Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding) of Harmony (Kedzierska et al. 2025) on Pancreas (16k) (Kedzierska et al. 2025)
0.66 Scib asw batch (batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding)
Methods
- Tested configuration
- Harmony (Kedzierska et al. 2025)
- Protocol
- Kedzierska et al. 2025 cell embedding scoring after UMAP projection
- Dataset subset
- Pancreas (16k) (Kedzierska et al. 2025)
- Procedure
- Kedzierska et al. 2025 cell embedding scoring after UMAP projection
- Evaluation
- Harmony UMAP-projected embedding on Pancreas (16k) (Kedzierska et al. 2025)
- Coverage
- Not reported scored / Not reported eligible
- Uncertainty
- Not reported by the source
- Evidence
- Independent external evaluation · source checkedKedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Additional file 1, sheet 'TableS7' cell E27, metric block 'Batch integration', row 'Pancreas (16k)', column 'Harmony' (single-value column)
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: source checked. Source checked does not mean independently reproduced.
Reproduction
- Split
- No split; each whole dataset embedded and scored
- Adaptation
- scGPT and Geneformer zero-shot from pretrained weights (scGPT random: no pretraining); scVI and Harmony fitted on each dataset with batch labels; HVG computed from each dataset
- Scoring implementation
- scib 1.0.4. ASW of cell-type labels rescaled to [0, 1]; NMI and ARI on Louvain clusters at the resolution with the highest NMI out of 20; batch integration = 1 minus absolute batch silhouette per cell type, averaged; PCR = change in variance explained by batch between the original data and the embedding (Methods, pages 9-10).
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Reported result 0.66 Individual claims | Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) Additional file 1, sheet 'TableS7' cell E27, metric block 'Batch integration', row 'Pancreas (16k)', column 'Harmony' (single-value column) Version: Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record | source checked ["source-hash-verification","deterministic-table-parse","independent-cell-check"] · 2026-10-14 independent paper Audit detailsExtraction: Read sheet 'TableS7' of the pinned workbook with a stdlib OOXML reader (extract/ooxml.py); sheet title, model headers C2:Q2, metric labels in column A and dataset labels in column B asserted; printed_value is the Excel General display of the stored number. Independent review 2026-10-14: matched. The single-value columns are whole-dataset scores: medians of these columns across the five main datasets reproduce 54 of the 56 TableS3 ranks (the bracketed columns reproduce 39). Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
2 source records and release history
- Kedzierska et al. 2025, Additional file 1 (Supplementary Tables S1-S7, xlsx) · Original source · Additional file 1 (13059_2025_3574_MOESM1_ESM.xlsx) of the version of record
- 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
Technical metadata and extraction receipts
Stable ID: gfm-guides-20261014-kedzierska2025-result-umap-pancreas-16k-harmony-batch-integration
- metric
- scib-asw-batch
- metric direction
- higher
- unit
- unitless
- printed value
- 0.66
- numeric value
- 0.66
- metric qualifier
- batch integration score (batch ASW per cell type); whole dataset; UMAP projection of the embedding
- source locator
- Additional file 1, sheet 'TableS7' cell E27, metric block 'Batch integration', row 'Pancreas (16k)', column 'Harmony' (single-value column)
- review
- method: source-hash-verification; deterministic-table-parse; independent-cell-check; method note: Workbook re-downloaded from the publisher (SHA-256 matches). An independent openpyxl reader compared every one of the 600 workbook results with the cell its locator names: value, Excel General display, metric block, dataset row, model column, protocol (full or UMAP) and evaluation links; every expected cell was found exactly once. Six cells also checked by hand.; 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: Extraction: Read sheet 'TableS7' of the pinned workbook with a stdlib OOXML reader (extract/ooxml.py); sheet title, model headers C2:Q2, metric labels in column A and dataset labels in column B asserted; printed_value is the Excel General display of the stored number. Independent review 2026-10-14: matched. The single-value columns are whole-dataset scores: medians of these columns across the five main datasets reproduce 54 of the 56 TableS3 ranks (the bracketed columns reproduce 39).
- missing metadata
- uncertainty: reason: unreported
- raw xml value
- 0.66
- workbook number format
- General