Evidence claim

Relevance of Replogle K562 Perturb-seq to "Assess models for genetic perturbation experiments"

Use case: Assess models for genetic perturbation experiments
Assessed by: Chen et al. 2026 genetic perturbation prediction, Replogle
Relevance: Proxy evidence
Endpoint: MSE, Pearson and Pearson delta (all genes and DE genes) of predicted post-perturbation expression on Replogle K562 Perturb-seq for CellPLM, scGPT-spatial, GenePT-w and scELMo with a shared GEARS decoder

Compares foundation-model representations as inputs to the same GEARS perturbation decoder on held-out perturbations. Proxy and narrow: no no-change, mean or linear control is reported, which the use case asks for, and the endpoint is expression agreement only.

4 reviewed evaluations

Evidence

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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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 3 values Inspect every linked evaluation's source locator before citing a result. Do not compare with other sources' Norman, Adamson or Replogle results; gene sets and splits differ. Use Pearson Delta and the DE-gene metrics; global Pearson is about 0.98-0.99 for every model (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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 MSE, Pearson and Pearson delta (all genes and DE genes) of predicted post-perturbation expression on Replogle K562 Perturb-seq for CellPLM, scGPT-spatial, GenePT-w and scELMo with a shared GEARS decoder 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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-perturbation-replogle 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 pearson-delta 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 3 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. DE metrics use the top 20 differentially expressed genes per perturbation condition (Methods); the DE gene sets are not printed. 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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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lit-cells-networks-20261011-chen2026-source-chen2026 fields status attributes.artifact_sha256 sha256 0b42f541d5ca376dc4e14f043f2eef02b5f307d7820685e0a1e3ef4a31def2b5 record id use-case-genetic-perturbation-response fields status name description facets attributes.question attributes.decision attributes.inputs attributes.output attributes.exclusions attributes.setting attributes.clinical_scope attributes.intended_users sha256 440f0f2e30cb7c828212bed728de2420ba8e13521280be58be7bdcdfe57ac973 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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 Compares foundation-model representations as inputs to the same GEARS perturbation decoder on held-out perturbations. Proxy and narrow: no no-change, mean or linear control is reported, which the use case asks for, and the endpoint is expression agreement only. 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 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling' 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

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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-perturbation-replogle

field: links:assessed_by:lit-cells-networks-20261011-chen2026-protocol-perturbation-replogle
value: lit-cells-networks-20261011-chen2026-protocol-perturbation-replogle
relevance: proxy
endpoint: MSE, Pearson and Pearson delta (all genes and DE genes) of predicted post-perturbation expression on Replogle K562 Perturb-seq for CellPLM, scGPT-spatial, GenePT-w and scELMo with a shared GEARS decoder
rationale: Compares foundation-model representations as inputs to the same GEARS perturbation decoder on held-out perturbations. Proxy and narrow: no no-change, mean or linear control is reported, which the use case asks for, and the endpoint is expression agreement only.
constraints: Inspect every linked evaluation's source locator before citing a result.; Do not compare with other sources' Norman, Adamson or Replogle results; gene sets and splits differ.; Use Pearson Delta and the DE-gene metrics; global Pearson is about 0.98-0.99 for every model (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.; DE metrics use the top 20 differentially expressed genes per perturbation condition (Methods); the DE gene sets are not printed.
citation locators: source id: lit-cells-networks-20261011-chen2026-source-chen2026; locator: Table 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling'
source locator: lit-cells-networks-20261011-chen2026-source-chen2026: Table 5; Results 'Perturbation prediction separates expression reconstruction from functional response modelling'
headline metric: pearson-delta
comparison group: chen2026-harmonised-fm
comparison title: Harmonised single-cell and spatial foundation model benchmark (Chen et al. 2026)
stratum label: Replogle K562 Perturb-seq
stratum order: 3
reviewed evaluations: lit-cells-networks-20261011-chen2026-eval-perturbation-replogle-cellplm; lit-cells-networks-20261011-chen2026-eval-perturbation-replogle-genept-w; lit-cells-networks-20261011-chen2026-eval-perturbation-replogle-scelmo; lit-cells-networks-20261011-chen2026-eval-perturbation-replogle-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: Assess models for genetic perturbation experiments

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