Gene-regulatory signal prediction tests whether combined representations generalize beyond repeated gene identities.
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Regulatory-edge evaluation across tissue domains; exact dataset releases remain unextracted.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Splits | Nested outer-split evaluation is complemented by leave-TF-out, leave-target-out and leave-both-out tests.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Metrics | AUROC in the reviewed stacked-model comparison.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Baselines | Combined representation is compared with the individual model branches.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Leakage controls | Nested validation separates feature construction from testing; entity-grouped tests address gene-identity carryover.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Uncertainty | Bootstrap confidence intervals support reported comparisons.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Entity type | Paper-specific computational evaluation protocol.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Organisms | Human tissues from the Tabula Sapiens atlas.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Assays | Tabula Sapiens single-cell RNA-seq with TRRUST regulatory reference annotations.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Allowed inputs | Candidate transcription-factor/target pairs and model representations.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
| Adaptation | Supervised prediction with nested splits and TF/target holdout stress tests.SourcesResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages |
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Regulatory-edge evaluation across tissue domains; exact dataset releases remain unextracted. Nested outer-split evaluation is complemented by leave-TF-out, leave-target-out and leave-both-out tests. AUROC in the reviewed stacked-model comparison. Combined representation is compared with the individual model branches. Nested validation separates feature construction from testing; entity-grouped tests address gene-identity carryover. Bootstrap confidence intervals support reported comparisons.
Each evaluation records what was tested and under which conditions.
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| scGPT + residual geometry: gene-regulatory signal prediction Asymmetric extraction, PCA-64 centered cosine geometry added to scGPT baseline Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.677 AUROC Unit: fraction · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedResidual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues · Table 4, Immune row, scGPT > +geom AUROC column Source checking is not independent reproduction. |
Last literature check: 2026-09-17. Primary-paper discovery and source inspection. Source-checked results are not independently reproduced experiments.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues | version of record | Read source DOI: 10.1186/s12859-026-06538-5 |
primary comparison table screened
Task-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced.
Stable record: reported-task-99afd88cb12895Trace 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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Input: Candidate transcription-factor/target pairs and model representations.","Evaluation: Supervised prediction with nested splits and TF/target holdout stress tests.","Readout: AUROC in the reviewed stacked-model comparison."] Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets Regulatory-edge evaluation across tissue domains; exact dataset releases remain unextracted. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Nested outer-split evaluation is complemented by leave-TF-out, leave-target-out and leave-both-out tests. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Supervised prediction with nested splits and TF/target holdout stress tests. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics AUROC in the reviewed stacked-model comparison. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Combined representation is compared with the individual model branches. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Nested validation separates feature construction from testing; entity-grouped tests address gene-identity carryover. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty Bootstrap confidence intervals support reported comparisons. Individual claims | Residual-stream geometry of single-cell foundation models carries incremental gene-regulatory signal across tissues Results: nested cross-validation; Grouped cross-validation; cached text lines 48–56; Methods dataset and scGPT passages Version: version of record | source checked automated source review · 2026-09-16 Audit detailsTask-specific computational methodology and field context checked in the cited primary-source artifact. Source-backed fields, inapplicable evaluator dimensions and unresolved details are distinguished. Numerical results were not reproduced. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: needs review
Stable ID: reported-task-99afd88cb12895