Evaluation

ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type

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.

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Release 2026-09-29-06401fd5b220 · Evidence verified: Not verified

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Evaluation results

1 evaluation · 2 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)	Protocol: FLIP2 Rhomax by_wild_type Dataset subset: FLIP2 Rhomax by_wild_type test subset	0.907 ndcg dimensionless · higher Uncertainty: Not reported Coverage: 184/184	Rewire evaluation · Source checked Methods, coverage and source ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type FLIP2 Rhomax by_wild_type Aggregation: Not reported ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report; ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · metrics.ndcg
Configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)	Protocol: FLIP2 Rhomax by_wild_type Dataset subset: FLIP2 Rhomax by_wild_type test subset	-0.222 spearman dimensionless · higher Uncertainty: Not reported Coverage: 184/184	Rewire evaluation · Source checked Methods, coverage and source ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) on FLIP2 Rhomax by_wild_type FLIP2 Rhomax by_wild_type Aggregation: Not reported ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report; ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · metrics.spearman

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Evaluation procedure

FLIP2 Rhomax by_wild_type

Configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)
Protocol: FLIP2 Rhomax by_wild_type
Dataset subset: FLIP2 Rhomax by_wild_type test subset

origin: Rewire evaluation
configuration: 1
protocol id: rewire-protocol-flip2-rhomax-by-wild-type-v1
dataset version: rewire-dataset-flip2-rhomax-by-wild-type-v3
split: canonical test
subset: flip2-rhomax-by-wild-type
population: 184/184
inputs: Complete amino-acid sequences; no labels enter encoder; no MSA/templates
adaptation: fixed train-only ridge on frozen representations
metric implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce
aggregation: all held-out test rows of the selected target
budget: one local CPU evaluation; no held-out hyperparameter selection

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

Reproduction

Split: canonical test
Adaptation: fixed train-only ridge on frozen representations
Scoring implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce

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Access requirements and official instructions: FLIP2 Rhomax by_wild_type

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.

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363 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
attributes.comparison.adaptation fixed train-only ridge on frozen representations Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `27dca7c2ac34ab35a7c2bd5ae80969e5ac10cf8e4e03bd969ac4a593cae397b7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation fixed train-only ridge on frozen representations Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `075be1919b8364a3ef1028f9204431d3caa7c3b4da586212d0ed6dd4b024c8da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.adaptation fixed train-only ridge on frozen representations Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `29d7c0ae7f47d45861a769eb8813bf8c650c9a95b3a6821c524b216b0b907ef0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation all held-out test rows of the selected target Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `27dca7c2ac34ab35a7c2bd5ae80969e5ac10cf8e4e03bd969ac4a593cae397b7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation all held-out test rows of the selected target Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `075be1919b8364a3ef1028f9204431d3caa7c3b4da586212d0ed6dd4b024c8da` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation all held-out test rows of the selected target Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `29d7c0ae7f47d45861a769eb8813bf8c650c9a95b3a6821c524b216b0b907ef0` 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	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `27dca7c2ac34ab35a7c2bd5ae80969e5ac10cf8e4e03bd969ac4a593cae397b7` 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	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `075be1919b8364a3ef1028f9204431d3caa7c3b4da586212d0ed6dd4b024c8da` 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	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `29d7c0ae7f47d45861a769eb8813bf8c650c9a95b3a6821c524b216b0b907ef0` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version rewire-dataset-flip2-rhomax-by-wild-type-v3 Context-only references	ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): 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: `27dca7c2ac34ab35a7c2bd5ae80969e5ac10cf8e4e03bd969ac4a593cae397b7` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: source checked

3 source records and release history

ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): report · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): audit · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191
ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): execution and verification instructions · Original source · 1663d1f04b2bbd6dfcff77fea78129d30b0de191

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Technical metadata and extraction receipts

