Datasets
PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency.
Task
translation-efficiency prediction
Translation-efficiency assessment uses published full-transcript measurements and is distinct from the paper’s CDS-only tasks.
Sources
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results tableOverview
Metrics
R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics.
Allowed inputs
Full-length mRNA sequence.
Sources
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results tableEvaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results tablelimited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 1 result. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: mRNABERT | Task: translation-efficiency prediction Dataset: human ultra-long mRNAs | 0.669 R-squared unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcemRNABERT: translation-efficiency prediction human translation-efficiency regression at 3066-nt input Aggregation: Not reported mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Table 2, mRNABERT (3066) row, Human R-squared column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency. R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics. Comparison models are fine-tuned using a common model library for the full-length mRNA task.
Sources
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results tableRecorded evaluations
Each evaluation records what was tested and under which conditions.
Run 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 and considerations
No source-reviewed explanatory claims are recorded here yet.
Limitations and conditions
- PERSIST-seq full-transcript traits and the human/mouse TE atlas are different evaluations. The supplementary section identifies them separately but does not supply an atlas partition or uncertainty protocol.
Sources (2)
mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table ; Supplementary Information task sections
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-f7142c3b3e0f3cSpecifications
Inputs, training, access and other details
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 | PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Splits | The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. · Not reported in inspected sourcesSources (2)mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 |
| Metrics | R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Baselines | Comparison models are fine-tuned using a common model library for the full-length mRNA task.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Leakage controls | The main and supplementary TE-atlas descriptions provide sequence-length and dataset summaries but do not describe exclusion of homologous transcripts, shared genes or pretraining overlap for that experiment. Controls described for other downstream datasets are not atlas controls. · Not reported in inspected sourcesSources (2)mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Methods: translation efficiency; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 |
| Uncertainty | The TE-atlas comparison has no task-specific repeat count or confidence-interval method in the inspected main and supplementary sections. The five-fold means/standard deviations for the separate PERSIST-seq evaluation do not define atlas uncertainty. · Not reported in inspected sourcesSources (2)mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset; mrnabert journal Supplementary Information — pinned PDF · Main TE-atlas results; Supplementary Information Full-Length mRNA, pp19–21 |
| Entity type | Paper-specific computational evaluation protocol.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Organisms | Human and mouse.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Assays | PERSIST-seq and ribosome-profiling translation-efficiency measurements.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Allowed inputs | Full-length mRNA sequence.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
| Adaptation | Task fine-tuning through a common comparison-model library.SourcesmRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table |
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 |
|---|---|---|
| mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset | journal full text in PMC | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 1 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset 10.1038/s41467-025-65340-8
Evidence locations
- Table 1; XML table Tab1
- Table 2; XML table Tab2
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.
21 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 | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets PERSIST-seq full-length mRNA measurements and a ribosome-profiling atlas of human/mouse translation efficiency. Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. Individual claims | mrnabert journal Supplementary Information — pinned PDF Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: 41467_2025_65340_MOESM1_ESM.pdf |
| Splits The supplementary full-length section distinguishes PERSIST-seq traits from the human/mouse TE atlas, but gives no TE-atlas train/validation/test membership or partition rule. Five-fold reporting for PERSIST-seq or other downstream tasks cannot be assigned to the atlas result. Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Main full-length mRNA results/Methods; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: journal full text in PMC | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Task fine-tuning through a common comparison-model library. Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics R-squared and Spearman correlation for the human/mouse translation-efficiency atlas; separate mRNA tasks use their own metrics. Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines Comparison models are fine-tuned using a common model library for the full-length mRNA task. Individual claims | mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table Version: journal full text in PMC | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls The main and supplementary TE-atlas descriptions provide sequence-length and dataset summaries but do not describe exclusion of homologous transcripts, shared genes or pretraining overlap for that experiment. Controls described for other downstream datasets are not atlas controls. Individual claims | mrnabert journal Supplementary Information — pinned PDF Methods: translation efficiency; Supplementary Information Full-Length mRNA, pp19–21, Tables 12–13 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Archive member: 41467_2025_65340_MOESM1_ESM.pdf |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
3 source records and release history
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Original source · journal full text in PMC
- mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset · Original source · journal full text in PMC
- mrnabert journal Supplementary Information — pinned PDF · Original source · Published supplementary PDF 41467_2025_65340_MOESM1_ESM.pdf; sha256:2820d9385389e41e9213223608b26c84bf6bffbba57ff48fd5dda17fb78a8aed
Technical metadata and extraction receipts
Stable ID: reported-task-f7142c3b3e0f3c
- areas
- rna-transcriptomes
- tasks
- translation-efficiency prediction
- entity level
- task
- version
- Not reported
- task
- translation-efficiency prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-mrnabert-2025-ff08ba89; inspected locators: Table 1; XML table Tab1; Table 2; XML table Tab2; searched queries: mRNABERT: advancing mRNA sequence design with a universal language model and comprehensive dataset 10.1038/s41467-025-65340-8; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; 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_reported_in_legacy_extract
- 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 source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: mrnabert-2025; source locator: Methods: full-length mRNA datasets and translation efficiency; cached text lines 119–120; task metric definitions and corresponding results table; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: human ultra-long mRNAs
- benchmark: mRNABERT: translation-efficiency prediction