Kedzierska et al. 2025 cell embedding scoring after UMAP projection
As the full-dimension protocol, but the scIB metrics are computed on the UMAP projection of each embedding.
Overview
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56 recorded evaluations, 360 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
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All evaluations
56 evaluations · 360 results. Different protocols are not a single leaderboard.
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Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Geneformer UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- Harmony UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- HVG UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- scGPT blood UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- scGPT human UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- scGPT kidney UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- scGPT random UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- scVI UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- Geneformer UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- Harmony UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- HVG UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- scGPT blood UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
Baseline coverage
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- External evaluations
- 56
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Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Evidence
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Evidence table
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
2 source records and release history
- Zero-shot evaluation reveals limitations of single-cell foundation models (Kedzierska et al. 2025, Genome Biology 26:101) · Original source · Version of record, Genome Biology 26:101, published 2025-04-18
- Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Original source · Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-kedzierska2025-protocol-umap-embedding
- areas
- single-cell
- contexts
- research
- protocol
- Project each embedding with UMAP, then compute the same scIB metrics against cell-type and batch labels.
- version
- Genome Biology 26:101
- metric implementation
- scib 1.0.4. ASW of cell-type labels rescaled to [0, 1]; NMI and ARI on Louvain clusters at the resolution with the highest NMI out of 20; batch integration = 1 minus absolute batch silhouette per cell type, averaged; PCR = change in variance explained by batch between the original data and the embedding (Methods, pages 9-10).
- unit
- unitless
- limitations
- UMAP parameters are not stated in the article.
- source locator
- Page 4-5 'Results and discussion' (Additional file 1: Fig. S6A, Table S5); Additional file 1 sheet TableS7
Related records
- part of: Zero-shot cell embedding evaluation of single-cell foundation models (Kedzierska et al. 2025)
- used in: Evaluated datasets, aggregated (Kedzierska et al. 2025)
- used in: Immune (330k) (Kedzierska et al. 2025)
- used in: Pancreas (16k) (Kedzierska et al. 2025)
- used in: Pancreas (8k) (Kedzierska et al. 2025)
- used in: PBMC (12k) (Kedzierska et al. 2025)
- used in: PBMC (95k) (Kedzierska et al. 2025)
- used in: Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on evaluated datasets (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on Immune (330k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on Pancreas (8k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on PBMC (12k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on PBMC (95k) (Kedzierska et al. 2025)
- assessment: Geneformer UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: Harmony UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: HVG UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: scGPT blood UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: scGPT human UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: scGPT kidney UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: scGPT random UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
- assessment: scVI UMAP-projected embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)