Orthrus | 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
OrthrusEvaluation	MIMIC mRNABench probes RNA Localization: RNA Localization prediction, mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.789 (best in column)	Not reported
OrthrusEvaluation	MIMIC mRNABench probes eCLIP: eCLIP prediction, mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.465	Not reported
OrthrusEvaluation	MIMIC mRNABench probes GO: GO prediction, mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.435	Not reported
OrthrusEvaluation	MIMIC mRNABench probes Protein Localization: Protein Localization prediction, mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.396	Not reported
OrthrusEvaluation	MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction, mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.633
OrthrusEvaluation	MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction, mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.46
OrthrusEvaluation	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	0.696 (best in column)

All 7 result rows with coverage, uncertainty and sources

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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: Orthrus	Protocol: MIMIC mRNABench probes eCLIP: eCLIP prediction Dataset subset: mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.465 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 Orthrus 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 10 (Orthrus [ 74 ]), column 2 (eCLIP)
Pipeline: Orthrus	Protocol: MIMIC mRNABench probes GO: GO prediction Dataset subset: mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.435 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 Orthrus 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 10 (Orthrus [ 74 ]), column 3 (GO)
Pipeline: Orthrus	Protocol: MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction Dataset subset: mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.633 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 Orthrus 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 10 (Orthrus [ 74 ]), column 6 (MRL (LBKWK))
Pipeline: Orthrus	Protocol: MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction Dataset subset: mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.46 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 Orthrus 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 10 (Orthrus [ 74 ]), column 7 (MRL (Sugimoto))
Pipeline: Orthrus	Protocol: MIMIC mRNABench probes Protein Localization: Protein Localization prediction Dataset subset: mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.396 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 Orthrus 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 10 (Orthrus [ 74 ]), column 4 (Protein Localization)
Pipeline: Orthrus	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)	0.696 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 Orthrus 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 10 (Orthrus [ 74 ]), column 8 (RNA Half Life)
Pipeline: Orthrus	Protocol: MIMIC mRNABench probes RNA Localization: RNA Localization prediction Dataset subset: mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.789 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 Orthrus 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 10 (Orthrus [ 74 ]), 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 Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, 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-orthrus: 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: every stated fact is supported by the cited text. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-537009fffad931e39f1d Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Embeds mature mRNA with Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, 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-orthrus: 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: every stated fact is supported by the cited text. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-537009fffad931e39f1d Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Embeds mature mRNA with Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, for the mRNABench property prediction tasks. Individual claims	Abstract: Orthrus: toward evolutionary and functional RNA foundation models Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-orthrus: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/41998407 (title and abstract), Nature methods 2026 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: every stated fact is supported by the cited text. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Orthrus, a Mamba-based mature RNA foundation model pretrained with a contrastive objective over splice isoforms and orthologous transcripts, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-537009fffad931e39f1d Source artifact SHA-256: `034ea6203ceabdd648e25bbb718ab4fa5ddd86720a7535d89a1a3883c67db9ef` 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: Orthrus: toward evolutionary and functional RNA foundation models · Original source · Europe PMC core record MED/41998407 (title and abstract), Nature methods 2026

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Technical metadata and extraction receipts

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

areas: rna-transcriptomes
source locator: Table S11, row Orthrus [ 74 ]; 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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