MFASS: matched GENCODE 44 canonical annotation
Current source-reviewed mapping
Proxy evidence: transfer to this question is limited
The recorded endpoint informs assay-oriented prioritisation under its declared conditions. Selecting variants for a different follow-up experiment requires transfer validation; the endpoint is not patient RNA or clinical pathogenicity.
- Assessed endpoint
- Ranking held-out MFASS SNVs by reporter-assay splice disruption under matched canonical annotation.
- Evaluation protocol
- MFASS: matched GENCODE 44 canonical annotation
- Computational task
- MFASS splice-variant prioritisation (Not yet reviewed)
- Input and population constraints
- Identical scored population: 8,297 of 8,324 held-out variants, 314 scored positives and 460 groups in all four configurations.
- Shared GENCODE 44 canonical transcript selection and FASTA; 50-base distance; distinct SpliceAI and Pangolin masking settings.
- Keep historical annotation conditions and scoring populations in their existing separate comparison groups.
Limits on interpretation
- 23 assembly-orientation mismatches and four canonical-transcript-span exclusions remain unscored. The latter are protocol exclusions, not established faulty variants; full-population performance is unknown.
- No top-100 precision difference is established and masked Pangolin is tie-sensitive. Paired contrast intervals are not individual-condition intervals.
- Exploratory source review only; no independent human review, replication or clinical validation. Assembly-issue author confirmation is not established.
Automated source review · 2026-09-25 · Codex research curation
Reviewed exact configuration and population scope against pinned source bytes. Applicability remains proxy evidence; no human domain review or clinical validation.
Evaluated configurations
Each configuration below belongs to this protocol. Inspect its inputs, population and scoring conditions before comparing it with another evaluation.
SpliceAI 1.3.1 · mask 0 (S0)
Rewire evaluation · Source checked
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.
- Population and split
- 8297/8324 · split-v2 test
- Inputs and adaptation
- GRCh38 genomic context; matched GENCODE44 canonical annotation · zero-shot pretrained specialists
- Evaluation budget
- one frozen execution per condition
- Runtime and memory
Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.
Uncertainty: Point estimate; paired contrast intervals are reported separately in the source and must not be used as intervals for this individual condition.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
SpliceAI 1.3.1 · mask 1 (S1)
Rewire evaluation · Source checked
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.
- Population and split
- 8297/8324 · split-v2 test
- Inputs and adaptation
- GRCh38 genomic context; matched GENCODE44 canonical annotation · zero-shot pretrained specialists
- Evaluation budget
- one frozen execution per condition
- Runtime and memory
Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.
Uncertainty: Point estimate; paired contrast intervals are reported separately in the source and must not be used as intervals for this individual condition.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
Pangolin 1.0.2 + per-gene masking patch · mask False (P0)
Rewire evaluation · Source checked
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.
- Population and split
- 8297/8324 · split-v2 test
- Inputs and adaptation
- GRCh38 genomic context; matched GENCODE44 canonical annotation · zero-shot pretrained specialists
- Evaluation budget
- one frozen execution per condition
- Runtime and memory
Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.
Uncertainty: Point estimate; paired contrast intervals are reported separately in the source and must not be used as intervals for this individual condition.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
Pangolin 1.0.2 + per-gene masking patch · mask True (P1)
Rewire evaluation · Source checked
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.
- Population and split
- 8297/8324 · split-v2 test
- Inputs and adaptation
- GRCh38 genomic context; matched GENCODE44 canonical annotation · zero-shot pretrained specialists
- Evaluation budget
- one frozen execution per condition
- Runtime and memory
Runtime and memory measurements are not reported in this evaluation. A study budget is not a runtime or memory measurement.
Uncertainty: Point estimate; paired contrast intervals are reported separately in the source and must not be used as intervals for this individual condition.
Evaluation methods, evidence and reproduction
No execution recipe has been verified for this exact configuration and evaluation. Inspect its methods and original run documentation before attempting reproduction.
Open the protocol's results and comparison checks →
Original execution documentation ↗
Mapping sources and review metadata
- MFASS matched canonical annotation v1: report.json · Original source ↗
/conditions/{S0,S1,P0,P1}/coverage; /conditions/{S0,S1,P0,P1}/metrics; /conditions/{S0,S1,P0,P1}/ties; /contrasts/{S1-S0,P1-P0,P0-S0}/paired/precision_at_capacity - MFASS matched canonical annotation v1: manifest-v1.json · Original source ↗
/conditions; /distance; /resources_sha256; /code - MFASS matched canonical annotation v1: exclusion-verification.json · Original source ↗
/exclusion_counts; /conditions; /checks - MFASS matched study intake: coverage and interpretation · Reviewed source copy ↗ · Original repository location ↗
Opening coverage, exclusion, annotation and interpretation paragraphs; Review and validation - MFASS benchmark: corrected v2 protocol and reproducibility instructions · Original source ↗
Dataset; Limits
Mapping use-case-mapping-splicing-mfass-matched-v1 · revision 1
Initial bounded applicability review of the matched MFASS study.
Reviewed evidence fingerprint c4cfbe66c30d59308fc8d2226f42720a09a6e54d2f407c7141b08e01e39c0a47