FLIP2 Rhomax by_wild_type
Current source-reviewed mapping
Proxy evidence: transfer to this question is limited
The archived background split directly tests one transfer setting; choosing constructs in a new experiment requires validation beyond those 184 rows.
- Assessed endpoint
- Spearman rank association and full-ranking NDCG for absorption-wavelength predictions on 184 held-out Rhomax sequences.
- Evaluation protocol
- FLIP2 Rhomax by_wild_type
- Computational task
- A reviewed task relationship is not recorded for this protocol.
- Input and population constraints
- The same frozen Rhomax by_wild_type assignments cover 584 training, 116 validation and 184 test records. Validation labels do not select these fixed settings.
- Two exact ESM-2 checkpoints use frozen final-layer residue means, no MSA or templates, and a train-only alpha-10 ridge probe with train-only target scaling. They are not zero-shot likelihood scorers.
- The 40-feature and 22-feature composition controls are distinct configurations. Training mean is the existing constant-control evaluation; repeated control checks do not add replications.
Limits on interpretation
- A spectral-tuning endpoint is not opsin activation efficiency, expression, photostability, cellular function, general protein fitness or clinical usefulness.
- Spearman and full-ranking NDCG do not establish wavelength calibration, top-k precision or a prospective experimental hit rate. Constant predictions have undefined Spearman; their NDCG is a control value, not strong predictive evidence.
- No intervals or seed-variability estimates. The 35M checkpoint was chosen after seeing the 8M outcome; the source describes an exploratory follow-up, not a preregistered family-scale comparison.
- ESM-2 pretraining overlap is unresolved. A frozen linear probe result does not establish the value of alternative pooling, fine-tuning or every model-family configuration.
- Recorded timing covers sections of execution and is not a hardware-normalised deployment-cost comparison. Human domain review and external replication are not established.
Automated source review · 2026-09-28 · Codex research curation
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.
Evaluated configurations
Each configuration below belongs to this protocol. Inspect its inputs, population and scoring conditions before comparing it with another evaluation.
Amino-acid composition + fixed ridge (FLIP2 Rhomax by_wild_type)
Rewire evaluation · Source checked
Predict measured Rhomax wavelengths (nm) from amino-acid sequence on all 184 held-out archived test records. This selected split is not a complete FLIP2 score.
- Population and split
- 184/184 · canonical test
- Inputs and adaptation
- Complete source sequence only; no assay labels during prediction · train-only fitting
- Evaluation budget
- one local CPU evaluation; no hyperparameter search outside training
- Runtime and memory
Inference and fit section: 0.012 s.
Metric evaluation section: 0.0109 s.
Device: Not reported. Batch size: 32.
These timings describe the recorded sections of this run, not total runtime or a general hardware benchmark. Peak memory is not reported.
| Metric | Value | Coverage | Uncertainty and source |
|---|---|---|---|
| ndcg | 0.955 dimensionless · higher | 184/184 | Not reported Result provenance |
| spearman | 0.418 dimensionless · higher | 184/184 | Not reported Result provenance |
Uncertainty: Not estimated; one complete selected evaluation.
Evaluation methods, evidence and reproduction
Recipe: generate and evaluate predictions
This committed script regenerates the selected local evaluation with the recorded inputs and configuration. Sequence-control instructions execute all four controls; select this evaluation from their outputs. Raw prior predictions are private, so public evidence alone cannot rescore them.
Training-mean control (FLIP2 Rhomax by_wild_type)
Rewire evaluation · Source checked
Predict measured Rhomax wavelengths (nm) from amino-acid sequence on all 184 held-out archived test records. This selected split is not a complete FLIP2 score.
- Population and split
- 184/184 · canonical test
- Inputs and adaptation
- Complete source sequence only; no assay labels during prediction · train-only fitting
- Evaluation budget
- one local CPU evaluation; no hyperparameter search outside training
- Runtime and memory
Inference and fit section: 0.000942 s.
Metric evaluation section: 0.0165 s.
Device: Not reported. Batch size: 32.
These timings describe the recorded sections of this run, not total runtime or a general hardware benchmark. Peak memory is not reported.
| Metric | Value | Coverage | Uncertainty and source |
|---|---|---|---|
| ndcg | 0.921 dimensionless · higher | 184/184 | Not reported Result provenance |
| spearman | undefined dimensionless · higher | 184/184 | Not reported Result provenance
|
Uncertainty: Not estimated; one complete selected evaluation.
