Source

Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx)

Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record · Peer-reviewed

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Records in this release that cite this source. A record can cite several sources.

1 benchmark
2 protocols
7 dataset subsets
112 evaluations
776 results
5 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Claims

Statements this source supports, each with where in the source it was checked.

Immune (330k): overlap with scGPT pretraining (Kedzierska et al. 2025): Pretraining overlap:scGPT The Immune (Cross-tissue Immune Cell Atlas) dataset was included in the scGPT pretraining data (CELLxGENE May 2023 census). (Additional file 1, sheet 'TableS2' cell H12 (column 'scGPT', row 'Immune (330k)'); page 9 'Datasets')
Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx): attributes.evidence_concerns: Evidence concerns [] (moved to attributes.limitations) (Sheets TableS3 and TableS6; article page 4-5 and page 10 'Supplementary information')
Pancreas (8k) (Kedzierska et al. 2025): description: Description Row labelled 'Pancreas (8k)' in the score sheets: the Pancreas subset without GEO GSE84133, which was in Geneformer pretraining. The Methods (page 9) say both the complete Pancreas dataset and its non-overlapping subset were scored 'in Additional file 1: Tables S1 and S5', which are the two score sheets, and this is their only extra Pancreas row. The workbook itself does not name the subset. (Article page 9 'Datasets' paragraph 3; Additional file 1 sheets TableS6 and TableS7 row 'Pancreas (8k)')
Pancreas (16k): overlap with Geneformer pretraining (Kedzierska et al. 2025): Pretraining overlap:Geneformer The Pancreas study GSE84133 (Baron et al.) was included in Geneformer pretraining; the other five Pancreas studies were not. (Additional file 1, sheet 'TableS2' cell G6 (column 'Geneformer', row 'GEO - GSE84133'); page 9 'Datasets')
Tabula Sapiens (483k): overlap with scGPT pretraining (Kedzierska et al. 2025): Pretraining overlap:scGPT Tabula Sapiens was included in the scGPT pretraining data (CELLxGENE May 2023 census). (Additional file 1, sheet 'TableS2' cell H11 (column 'scGPT', row 'Tabula Sapiens (483k)'); page 9 'Datasets')

Models, benchmarks and other records

Benchmarks (1)

Zero-shot cell embedding evaluation of single-cell foundation models (Kedzierska et al. 2025)

Protocols (2)

Dataset subsets (7)

Evaluations (112)

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

26 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03574-x/MediaObjects/13059_2025_3574_MOESM1_ESM.xlsx Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Doi 10.1186/s13059-025-03574-x Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.doi` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Licence CC-BY-4.0 Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.licence` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 3 values Each model has two columns under one merged header: a single value and a value with a bracketed range. Neither column is labelled; the caption says scores were calculated on the whole dataset and in 10 repeats on 10% subsamples. Only the single-value (whole-dataset) columns are extracted. The workbook numbers its tables differently from the article caption: workbook TableS1 is caption S7, TableS2 is S3, TableS3 is S2, TableS4 is S4, TableS5 is S6, TableS6 is S1 and TableS7 is S5. Locators use the workbook sheet names. Each model has an unlabelled single-value column and a bracketed column. Medians of the single-value columns over the five main datasets reproduce 54 of the 56 TableS3 ranks, against 39 for the bracketed central values, so the single values are the whole-dataset scores the paper ranks. The central statistic and the range type of the bracketed (10-repeat subsample) column are not stated. Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.limitations` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Media type application/vnd.openxmlformats-officedocument.spreadsheetml.sheet Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.media_type` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Publication status peer_reviewed Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.publication_status` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-10-14T12:01:36Z Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Review: artifact sha256 7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.review.artifact_sha256` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Review: date 2026-10-14 Source metadata	Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Original source ↗ No field-specific location recorded Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record Retrieved: 2026-10-14T12:01:36Z	catalogued No individual claim review recorded Audit details Field: `attributes.review.date` Source artifact SHA-256: `7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-10-23-5347695500ed · Record review: source checked

Supplementary workbook of the article, retrieved from the publisher (Springer static content) and hashed for the 2026-10-14 genomic foundation model guide fixes.

