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Evaluation

Protein composition + fixed ridge probe 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.

Research readiness

These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.

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

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • metric replay: verification is missing
  • annotations: verification is missing
  • dependence: verification is missing

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • recipe pinned: verification is missing
  • resource estimate: verification is missing

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • artifact hashes: verification is missing
  • join integrity: verification is missing
  • score semantics: verification is missing
  • independent validation: verification is missing
  • overlap checked: verification is missing

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Read reviewed discrepancy investigations

Evaluation results

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

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: Protein composition + fixed ridge probe (FLIP2 Rhomax by_wild_type)Protocol: FLIP2 Rhomax by_wild_type
Dataset subset: FLIP2 Rhomax by_wild_type test subset		0.955 ndcg
dimensionless · higher

Uncertainty: Not reported

Coverage: 184/184

Rewire evaluation · Source checked
Methods, coverage and source

Protein composition + fixed ridge probe on FLIP2 Rhomax by_wild_type

FLIP2 Rhomax by_wild_type

Aggregation: Not reported

Protein composition + fixed ridge probe: report; Protein composition + fixed ridge probe: audit · metrics.ndcg
Configuration: Protein composition + fixed ridge probe (FLIP2 Rhomax by_wild_type)Protocol: FLIP2 Rhomax by_wild_type
Dataset subset: FLIP2 Rhomax by_wild_type test subset		0.418 spearman
dimensionless · higher

Uncertainty: Not reported

Coverage: 184/184

Rewire evaluation · Source checked
Methods, coverage and source

Protein composition + fixed ridge probe on FLIP2 Rhomax by_wild_type

FLIP2 Rhomax by_wild_type

Aggregation: Not reported

Protein composition + fixed ridge probe: report; Protein composition + fixed ridge probe: audit · metrics.spearman

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

Evaluation procedure

FLIP2 Rhomax by_wild_type

Configuration
Protein composition + fixed ridge probe (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
protocol allowlisted biological inputs; see baseline configuration for extra inputs
adaptation
fixed train-only ridge on frozen representations
metric implementation
9350e367b20ec48d9ce1195cb5b73c4bd98ce8530a2d1f7ba2157fc8be75fa34
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
9350e367b20ec48d9ce1195cb5b73c4bd98ce8530a2d1f7ba2157fc8be75fa34

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.

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.

279 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statementOriginal source and locationReview and provenance
attributes.comparison.adaptation
fixed train-only ridge on frozen representations
Context-only references		Protein composition + fixed ridge probe: 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: 4126d97686aaa026bab6989f85c405e097b383831e4b8012232394c2ec9178de

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		Protein composition + fixed ridge probe: 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		Protein composition + fixed ridge probe: 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: 2071ac2487d56df4150109b944a42944ed12e1398d00899c054580f709921317

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		Protein composition + fixed ridge probe: 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: 4126d97686aaa026bab6989f85c405e097b383831e4b8012232394c2ec9178de

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		Protein composition + fixed ridge probe: 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		Protein composition + fixed ridge probe: 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: 2071ac2487d56df4150109b944a42944ed12e1398d00899c054580f709921317

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		Protein composition + fixed ridge probe: 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: 4126d97686aaa026bab6989f85c405e097b383831e4b8012232394c2ec9178de

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		Protein composition + fixed ridge probe: 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		Protein composition + fixed ridge probe: 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: 2071ac2487d56df4150109b944a42944ed12e1398d00899c054580f709921317

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		Protein composition + fixed ridge probe: 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: 4126d97686aaa026bab6989f85c405e097b383831e4b8012232394c2ec9178de

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

All evidence (CSV)All evidence (JSONL)How to read the evidence

Sources and history

View linked audit checks and correction history

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

3 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: rewire-local-20260921-evaluation-composition22

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: protocol allowlisted biological inputs; see baseline configuration for extra inputs; adaptation: fixed train-only ridge on frozen representations; metric implementation: 9350e367b20ec48d9ce1195cb5b73c4bd98ce8530a2d1f7ba2157fc8be75fa34; aggregation: all held-out test rows of the selected target; budget: one local CPU evaluation; no held-out hyperparameter selection
input information
protocol allowlisted biological inputs; see baseline configuration for extra inputs
model configuration
alphabet: ACDEFGHIKLMNPQRSTVWY; baseline id: protein-composition-probe-v1; baseline version: 1; features: log1p length, residue fractions, unknown fraction; head: protocol-owned alpha-10 ridge
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
0a214b7dbad99d3684353cf3d56c5c57bae1e2dfa67eb88f67e3f32c66313dd7
prepared sha256
f417d43497e0c8c453bd7c66cfea05959b4d6d47462283096e42a2dae8b72419
execution
adapter: SequenceComposition; batch size: 32; fitting: protocol_owned_probe; inference and fit seconds: 0.010466667008586228; mode: local_adapter; prediction type: embedding
timing seconds
evaluation: 0.013304500011145137
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: 9350e367b20ec48d9ce1195cb5b73c4bd98ce8530a2d1f7ba2157fc8be75fa34; sif sha256: unreported
run url
https://github.com/rewire-bio/rewire-benchmarks/blob/1663d1f04b2bbd6dfcff77fea78129d30b0de191/research/baseline-programme-2026-09-21/rhomax/protein-composition-probe-v1.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.; The 40-feature and 22-feature composition controls are distinct configurations; do not consolidate them by name.
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