ProteinGym v1.3 AMFR seeded-random control
One seed-0 random ranking on all 2,972 AMFR variants. This is one complete assay, not the full ProteinGym track or an estimate of a chance-performance interval.
Overview
One seed-0 random ranking on all 2,972 AMFR variants. This is one complete assay, not the full ProteinGym track or an estimate of a chance-performance interval.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
1 evaluation · 5 metric rows. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay) | Protocol: ProteinGym v1.3 AMFR seeded-random control Dataset subset: ProteinGym v1.3 AMFR stability assay, 2,972 variants | 0.514 AUC dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972 | Rewire evaluation · source checkedMethods, coverage and sourceSeeded random ranking control on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported Seeded random ranking control: report; Seeded random ranking control: audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.AUC |
| Configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay) | Protocol: ProteinGym v1.3 AMFR seeded-random control Dataset subset: ProteinGym v1.3 AMFR stability assay, 2,972 variants | 0.019 MCC dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972 | Rewire evaluation · source checkedMethods, coverage and sourceSeeded random ranking control on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported Seeded random ranking control: report; Seeded random ranking control: audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.MCC |
| Configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay) | Protocol: ProteinGym v1.3 AMFR seeded-random control Dataset subset: ProteinGym v1.3 AMFR stability assay, 2,972 variants | 0.526 NDCG dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972 | Rewire evaluation · source checkedMethods, coverage and sourceSeeded random ranking control on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported Seeded random ranking control: report; Seeded random ranking control: audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.NDCG |
| Configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay) | Protocol: ProteinGym v1.3 AMFR seeded-random control Dataset subset: ProteinGym v1.3 AMFR stability assay, 2,972 variants | 0.008 Spearman dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972 | Rewire evaluation · source checkedMethods, coverage and sourceSeeded random ranking control on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported Seeded random ranking control: report; Seeded random ranking control: audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.Spearman |
| Configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay) | Protocol: ProteinGym v1.3 AMFR seeded-random control Dataset subset: ProteinGym v1.3 AMFR stability assay, 2,972 variants | 0.087 Top_recall dimensionless · higher Uncertainty: Not reported Coverage: 2972/2972 | Rewire evaluation · source checkedMethods, coverage and sourceSeeded random ranking control on ProteinGym v1.3 AMFR substitution assay ProteinGym v1.3 AMFR substitution assay Aggregation: Not reported Seeded random ranking control: report; Seeded random ranking control: audit · protocol_results.per_assay.AMFR_HUMAN_Tsuboyama_2023_4G3O.metrics.Top_recall |
Source checking is not independent reproduction. Release 2026-09-22-f58a0f1d267f.
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
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Recorded evaluations
Each evaluation records what was tested and under which conditions.
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
Evidence
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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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-proteingym Individual claims | Seeded random ranking control: report protocol_id; protocol_configuration; provenance.upstream_revision Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 | source checked No individual claim review recorded Audit detailsField: Claim: rewire-protocol-proteingym-amfr-random-v13-suite Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-22-f58a0f1d267f · Record review: source checked
3 source records and release history
- Seeded random ranking control: report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- Seeded random ranking control: audit · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
- Seeded random ranking control: execution and verification instructions · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
Technical metadata and extraction receipts
Stable ID: rewire-protocol-proteingym-amfr-random-v13
- areas
- proteins-complexes
- version
- 1.3
- protocol id
- proteingym-v1.3-dms-substitutions
- procedure
- aggregation: round_assay_3dp_then_mean_by_UniProt_and_selection_then_equal_category_mean; assays: AMFR HUMAN Tsuboyama 2023 4G3O: MSA Neff L category: Medium; UniProt ID: AMFR_HUMAN; expected count: 2972; prepared count: 2972; selection type: Stability; taxon: Human; binary labels: official_DMS_score_bin; official assay count: 217; official variant count: 2465767; score direction: higher_is_better
- score generation
- baseline id: seeded-random-v1; baseline version: 1; limitation: One seeded control is not an uncertainty estimate; IDs bind the run; method: SHA256(seed:prepared_id), first 64 bits / 2**64; seed: 0
- source locator
- protocol_configuration; model_configuration; protocol_results
- allowed information
- Opaque prepared mutation ID and fixed seed 0 only; no labels, pretrained model or fitting.
- reproduction url
- https://github.com/rewire-bio/rewire-benchmarks/blob/1663d1f04b2bbd6dfcff77fea78129d30b0de191/research/proteingym-null-2026-09-21/README.md
- reproducibility note
- Source-reviewed instructions for this one fixed-seed control; not the ESM-2 masked-marginal procedure.