Model type
RNA sequence language model; this record is the paper-specific evaluated configuration.
Configuration
RiNALMo
This RNA model is evaluated as a representation source for mature-mRNA prediction in mRNABench.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Introduction/Sequence Compressibility: (paragraph 1); Conclusion (paragraph 1)How it worksEvaluated procedure (conceptual)
Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1)At a glance
Biological inputs
Mature mRNA sequences or benchmark-defined segments
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Conclusion (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1)Outputs
Embeddings and task-specific mRNA-property predictions
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Related Works/Deep learning for mRNA property prediction: (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1)limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Evaluations and results
Release 2026-09-17-d277315f7d76 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| RiNALMo: Mean ribosome load from MPRA Linear probe; mean across ten random seeds. Independent external evaluation · Evaluation metadata: needs review | ||
| 0.74 Pearson R Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedmRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, RiNALMo row, MRL MPRA column Source checking is not independent reproduction. |
How it works
How the evaluated method works
The benchmark extracts nucleotide-model embeddings and evaluates task-specific predictors under standardised protocols.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1)Underlying method and version boundaries
RiNALMo produces nucleotide representations from RNA sequences. The documented large model has 650 million parameters and pretraining on 36 million non-coding RNA sequences; the benchmark row still requires its exact checkpoint identity.
Sources
lbcb-sci/RiNALMo README.md · README.md; introduction, model description, pretrained-model and usage sections at pinned revisionWhat was evaluated
The linked evaluation record identifies RiNALMo: Mean ribosome load from MPRA. Its dataset, split, adaptation and evidence origin remain attached to the reported results.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · The named evaluation’s methods and comparison table; exact preserved evaluation IDs: evaluation-lit-009Strengths and limitations
Strengths and considerations
- Tests a broad set of mature-mRNA properties across ten datasets and 59 tasks.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Conclusion (paragraph 1); Benchmarking Tasks (paragraph 1)
Limitations and conditions
- A model pretrained mainly on non-coding RNA may have different strengths on mature-mRNA tasks; aggregate results do not identify a universal RNA-model winner.
Sources
mRNABench: A curated benchmark for mature mRNA property and function prediction · Results/Sequence compressibility predicts model performance across genomic regions (paragraph 4); Conclusion (paragraph 1)
Profile review details
Primary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction.
Stable record: reported-model-3e58d0faf88d2eSpecifications
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 |
|---|---|
| Model type | RNA sequence language model; this record is the paper-specific evaluated configuration.Sourceslbcb-sci/RiNALMo README.md · README.md model description |
| Architecture / procedure | The benchmark extracts nucleotide-model embeddings and evaluates task-specific predictors under standardised protocols.SourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) |
| Biological inputs | Mature mRNA sequences or benchmark-defined segmentsSourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Conclusion (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1) |
| Outputs | Embeddings and task-specific mRNA-property predictionsSourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Related Works/Deep learning for mRNA property prediction: (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1) |
| Parameters | 650M parameters (Table 1).SourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Table1; RiNALMo row |
| Known versions / configuration | RiNALMo ncRNA encoder listed as rinalmo in the comparison tables.SourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Introduction (paragraph 1); Introduction (paragraph 3) |
| Training data / fitting | Task-specific adaptation uses the mRNABench partitions; the encoder’s original RNA pretraining is distinct.SourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1); Appendix Contents/Dataset Processing Protocols/Mean Ribosome Load (paragraph 1) |
| Context limits | 1,024-token context listed in Table 1; the benchmark chunks longer sequences before probing.SourcesmRNABench: A curated benchmark for mature mRNA property and function prediction · Table1 RiNALMo row; Methods / Linear Probing |
| Access | Official upstream implementation and usage documentation: https://github.com/lbcb-sci/RiNALMo/blob/2c2c5c14a5ae609d8c560a5d9ca32e51e0288955/README.md. This pinned documentation revision is not automatically the evaluated weight revision.Sourceslbcb-sci/RiNALMo README.md · README.md; installation, model download and usage instructions |
| Code licence | Apache 2.0 (upstream repository code at the cited revision; this does not establish every dependency or historical checkpoint licence).Sourceslbcb-sci/RiNALMo LICENSE · LICENSE; complete licence text |
| Weights licence | CC BY 4.0 for RiNALMo model parameters; code is separately Apache 2.0.Sourceslbcb-sci/RiNALMo README.md · README.md; Model Parameters License |
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.
20 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual input–method–output guide. Check the procedure text and linked evaluation for fitted components, additional inputs and exact settings. Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram steps ["Mature mRNA sequences or benchmark-defined segments","RiNALMo","Embeddings and task-specific mRNA-property predictions"] Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Evaluated procedure (conceptual) Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Model type RNA sequence language model; this record is the paper-specific evaluated configuration. Individual claims | lbcb-sci/RiNALMo README.md README.md model description Version: 2c2c5c14a5ae609d8c560a5d9ca32e51e0288955 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Architecture / procedure The benchmark extracts nucleotide-model embeddings and evaluates task-specific predictors under standardised protocols. Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Weights licence CC BY 4.0 for RiNALMo model parameters; code is separately Apache 2.0. Individual claims | lbcb-sci/RiNALMo README.md README.md; Model Parameters License Version: 2c2c5c14a5ae609d8c560a5d9ca32e51e0288955 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Biological inputs Mature mRNA sequences or benchmark-defined segments Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Conclusion (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Outputs Embeddings and task-specific mRNA-property predictions Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Related Works/Deep learning for mRNA property prediction: (paragraph 1); Appendix Contents/Dataset Processing Protocols/Variant Effect Prediction (paragraph 1) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Parameters 650M parameters (Table 1). Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Table1; RiNALMo row Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Known versions / configuration RiNALMo ncRNA encoder listed as rinalmo in the comparison tables. Individual claims | mRNABench: A curated benchmark for mature mRNA property and function prediction Introduction (paragraph 1); Introduction (paragraph 3) Version: preprint archived 2025-07-08 | source checked automated source review · 2026-09-16 Audit detailsPrimary full text and the available official implementation/model documentation were inspected. Explanatory claims are source-backed; unresolved exact-configuration metadata is labelled explicitly. This is automated review, not a human review or independent benchmark reproduction. 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: needs review
3 source records and release history
- mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08
- lbcb-sci/RiNALMo README.md · Original source · 2c2c5c14a5ae609d8c560a5d9ca32e51e0288955
- lbcb-sci/RiNALMo LICENSE · Original source · 2c2c5c14a5ae609d8c560a5d9ca32e51e0288955
Technical metadata and extraction receipts
Stable ID: reported-model-3e58d0faf88d2e
- areas
- rna-transcriptomes
- entity level
- method
- version
- Not reported
- reported name
- RiNALMo
- historical missing metadata
- version: not_reported_in_legacy_extract; checkpoint revision: not_reported_in_legacy_extract; training data: not_reported_in_legacy_extract; licence: 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
- model
- entity classification
- review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: mrnabench-2025; evidence-reported-base-rinalmo-readme-md; source locator: Results/Nucleotide foundation models perform poorly at compositional generalization (paragraph 3); Methods/Linear Probing (paragraph 1) | README.md model description | Introduction/Sequence Compressibility: (paragraph 1); Conclusion (paragraph 1); ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.