Perturbation-response prediction asks whether a model can predict molecular measurements under a changed cellular condition.
Explanatory profile: source reviewed · 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 |
|---|---|
| Entity type | Task guide; concrete protocol identities remain separate.Sourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Allowed inputs | Control-cell measurements, requested condition and permitted covariates; predictions and observed responses aligned to the same features.Sourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Metrics | PerturBench supports expression-error, correlation, change-from-control and distributional metrics; aggregation and ranking settings are explicit configuration choices.Sourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
| Baselines | Choose the baselines supplied by the selected protocol and record their access to controls and training conditions. No baseline result is asserted by this guide.Sourcesaltoslabs/perturbench official source · README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation |
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
A concrete protocol defines which conditions are observed during fitting and which are held out. Compare predicted and measured responses with matched covariates and a declared aggregation. PerturBench separates average expression, changes from controls and distributional comparisons; these answer different questions. Report the dataset-specific split rather than assuming that a random cell split tests unseen perturbations.
This is a task guide, not a single versioned benchmark protocol. The connected resources provide examples or concrete procedures. A candidate method or proposed control is not evidence that an evaluation has been completed.
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
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 |
|---|---|---|
| Predicting transcriptional outcomes of novel multigene perturbations with GEARS | PMC full-text XML snapshot PMC11180609 at retrieval; byte-pinned by SHA-256 | Read source DOI: 10.1038/s41587-023-01905-6 |
| Towards Principled Evaluation of Single-Cell Perturbation Prediction Models | bioRxiv 2026.07.23.740433v1 | Read source DOI: 10.64898/2026.07.23.740433 |
broad task primary protocol linked
Reviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol.
Stable record: catalog-task-cell-perturbationTrace 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.
17 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Select data and held-out conditions","Specify allowed controls and covariates","Predict molecular responses","Score declared aggregates and distributions"] Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Conceptual evaluation workflow Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Entity type Task guide; concrete protocol identities remain separate. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Organisms No shared organism population is defined at this guide level. Record it for each selected dataset. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Assays No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits No executable split is attached to this task identity. Use the selected protocol’s split manifest. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Allowed inputs Control-cell measurements, requested condition and permitted covariates; predictions and observed responses aligned to the same features. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | source checked automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. Individual claims | altoslabs/perturbench official source README: Downloading and Preparing Datasets, Data Splitting, Evaluator Class and Automated Evaluation Version: c84038bc1ea409aa54f3832cfa6f34f5059adf0c | inapplicable automated source review · 2026-09-16 Audit detailsReviewed named primary documentation and existing protocol records. Editorial task scope is distinguished from source-reported procedures. No model execution or new numerical result; a reviewed guide is not a complete runnable protocol. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Release 2026-09-17-d277315f7d76 · Record review: discovered
Stable ID: catalog-task-cell-perturbation