Datasets
A separately generated flu-vaccine mRNA dataset with measured expression-related labels.
Task
flu-vaccine mRNA property prediction
The flu-vaccine entry refers to a supervised mRNA-property evaluation dataset within the CodonBERT paper.
Sources
CodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captionsOverview
Metrics
Spearman rank correlation for the vaccine-expression regression task; classification accuracy belongs to a different E. coli task.
Allowed inputs
mRNA sequence representations.
Sources
CodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captionsEvaluation 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
CodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captionslimited 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: CodonBERT | Task: flu-vaccine mRNA property prediction Dataset: flu-vaccine sequences | 0.81 Spearman rho unitless · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCodonBERT: flu-vaccine mRNA property prediction codon-based model fine-tuned for downstream regression Aggregation: Not reported CodonBERT large language model for mRNA vaccines · Table 2, CodonBERT row, Flu vaccines Spearman correlation 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
A separately generated flu-vaccine mRNA dataset with measured expression-related labels. Each downstream dataset uses a shared 70:15:15 training/validation/test split across methods, according to Table 1. Spearman rank correlation for the vaccine-expression regression task; classification accuracy belongs to a different E. coli task. Plain TextCNN, RNABERT/TextCNN, RNA-FM/TextCNN, TF-IDF and Codon2vec/TextCNN configurations in the expression-regression table. The shared split controls partition differences between methods. Homology or construct-family exclusion is not specified in the checked downstream-task split statement. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
CodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captionsRecorded 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
- Exact split membership, regression aggregation, baseline execution remain unresolved for the separate vaccine-expression dataset.
Sources
CodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions
Profile review details
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-1c74661df2c401Specifications
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 | A separately generated flu-vaccine mRNA dataset with measured expression-related labels.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Splits | Each downstream dataset uses a shared 70:15:15 training/validation/test split across methods, according to Table 1.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Metrics | Spearman rank correlation for the vaccine-expression regression task; classification accuracy belongs to a different E. coli task.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Baselines | Plain TextCNN, RNABERT/TextCNN, RNA-FM/TextCNN, TF-IDF and Codon2vec/TextCNN configurations in the expression-regression table.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Leakage controls | The shared split controls partition differences between methods. Homology or construct-family exclusion is not specified in the checked downstream-task split statement.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Entity type | Paper-specific computational evaluation protocol.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Organisms | Influenza-vaccine mRNA constructs.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Assays | Measured expression-related mRNA labels.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Allowed inputs | mRNA sequence representations.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
| Adaptation | Supervised downstream expression regression; all methods use the same task split.SourcesCodonBERT large language model for mRNA vaccines · Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions |
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 |
|---|---|---|
| CodonBERT large language model for mRNA vaccines | 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
- CodonBERT large language model for mRNA vaccines 10.1101/gr.278870.123
Evidence locations
- Table 2.; XML table GR278870LITB2
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 summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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
| CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 A separately generated flu-vaccine mRNA dataset with measured expression-related labels. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 Each downstream dataset uses a shared 70:15:15 training/validation/test split across methods, according to Table 1. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 downstream expression regression; all methods use the same task split. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 Spearman rank correlation for the vaccine-expression regression task; classification accuracy belongs to a different E. coli task. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 Plain TextCNN, RNABERT/TextCNN, RNA-FM/TextCNN, TF-IDF and Codon2vec/TextCNN configurations in the expression-regression table. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 The shared split controls partition differences between methods. Homology or construct-family exclusion is not specified in the checked downstream-task split statement. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | 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 The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | CodonBERT large language model for mRNA vaccines Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions Version: journal full text in PMC | unreported 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 |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- CodonBERT large language model for mRNA vaccines · Original source · journal full text in PMC
- CodonBERT large language model for mRNA vaccines · Original source · journal full text in PMC
Technical metadata and extraction receipts
Stable ID: reported-task-1c74661df2c401
- areas
- rna-transcriptomes
- tasks
- flu-vaccine mRNA property prediction
- entity level
- task
- version
- Not reported
- task
- flu-vaccine mRNA property 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-codonbert-vaccines-2024-29680737; inspected locators: Table 2.; XML table GR278870LITB2; searched queries: CodonBERT large language model for mRNA vaccines 10.1101/gr.278870.123; 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: codonbert-vaccines-2024; source locator: Results: supervised learning datasets; cached text lines 14–17; task metric definitions and corresponding results table; matching task comparison table/ablation captions; 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: flu-vaccine sequences
- benchmark: CodonBERT: flu-vaccine mRNA property prediction