MFASS: matched GENCODE 44 canonical 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.
Overview
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.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
MFASS matched canonical annotation: Precision at 100
Precision at 100 (dimensionless) · Higher values are better.
MFASS: matched GENCODE 44 canonical annotation · MFASS v2 test: matched canonical annotation coverage
Evidence origin: Rewire evaluation.
MFASS matched canonical annotation v1: report.json; MFASS matched canonical annotation v1: manifest-v1.json; MFASS matched canonical annotation v1: verification.json; MFASS matched canonical annotation v1: provenance.json; MFASS matched canonical annotation v1: exclusion-verification.json · report.json: conditions.*.metrics.precision_at_capacity- 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.
Comparison details and 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.
Automated source review: 2026-09-25. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
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Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-25-d40cee0abe73. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
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Evidence
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10 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: evaluates task catalog-task-mfass-splice Individual claims | MFASS matched canonical annotation v1: exclusion-verification.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 4be7a98e2553fa2378c29625b13eb3e8ac2e58fb | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-evaluates-task-catalog-task-mfass-splice Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task catalog-task-mfass-splice Individual claims | MFASS matched canonical annotation v1: manifest-v1.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-evaluates-task-catalog-task-mfass-splice Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task catalog-task-mfass-splice Individual claims | MFASS matched canonical annotation v1: provenance.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-evaluates-task-catalog-task-mfass-splice Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task catalog-task-mfass-splice Individual claims | MFASS matched canonical annotation v1: report.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-evaluates-task-catalog-task-mfass-splice Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: evaluates task catalog-task-mfass-splice Individual claims | MFASS matched canonical annotation v1: verification.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-evaluates-task-catalog-task-mfass-splice Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of rewire-mfass-v2 Individual claims | MFASS matched canonical annotation v1: exclusion-verification.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 4be7a98e2553fa2378c29625b13eb3e8ac2e58fb | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-part-of-rewire-mfass-v2 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of rewire-mfass-v2 Individual claims | MFASS matched canonical annotation v1: manifest-v1.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-part-of-rewire-mfass-v2 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of rewire-mfass-v2 Individual claims | MFASS matched canonical annotation v1: provenance.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-part-of-rewire-mfass-v2 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of rewire-mfass-v2 Individual claims | MFASS matched canonical annotation v1: report.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-part-of-rewire-mfass-v2 Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Relationship: part of rewire-mfass-v2 Individual claims | MFASS matched canonical annotation v1: verification.json manifest-v1.json: study and conditions Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 093fd1ae198c80ce34408d84d6543bca4fc538f2 | source checked automated execution evidence review · 2026-09-25T11:24:56Z Audit detailsComputational source, coverage and metric checks only; not independent human review or published-score reproduction. Field: Claim: rewire-mfass-matched-v1-protocol-part-of-rewire-mfass-v2 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-protocol
- areas
- dna-genomes
- version
- matched-annotation-v1
- source locator
- manifest-v1.json; report.json
- 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.
