GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
Norman2019 perturbation-response Pearson DE. Scored with Pearson correlation of differential expression on Norman et al.2019 perturbation data used in GEARS Supplementary Table6. Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted.
Overview
Norman2019 perturbation-response Pearson DE. Scored with Pearson correlation of differential expression on Norman et al.2019 perturbation data used in GEARS Supplementary Table6. Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
pearson_delta_expression (correlation) · Higher values are better.
Every method GEARS Norman2019 CPA-control comparison reports on Norman2019 perturbation-response Pearson DE, scored with Pearson correlation of differential expression on Norman et al.2019 perturbation data used in GEARS Supplementary Table6.
GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE · Norman et al.2019 perturbation data used in GEARS Supplementary Table6 (GEARS Norman2019 CPA-control comparison split)
Evidence origin: Author-reported evaluation. Numerical source review does not establish independent reproduction.
GEARS primary supplement, Table6 · Supplementary Table6, printed p34 / PDF p35; metric definitions Table1; Supplementary Note5.Complete four-method table; author-reported results, not reproduced.
All comparison limitations (5)
- Complete four-method table; author-reported results, not reproduced.
- The table prints ± spreads without defining SD, SE or CI in its caption. Preserve the printed values and mark spread type unreported.
- The table labels MSE without explicitly restating the scored gene subset. Top20 is usual in this paper, but is not silently inferred for this table.
- Exact split manifests, assay counts scored, checkpoint revision and evaluator commit are unextracted.
- No Perturb also occurs in Table5 and may be reused evidence; no independent replicate is claimed.
Automated source review: 2026-09-23.
No unavailable values; missing scores remain labelled and are never plotted as zero.
Showing 4 of 4 matching rows.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
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- CPA on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- CPA + KG on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- GEARS on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- No Perturb on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 4
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
No-change prediction under matched control conditions
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Training-only mean-effect or linear prediction
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-23-2b89723c6dd9. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Strengths, limitations and unresolved questions
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 |
|---|---|---|
| Relationship: part of model-coverage-gears-norman-cpa-controls Individual claims | GEARS primary supplement, Table6 Supplementary Table6, printed p34 / PDF p35; metric definitions Table1; Supplementary Note5. Version: 10.1038/s41587-023-01905-6 publisher supplement | source checked automated source review · 2026-09-23 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: gears-2023-supp-table6-association-pearson-de Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-23-2b89723c6dd9 · Record review: source checked
1 source records and release history
- GEARS primary supplement, Table6 · Original source · 10.1038/s41587-023-01905-6 publisher supplement
Technical metadata and extraction receipts
Stable ID: gears-2023-supp-table6-task-pearson-de
- areas
- cells-spatial-multiomics
- tasks
- Norman2019 perturbation-response Pearson DE
- metric
- Pearson correlation of differential expression
- metric direction
- higher
- dataset
- Norman et al.2019 perturbation data used in GEARS Supplementary Table6
- protocol
- Predict post-perturbation expression on Norman2019. MSE compares predicted and true expression; Pearson DE compares predicted versus true change over unperturbed controls (Supplementary Table1). Exact Table6 scoring gene subset and split manifest remain unextracted.
- source locator
- Supplementary Table6, printed p34 / PDF p35; metric definitions Table1; Supplementary Note5.
- comparison panels
- id: gears-2023-supp-table6-panel-pearson-de; title: GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE; protocol id: gears-2023-supp-table6-task-pearson-de; dataset id: gears-2023-supp-table6-dataset-norman-et-al-2019-perturbation-data-used-in-gears-supplementary-table6; metric: pearson_delta_expression; unit: correlation; direction: higher; result ids: gears-2023-supp-table6-result-no-perturb-pearson-de-pearson-delta-expression; gears-2023-supp-table6-result-cpa-pearson-de-pearson-delta-expression; gears-2023-supp-table6-result-cpa-plus-kg-pearson-de-pearson-delta-expression; gears-2023-supp-table6-result-gears-pearson-de-pearson-delta-expression; source ids: coverage-source-gears-supp; source locator: Supplementary Table6, printed p34 / PDF p35; metric definitions Table1; Supplementary Note5.; context: Every method GEARS Norman2019 CPA-control comparison reports on Norman2019 perturbation-response Pearson DE, scored with Pearson correlation of differential expression on Norman et al.2019 perturbation data used in GEARS Supplementary Table6.; caveats: Complete four-method table; author-reported results, not reproduced.; The table prints ± spreads without defining SD, SE or CI in its caption. Preserve the printed values and mark spread type unreported.; The table labels MSE without explicitly restating the scored gene subset. Top20 is usual in this paper, but is not silently inferred for this table.; Exact split manifests, assay counts scored, checkpoint revision and evaluator commit are unextracted.; No Perturb also occurs in Table5 and may be reused evidence; no independent replicate is claimed.; review: method: automated_source_review; date: 2026-09-23
- entity level
- protocol
Related records
- part of: GEARS Norman2019 CPA-control comparison
- subject: GEARS Norman2019 CPA-control comparison Pearson DE: part of model-coverage-gears-norman-cpa-controls
- benchmark: CPA on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- benchmark: CPA + KG on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- benchmark: GEARS on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE
- benchmark: No Perturb on GEARS Norman2019 CPA-control comparison Pearson DE: Norman2019 perturbation-response Pearson DE