Protocol

FramePool study MRL: Random 25-100nt

Pearson correlation of predicted and observed MRL on source held-out MPRA sequences.

Overview

Pearson correlation of predicted and observed MRL on source held-out MPRA sequences.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

10 recorded evaluations, 10 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

10 evaluations · 10 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: 3mer_random_forest	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.616 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3mer_random_forest random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C2; row 3mer_random_forest; S7–S8 MPRA correlation plots
Configuration: 4mer_random_forest	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.647 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 4mer_random_forest random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C3; row 4mer_random_forest; S7–S8 MPRA correlation plots
Configuration: 5mer_frame_forest	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.73 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 5mer_frame_forest random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C6; row 5mer_frame_forest; S7–S8 MPRA correlation plots
Configuration: frame_forest (4mer)	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.772 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source frame_forest (4mer) random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C4; row frame_forest (4mer); S7–S8 MPRA correlation plots
Configuration: frame_forest_hyperopt	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.778 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source frame_forest_hyperopt random-25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S4 · S4 Table cell C5; row frame_forest_hyperopt; S7–S8 MPRA correlation plots
Configuration: FramePool 100	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.903 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FramePool 100 Random 25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S1 · S1 Table cell E3; row Random 25-100nt, column FramePool 100; main text Evaluating frame pooling on MPRA data identifies Pearson correlation
Configuration: FramePool 50	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.901 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FramePool 50 Random 25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S1 · S1 Table cell C3; row Random 25-100nt, column FramePool 50; main text Evaluating frame pooling on MPRA data identifies Pearson correlation
Configuration: FramePool Combined	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.914 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source FramePool Combined Random 25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S1 · S1 Table cell F3; row Random 25-100nt, column FramePool Combined; main text Evaluating frame pooling on MPRA data identifies Pearson correlation
Configuration: Optimus 100	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.915 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Optimus 100 Random 25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S1 · S1 Table cell D3; row Random 25-100nt, column Optimus 100; main text Evaluating frame pooling on MPRA data identifies Pearson correlation
Configuration: Optimus 50	Protocol: FramePool study MRL: Random 25-100nt Dataset subset: Sample MPRA Random 25-100nt	0.743 pearson_r correlation · higher Uncertainty: type: unreported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Optimus 50 Random 25-100nt Not reported Aggregation: Not reported FramePool 2021 primary article; FramePool Supplementary Table S1 · S1 Table cell B3; row Random 25-100nt, column Optimus 50; main text Evaluating frame pooling on MPRA data identifies Pearson correlation

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

FramePool translation-prediction study

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 10

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set mean where supervised fitting is permitted

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Simple features with train-only ridge regression

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Applicable tests and references

Applicability is distinct from a completed evaluation.

3mer_random_forest MRL comparator · source_supported
4mer_random_forest MRL comparator · source_supported
5mer_frame_forest MRL comparator · source_supported
frame_forest (4mer) MRL comparator · source_supported
frame_forest_hyperopt MRL comparator · source_supported

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statement	Original source and location	Review and provenance
Relationship: part of uc20260930-benchmark-framepool Individual claims	FramePool 2021 primary article Original source ↗ Supplementary Tables S1 and S4; Model training and testing Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 journal article XML; PMC8136849.1 Retrieved: 2026-09-30	source checked automated source review · 2026-09-30T21:44:09.612264+00:00 Audit details Field: `links:part_of:uc20260930-benchmark-framepool` Claim: uc20260930-protocol-parent-9c66a82c516b230d Source artifact SHA-256: `689af3ecab7b5a928eacc5a76d965960708cbb253fc7cdeae463b16d30ffd2e3` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Relationship: part of uc20260930-benchmark-framepool Individual claims	FramePool Supplementary Table S1 Original source ↗ Supplementary Tables S1 and S4; Model training and testing Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2021 published S1 XLSX Retrieved: 2026-09-30	source checked automated source review · 2026-09-30T21:44:09.612264+00:00 Audit details Field: `links:part_of:uc20260930-benchmark-framepool` Claim: uc20260930-protocol-parent-9c66a82c516b230d Source artifact SHA-256: `4ed99aebadc607b43fca67bc2c6336cf4f167cc4b9cdd57b0abfcad0d2a06562` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

Release 2026-09-30-e37e3ab1284d · Record review: source checked

2 source records and release history

FramePool 2021 primary article · Original source · 2021 journal article XML; PMC8136849.1
FramePool Supplementary Table S1 · Original source · 2021 published S1 XLSX

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Technical metadata and extraction receipts

Stable ID: uc20260930-framepool-protocol-random-25-100nt

areas: rna-transcriptomes
source locator: S1 Table; Model training; Model testing
review: method: automated_source_review; reviewer: Codex experimental-use-case curation; date: 2026-09-30; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.
limitations: Distinct from mRNABench designed-MRL split; no merging of scores.; Optimus models truncate sequences to maximum trained length.

Related records

part of: FramePool translation-prediction study
applicable to: 3mer_random_forest MRL comparator
applicable to: 4mer_random_forest MRL comparator
applicable to: 5mer_frame_forest MRL comparator
applicable to: frame_forest (4mer) MRL comparator
applicable to: frame_forest_hyperopt MRL comparator
protocol: 3mer_random_forest random-25-100nt
protocol: 4mer_random_forest random-25-100nt
protocol: 5mer_frame_forest random-25-100nt
protocol: frame_forest (4mer) random-25-100nt
protocol: frame_forest_hyperopt random-25-100nt
protocol: FramePool 100 Random 25-100nt
protocol: FramePool 50 Random 25-100nt
protocol: FramePool Combined Random 25-100nt
protocol: Optimus 100 Random 25-100nt
protocol: Optimus 50 Random 25-100nt
subject: FramePool study MRL: Random 25-100nt study membership

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