity. However, dropout events in single-cell RNA-seq data severely hinder the effectiveness and accuracy of downstream analysis. Therefore, data preprocessing with imputation methods is crucial to scRNA-seq analysis.
resultsTo address the issue of oversmoothing in smoothing-based imputation methods, the presented AcImpute, an unsupervised method that enhances imputation accuracy by constraining the smoothing weights among cells for genes with different expression levels. Compared with nine other imputation methods in cluster analysis and trajectory inference, the experimental results can demonstrate that AcImpute effectively restores gene expression, preserves inter-cell variability, preventing oversmoothing and improving clustering and trajectory inference performance. AVAILABILITY AND IMPLEMENTATION: The code is available at https://github.com/Liutto/AcImpute.
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