ArticleNature biotechnology2026
Limitations of cell embedding metrics assessed using drifting islands.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- Article
- Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer.PLoS computational biology · 2026Article
- Atlas-Level Single-Cell and Spatial Transcriptomics Data Integration via PRIME.bioRxiv : the preprint server for biology · 2026Article
- Representation learning of single-cell RNA-seq data.RNA (New York, N.Y.) · 2026Review
- Toward trustworthy virtual cells: a roadmap for perturbation-resolved, context-aware, and experimentally validated cell models.Frontiers in cell and developmental biology · 2026Review
- A computational framework to dissect imputation strategies for single-cell histone modification data.NAR genomics and bioinformatics · 2025Article
- Biology-driven insights into the power of single-cell foundation models.Genome biology · 2025Article
- On metrics for subpopulation detection in single-cell and spatial omics data.Nucleic acids research · 2025Article
- Revealing a coherent cell state landscape across single cell datasets with CONCORD.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biological studies rely on embeddings of single-cell profiles but assessing the quality of these embeddings is challenging. Here we show that current evaluation metrics are incomplete by training a three-layer perceptron, Islander. Islander outperforms all leading embedding methods on a diverse set of cell atlases but it distorts biological structures, limiting its use for biological discovery. We then present a new metric, scGraph, to help flag such distortions.
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Registered trials
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