Limitations of cell embedding metrics assessed using drifting islands

2025/06/11 by Hanchen Wang, Jure Leskovec, Aviv Regev · 1 voice
Biochemistry, Genetics and Molecular Biology · Engineering · #Cell Image Analysis Techniques #Microfluidic and Bio-sensing Technologies #Single-cell and spatial transcriptomics

paper · doi:10.1038/s41587-025-02702-z

crossref issued 2025/06/11 · crossref published 2025/06/11 · crossref published-online 2025/06/11 · openalex publication_date 2025/06/11 · crossref created 2025/06/11 · openalex created_date 2025/10/10 · crossref published-print 2026/04/01 · crossref deposited 2026/04/17 · openalex updated_date 2026/07/28 · crossref indexed 2026/07/31

Citations

• A benchmark of batch-effect correction methods for single-cell RNA sequencing data
• Integrated analysis of multimodal single-cell data
• Benchmarking atlas-level data integration in single-cell genomics
• Transfer learning enables predictions in network biology
• Scientific discovery in the age of artificial intelligence
• Automatic cell-type harmonization and integration across Human Cell Atlas datasets
• Zero-shot evaluation reveals limitations of single-cell foundation models
• Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Discussions

• Brief communication by Hanchen Wang, Jure Leskovec & Aviv Regev in @natbiotech.nature.com on limitations of single cell embedding metrics. TL;DR: "Islanders" flag distortions in biological continuums, [bsky, 1 points, 0 comments]