Evaluation methods, evidence and reproduction
Recipe: generate and evaluate predictions
This committed script regenerates the selected local evaluation with the recorded inputs and configuration. Sequence-control instructions execute all four controls; select this evaluation from their outputs. Raw prior predictions are private, so public evidence alone cannot rescore them.
Protein composition + fixed ridge probe (FLIP2 Rhomax by_wild_type)
Rewire evaluation · Source checked
Frozen features with a fixed alpha-10 ridge head fitted only on training rows; all 184 Rhomax by_wild_type held-out proteins scored. This selected split is not a whole FLIP2 score.
- Population and split
- 184/184 · canonical test
- Inputs and adaptation
- protocol allowlisted biological inputs; see baseline configuration for extra inputs · fixed train-only ridge on frozen representations
- Evaluation budget
- one local CPU evaluation; no held-out hyperparameter selection
- Runtime and memory
Inference and fit section: 0.0105 s.
Metric evaluation section: 0.0133 s.
Device: Not reported. Batch size: 32.
These timings describe the recorded sections of this run, not total runtime or a general hardware benchmark. Peak memory is not reported.
| Metric | Value | Coverage | Uncertainty and source |
|---|---|---|---|
| ndcg | 0.955 dimensionless · higher | 184/184 | Not reported Result provenance |
| spearman | 0.418 dimensionless · higher | 184/184 | Not reported Result provenance
|
Uncertainty: Not estimated; one selected evaluation.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)
Rewire evaluation · Source checked
Frozen features with a fixed alpha-10 ridge head fitted only on training rows; all 184 Rhomax by_wild_type held-out proteins scored. This selected split is not a whole FLIP2 score.
- Population and split
- 184/184 · canonical test
- Inputs and adaptation
- Complete amino-acid sequences; no labels enter encoder; no MSA/templates · fixed train-only ridge on frozen representations
- Evaluation budget
- one local CPU evaluation; no held-out hyperparameter selection
- Runtime and memory
Inference and fit section: 64.1 s.
Metric evaluation section: 0.162 s.
Device: cpu. Batch size: 4.
These timings describe the recorded sections of this run, not total runtime or a general hardware benchmark. Peak memory is not reported.
| Metric | Value | Coverage | Uncertainty and source |
|---|---|---|---|
| ndcg | 0.907 dimensionless · higher | 184/184 | Not reported Result provenance |
| spearman | -0.222 dimensionless · higher | 184/184 | Not reported Result provenance |
Uncertainty: Not estimated; one selected evaluation.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)
Rewire evaluation · Source checked
Frozen features with a fixed alpha-10 ridge head fitted only on training rows; all 184 Rhomax by_wild_type held-out proteins scored. This selected split is not a whole FLIP2 score.
- Population and split
- 184/184 · canonical test
- Inputs and adaptation
- Complete amino-acid sequences; no labels enter encoder; no MSA/templates · fixed train-only ridge on frozen representations
- Evaluation budget
- one local CPU evaluation; no held-out hyperparameter selection
- Runtime and memory
Inference and fit section: 17.6 s.
Metric evaluation section: 0.0481 s.
Device: cpu. Batch size: 4.
These timings describe the recorded sections of this run, not total runtime or a general hardware benchmark. Peak memory is not reported.
| Metric | Value | Coverage | Uncertainty and source |
|---|---|---|---|
| ndcg | 0.896 dimensionless · higher | 184/184 | Not reported Result provenance |
| spearman | -0.146 dimensionless · higher | 184/184 | Not reported Result provenance |
Uncertainty: Not estimated; one selected evaluation.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
Open the protocol's results and comparison checks →
Original execution documentation ↗
Mapping sources and review metadata
- ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions · Original source ↗
Matched Rhomax evaluations; Procedure and evidence; Re-run or inspect - ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source ↗
/metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance - ESM-2 8M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source ↗
/metrics; /coverage; /model_configuration; /protocol_configuration; /execution; /provenance - Protein composition + fixed ridge probe: report · Original source ↗
/metrics; /model_configuration; /protocol_configuration - Training-mean control: local execution report (20 September 2026) · Original source ↗
/metrics; /coverage; /model_configuration - Amino-acid composition + fixed ridge: local execution report (20 September 2026) · Original source ↗
/metrics; /coverage; /model_configuration; /provenance
Mapping use-case-mapping-rhodopsin-wavelength-rhomax-fixed-probes · revision 1
Initial applicability review: primary sources and separate automated cross-review support this exact protocol, its complete selected comparator group and the stated limits.
Reviewed evidence fingerprint a012ef5867a510fe9861d1a3de019095e38fb8718f0dbd3581ddd1c5b9a51783