Pipeline

Evo2

Embeds mature mRNA with Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, for the mRNABench property prediction tasks.

7 evaluations · 7 results

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
Evo2Evaluation	MIMIC mRNABench probes RNA Localization: RNA Localization prediction, mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.767 (best in column)	Not reported
Evo2Evaluation	MIMIC mRNABench probes eCLIP: eCLIP prediction, mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.473	Not reported
Evo2Evaluation	MIMIC mRNABench probes GO: GO prediction, mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.467	Not reported
Evo2Evaluation	MIMIC mRNABench probes Protein Localization: Protein Localization prediction, mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.408	Not reported
Evo2Evaluation	MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction, mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.507
Evo2Evaluation	MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction, mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.455
Evo2Evaluation	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	0.661 (best in column)

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Pipeline: Evo2	Protocol: MIMIC mRNABench probes eCLIP: eCLIP prediction Dataset subset: mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.473 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 Evo2 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 7 (Evo2 [ 29 ]), column 2 (eCLIP)
Pipeline: Evo2	Protocol: MIMIC mRNABench probes GO: GO prediction Dataset subset: mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.467 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 Evo2 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 7 (Evo2 [ 29 ]), column 3 (GO)
Pipeline: Evo2	Protocol: MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction Dataset subset: mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.507 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 Evo2 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 7 (Evo2 [ 29 ]), column 6 (MRL (LBKWK))
Pipeline: Evo2	Protocol: MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction Dataset subset: mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.455 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 Evo2 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 7 (Evo2 [ 29 ]), column 7 (MRL (Sugimoto))
Pipeline: Evo2	Protocol: MIMIC mRNABench probes Protein Localization: Protein Localization prediction Dataset subset: mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.408 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 Evo2 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 7 (Evo2 [ 29 ]), column 4 (Protein Localization)
Pipeline: Evo2	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)	0.661 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 Evo2 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 7 (Evo2 [ 29 ]), column 8 (RNA Half Life)
Pipeline: Evo2	Protocol: MIMIC mRNABench probes RNA Localization: RNA Localization prediction Dataset subset: mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.767 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 Evo2 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 7 (Evo2 [ 29 ]), column 5 (RNA Localization)

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

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Underlying model: Evo 2. Results on this page belong to this pipeline and its evaluated settings.

Evidence

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Evidence table

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4 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 Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, 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-evo2: 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 'with 7B and 40B parameters': the record does not identify the Evo 2 checkpoint quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-b3e37a3de3e9650701cb Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Embeds mature mRNA with Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, 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-evo2: 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 'with 7B and 40B parameters': the record does not identify the Evo 2 checkpoint quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-b3e37a3de3e9650701cb Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Embeds mature mRNA with Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, for the mRNABench property prediction tasks. Individual claims	Abstract: Genome modeling and design across all domains of life with Evo 2 Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-evo2: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record PPR/PPR981265 (title and abstract), bioRxiv 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 'with 7B and 40B parameters': the record does not identify the Evo 2 checkpoint quoted. Conflicting source claim: `"mRNABench evaluation of mature mRNA embeddings from Evo 2, a DNA foundation model trained on 9.3 trillion base pairs from all domains of life with a context of up to 1 million nucleotides, with task scores quoted from prior work in MIMIC Table S11."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-b3e37a3de3e9650701cb Source artifact SHA-256: `ab65a131aa7ac7f648df4887875a9c3b1bd39cd9ae35d12546b4a6f77e4e2876` 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
Relationship: uses model discovery-model-evo-2 Individual claims	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ Table S11, row Evo2 [ 29 ]; Appendix D.3 Version: arXiv version 1 Retrieved: 2026-09-23	source checked ["automated-source-review"] · 2026-09-23 Audit details Source-backed evaluated identity only; no independent reproduction. Field: `links:uses_model:discovery-model-evo-2` Claim: mimic-2026-mrnabench-method-evo2-discovery-model-evo-2-identity-claim Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record 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: Genome modeling and design across all domains of life with Evo 2 · Original source · Europe PMC core record PPR/PPR981265 (title and abstract), bioRxiv 2025

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Technical metadata and extraction receipts

Stable ID: mimic-2026-mrnabench-method-evo2

areas: rna-transcriptomes
source locator: Table S11, row Evo2 [ 29 ]; 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.

Related records

uses model: Evo 2
subject: Evo2: description
system: Evo2 on MIMIC mRNABench probes eCLIP: eCLIP prediction
system: Evo2 on MIMIC mRNABench probes GO: GO prediction
system: Evo2 on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
system: Evo2 on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
system: Evo2 on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
system: Evo2 on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
system: Evo2 on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
subject: Evo2: uses model discovery-model-evo-2

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