MIMIC v1: Table S11 and Appendix D.3; arXiv version 1

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12 pipelines
7 protocols
7 dataset subsets
84 evaluations
84 results
22 evidence claims

Results

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Model or configuration	Metric	Value	Dataset	Evaluation
AIDO-RNA	AUPRC	0.420 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes eCLIP: eCLIP prediction
AIDO-RNA	AUPRC	0.366 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes GO: GO prediction
AIDO-RNA	Pearson	0.534 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
AIDO-RNA	Pearson	0.360 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
AIDO-RNA	AUPRC	0.343 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
AIDO-RNA	Pearson	0.555 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
AIDO-RNA	AUPRC	0.734 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	AIDO-RNA on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
Dilated ResNet	AUPRC	0.421 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes eCLIP: eCLIP prediction
Dilated ResNet	AUPRC	0.155 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes GO: GO prediction
Dilated ResNet	Pearson	0.411 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
Dilated ResNet	Pearson	0.448 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
Dilated ResNet	AUPRC	0.169 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
Dilated ResNet	Pearson	0.647 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
Dilated ResNet	AUPRC	0.645 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Dilated ResNet on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
DNABERT-S	AUPRC	0.374 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes eCLIP: eCLIP prediction
DNABERT-S	AUPRC	0.318 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes GO: GO prediction
DNABERT-S	Pearson	0.393 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
DNABERT-S	Pearson	0.292 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
DNABERT-S	AUPRC	0.311 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
DNABERT-S	Pearson	0.467 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
DNABERT-S	AUPRC	0.685 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT-S on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
DNABERT2	AUPRC	0.371 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes eCLIP: eCLIP prediction
DNABERT2	AUPRC	0.326 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes GO: GO prediction
DNABERT2	Pearson	0.534 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
DNABERT2	Pearson	0.286 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
DNABERT2	AUPRC	0.325 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
DNABERT2	Pearson	0.475 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
DNABERT2	AUPRC	0.675 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	DNABERT2 on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
ERNIE-RNA	AUPRC	0.373 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes eCLIP: eCLIP prediction
ERNIE-RNA	AUPRC	0.341 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes GO: GO prediction
ERNIE-RNA	Pearson	0.503 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
ERNIE-RNA	Pearson	0.328 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
ERNIE-RNA	AUPRC	0.338 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
ERNIE-RNA	Pearson	0.518 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
ERNIE-RNA	AUPRC	0.691 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	ERNIE-RNA on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
Evo2	AUPRC	0.473 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes eCLIP: eCLIP prediction
Evo2	AUPRC	0.467 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes GO: GO prediction
Evo2	Pearson	0.507 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
Evo2	Pearson	0.455 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
Evo2	AUPRC	0.408 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
Evo2	Pearson	0.661 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
Evo2	AUPRC	0.767 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Evo2 on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
HyenaDNA	AUPRC	0.374 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes eCLIP: eCLIP prediction
HyenaDNA	AUPRC	0.308 fraction	mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes GO: GO prediction
HyenaDNA	Pearson	0.506 unitless	mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction
HyenaDNA	Pearson	0.287 unitless	mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction
HyenaDNA	AUPRC	0.311 fraction	mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes Protein Localization: Protein Localization prediction
HyenaDNA	Pearson	0.462 unitless	mRNABench RNA Half Life as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes RNA Half Life: RNA Half Life prediction
HyenaDNA	AUPRC	0.670 fraction	mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	HyenaDNA on MIMIC mRNABench probes RNA Localization: RNA Localization prediction
MIMIC	AUPRC	0.470 fraction	mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	MIMIC on MIMIC mRNABench probes eCLIP: eCLIP prediction

Claims

Statements this source supports, each with where in the source it was checked.

