RNABERT | configuration

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Evaluations and results

10 evaluations · 10 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
RNABERTEvaluation	mRNABench MRNA-LOC-LR: mRNA localisation, long range, mRNABench mRNA Loc-LR (mRNABench split)	68.3% (best in column)	Not reported
RNABERTEvaluation	mRNABench MRNA-LOC-SR: mRNA localisation, short range, mRNABench mRNA Loc-SR (mRNABench split)	57.5%	Not reported
RNABERTEvaluation	mRNABench PROT-LOC: Protein localisation, mRNABench Prot Loc (mRNABench split)	28%	Not reported
RNABERTEvaluation	mRNABench GO: Gene Ontology term prediction, mRNABench GO (mRNABench split)	23.8%	Not reported
RNABERTEvaluation	mRNABench ECLIP: eCLIP binding site prediction, mRNABench eCLIP (mRNABench split)	19.2%	Not reported
RNABERTEvaluation	mRNABench VEP: Variant effect prediction, mRNABench VEP (mRNABench split)	19.2%	Not reported
RNABERTEvaluation	mRNABench HL: mRNA half life, mRNABench HL (mRNABench split)	Not reported	0.21
RNABERTEvaluation	mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life, mRNABench MRL-HL-Pair (mRNABench split)	Not reported	0.32 (best in column)
RNABERTEvaluation	mRNABench MRL-MPRA: Mean ribosome load on an MPRA library, mRNABench MRL MPRA (mRNABench split)	Not reported	0.24
RNABERTEvaluation	mRNABench MRL: Mean ribosome load, mRNABench MRL (mRNABench split)	Not reported	0.06

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: RNABERT	Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split)	19.2% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench ECLIP: eCLIP binding site prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(eCLIP)
Configuration: RNABERT	Task: mRNABench GO: Gene Ontology term prediction Dataset subset: mRNABench GO (mRNABench split)	23.8% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench GO: Gene Ontology term prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(GO)
Configuration: RNABERT	Task: mRNABench HL: mRNA half life Dataset subset: mRNABench HL (mRNABench split)	0.21 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench HL: mRNA half life A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(HL)
Configuration: RNABERT	Task: mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life Dataset subset: mRNABench MRL-HL-Pair (mRNABench split)	0.32 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(MRL-HL-Pair)
Configuration: RNABERT	Task: mRNABench MRL-MPRA: Mean ribosome load on an MPRA library Dataset subset: mRNABench MRL MPRA (mRNABench split)	0.24 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench MRL-MPRA: Mean ribosome load on an MPRA library A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(MRL MPRA)
Configuration: RNABERT	Task: mRNABench MRL: Mean ribosome load Dataset subset: mRNABench MRL (mRNABench split)	0.06 Pearson unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench MRL: Mean ribosome load A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(MRL)
Configuration: RNABERT	Task: mRNABench MRNA-LOC-LR: mRNA localisation, long range Dataset subset: mRNABench mRNA Loc-LR (mRNABench split)	68.3% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench MRNA-LOC-LR: mRNA localisation, long range A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(mRNA Loc-LR)
Configuration: RNABERT	Task: mRNABench MRNA-LOC-SR: mRNA localisation, short range Dataset subset: mRNABench mRNA Loc-SR (mRNABench split)	57.5% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench MRNA-LOC-SR: mRNA localisation, short range A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(mRNA Loc-SR)
Configuration: RNABERT	Task: mRNABench PROT-LOC: Protein localisation Dataset subset: mRNABench Prot Loc (mRNABench split)	28% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench PROT-LOC: Protein localisation A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(Prot Loc)
Configuration: RNABERT	Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split)	19.2% AUPRC percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source RNABERT on mRNABench VEP: Variant effect prediction A linear probe over frozen embeddings, scored as the mean over ten random seeds. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 2, row(RNABERT), column(VEP)

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

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mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08

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Technical metadata and extraction receipts

Stable ID: mrnabench-method-rnabert

areas: rna-transcriptomes
source locator: Table 2, row(RNABERT)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Best checkpoint of this model family, as selected by the mRNABench authors and listed in their Appendix D.

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