Configuration

Geneformer (Kedzierska et al. 2025)

Configuration of Geneformer: Geneformer cell representation; Zero-shot; pretrained weights, no fine-tuning; Mean of gene embeddings per cell.

15 evaluations · 99 results 2 open disagreements between studies involve its model

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

15 evaluations · 99 results. Different protocols are not a single leaderboard.

Sorted by Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding)	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)	Avg bio (AvgBIO (mean of cell-type ASW, NMI and ARI; NMI and ARI on Louvain clusters at the best-NMI resolution); whole dataset; UMAP projection of the embedding)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions)	Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; UMAP projection of the embedding)	Scib asw label (cell-type ASW; whole dataset; full embedding dimensions)	Scib asw label (cell-type ASW; whole dataset; UMAP projection of the embedding)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions)	Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; UMAP projection of the embedding)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions)	Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); UMAP projection of the embedding)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions)	Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding)	Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions)	Scib pcr batch (principal component regression on batch; whole dataset; UMAP projection of the embedding)	Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; best value across datasets)	Pearson (Geneformer input versus predicted gene ranking, all genes unmasked; median across datasets)	Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); full embedding dimensions)	Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); UMAP projection of the embedding)	Rank (rank of the median ARI score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median ASW score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median Average batch score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median Average BIO score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median Batch integration score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median NMI score across datasets among the eight representations (1 = best); full embedding dimensions)	Rank (rank of the median PCR score across datasets among the eight representations (1 = best); full embedding dimensions)
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (12k) (Kedzierska et al. 2025)	0.6 (best in column)	Not reported	0.59 (best in column)	Not reported	0.65 (best in column)	Not reported	0.51 (best in column)	Not reported	0.48 (best in column)	Not reported	8	Not reported	0.97 (best in column)	Not reported	0 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (95k) (Kedzierska et al. 2025)	0.4	Not reported	0.52	Not reported	0.65 (best in column)	Not reported	0.51 (best in column)	Not reported	Not reported	Not reported	6 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Immune (330k) (Kedzierska et al. 2025)	0.19	Not reported	0.35	Not reported	0.42	Not reported	0.45	Not reported	0.38	Not reported	8	Not reported	0.76	Not reported	0 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.14	Not reported	0.3	Not reported	0.35	Not reported	0.41	Not reported	0.45	Not reported	8	Not reported	0.9	Not reported	0 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (16k) (Kedzierska et al. 2025)	0.09	Not reported	0.24	Not reported	0.26	Not reported	0.37	Not reported	0.3	Not reported	8	Not reported	0.6	Not reported	0 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (8k) (Kedzierska et al. 2025)	0.05	Not reported	0.22	Not reported	0.16	Not reported	0.46	Not reported	0.36	Not reported	Not reported	Not reported	0.73	Not reported	0 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Evaluated datasets, aggregated (Kedzierska et al. 2025)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	8	Not reported	7	8	8	7	7	8	8
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 Geneformer pretraining-objective reconstruction, Evaluated datasets, aggregated (Kedzierska et al. 2025)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.95	0.56	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Evaluated datasets, aggregated (Kedzierska et al. 2025)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	8	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Immune (330k) (Kedzierska et al. 2025)	Not reported	0.12	Not reported	0.29	Not reported	0.34	Not reported	0.4	Not reported	0.24	Not reported	8	Not reported	0.49	Not reported	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (16k) (Kedzierska et al. 2025)	Not reported	0.07	Not reported	0.22	Not reported	0.24	Not reported	0.35	Not reported	0.18	Not reported	8	Not reported	0.37	Not reported	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (8k) (Kedzierska et al. 2025)	Not reported	0.02	Not reported	0.2	Not reported	0.16	Not reported	0.42	Not reported	0.26	Not reported	Not reported	Not reported	0.53	Not reported	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (12k) (Kedzierska et al. 2025)	Not reported	0.37 (best in column)	Not reported	0.51 (best in column)	Not reported	0.58 (best in column)	Not reported	0.6 (best in column)	Not reported	0.71 (best in column)	Not reported	7	Not reported	0.89 (best in column)	Not reported	0.53 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (95k) (Kedzierska et al. 2025)	Not reported	0.3	Not reported	0.45	Not reported	0.48	Not reported	0.58	Not reported	Not reported	Not reported	6 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Geneformer (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Tabula Sapiens (483k) (Kedzierska et al. 2025)	Not reported	0.11	Not reported	0.22	Not reported	0.3	Not reported	0.26	Not reported	0.35	Not reported	8	Not reported	0.71	Not reported	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 99 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	8 Rank (overall average ranking across datasets, based