Evidence claim

Systematic evaluation of single-cell foundation model interpretability: attentio: evidence concerns

Evidence concerns of Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634)

[] (moved to attributes.limitations; the two CRISPRa results are disputed)

A source-level concern blocked comparison of all 20 results. The CRISPRa citation problem affects only the two CRISPRa results, which are now disputed; the differing perturbation sets are different analyses held as separate dataset subsets, not a conflict.

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.

7 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Claimed field attributes.evidence_concerns Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.field` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Previous value [{"source_id": "gfm-guides-20261014-kendiukhov2026-source-article", "message": "The K562 CRISPRa analysis cites reference 25, Adamson et al. 2016 (Cell 167:1867), which is a CRISPRi Perturb-seq study of the unfolded protein response. The Data availability statement lists 'Dixit/Adamson/Shifrut datasets'. The CRISPRa dataset identity should be checked before the CRISPRa results are compared.", "source_locator": "Page 10, 'Context-dependent attention-correlation relationship', sentence 2 ('On K562 CRISPRa [25] (n = 77)'); reference 25; 'Data availability'", "artifact_sha256": "4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe", "review_date": "2026-10-14"}, {"source_id": "gfm-guides-20261014-kendiukhov2026-source-article", "message": "K562 CRISPRi results are reported on two perturbation sets: n = 151 for correlation edges and the gene-level baselines (Fig. 3) and n = 280 evaluable perturbations for the attention versus correlation comparison, where correlation scores 0.703 against 0.696 on the 151 set. The article does not say how the two sets relate. RPE1 is likewise reported at n = 1,251 (attention versus correlation) and n = 1,167 (confound battery), with attention 0.748 (L15) and 0.747 (layer not stated).", "source_locator": "Page 7, 'Perturbation-first validation reveals gene-level dominance', paragraphs 1-3; page 10, 'Context-dependent attention-correlation relationship' and 'Cross-cell-type generalisation of confound pattern'", "artifact_sha256": "4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe", "review_date": "2026-10-14"}] Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.previous_value` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Claimed value [] (moved to attributes.limitations; the two CRISPRa results are disputed) Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `attributes.value` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description A source-level concern blocked comparison of all 20 results. The CRISPRa citation problem affects only the two CRISPRa results, which are now disputed; the differing perturbation sets are different analyses held as separate dataset subsets, not a conflict. Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: subject gfm-guides-20261014-kendiukhov2026-source-article Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `links:subject:gfm-guides-20261014-kendiukhov2026-source-article` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name Systematic evaluation of single-cell foundation model interpretability: attentio: attributes.evidence_concerns Context-only references	Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) Original source ↗ Page 7 paragraphs 1-3; page 10; Table 1; reference 25 Version: Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14) Retrieved: 2026-10-14T12:01:07Z	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634) · Original source · Version of record, BMC Genomics 27:634, published 2026-07-22 (received 2026-03-10, accepted 2026-05-14)

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Technical metadata and extraction receipts

Stable ID: metadata-correction-069716ac96f366b526cd

field: attributes.evidence_concerns
previous value: [{"source_id": "gfm-guides-20261014-kendiukhov2026-source-article", "message": "The K562 CRISPRa analysis cites reference 25, Adamson et al. 2016 (Cell 167:1867), which is a CRISPRi Perturb-seq study of the unfolded protein response. The Data availability statement lists 'Dixit/Adamson/Shifrut datasets'. The CRISPRa dataset identity should be checked before the CRISPRa results are compared.", "source_locator": "Page 10, 'Context-dependent attention-correlation relationship', sentence 2 ('On K562 CRISPRa [25] (n = 77)'); reference 25; 'Data availability'", "artifact_sha256": "4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe", "review_date": "2026-10-14"}, {"source_id": "gfm-guides-20261014-kendiukhov2026-source-article", "message": "K562 CRISPRi results are reported on two perturbation sets: n = 151 for correlation edges and the gene-level baselines (Fig. 3) and n = 280 evaluable perturbations for the attention versus correlation comparison, where correlation scores 0.703 against 0.696 on the 151 set. The article does not say how the two sets relate. RPE1 is likewise reported at n = 1,251 (attention versus correlation) and n = 1,167 (confound battery), with attention 0.748 (L15) and 0.747 (layer not stated).", "source_locator": "Page 7, 'Perturbation-first validation reveals gene-level dominance', paragraphs 1-3; page 10, 'Context-dependent attention-correlation relationship' and 'Cross-cell-type generalisation of confound pattern'", "artifact_sha256": "4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe", "review_date": "2026-10-14"}]
value: [] (moved to attributes.limitations; the two CRISPRa results are disputed)
source locator: Page 7 paragraphs 1-3; page 10; Table 1; reference 25
review: method: source-hash-verification; scope-review; method note: Re-read pages 7-10, Table 1, the Fig. 3 caption and reference 25 in the archived PDF.; reviewer: claude; reviewer note: Claude (Opus 5.5) research agent, independent of the extractor; no human review claimed; date: 2026-10-14; artifact sha256: 4c1699cb964ae588117a6737f5e9e189eb9a5ef5ff78568d2a99e7a13d6608fe; retrieval url: https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-026-12965-8.pdf; note: See docs/reviews/2026-10-14-gfm-guide-evidence-review.md.

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subject: Systematic evaluation of single-cell foundation model interpretability: attention-derived edge scores add no incremental value over gene-level features for perturbation-target prediction (Kendiukhov 2026, BMC Genomics 27:634)

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