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Stable ID: gfm-guides-20261014-kedzierska2025-source-additional-file-1

areas: single-cell
contexts: research
url: https://doi.org/10.1186/s13059-025-03574-x
artifact url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03574-x/MediaObjects/13059_2025_3574_MOESM1_ESM.xlsx
version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record
retrieved at: 2026-10-14T12:01:36Z
artifact sha256: 7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e
doi: 10.1186/s13059-025-03574-x
publication status: peer_reviewed
licence: CC-BY-4.0
media type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
limitations: Each model has two columns under one merged header: a single value and a value with a bracketed range. Neither column is labelled; the caption says scores were calculated on the whole dataset and in 10 repeats on 10% subsamples. Only the single-value (whole-dataset) columns are extracted.; The workbook numbers its tables differently from the article caption: workbook TableS1 is caption S7, TableS2 is S3, TableS3 is S2, TableS4 is S4, TableS5 is S6, TableS6 is S1 and TableS7 is S5. Locators use the workbook sheet names.; Each model has an unlabelled single-value column and a bracketed column. Medians of the single-value columns over the five main datasets reproduce 54 of the 56 TableS3 ranks, against 39 for the bracketed central values, so the single values are the whole-dataset scores the paper ranks. The central statistic and the range type of the bracketed (10-repeat subsample) column are not stated.
review: method: source-hash-verification; method note: Re-downloaded from the publisher on 2026-10-14; SHA-256 matches.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: 7adee1211206c4071981a402617c293048baeeeaf415b68ecd13383678003b5e; retrieval url: https://static-content.springer.com/esm/art%3A10.1186%2Fs13059-025-03574-x/MediaObjects/13059_2025_3574_MOESM1_ESM.xlsx; note: Independent review 2026-10-14.

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subject: Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx): attributes.evidence_concerns

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Model or configuration	Metric	Value	Dataset	Evaluation
Geneformer (Kedzierska et al. 2025)	Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); full embedding dimensions)	8 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median ARI score across datasets among the eight representations (1 = best); full embedding dimensions)	7 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median ASW score across datasets among the eight representations (1 = best); full embedding dimensions)	8 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median Average batch score across datasets among the eight representations (1 = best); full embedding dimensions)	8 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median Average BIO score across datasets among the eight representations (1 = best); full embedding dimensions)	7 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median Batch integration score across datasets among the eight representations (1 = best); full embedding dimensions)	7 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median NMI score across datasets among the eight representations (1 = best); full embedding dimensions)	8 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank of the median PCR score across datasets among the eight representations (1 = best); full embedding dimensions)	8 unitless	Evaluated datasets, aggregated (Kedzierska et al. 2025)	Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.19 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	0.38 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.35 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.42 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	8 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	0.76 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	0.45 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions)	0 unitless	Immune (330k) (Kedzierska et al. 2025)	Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.05 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	0.36 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.22 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.16 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	0.73 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	0.46 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions)	0 unitless	Pancreas (8k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.09 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	0.3 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.24 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.26 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	8 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	0.6 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	0.37 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions)	0 unitless	Pancreas (16k) (Kedzierska et al. 2025)	Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.6 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	0.48 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.59 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.65 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	8 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	0.97 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	0.51 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions)	0 unitless	PBMC (12k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (12k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.4 unitless	PBMC (95k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (95k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.52 unitless	PBMC (95k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (95k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.65 unitless	PBMC (95k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (95k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	6 unitless	PBMC (95k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (95k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	0.51 unitless	PBMC (95k) (Kedzierska et al. 2025)	Geneformer cell embedding on PBMC (95k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.14 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	0.45 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; full embedding dimensions)	0.3 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	0.35 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	8 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)
Geneformer (Kedzierska et al. 2025)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	0.9 unitless	Tabula Sapiens (483k) (Kedzierska et al. 2025)	Geneformer cell embedding on Tabula Sapiens (483k) (Kedzierska et al. 2025)