Pangolin 1.0.2 + per-gene masking patch · mask True (P1) on MFASS matched annotation
8,297 of 8,324 held-out variants scored in every configuration (314 positives, 460 exon groups). The same 27 rows are excluded: 23 assembly-orientation mismatches and four outside the selected canonical transcript spans. Missing scores are not zero or negative predictions.
Evaluation results
1 evaluation · 4 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
Source checking is not independent reproduction. Release 2026-09-25-d40cee0abe73.
Evaluation procedure
MFASS matched GENCODE 44 canonical annotation
- Configuration
- Pangolin 1.0.2 + per-gene masking patch · mask True (P1)
- Protocol
- MFASS: matched GENCODE 44 canonical annotation
- Dataset subset
- MFASS v2 test: matched canonical annotation coverage
- origin
- Rewire evaluation
- configuration
- 1
- protocol id
- rewire-mfass-matched-v1-protocol
- dataset version
- rewire-mfass-matched-v1-dataset
- split
- split-v2 test
- subset
- identical 8297 scored IDs; 27 excluded
- population
- 8297/8324
- inputs
- GRCh38 genomic context; matched GENCODE44 canonical annotation
- adaptation
- zero-shot pretrained specialists
- metric implementation
- 4030374ed11d38e523fc9991ddd792f8800e7739ac71588085bfff91f912d7f7
- aggregation
- common scored variants
- budget
- one frozen execution per condition
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- split-v2 test
- Adaptation
- zero-shot pretrained specialists
- Scoring implementation
- 4030374ed11d38e523fc9991ddd792f8800e7739ac71588085bfff91f912d7f7
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.
215 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation zero-shot pretrained specialists Context-only references | MFASS matched canonical annotation v1: exclusion-verification.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 4be7a98e2553fa2378c29625b13eb3e8ac2e58fb | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.adaptation zero-shot pretrained specialists Context-only references | MFASS matched canonical annotation v1: manifest-v1.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.adaptation zero-shot pretrained specialists Context-only references | MFASS matched canonical annotation v1: provenance.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.adaptation zero-shot pretrained specialists Context-only references | MFASS matched canonical annotation v1: report.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.adaptation zero-shot pretrained specialists Context-only references | MFASS matched canonical annotation v1: verification.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation common scored variants Context-only references | MFASS matched canonical annotation v1: exclusion-verification.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 4be7a98e2553fa2378c29625b13eb3e8ac2e58fb | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation common scored variants Context-only references | MFASS matched canonical annotation v1: manifest-v1.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation common scored variants Context-only references | MFASS matched canonical annotation v1: provenance.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation common scored variants Context-only references | MFASS matched canonical annotation v1: report.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation common scored variants Context-only references | MFASS matched canonical annotation v1: verification.json report.json: conditions.P1 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | not individually reviewed No individual claim review recorded rewire run Audit detailsField: 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 2026-09-25-d40cee0abe73 · Record review: source checked
5 source records and release history
- MFASS matched canonical annotation v1: report.json · Original source · 093fd1ae198c80ce34408d84d6543bca4fc538f2
- MFASS matched canonical annotation v1: manifest-v1.json · Original source · 093fd1ae198c80ce34408d84d6543bca4fc538f2
- MFASS matched canonical annotation v1: verification.json · Original source · 093fd1ae198c80ce34408d84d6543bca4fc538f2
- MFASS matched canonical annotation v1: provenance.json · Original source · 093fd1ae198c80ce34408d84d6543bca4fc538f2
- MFASS matched canonical annotation v1: exclusion-verification.json · Original source · 4be7a98e2553fa2378c29625b13eb3e8ac2e58fb
Technical metadata and extraction receipts
Stable ID: rewire-mfass-matched-v1-evaluation-p1
- areas
- dna-genomes
- origin
- rewire_run
- execution scope
- partial_selected_evaluation
- suite complete
- false
- published score reproduction
- false
- eligible count
- 8324
- scored count
- 8297
- missing count
- 27
- coverage
- 8297/8324
- positive count
- 314
- independent groups
- 460
- exclusion counts
- assembly orientation: 23; canonical transcript span: 4
- scored ids sha256
- 89b5568e2d819b892ba5e6db680d85e41224d6a69fec4b09a85c5075cade39d8
- predictions sha256
- 9fba694b636899feed60d955506849f68701fc6ecb9cec5c1fc6ba7f92728e1e
- unscored sha256
- f8f274522c28f428e97bf84458294e235979466b7c9433746a6ad1adef37fe5a
- protocol
- MFASS matched GENCODE 44 canonical annotation
- version
- 1
- input information
- GRCh38 genomic context; distance 50; matched canonical annotation; no assay labels during prediction
- comparison
- protocol id: rewire-mfass-matched-v1-protocol; dataset version: rewire-mfass-matched-v1-dataset; split: split-v2 test; subset: identical 8297 scored IDs; 27 excluded; population: 8297/8324; inputs: GRCh38 genomic context; matched GENCODE44 canonical annotation; adaptation: zero-shot pretrained specialists; metric implementation: 4030374ed11d38e523fc9991ddd792f8800e7739ac71588085bfff91f912d7f7; aggregation: common scored variants; budget: one frozen execution per condition
- run url
- https://github.com/rewire-bio/rewire-benchmarks/blob/093fd1ae198c80ce34408d84d6543bca4fc538f2/benchmarks/mfass/results/matched-annotation-v1/report.json
- reproduction url
- https://github.com/rewire-bio/rewire-benchmarks/blob/093fd1ae198c80ce34408d84d6543bca4fc538f2/benchmarks/mfass/results/matched-annotation-v1/README.md
- source locator
- report.json: conditions.P1
- ties
- scored: 8297; score at capacity: 0.54; above cutoff: 98; tied at cutoff: 3; slots filled from ties: 2; tie break: label-independent permutation, rewirebench.metrics.precision_at_n
- limitations
- 8,297 of 8,324 held-out variants scored in every configuration (314 positives, 460 exon groups). The same 27 rows are excluded: 23 assembly-orientation mismatches and four outside the selected canonical transcript spans. Missing scores are not zero or negative predictions.; Exploratory comparison: prior results were known. Paired contrast intervals are unadjusted and do not establish a universal model ranking.; Pangolin uses the recorded per-gene masking patch; these are exact configurations, not unqualified upstream model scores.; Precision at 100 is sensitive to tied-score ordering, especially P1. Numerical source checking is automated, not human review or independent reproduction.; Assembly-orientation issue reported at https://github.com/KosuriLab/MFASS/issues/1. Original v1 outputs remain unchanged; corrections require a new version.
- review
- method: automated_execution_evidence_review; reviewed at: 2026-09-25T11:24:56Z; notes: Computational source, coverage and metric checks only; not independent human review or published-score reproduction.
Related records
- configuration: Pangolin 1.0.2 + per-gene masking patch · mask True (P1)
- protocol: MFASS: matched GENCODE 44 canonical annotation
- dataset subset: MFASS v2 test: matched canonical annotation coverage
- evaluation: Pangolin 1.0.2 + per-gene masking patch · mask True (P1): AUROC
- evaluation: Pangolin 1.0.2 + per-gene masking patch · mask True (P1): Average precision
- evaluation: Pangolin 1.0.2 + per-gene masking patch · mask True (P1): Precision at 100
- evaluation: Pangolin 1.0.2 + per-gene masking patch · mask True (P1): Recall at 100