Stable ID: rewire-local-20260921-evaluation-esm2-35m

areas: proteins-complexes
origin: rewire_run
execution scope: complete_selected_evaluation
published score reproduction: false
protocol: FLIP2 Rhomax by_wild_type
version: 1
source locator: metrics; coverage; protocol_results
original sdk scope: full
original sdk completion: complete
suite complete: false
eligible count: 184
scored count: 184
missing count: 0
coverage: 184/184
comparison: protocol id: rewire-protocol-flip2-rhomax-by-wild-type-v1; dataset version: rewire-dataset-flip2-rhomax-by-wild-type-v3; split: canonical test; subset: flip2-rhomax-by-wild-type; population: 184/184; inputs: Complete amino-acid sequences; no labels enter encoder; no MSA/templates; adaptation: fixed train-only ridge on frozen representations; metric implementation: 08cbbaac2aa8f60af5c43af7a83410e9690b44c5e4d162fbe1e5766885952fce; aggregation: all held-out test rows of the selected target; budget: one local CPU evaluation; no held-out hyperparameter selection
input information: Complete amino-acid sequences; no labels enter encoder; no MSA/templates
model configuration: checkpoint: esm2_t12_35M_UR50D; device: cpu; dimension: 480; encoder frozen: true; head: alpha: 10; feature scaling: none; fit intercept: true; max iter: 1000000; name: rewire-frozen-embedding-ridge-v1; refit: train only; relationship to published baseline: Frozen-embedding extension of upstream alpha-10 ridge. The published baseline uses one-hot features and scales targets using train plus validation rows. This extension is not that published baseline.; solver: auto; target scaling: StandardScaler fitted only on train labels; tol: 0.00001; validation use: none; fixed hyperparameters; pooling: mean over residues excluding BOS/EOS and padding; representation layer: 12; scope: one complete Rhomax split, not FLIP2 suite; torch seed: 0; torch threads: 4; validation used: false
protocol configuration: adapter input contract: opaque-sequence-inputs-v1; canonical split counts: test: 184; train: 584; validation: 116; canonical test count: 184; data verification: pinned_source_bytes; dataset: rhomax; embedding probe: alpha: 10; feature scaling: none; fit intercept: true; max iter: 1000000; name: rewire-frozen-embedding-ridge-v1; refit: train only; relationship to published baseline: Frozen-embedding extension of upstream alpha-10 ridge. The published baseline uses one-hot features and scales targets using train plus validation rows. This extension is not that published baseline.; solver: auto; target scaling: StandardScaler fitted only on train labels; tol: 0.00001; validation use: none; fixed hyperparameters; input representation: amino-acid sequence; metric: spearman; metric direction: higher; metrics: spearman; ndcg; prepared rows sha256: d86fe3926529df72649f4638ffa0d89ec62460d831ceb62ad47ff86249469a12; smoke limit per split: Not reported; source note: Not reported; source reuse terms: CC-BY-4.0 archive; source attribution under resources/flip2; split: by_wild_type; suite complete: false; target units: nm; task: regression
provenance: data verification: pinned_source_bytes; dataset version: zenodo-18433203-v3; evaluator url: https://github.com/J-SNACKKB/FLIP/blob/62cace8735f5610e2743cf06ce0f944b37fffaa6/baselines/aggregate.py#L131-L135; source csv sha256: 8e78f6a16cd5298131dca83130d4b94cc0ab4ae9c699460880441c19a65f656f; source sha256: 7c6d2f02cb89310378ac9897c321fbbd909fb0757ac88803dcce84f5f6b05ce3; source url: https://zenodo.org/api/records/18433203/files/rhomax/by_wild_type.csv.gz/content; split origin: Archived assignments: validation=True held out of training; upstream revision: 62cace8735f5610e2743cf06ce0f944b37fffaa6
predictions sha256: 96e8a0c6663dd0a471b984fb86506e483d252a6036a9617cf5f4487664274abd
prepared sha256: f417d43497e0c8c453bd7c66cfea05959b4d6d47462283096e42a2dae8b72419
execution: adapter: ESM2Embeddings; adapter provenance: checkpoint sha256: 7f21e80e61d16a71735163ef555d3009afb0c98da74c48e29df08606973cc55e; checkpoint url: https://dl.fbaipublicfiles.com/fair-esm/models/esm2_t12_35M_UR50D.pt; device: cpu; fair esm version: 2.0.0; implementation sha256: bb46676af95050012cf0bf8a8309581b400f660d2722519889693f4084559d73; maximum sequence length: 1022; model: esm2_t12_35M_UR50D; published result reproduction: false; reference: https://github.com/facebookresearch/esm/blob/2b369911bb5b4b0dda914521b9475cad1656b2ac/README.md#usage; representation layer: 12; strategy: frozen_final_layer_residue_mean_excluding_special_tokens; training overlap: unreported; UniRef50 pretraining may overlap benchmark proteins; batch size: 4; fitting: protocol_owned_probe; inference and fit seconds: 64.14407666699844; mode: local_adapter; prediction type: embedding
timing seconds: evaluation: 0.1622792090056464
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/baseline-programme-2026-09-21/rhomax-35m/esm2.report.json
reproduction url: https://github.com/rewire-bio/rewire-benchmarks/blob/1663d1f04b2bbd6dfcff77fea78129d30b0de191/research/baseline-programme-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.; Pretraining overlap is unreported; conclusions apply to the exact evaluated configuration.

Related records

configuration: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire) (FLIP2 Rhomax by_wild_type)
protocol: FLIP2 Rhomax by_wild_type
dataset: FLIP2 Rhomax by_wild_type test subset
evaluation: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): ndcg
evaluation: ESM-2 35M frozen residue-mean embeddings + fixed ridge (Rewire): spearman

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