Strengths supported by sources
- A two-part assessment can expose overcorrection that a batch-mixing score alone misses.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools
Task
Batch integration
Batch integration asks whether measurements from different experiments can be combined while preserving biological differences.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration ToolsAt a glance
Inputs, training, access and other details
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.Sourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Allowed inputs | Single-cell measurements with batch labels and biological annotations; the chosen method may return a corrected matrix, embedding or graph.Sourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Metrics | scIB includes cell-type silhouette, ARI/NMI and trajectory conservation for biology; batch silhouette, iLISI, kBET and graph connectivity for batch effects.Sourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
| Baselines | Documented integration comparators include Harmony, MNN, scVI and Seurat. Versions and preprocessing are part of the configuration.Sourcestheislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools |
How it works
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration ToolsChoosing an evaluation
Assess two objectives separately: removal of technical batch effects and retention of cell identities and biological variation. scIB supplies metrics for both. A model that mixes every cell together can score well on mixing while destroying useful biology, so one objective cannot substitute for the other. Use a concrete scIB or Open Problems protocol for datasets, preprocessing and scoring; those resources are not interchangeable.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration ToolsTask scope
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.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration ToolsEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Tested entities and results
Release 2026-09-17-d277315f7d76 · 0 evaluations · 0 metric rows. Different protocols are not a single leaderboard.
No evaluations linked in this release.
Papers and result coverage
Last literature check: 2026-09-17. Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Benchmarking atlas-level data integration in single-cell genomics | PMC8748196 | Read source DOI: 10.1038/s41592-021-01336-8 |
What is still missing
- Bio-conservation and batch-removal components depend on datasets and preprocessing. Figures do not justify new exact numerical scores; official source-data matrix extraction remains pending. Broad batch integration is not identical to scIB or Open Problems.
Search and extraction details
broad task requires concrete protocol links
Searches
- Batch integration primary paper benchmark results
Evidence locations
- Table1 tasks and integration-evaluation methods; result figures
Strengths and limitations
Limitations and conditions
- Metric choice depends on available labels and output representation. This guide supplies neither a shared cohort nor a universal combined score.
Sources
theislab/scib official source · README: Metrics, Biological Conservation, Batch Correction and Integration Tools
Profile review details
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-batch-integrationApplicable tests and references
Applicability is distinct from a completed evaluation.
- scVI · proposed
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.
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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 annotated datasets and protocol","Apply the integration method","Measure retained biological variation","Measure residual batch effects"] Individual claims | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 Single-cell measurements with batch labels and biological annotations; the chosen method may return a corrected matrix, embedding or graph. Individual claims | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 | theislab/scib official source README: Metrics, Biological Conservation, Batch Correction and Integration Tools Version: cd67913396b4c0430710b3d90f1d1841f5fa4468 | 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 |
Sources and history
Release 2026-09-17-d277315f7d76 · Record review: discovered
4 source records and release history
- scGPT official resource · Original source · Not reported
- scVI official resource · Original source · Not reported
- Benchmarking atlas-level data integration in single-cell genomics · Original source · PMC8748196
- theislab/scib official source · Original source · cd67913396b4c0430710b3d90f1d1841f5fa4468
Technical metadata and extraction receipts
Stable ID: catalog-task-cell-batch-integration
- areas
- cells-tissues
- entity level
- task
- version
- Not reported
- task
- Batch integration
- scope note
- Test whether cell identity is retained across donors and batches.
- benchmark research
- review date: 2026-09-17; status: broad_task_requires_concrete_protocol_links; primary sources: evidence-expansion-p2-evidence-discovery-final-scib-f65dd8b63336; inspected locators: Table1 tasks and integration-evaluation methods; result figures; searched queries: Batch integration primary paper benchmark results; gaps: Bio-conservation and batch-removal components depend on datasets and preprocessing. Figures do not justify new exact numerical scores; official source-data matrix extraction remains pending. Broad batch integration is not identical to scIB or Open Problems.; claim scope: Primary-source discovery and table/protocol screening; source checked is not independently reproduced. Raw acquisitions not automatically numerical publication approval.
- historical missing metadata
- protocol version: not_yet_extracted
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This record identifies the biological prediction question or a suite-specific task, rather than a uniquely fixed evaluated procedure. Preserve its task identity and leave split, model adaptation and scoring details on linked protocols/evaluations.; source ids: src-discovery-theislab-scib; source locator: README: Metrics, Biological Conservation, Batch Correction and Integration Tools; ambiguities: None recorded
Related records
- applicable to: scVI
- evaluates task: Open Problems
- evaluates task: scIB