Relevance of mRNABench Sample designed MRL to "Set baselines for UTR translation experiments"

Stable ID: use-case-mapping-utr-translation-baselines-designed-v1

field

links:assessed_by:rewire-protocol-mrnabench-designed-mrl-v1

value

rewire-protocol-mrnabench-designed-mrl-v1

relevance

direct

endpoint

Predicting target_mrl_designed on the complete 15,003-record canonical test split of the Sample designed reporter dataset.

rationale

The matched sequence-composition and training-mean controls provide an auditable starting point for deciding whether a more complex method adds predictive value on this defined endpoint. They do not establish transfer to a different library or supply a pretrained-model comparison.

constraints

Both controls use the same full processed sequences, seed-2541 split, training labels and complete held-out test population. No validation or test labels select hyperparameters.; Composition features are log1p length, A/C/G/T fractions and unknown fraction, fitted with train-only RidgeCV over the recorded five alpha values and no normalization. The constant control is the training-target arithmetic mean.; MSE is the matched primary endpoint. Constant-control Pearson and Spearman are unavailable; do not replace missing values with zeros.

limitations

One target, one split and one execution per method; no uncertainty or seed variability. No homology-separated or compositional-generalisation claim.; This training-only protocol differs from upstream probing and is not an aggregate mRNABench score or a reproduction of a published model result.; The original run’s raw inputs and saved predictions are not publicly archived. The recipe obtains source data and runs the controls again, including separate protein controls; it does not rescore prior predictions. Source-data reuse terms and cross-platform reproducibility remain unresolved.; Research baseline evidence only, with no new execution, human domain review or clinical validation.

revision

1

reason

Initial applicability review: primary sources and separate automated cross-review support this exact protocol, its complete selected comparator group and the stated limits.

citation locators

source id: rewire-local-20260920-source-mrnabench-composition; locator: /coverage; /model_configuration; /protocol_configuration; /protocol_results; /provenance; source id: rewire-local-20260920-source-mrnabench-train-mean; locator: /coverage; /model_configuration; /protocol_results/metric_unavailable_reasons; /provenance; source id: rewire-local-20260920-instructions-mrnabench; locator: Results: RNA evaluation paragraph; Provenance and review; Reproduce the four sequence controls

source locator

rewire-local-20260920-source-mrnabench-composition: /coverage; /model_configuration; /protocol_configuration; /protocol_results; /provenance; rewire-local-20260920-source-mrnabench-train-mean: /coverage; /model_configuration; /protocol_results/metric_unavailable_reasons; /provenance; rewire-local-20260920-instructions-mrnabench: Results: RNA evaluation paragraph; Provenance and review; Reproduce the four sequence controls

review

method: automated-source-review; reviewer: codex; reviewer note: Codex research curation; reviewed at: 2026-09-28T12:15:35.948Z; note: Primary-source curation and separate automated cross-review checked exact evidence identities, comparator coverage, endpoint relevance and transfer limits. No new execution, human scientific review, independent replication or clinical validation.

reviewed evaluations

rewire-local-20260920-evaluation-mrnabench-composition; rewire-local-20260920-evaluation-mrnabench-train-mean

pins

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• subject: Set baselines for UTR translation experiments