AIDO-RNA: description: Description mRNABench evaluation of mature mRNA embeddings from AIDO.RNA, an RNA foundation model pretrained on 42 million non-coding RNA sequences at single-nucleotide resolution, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-aido-rna: abstract)
Dilated ResNet: description: Description Supervised dilated convolutional network baseline, built from three or four DilatedResNet blocks and trained from scratch on each task's training split. (expansion-p3-mrnabench-2025: Appendix A, Overview of Evaluated Models (baselines paragraph); coverage-source-mimic-2026-v1-html: Table S11 and Appendix D.3)
DNABERT-S: description: Description mRNABench evaluation of mature mRNA embeddings from DNABERT-S, a genome model built on DNABERT-2 and trained with contrastive objectives to give species-aware DNA embeddings, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert-s: abstract)
DNABERT2: description: Description mRNABench evaluation of mature mRNA embeddings from DNABERT-2, a genome foundation model that tokenises DNA with byte pair encoding instead of k-mers, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-dnabert2: abstract)
DNABERT2: uses model discovery-model-dnabert-2: Uses model DNABERT-2 (Table S11, row DNABERT2 [ 33 ]; Appendix D.3)
ERNIE-RNA: description: Description mRNABench evaluation of mature mRNA embeddings from ERNIE-RNA, an RNA language model based on a modified BERT with a base-pairing restriction, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-ernie-rna: abstract)
Evo2: description: Description 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. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-evo2: abstract)
Evo2: uses model discovery-model-evo-2: Uses model Evo 2 (Table S11, row Evo2 [ 29 ]; Appendix D.3)
HyenaDNA: description: Description mRNABench evaluation of mature mRNA embeddings from HyenaDNA, a genomic foundation model built on Hyena implicit convolutions and pretrained on the human reference genome with single-nucleotide tokens and contexts of up to 1 million tokens, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-hyenadna: abstract)
MIMIC mRNABench probes eCLIP: part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), eCLIP column; Appendix D.3)
MIMIC mRNABench probes GO: part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), GO column; Appendix D.3)
MIMIC mRNABench probes MRL (LBKWK): part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), MRL (LBKWK) column; Appendix D.3)
MIMIC mRNABench probes MRL (Sugimoto): part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), MRL (Sugimoto) column; Appendix D.3)
MIMIC mRNABench probes Protein Localization: part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), Protein Localization column; Appendix D.3)
MIMIC mRNABench probes RNA Half Life: part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), RNA Half Life column; Appendix D.3)
MIMIC mRNABench probes RNA Localization: part of discovery-benchmark-mrnabench: Part of mRNABench (Table S11 (HTML A4.T11), RNA Localization column; Appendix D.3)
MIMIC: uses model catalog-model-mimic: Uses model MIMIC (Table S11, row MIMIC; Appendix D.3)
NT-v2: description: Description mRNABench evaluation of mature mRNA embeddings from a Nucleotide Transformer model reported as NT-v2, from a family of transformer DNA foundation models (50 million to 2.5 billion parameters, integrating information from 3,202 human genomes and 850 genomes of other species), with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-nt-v2: abstract)
NT-v2: uses model discovery-model-nucleotide-transformer: Uses model Nucleotide Transformer (Table S11, row NT-v2 [ 121 ]; Appendix D.3)
Orthrus: description: Description 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. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-orthrus: abstract)
RiNALMo: description: Description 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. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-rinalmo: abstract)
SpliceBERT: description: Description mRNABench evaluation of mature mRNA embeddings from SpliceBERT, a language model pretrained by masked language modelling on primary RNA sequences from 72 vertebrates, with task scores quoted from prior work in MIMIC Table S11. (coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-splicebert: abstract)

Models, benchmarks and other records

Pipelines (12)

Protocols (7)

Dataset subsets (7)

Evaluations (84)

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Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Artifact SHA-256 6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0 Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_sha256` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Artifact url https://arxiv.org/html/2604.24506v1 Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `attributes.artifact_url` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Retrieved at 2026-09-23 Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `attributes.retrieved_at` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Url https://arxiv.org/html/2604.24506v1 Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `attributes.url` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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Version arXiv version 1 Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `attributes.version` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Pinned primary artifact. Review is limited to the cited rows. Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Facets: areas 1 values rna-transcriptomes Source metadata	MIMIC v1: Table S11 and Appendix D.3 Original source ↗ No field-specific location recorded Version: arXiv version 1 Retrieved: 2026-09-23	catalogued No individual claim review recorded Audit details Field: `facets.areas` Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
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Stable ID: coverage-source-mimic-2026-v1-html

areas: rna-transcriptomes
url: https://arxiv.org/html/2604.24506v1
artifact url: https://arxiv.org/html/2604.24506v1
artifact sha256: 6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0
retrieved at: 2026-09-23
venue: arXiv preprint
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