Configuration

Harmony (Kedzierska et al. 2025)

Configuration of Harmony: Fitted on each target dataset using its batch labels; Harmony-adjusted embedding.

Overview

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

Evaluations and results

14 evaluations · 97 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)	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)
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (16k) (Kedzierska et al. 2025)	0.93 (best in column)	Not reported	0.82 (best in column)	Not reported	0.89 (best in column)	Not reported	0.66 (best in column)	Not reported	0.79	Not reported	1 (best in column)	Not reported	0.82	Not reported	0.77	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Pancreas (8k) (Kedzierska et al. 2025)	0.87	Not reported	0.79	Not reported	0.86	Not reported	0.63	Not reported	0.64	Not reported	Not reported	Not reported	0.83	Not reported	0.45	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (12k) (Kedzierska et al. 2025)	0.72	Not reported	0.72	Not reported	0.82	Not reported	0.62	Not reported	0.89 (best in column)	Not reported	1 (best in column)	Not reported	0.97 (best in column)	Not reported	0.82 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, PBMC (95k) (Kedzierska et al. 2025)	0.6	Not reported	0.63	Not reported	0.74	Not reported	0.55	Not reported	Not reported	Not reported	2	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
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Immune (330k) (Kedzierska et al. 2025)	0.51	Not reported	0.57	Not reported	0.67	Not reported	0.52	Not reported	0.74	Not reported	1 (best in column)	Not reported	0.8	Not reported	0.67	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions, Tabula Sapiens (483k) (Kedzierska et al. 2025)	0.27	Not reported	0.39	Not reported	0.51	Not reported	0.39	Not reported	0.41	Not reported	7	Not reported	0.74	Not reported	0.08	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (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	2	Not reported	2	1	2	2	8	2	2
Harmony (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	2	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Immune (330k) (Kedzierska et al. 2025)	Not reported	0.5	Not reported	0.55	Not reported	0.66	Not reported	0.49	Not reported	0.57	Not reported	1 (best in column)	Not reported	0.54	Not reported	0.6	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (16k) (Kedzierska et al. 2025)	Not reported	0.57	Not reported	0.71	Not reported	0.78	Not reported	0.77 (best in column)	Not reported	0.67	Not reported	1 (best in column)	Not reported	0.66	Not reported	0.69	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Pancreas (8k) (Kedzierska et al. 2025)	Not reported	0.63 (best in column)	Not reported	0.72 (best in column)	Not reported	0.8 (best in column)	Not reported	0.73	Not reported	0.49	Not reported	Not reported	Not reported	0.69	Not reported	0.28	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (12k) (Kedzierska et al. 2025)	Not reported	0.5	Not reported	0.66	Not reported	0.73	Not reported	0.75	Not reported	0.94 (best in column)	Not reported	2	Not reported	0.91 (best in column)	Not reported	0.96 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, PBMC (95k) (Kedzierska et al. 2025)	Not reported	0.56	Not reported	0.63	Not reported	0.71	Not reported	0.64	Not reported	Not reported	Not reported	2	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
Harmony (Kedzierska et al. 2025)Evaluation	Kedzierska et al. 2025 cell embedding scoring after UMAP projection, Tabula Sapiens (483k) (Kedzierska et al. 2025)	Not reported	0.2	Not reported	0.32	Not reported	0.5	Not reported	0.25	Not reported	0.27	Not reported	7	Not reported	0.55	Not reported	0	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

All 97 result rows with coverage, uncertainty and sources

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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: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 B4, row 'Harmony', column 'Average ranking'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 D4, row 'Harmony', column 'ARI'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	1 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 Harmony 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 C4, row 'Harmony', column 'ASW'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 F4, row 'Harmony', column 'Average batch'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 B4, row 'Harmony', column 'Average BIO'
Configuration: Harmony (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 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 Harmony 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 G4, row 'Harmony', column 'Batch integration'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 E4, row 'Harmony', column 'NMI'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Evaluated datasets, aggregated (Kedzierska et al. 2025)	2 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 Harmony 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 H4, row 'Harmony', column 'PCR'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.51 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 Harmony 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 E19, metric block 'ARI', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.52 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 Harmony 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 E7, metric block 'ASW', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.74 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 Harmony 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 E40, metric block 'Average batch', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.57 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 Harmony 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 E25, metric block 'AvgBIO', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.8 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 Harmony 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 E30, metric block 'Batch integration', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.67 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 Harmony 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 E13, metric block 'NMI', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	0.67 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 Harmony 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 E35, metric block 'PCR', row 'Immune (330k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Immune (330k) (Kedzierska et al. 2025)	1 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 Harmony 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 F4, row 'Harmony', column 'Immune (330k)'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.93 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 Harmony 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 E15, metric block 'ARI', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.66 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 Harmony 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 E3, metric block 'ASW', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.79 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 Harmony 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 E37, metric block 'Average batch', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.82 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 Harmony 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 E21, metric block 'AvgBIO', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.82 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 Harmony 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 E27, metric block 'Batch integration', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.89 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 Harmony 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 E9, metric block 'NMI', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	0.77 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 Harmony 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 E32, metric block 'PCR', row 'Pancreas (16k)', column 'Harmony' (single-value column)
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (16k) (Kedzierska et al. 2025)	1 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 Harmony 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 C4, row 'Harmony', column 'Pancreas (16k)'
Configuration: Harmony (Kedzierska et al. 2025)	Protocol: Kedzierska et al. 2025 cell embedding scoring, full embedding dimensions Dataset subset: Pancreas (8k) (Kedzierska et al. 2025)	0.87 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 Harmony 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 E16, metric block 'ARI', row 'Pancreas (8k)', column 'Harmony' (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-harmony

areas: single-cell
contexts: research
method types: specialist
reported name: Harmony
foundation model eligible: false
training setting: Fitted on each target dataset using its batch labels
representation: Harmony-adjusted embedding
missing metadata: hyperparameters: reason: unreported; version: reason: unreported
source locator: Pages 7-8 'Models and baselines'; page 11 'Code availability'
provenance note: Harmony baseline as run by Kedzierska et al. 2025.

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