Supervised CNN
Baseline trained from scratch by the mRNABench authors.
Overview
Baseline trained from scratch by the mRNABench authors.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
10 evaluations · 10 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Method: Supervised CNN | Task: mRNABench ECLIP: eCLIP binding site prediction Dataset subset: mRNABench eCLIP (mRNABench split) | 42% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(eCLIP) |
| Method: Supervised CNN | Task: mRNABench GO: Gene Ontology term prediction Dataset subset: mRNABench GO (mRNABench split) | 15.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(GO) |
| Method: Supervised CNN | Task: mRNABench HL: mRNA half life Dataset subset: mRNABench HL (mRNABench split) | 0.65 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(HL) |
| Method: Supervised CNN | Task: mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life Dataset subset: mRNABench MRL-HL-Pair (mRNABench split) | 0.41 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(MRL-HL-Pair) |
| Method: Supervised CNN | Task: mRNABench MRL-MPRA: Mean ribosome load on an MPRA library Dataset subset: mRNABench MRL MPRA (mRNABench split) | 0.77 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(MRL MPRA) |
| Method: Supervised CNN | Task: mRNABench MRL: Mean ribosome load Dataset subset: mRNABench MRL (mRNABench split) | 0.45 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(MRL) |
| Method: Supervised CNN | Task: mRNABench MRNA-LOC-LR: mRNA localisation, long range Dataset subset: mRNABench mRNA Loc-LR (mRNABench split) | 73.7% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(mRNA Loc-LR) |
| Method: Supervised CNN | Task: mRNABench MRNA-LOC-SR: mRNA localisation, short range Dataset subset: mRNABench mRNA Loc-SR (mRNABench split) | 64.5% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(mRNA Loc-SR) |
| Method: Supervised CNN | Task: mRNABench PROT-LOC: Protein localisation Dataset subset: mRNABench Prot Loc (mRNABench split) | 17% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(Prot Loc) |
| Method: Supervised CNN | Task: mRNABench VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 33.2% auprc percent · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised CNN 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(Supervised CNN), column(VEP) |
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Evidence
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Sources and history
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Release 2026-09-29-06401fd5b220 · Record review: source checked
1 source records and release history
- mRNABench: A curated benchmark for mature mRNA property and function prediction · Original source · preprint archived 2025-07-08
Technical metadata and extraction receipts
Stable ID: mrnabench-method-supervised-cnn
- areas
- rna-transcriptomes
- source locator
- Table 2, row(Supervised CNN)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: Supervised CNN on mRNABench ECLIP: eCLIP binding site prediction
- model: Supervised CNN on mRNABench GO: Gene Ontology term prediction
- model: Supervised CNN on mRNABench HL: mRNA half life
- model: Supervised CNN on mRNABench MRL: Mean ribosome load
- model: Supervised CNN on mRNABench MRL-HL-PAIR: Paired mean ribosome load and half life
- model: Supervised CNN on mRNABench MRL-MPRA: Mean ribosome load on an MPRA library
- model: Supervised CNN on mRNABench MRNA-LOC-LR: mRNA localisation, long range
- model: Supervised CNN on mRNABench MRNA-LOC-SR: mRNA localisation, short range
- model: Supervised CNN on mRNABench PROT-LOC: Protein localisation
- model: Supervised CNN on mRNABench VEP: Variant effect prediction