on mean biological-conservation and batch-mixing scores (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell B10, row 'Geneformer', column 'Average ranking'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	7 Rank (rank of the median ARI score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell D9, row 'Geneformer', column 'ARI'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	8 Rank (rank of the median ASW score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell C9, row 'Geneformer', column 'ASW'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	8 Rank (rank of the median Average batch score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell F9, row 'Geneformer', column 'Average batch'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	7 Rank (rank of the median Average BIO score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell B9, row 'Geneformer', column 'Average BIO'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	7 Rank (rank of the median Batch integration score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell G9, row 'Geneformer', column 'Batch integration'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	8 Rank (rank of the median NMI score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell E9, row 'Geneformer', column 'NMI'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	8 Rank (rank of the median PCR score across datasets among the eight representations (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on evaluated datasets (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS3' cell H9, row 'Geneformer', column 'PCR'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.19 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q19, metric block 'ARI', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.45 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q7, metric block 'ASW', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.38 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q40, metric block 'Average batch', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.35 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q25, metric block 'AvgBIO', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.76 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q30, metric block 'Batch integration', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.42 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q13, metric block 'NMI', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q35, metric block 'PCR', row 'Immune (330k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	8 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Immune (330k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell F10, row 'Geneformer', column 'Immune (330k)'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.09 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q15, metric block 'ARI', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.37 Scib asw label (cell-type ASW; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q3, metric block 'ASW', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.3 Average batch score (average batch score (mean of batch integration score and PCR batch score); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q37, metric block 'Average batch', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.24 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) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q21, metric block 'AvgBIO', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.6 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q27, metric block 'Batch integration', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.26 Normalized mutual information (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q9, metric block 'NMI', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0 Scib pcr batch (principal component regression on batch; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q32, metric block 'PCR', row 'Pancreas (16k)', column 'Geneformer' (single-value column)
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	8 Rank (rank among the eight representations by mean biological-conservation and batch-mixing scores on this dataset (1 = best); full embedding dimensions) unitless · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (16k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS4' cell C10, row 'Geneformer', column 'Pancreas (16k)'
Configuration: Geneformer (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (8k) (Kedzierska et al. 2025)	0.05 Adjusted rand index (Louvain clusters at best-NMI resolution versus cell-type labels; whole dataset; full embedding dimensions) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Geneformer cell embedding on Pancreas (8k) (Kedzierska et al. 2025) gfm-guides-20261014-kedzierska2025-protocol-cell-embedding Aggregation: Not reported Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS6' cell Q16, metric block 'ARI', row 'Pancreas (8k)', column 'Geneformer' (single-value column)

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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

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Stable ID: gfm-guides-20261014-kedzierska2025-config-geneformer

areas: single-cell
contexts: research
method types: foundation_model
reported name: Geneformer
foundation model eligible: true
training setting: Zero-shot; pretrained weights, no fine-tuning
representation: Mean of gene embeddings per cell
version: Geneformer commit 5d0082c (2023-11-21)
checkpoint: Geneformer code at commit 5d0082c (2023-11-21); 6 Transformer layers, 4 attention heads, pretrained on 27.4M human single-cell transcriptomes (Methods); cell embedding = average of gene embeddings
access reuse: Evaluation code: github.com/microsoft/zero-shot-scfoundation (MIT), archived on Zenodo; not pinned to a commit in the article
source locator: Pages 7-8 'Models and baselines'; page 11 'Code availability'
provenance note: Geneformer cell representation as evaluated zero-shot by Kedzierska et al. 2025.

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