Relevance of GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE to "Assess models for genetic perturbation experiments"
- Use case
- Assess models for genetic perturbation experiments
- Assessed by
- GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE
- Relevance
- Proxy evidence
- Endpoint
- Mean squared error of predicted versus observed post-perturbation expression; lower is better.
The complete comparison includes a no-change control, CPA, CPA with knowledge-graph features and GEARS. It can inform which controls to include in a pilot; aggregate expression agreement does not directly measure follow-up experiment yield.
4 reviewed evaluations
- CPA on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE
- CPA + KG on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE
- GEARS on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE
- No Perturb on GEARS Norman2019 CPA-control comparison MSE: Norman2019 perturbation-response MSE
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.
30 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Citation locations2 values
| GEARS primary supplement, Table6 coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41587-023-01905-6 publisher supplement | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Citation locations2 values
| snap-stanford/GEARS: README.md coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f374e43e197b295016d80395d7a54ddb81cc6769 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Constraints2 values
| GEARS primary supplement, Table6 coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41587-023-01905-6 publisher supplement | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Constraints2 values
| snap-stanford/GEARS: README.md coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f374e43e197b295016d80395d7a54ddb81cc6769 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Endpoint Mean squared error of predicted versus observed post-perturbation expression; lower is better. Context-only references | GEARS primary supplement, Table6 coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41587-023-01905-6 publisher supplement | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Endpoint Mean squared error of predicted versus observed post-perturbation expression; lower is better. Context-only references | snap-stanford/GEARS: README.md coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f374e43e197b295016d80395d7a54ddb81cc6769 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Claimed field links:assessed_by:gears-2023-supp-table6-task-mse Context-only references | GEARS primary supplement, Table6 coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41587-023-01905-6 publisher supplement | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field links:assessed_by:gears-2023-supp-table6-task-mse Context-only references | snap-stanford/GEARS: README.md coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f374e43e197b295016d80395d7a54ddb81cc6769 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Limitations3 values
| GEARS primary supplement, Table6 coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 10.1038/s41587-023-01905-6 publisher supplement | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Limitations3 values
| snap-stanford/GEARS: README.md coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54). Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: f374e43e197b295016d80395d7a54ddb81cc6769 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
2 source records and release history
- GEARS primary supplement, Table6 · Original source · 10.1038/s41587-023-01905-6 publisher supplement
- snap-stanford/GEARS: README.md · Original source · f374e43e197b295016d80395d7a54ddb81cc6769
Technical metadata and extraction receipts
Stable ID: use-case-map-gears-norman-table6-mse
- field
- links:assessed_by:gears-2023-supp-table6-task-mse
- value
- gears-2023-supp-table6-task-mse
- relevance
- proxy
- endpoint
- Mean squared error of predicted versus observed post-perturbation expression; lower is better.
- rationale
- The complete comparison includes a no-change control, CPA, CPA with knowledge-graph features and GEARS. It can inform which controls to include in a pilot; aggregate expression agreement does not directly measure follow-up experiment yield.
- constraints
- Use the exact Norman2019 K562 source-table protocol and configurations; do not combine this evidence with PerturBench or other GEARS splits.; Read both Table 6 endpoints together while retaining their separate metrics and shared experimental provenance.
- limitations
- Exact Table 6 split and scored gene subset remain unextracted; checkpoint and runtime requirements are not established by these catalogue evaluations.; Reported spreads have unspecified type. A numerical difference is not a significance test.; Predictions need validation in the intended cell system before experiment selection.
- revision
- 1
- reason
- Initial applicability review: primary sources and separate automated cross-review support this exact protocol, its complete selected comparator group and the stated limits.
- citation locators
- source id: coverage-source-gears-supp; locator: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; source id: evidence-official-c037e3419c04936262a0; locator: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54).
- source locator
- coverage-source-gears-supp: Supplementary Table 6, printed page 34 / PDF page 35; Supplementary Table 1, PDF page 30; Supplementary Notes 5 and 14 (K562 context).; evidence-official-c037e3419c04936262a0: README.md at f374e43e197b295016d80395d7a54ddb81cc6769, A note on usage (lines 15–19) and Core API Interface (lines 20–54).
- review
- method: automated-source-review; reviewer: codex; reviewer note: Codex research curation; reviewed at: 2026-09-28T12:11:40.845Z; note: Primary-source curation and separate automated cross-review checked exact evidence identities, comparator coverage, endpoint relevance and transfer limits. No new execution, human scientific review, independent replication or clinical validation.
- reviewed evaluations
- gears-2023-supp-table6-evaluation-cpa-mse; gears-2023-supp-table6-evaluation-cpa-plus-kg-mse; gears-2023-supp-table6-evaluation-gears-mse; gears-2023-supp-table6-evaluation-no-perturb-mse
- pins
- record id: coverage-source-gears-supp; fields: status; attributes.artifact_sha256; sha256: 0324d8e1d9aede1256f962ee1166112283d833bba69d4e5cbadd0855f4bc15dc; record id: evidence-official-c037e3419c04936262a0; fields: status; attributes.artifact_sha256; sha256: 6b31c24a5be44e39f4688991d77ec0debc638be9498dfa24e494144ec6563949; record id: gears-2023-supp-table6-evaluation-cpa-mse; fields: status; links; attributes.origin; attributes.comparison; sha256: a06e7c5ce8dfd87d57ea294058f2cece60869e7f0e0f09c39fd453a727f8fbc0; record id: gears-2023-supp-table6-evaluation-cpa-plus-kg-mse; fields: status; links; attributes.origin; attributes.comparison; sha256: ddad4dedfeaed30420e386e6c114529992da0e8387fe448b438ce9f2d6f4cf9b; record id: gears-2023-supp-table6-evaluation-gears-mse; fields: status; links; attributes.origin; attributes.comparison; sha256: 4bce02cfc88ad003da3ed500229510817282616024295fe8498aed2aa627be72; record id: gears-2023-supp-table6-evaluation-no-perturb-mse; fields: status; links; attributes.origin; attributes.comparison; sha256: 91656a916798eb7533498675ef6051b748a758e10e1de0828197a496ffd75c6e; record id: gears-2023-supp-table6-result-cpa-mse-mse; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: a7ac5338db77f2f899ead6b65c9fe5c77c2122529530c7a32276433245e228de; record id: gears-2023-supp-table6-result-cpa-plus-kg-mse-mse; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 49967984ef6c6336ee5bfb58c3b5c9088d80301205e29658cef9cd41c52a325e; record id: gears-2023-supp-table6-result-gears-mse-mse; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 43d7edef1d4abb986c1a3407da572c820ec46ba294f3dc4f4c3c13a623e20abb; record id: gears-2023-supp-table6-result-no-perturb-mse-mse; fields: status; attributes.metric; attributes.metric_qualifier; attributes.printed_value; attributes.numeric_value; sha256: 6c322baf94414b1f1891fe2209658f5f006ecaeaedb140d7605ad60ac2ac3fbd; record id: gears-2023-supp-table6-task-mse; fields: status; name; description; facets; source_ids; links; attributes; sha256: e73fc238dc962d54bcba2b835930fbc95b7857f84bd83f6e390f69786ea62fae; 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