RiNALMo | pipeline

Overview

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Evaluations and results

7 evaluations · 7 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	AUPRC	Pearson
RiNALMoEvaluation	MIMIC mRNABench probes RNA Localization: RNA Localization prediction, mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.69 (best in column)	Not reported
RiNALMoEvaluation	MIMIC mRNABench probes eCLIP: eCLIP prediction, mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.393	Not reported
RiNALMoEvaluation	MIMIC mRNABench probes GO: GO prediction, mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.347	Not reported
RiNALMoEvaluation	MIMIC mRNABench probes Protein Localization: Protein Localization prediction, mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.327	Not reported
RiNALMoEvaluation	MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction, mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.466
RiNALMoEvaluation	MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction, mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.416
RiNALMoEvaluation	MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction, mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.532 (best in column)

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes eCLIP: eCLIP prediction Dataset subset: mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.393 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes eCLIP: eCLIP prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 2 (eCLIP)
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes GO: GO prediction Dataset subset: mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.347 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes GO: GO prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 3 (GO)
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction Dataset subset: mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.466 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 6 (MRL (LBKWK))
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction Dataset subset: mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.416 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 7 (MRL (Sugimoto))
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes Protein Localization: Protein Localization prediction Dataset subset: mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.327 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes Protein Localization: Protein Localization prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 4 (Protein Localization)
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction Dataset subset: mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.532 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 8 (RNA Half Life)
Pipeline: RiNALMo	Protocol: MIMIC mRNABench probes RNA Localization: RNA Localization prediction Dataset subset: mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.69 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Result quoted from another source · Source checked Methods, coverage and source RiNALMo on MIMIC mRNABench probes RNA Localization: RNA Localization prediction MIMIC uses concatenated register tokens and mean-pooled RNA-track representations with supervised probes. Nucleotide/codon/amino-acid conditioning is selected per task on validation data; predictions are averaged across selected modality subsets. Comparator scores are quoted from prior mRNABench work. Aggregation: Not reported MIMIC v1: Table S11 and Appendix D.3 · Table S11 (HTML A4.T11), data row 11 (RiNALMo [ 122 ]), column 5 (RNA Localization)

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Evidence

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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.

3 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Description Embeds mature mRNA with RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, for the mRNABench property prediction tasks. Individual claims	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-rinalmo: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv version 1 Retrieved: 2026-09-23	conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit details Description written from the cited source text; provenance text moved to attributes.source_locator. Independent review 2026-10-10: corrected. Removed '650-million-parameter': mRNABench reports the best model per family and neither MIMIC nor the record identifies which RiNALMo checkpoint was quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-3935e0ad3b37f81f3821 Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Embeds mature mRNA with RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, for the mRNABench property prediction tasks. Individual claims	mRNABench: A curated benchmark for mature mRNA property and function prediction Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-rinalmo: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: preprint archived 2025-07-08 Retrieved: 2026-09-16T10:41:16.497221+00:00	conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit details Description written from the cited source text; provenance text moved to attributes.source_locator. Independent review 2026-10-10: corrected. Removed '650-million-parameter': mRNABench reports the best model per family and neither MIMIC nor the record identifies which RiNALMo checkpoint was quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-3935e0ad3b37f81f3821 Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Embeds mature mRNA with RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, for the mRNABench property prediction tasks. Individual claims	Abstract: RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-rinalmo: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/40593636 (title and abstract), Nature communications 2025 Retrieved: 2026-10-10T06:44:13Z	conflicting claim ["automated-source-review","ai-assisted-source-review"] · 2026-10-10 Audit details Description written from the cited source text; provenance text moved to attributes.source_locator. Independent review 2026-10-10: corrected. Removed '650-million-parameter': mRNABench reports the best model per family and neither MIMIC nor the record identifies which RiNALMo checkpoint was quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from RiNALMo, an RNA language model pretrained on 36 million non-coding RNA sequences, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-3935e0ad3b37f81f3821 Source artifact SHA-256: `e9c58b7facff44a129edf7c942747be63d0263b00ce0cca3d7d4183a96d2987a` Hash scope: SHA-256 of one retrieval of a Europe PMC REST search response. The response is not byte-stable: on 2026-10-10 a second retrieval of 10 of these 31 records differed only in JSON key order and parsed to identical content. The title and abstractText fields are the evidence. Inspected artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

3 source records and release history

MIMIC v1: Table S11 and Appendix D.3 · Original source · arXiv version 1
mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08
Abstract: RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks · Original source · Europe PMC core record MED/40593636 (title and abstract), Nature communications 2025

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Technical metadata and extraction receipts

Stable ID: mimic-2026-mrnabench-method-rinalmo

areas: rna-transcriptomes
source locator: Table S11, row RiNALMo [ 122 ]; Appendix D.3; Prior mRNABench evaluated pipeline, quoted in MIMIC Table S11; not a new execution
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Task scores quoted from prior work in MIMIC Table S11; not a new execution.

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