- reproduction url
- https://github.com/rewire-bio/rewire-benchmarks/blob/093fd1ae198c80ce34408d84d6543bca4fc538f2/benchmarks/mfass/results/matched-annotation-v1/README.md
- comparison panels
- id: rewire-mfass-matched-v1-precision-at-capacity; title: MFASS matched canonical annotation: Precision at 100; protocol id: rewire-mfass-matched-v1-protocol; dataset id: rewire-mfass-matched-v1-dataset; metric: Precision at 100; unit: dimensionless; direction: higher; result ids: rewire-mfass-matched-v1-result-s0-precision-at-capacity; rewire-mfass-matched-v1-result-s1-precision-at-capacity; rewire-mfass-matched-v1-result-p0-precision-at-capacity; rewire-mfass-matched-v1-result-p1-precision-at-capacity; source ids: rewire-mfass-matched-v1-source-report; rewire-mfass-matched-v1-source-manifest-v1; rewire-mfass-matched-v1-source-verification; rewire-mfass-matched-v1-source-provenance; rewire-mfass-matched-v1-source-exclusion-verification; source locator: report.json: conditions.*.metrics.precision_at_capacity; context: 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.; caveats: 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_source_review; date: 2026-09-25; id: rewire-mfass-matched-v1-recall-at-capacity; title: MFASS matched canonical annotation: Recall at 100; protocol id: rewire-mfass-matched-v1-protocol; dataset id: rewire-mfass-matched-v1-dataset; metric: Recall at 100; unit: dimensionless; direction: higher; result ids: rewire-mfass-matched-v1-result-s0-recall-at-capacity; rewire-mfass-matched-v1-result-s1-recall-at-capacity; rewire-mfass-matched-v1-result-p0-recall-at-capacity; rewire-mfass-matched-v1-result-p1-recall-at-capacity; source ids: rewire-mfass-matched-v1-source-report; rewire-mfass-matched-v1-source-manifest-v1; rewire-mfass-matched-v1-source-verification; rewire-mfass-matched-v1-source-provenance; rewire-mfass-matched-v1-source-exclusion-verification; source locator: report.json: conditions.*.metrics.recall_at_capacity; context: 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.; caveats: 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_source_review; date: 2026-09-25; id: rewire-mfass-matched-v1-average-precision-sklearn; title: MFASS matched canonical annotation: Average precision; protocol id: rewire-mfass-matched-v1-protocol; dataset id: rewire-mfass-matched-v1-dataset; metric: Average precision; unit: dimensionless; direction: higher; result ids: rewire-mfass-matched-v1-result-s0-average-precision-sklearn; rewire-mfass-matched-v1-result-s1-average-precision-sklearn; rewire-mfass-matched-v1-result-p0-average-precision-sklearn; rewire-mfass-matched-v1-result-p1-average-precision-sklearn; source ids: rewire-mfass-matched-v1-source-report; rewire-mfass-matched-v1-source-manifest-v1; rewire-mfass-matched-v1-source-verification; rewire-mfass-matched-v1-source-provenance; rewire-mfass-matched-v1-source-exclusion-verification; source locator: report.json: conditions.*.metrics.average_precision_sklearn; context: 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.; caveats: 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_source_review; date: 2026-09-25; id: rewire-mfass-matched-v1-auroc; title: MFASS matched canonical annotation: AUROC; protocol id: rewire-mfass-matched-v1-protocol; dataset id: rewire-mfass-matched-v1-dataset; metric: AUROC; unit: dimensionless; direction: higher; result ids: rewire-mfass-matched-v1-result-s0-auroc; rewire-mfass-matched-v1-result-s1-auroc; rewire-mfass-matched-v1-result-p0-auroc; rewire-mfass-matched-v1-result-p1-auroc; source ids: rewire-mfass-matched-v1-source-report; rewire-mfass-matched-v1-source-manifest-v1; rewire-mfass-matched-v1-source-verification; rewire-mfass-matched-v1-source-provenance; rewire-mfass-matched-v1-source-exclusion-verification; source locator: report.json: conditions.*.metrics.auroc; context: 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.; caveats: 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_source_review; date: 2026-09-25
Related records
- part of: MFASS v2
- evaluates task: MFASS splice-variant prioritisation
- protocol: Pangolin 1.0.2 + per-gene masking patch · mask False (P0) on MFASS matched annotation
- protocol: Pangolin 1.0.2 + per-gene masking patch · mask True (P1) on MFASS matched annotation
- protocol: SpliceAI 1.3.1 · mask 0 (S0) on MFASS matched annotation
- protocol: SpliceAI 1.3.1 · mask 1 (S1) on MFASS matched annotation
- subject: This matched-annotation protocol directly evaluates the MFASS splice-variant prioritisation task on its documented filtered test subset.
- subject: This matched-annotation protocol evaluates MFASS splice-variant prioritisation.