Datasets
No single dataset is fixed by this guide. Select a linked protocol and its versioned data release.
inapplicable
Task
RNA splice-site mapping
Splice-site mapping evaluates where splice-related labels occur along a sequence. It is distinct from scoring the effect of a particular variant.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variantsNo reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.
Overview
Metrics
The chosen protocol must define site-level scoring, matching tolerance and class balance; this guide does not supply one universal metric.
Allowed inputs
Sequence windows and position-level splice labels under the selected task’s coordinate and strand conventions.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variantsEvaluation procedure diagram
How it worksConceptual evaluation workflow
Conceptual task guide. Dataset preparation, parameters and scoring must come from a separately identified protocol.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variantsSource reviewed · Automated source review, 2026-09-16. All specifications and missing details
Results
All evaluations
0 evaluations · 0 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
No evaluations linked in this release.
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Choosing an evaluation
Choose the task’s coordinate system, sequence window and label definition before interpreting scores. BEACON lists a SpliceAI-labelled downstream task and several splice-oriented representations. Their presence in the suite identifies a task area, not a shared checkpoint or proof of performance for every listed model.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variantsTask 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
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variantsRun instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths supported by sources
- Position-level labels test localisation, rather than only a sequence-wide classification.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants
Limitations and conditions
- A splice-site score is not a measured variant-effect score and does not establish clinical interpretation.
Sources
terry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants
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-rna-splice-sitesSpecifications
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.Sourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Datasets | No single dataset is fixed by this guide. Select a linked protocol and its versioned data release. · Not applicableSourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Organisms | No shared organism population is defined at this guide level. Record it for each selected dataset. · Not applicableSourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Assays | No single measurement assay is fixed by this guide; the endpoint and assay belong to the selected protocol. · Not applicableSourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Splits | No executable split is attached to this task identity. Use the selected protocol’s split manifest. · Not applicableSourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Allowed inputs | Sequence windows and position-level splice labels under the selected task’s coordinate and strand conventions.Sourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Adaptation | No common fitting regime is imposed here. Keep pretrained, frozen, probed, fine-tuned and conventional methods distinct where applicable. · Not applicableSourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Metrics | The chosen protocol must define site-level scoring, matching tolerance and class balance; this guide does not supply one universal metric.Sourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
| Baselines | Use the protocol’s sequence and splice-specialist comparators with matched inputs. Proposed applicability is separate from completed evaluation.Sourcesterry-r123/RNABenchmark official source · README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes | Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | Read source |
| Benchmarking splice variant prediction algorithms using massively parallel splicing assays | Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | Read source |
Historical gaps recorded on 2026-09-17
- complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.
Search and extraction details
primary protocol reviewed
Searches
- Pangolin SpliceAI MFASS splice variant benchmark rewire
Evidence locations
- GUE Table 6 SSP columns; splice-effect paper Results and Figure 2
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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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
| terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 Sequence windows and position-level splice labels under the selected task’s coordinate and strand conventions. Individual claims | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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 | terry-r123/RNABenchmark official source README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants Version: da7f9c7ac3f39605af27e1dfcdf879adba963d79 | 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
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: discovered
5 source records and release history
- RNA-FM official resource · Original source · Not reported
- MIMIC official resource · Original source · Not reported
- DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genomes · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- Benchmarking splice variant prediction algorithms using massively parallel splicing assays · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
- terry-r123/RNABenchmark official source · Original source · da7f9c7ac3f39605af27e1dfcdf879adba963d79
Technical metadata and extraction receipts
Stable ID: catalog-task-rna-splice-sites
- areas
- rna-transcriptomes
- entity level
- task
- version
- Not reported
- task
- RNA splice-site mapping
- scope note
- Predict splice-site classes from transcript sequence, using a held-out gene split.
- benchmark research
- review date: 2026-09-17; status: primary_protocol_reviewed; primary sources: evidence-expansion-gue-49300ace; evidence-expansion-splice-evaluation-6960a140; inspected locators: GUE Table 6 SSP columns; splice-effect paper Results and Figure 2; searched queries: Pangolin SpliceAI MFASS splice variant benchmark rewire; gaps: complete comparable numeric result batch: Specific candidate tables and protocol boundaries are documented; no graph values or incomplete winner-only selection are converted into publishable rows.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- 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-terry-r123-rnabenchmark; source locator: README: Tasks and Datasets (SpliceAI task); model inventory including SpliceBERT variants; ambiguities: None recorded