Evaluation

Seeded random ranking control on ProteinGym v1.3 AMFR substitution assay

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.

Evaluation results

1 evaluation · 5 metric rows. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
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 checked Methods, coverage and source Seeded 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 checked Methods, coverage and source Seeded 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 checked Methods, coverage and source Seeded 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 checked Methods, coverage and source Seeded 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 checked Methods, coverage and source Seeded 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.

Evaluation procedure

ProteinGym v1.3 AMFR substitution assay

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

origin: Rewire evaluation
configuration: 1.3
protocol id: rewire-protocol-proteingym-amfr-random-v13
dataset version: rewire-dataset-proteingym-amfr-random-v13
split: Full assay; no train/test split
subset: proteingym-dms-substitutions-v1.3
population: 2972/2972
inputs: protocol allowlisted biological inputs; see baseline configuration for extra inputs
adaptation: none; seed fixed before scoring
metric implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce
aggregation: single assay
budget: one local CPU evaluation; no held-out hyperparameter selection

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: Full assay; no train/test split
Adaptation: none; seed fixed before scoring
Scoring implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Access requirements and official instructions: ProteinGym v1.3 AMFR seeded-random control

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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.

216 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-22-f58a0f1d267f
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation none; seed fixed before scoring Context-only references	Seeded random ranking control: audit Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `e27576294fcc8b01fab73745df1f46787ca2b5864c2c55685b48ee3619b47666` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation none; seed fixed before scoring Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation none; seed fixed before scoring Context-only references	Seeded random ranking control: report Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation single assay Context-only references	Seeded random ranking control: audit Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `e27576294fcc8b01fab73745df1f46787ca2b5864c2c55685b48ee3619b47666` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation single assay Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation single assay Context-only references	Seeded random ranking control: report Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget one local CPU evaluation; no held-out hyperparameter selection Context-only references	Seeded random ranking control: audit Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `e27576294fcc8b01fab73745df1f46787ca2b5864c2c55685b48ee3619b47666` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget one local CPU evaluation; no held-out hyperparameter selection Context-only references	Seeded random ranking control: execution and verification instructions Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `09d4fcfdc0a014b21d7cd5a9419d8990425ea655031f21ecb1ca4bf1a2c9b63e` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget one local CPU evaluation; no held-out hyperparameter selection Context-only references	Seeded random ranking control: report Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `0f20a55715e3f223b9127792df28c6f37547fa7d0c18be55795b632c87019c58` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version rewire-dataset-proteingym-amfr-random-v13 Context-only references	Seeded random ranking control: audit Original source ↗ metrics; coverage; protocol_results Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 1663d1f04b2bbd6dfcff77fea78129d30b0de191 Retrieved: 2026-09-22T21:18:22Z	not individually reviewed No individual claim review recorded rewire run Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `e27576294fcc8b01fab73745df1f46787ca2b5864c2c55685b48ee3619b47666` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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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

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Technical metadata and extraction receipts

Stable ID: rewire-local-20260921-evaluation-proteingym-random

areas: proteins-complexes
origin: rewire_run
execution scope: complete_selected_evaluation
published score reproduction: false
protocol: ProteinGym v1.3 AMFR substitution assay
version: 1.3
source locator: metrics; coverage; protocol_results
original sdk scope: subset
original sdk completion: partial
suite complete: false
eligible count: 2972
scored count: 2972
missing count: 0
coverage: 2972/2972
comparison: protocol id: rewire-protocol-proteingym-amfr-random-v13; dataset version: rewire-dataset-proteingym-amfr-random-v13; split: Full assay; no train/test split; subset: proteingym-dms-substitutions-v1.3; population: 2972/2972; inputs: protocol allowlisted biological inputs; see baseline configuration for extra inputs; adaptation: none; seed fixed before scoring; metric implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce; aggregation: single assay; budget: one local CPU evaluation; no held-out hyperparameter selection
input information: protocol allowlisted biological inputs; see baseline configuration for extra inputs
model configuration: 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
protocol configuration: 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
provenance: assay sha256: AMFR HUMAN Tsuboyama 2023 4G3O: dd911d925eca79329a496eb6cb7b181ab448e15db244daf1c1f9c01e8a704c2a; data verification: local_bytes_hashed_not_independently_source_verified; expected hashes checked: AMFR_HUMAN_Tsuboyama_2023_4G3O; reference sha256: a8f498011532a74aa9fe556a50555a75e928c5837d19c06a87592ae04049b308; source url: https://github.com/OATML-Markslab/ProteinGym/tree/144fe22b07dfaeec2b366f2346203a9838a55b4c; upstream revision: 144fe22b07dfaeec2b366f2346203a9838a55b4c
predictions sha256: 37a020ad31e35d57a924397c395c10bfac152417f0a42207400cef789d3d5e02
prepared sha256: 9f0e0cce34942797364990ef4dc9fb8b382f7b2fd59e6c72de23efc2992fb148
execution: adapter: SeededRandomScore; batch size: 32; fitting: none; inference and fit seconds: 0.005387083001551218; mode: local_adapter; prediction type: scalar
timing seconds: evaluation: 0.05659729200124275
environment: architecture: arm64; container digest: unreported; container runtime: unreported; platform: macOS-26.6.2-arm64-arm-64bit; python: 3.11.13; rewirebench: 0.4.0; sdk code sha256: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce; sif sha256: unreported
run url: https://github.com/rewire-bio/rewire-benchmarks/blob/1663d1f04b2bbd6dfcff77fea78129d30b0de191/research/proteingym-null-2026-09-21/evidence/seeded-random.report.json
reproduction url: https://github.com/rewire-bio/rewire-benchmarks/blob/1663d1f04b2bbd6dfcff77fea78129d30b0de191/research/proteingym-null-2026-09-21/README.md
reproduction note: The linked pinned scripts describe this exact execution. No generic suite recipe is claimed to reproduce it; this review only checked existing artifacts.
limitations: No confidence intervals or seed variability estimate.; Source checking and local execution do not reproduce a published paper score.; One complete AMFR assay, not the full 217-assay track.; Input bytes were hashed locally, not independently verified against an upstream published checksum.; One fixed-seed random ranking, not a chance-performance interval.

Related records

configuration: Seeded random ranking control (ProteinGym v1.3 AMFR substitution assay)
protocol: ProteinGym v1.3 AMFR seeded-random control
dataset: ProteinGym v1.3 AMFR stability assay, 2,972 variants
evaluation: Seeded random ranking control: AUC
evaluation: Seeded random ranking control: MCC
evaluation: Seeded random ranking control: NDCG
evaluation: Seeded random ranking control: Spearman
evaluation: Seeded random ranking control: Top_recall

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