Evidence claim

Relevance of BMMC held-out annotation to "Transfer cell-type annotations to a new dataset"

Use case: Transfer cell-type annotations to a new dataset
Assessed by: Chen et al. 2026 supervised cell type annotation, BMMC
Relevance: Proxy evidence
Endpoint: Accuracy, precision, recall, macro-F1, PR-AUC and ROC-AUC of supervised cell type annotation on a stratified held-out split of BMMC

Scores foundation models fine-tuned on reference labels and tested on held-out cells of the same dataset. Proxy: the use case transfers labels to a new dataset, while this split keeps train and test cells from the same study and batch structure.

5 reviewed evaluations

Evidence

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Evidence table

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19 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
Citation locations 1 values source id lit-cells-networks-20261011-chen2026-source-chen2026 locator Table 4; Results on supervised annotation; Methods 'Cell type annotation' Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.citation_locators` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison group chen2026-harmonised-fm Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_group` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Comparison title Harmonised single-cell and spatial foundation model benchmark (Chen et al. 2026) Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.comparison_title` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Constraints 2 values Inspect every linked evaluation's source locator before citing a result. Prefer macro-F1 and PR-AUC; accuracy and ROC-AUC saturate on ATAA (Results). Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.constraints` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Endpoint Accuracy, precision, recall, macro-F1, PR-AUC and ROC-AUC of supervised cell type annotation on a stratified held-out split of BMMC Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.endpoint` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed field links:assessed_by:lit-cells-networks-20261011-chen2026-protocol-annotation-bmmc Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.field` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Headline metric macro-f1 Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.headline_metric` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Limitations 6 values Preprint; single run with seed 42 and no spread, so small differences are not testable. The authors did not develop any of the six models (independent comparison), but no conventional baseline is in the tables. Within-dataset stratified split, not cross-dataset transfer. PR-AUC and ROC-AUC are macro-averaged (Methods); precision and recall are called global without a definition and appear to be averaged differently between models (source evidence concern), so do not compare them across models. Reference labels are the datasets' curated marker-gene and expert annotations, not independent ground truth. No rejection of unseen cell types or unassigned output is evaluated. Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.limitations` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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f4ef70c0d86c1d3ea8ff8600431eb0792da0bd5f355e7137bc364a42aa284bd9 Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.pins` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Rationale Scores foundation models fine-tuned on reference labels and tested on held-out cells of the same dataset. Proxy: the use case transfers labels to a new dataset, while this split keeps train and test cells from the same study and batch structure. Context-only references	Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation Original source ↗ lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation' Version: arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19) Retrieved: 2026-10-11T21:29:34Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.rationale` Source artifact SHA-256: `8137338c6146f570a6546f30707d4244baca9dab848b32c51539665a5ba539da` 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

1 source record and release history

Harmonised benchmarking of foundation models for single-cell and spatial transcriptomics reveals context-dependent generalisation · Original source · arXiv 2607.17227v2, updated 2026-09-17 (v1 posted 2026-07-19)

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Technical metadata and extraction receipts

Stable ID: use-case-mapping-lit-cells-networks-20261011-chen2026-annotation-bmmc

field: links:assessed_by:lit-cells-networks-20261011-chen2026-protocol-annotation-bmmc
value: lit-cells-networks-20261011-chen2026-protocol-annotation-bmmc
relevance: proxy
endpoint: Accuracy, precision, recall, macro-F1, PR-AUC and ROC-AUC of supervised cell type annotation on a stratified held-out split of BMMC
rationale: Scores foundation models fine-tuned on reference labels and tested on held-out cells of the same dataset. Proxy: the use case transfers labels to a new dataset, while this split keeps train and test cells from the same study and batch structure.
constraints: Inspect every linked evaluation's source locator before citing a result.; Prefer macro-F1 and PR-AUC; accuracy and ROC-AUC saturate on ATAA (Results).
limitations: Preprint; single run with seed 42 and no spread, so small differences are not testable.; The authors did not develop any of the six models (independent comparison), but no conventional baseline is in the tables.; Within-dataset stratified split, not cross-dataset transfer.; PR-AUC and ROC-AUC are macro-averaged (Methods); precision and recall are called global without a definition and appear to be averaged differently between models (source evidence concern), so do not compare them across models.; Reference labels are the datasets' curated marker-gene and expert annotations, not independent ground truth.; No rejection of unseen cell types or unassigned output is evaluated.
citation locators: source id: lit-cells-networks-20261011-chen2026-source-chen2026; locator: Table 4; Results on supervised annotation; Methods 'Cell type annotation'
source locator: lit-cells-networks-20261011-chen2026-source-chen2026: Table 4; Results on supervised annotation; Methods 'Cell type annotation'
headline metric: macro-f1
comparison group: chen2026-harmonised-fm
comparison title: Harmonised single-cell and spatial foundation model benchmark (Chen et al. 2026)
stratum label: BMMC held-out annotation
stratum order: 3
reviewed evaluations: lit-cells-networks-20261011-chen2026-eval-annotation-bmmc-cellplm; lit-cells-networks-20261011-chen2026-eval-annotation-bmmc-genept-w; lit-cells-networks-20261011-chen2026-eval-annotation-bmmc-nicheformer; lit-cells-networks-20261011-chen2026-eval-annotation-bmmc-scelmo; lit-cells-networks-20261011-chen2026-eval-annotation-bmmc-scgpt-spatial
reason: Add a relevance judgement for a protocol from the 2026-10-11 cells-spatial and networks-mechanistic literature pass, reviewed in docs/reviews/2026-10-12-cells-networks-batches.md.
review: method: ai-assisted-source-review; scope-review; method note: Reviewer checked the endpoint against the use case's inputs, output and exclusions, the relevance rating and the limitations; every evaluation on the protocol had its values checked in the batch review. Corrections listed in review.md were applied by the extractor.; reviewer: claude; reviewer note: Claude review agent reviewer-cn-2, independent of the extractor lit-cells-networks; no human review claimed; reviewed at: 2026-10-12T08:44:00Z; note: Automated review; not human scientific review.
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subject: Transfer cell-type annotations to a new dataset

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