mRNABench variant probes evaluation of naive-4 on Variant effect prediction, scored with AUPRC.
1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: naive-4 | Protocol: mRNABench variant probes VEP: Variant effect prediction Dataset subset: mRNABench VEP (mRNABench split) | 0.195 ± 0.017 AUPRC fraction · higher Uncertainty: 95% CI ± 0.017 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcenaive-4 on mRNABench variant probes VEP: Variant effect prediction Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Aggregation: Not reported mRNABench: A curated benchmark for mature mRNA property and function prediction · Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 |
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Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics.
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13 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Adaptation Named naive feature or architecture control plus a task-specific probe; no pretrained-model claim. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: metric implementation AUPRC Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Comparison: protocol id mrnabench-variants-2025-task-vep Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Evidence experiment set id mrnabench-2025-linear-probing-default-splits Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Evidence overlap Same paper experiment set: mrnabench-2025-linear-probing-default-splits. Table 2 selects a best-overall variant per family from these measurements. Do not count the summary and per-variant tables as independent evidence. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Origin author_reported Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Protocol Frozen transcript representations with task-specific linear probes, or named supervised/naive controls. Homology splits where possible; random splits for MRL-MPRA, MRL-HL-Pair and VEP. Reported mean over ten splits; Appendix C enumerates nine seeds. Table captions say ten random splits, while Methods specify homology splits where possible. This source ambiguity and the nine explicitly listed seeds are retained; exact split manifests remain unextracted. Appendix C uses micro-averaged multilabel metrics. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Source location Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Description mRNABench variant probes evaluation of naive-4 on Variant effect prediction, scored with AUPRC. Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: assessment mrnabench-variants-2025-task-vep Context-only references | mRNABench: A curated benchmark for mature mRNA property and function prediction Table 5 (XML T2), data row 22, XML tr 24, column 6 (VEP | AUPRC), model naive-4 Version: preprint archived 2025-07-08 | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
Stable ID: mrnabench-variants-2025-evaluation-naive-4-vep