SpliceBERT | 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
SpliceBERTEvaluation	MIMIC mRNABench probes RNA Localization: RNA Localization prediction, mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.726 (best in column)	Not reported
SpliceBERTEvaluation	MIMIC mRNABench probes GO: GO prediction, mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.382	Not reported
SpliceBERTEvaluation	MIMIC mRNABench probes eCLIP: eCLIP prediction, mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.377	Not reported
SpliceBERTEvaluation	MIMIC mRNABench probes Protein Localization: Protein Localization prediction, mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.36	Not reported
SpliceBERTEvaluation	MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction, mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.514
SpliceBERTEvaluation	MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction, mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	Not reported	0.336
SpliceBERTEvaluation	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	0.531 (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: SpliceBERT	Protocol: MIMIC mRNABench probes eCLIP: eCLIP prediction Dataset subset: mRNABench eCLIP as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.377 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 2 (eCLIP)
Pipeline: SpliceBERT	Protocol: MIMIC mRNABench probes GO: GO prediction Dataset subset: mRNABench GO as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.382 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 3 (GO)
Pipeline: SpliceBERT	Protocol: MIMIC mRNABench probes MRL (LBKWK): MRL (LBKWK) prediction Dataset subset: mRNABench MRL (LBKWK) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.514 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 6 (MRL (LBKWK))
Pipeline: SpliceBERT	Protocol: MIMIC mRNABench probes MRL (Sugimoto): MRL (Sugimoto) prediction Dataset subset: mRNABench MRL (Sugimoto) as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.336 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 7 (MRL (Sugimoto))
Pipeline: SpliceBERT	Protocol: MIMIC mRNABench probes Protein Localization: Protein Localization prediction Dataset subset: mRNABench Protein Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.36 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 4 (Protein Localization)
Pipeline: SpliceBERT	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)	0.531 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 8 (RNA Half Life)
Pipeline: SpliceBERT	Protocol: MIMIC mRNABench probes RNA Localization: RNA Localization prediction Dataset subset: mRNABench RNA Localization as reported in MIMIC Table S11 (MIMIC mRNABench probes split)	0.726 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 SpliceBERT 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 12 (SpliceBERT [ 77 ]), column 5 (RNA Localization)

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

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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 SpliceBERT, a language model pretrained by masked language modelling on primary RNA sequences from 72 vertebrates, 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-splicebert: 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 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."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-51bc8bd036adadd6a826 Source artifact SHA-256: `6408e6fae37567837ca53bd8a1ebef6cf7d3787bbf00dae7556e1b62822ffff0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Embeds mature mRNA with SpliceBERT, a language model pretrained by masked language modelling on primary RNA sequences from 72 vertebrates, 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-splicebert: 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 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."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-51bc8bd036adadd6a826 Source artifact SHA-256: `79f6264ee883535203c63a313547e7c57baa85585f76b42f8d899eb17fb7e600` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Description Embeds mature mRNA with SpliceBERT, a language model pretrained by masked language modelling on primary RNA sequences from 72 vertebrates, for the mRNABench property prediction tasks. Individual claims	Abstract: Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction Original source ↗ coverage-source-mimic-2026-v1-html: Appendix D.3 and Table S11; expansion-p3-mrnabench-2025: abstract; qa-descriptions-20261010-source-splicebert: abstract Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Europe PMC core record MED/38605640 (title and abstract), Briefings in bioinformatics 2024 Retrieved: 2026-10-10T06:44:14Z	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 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."`. Claim record status: source_checked. Field: `description` Claim: metadata-correction-51bc8bd036adadd6a826 Source artifact SHA-256: `08d1dce96c933d04a7633bedd5707373ad380029bf833ee20663a6921a773ff1` 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: Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction · Original source · Europe PMC core record MED/38605640 (title and abstract), Briefings in bioinformatics 2024

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Technical metadata and extraction receipts

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

areas: rna-transcriptomes
source locator: Table S11, row SpliceBERT [ 77 ]; 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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