Configuration

Pangolin · mask=False

This MFASS evaluation uses Pangolin with masking disabled, scoring variants in genomic context.

Sources

MFASS v2 run_pangolin.py · run_pangolin.py module documentation and recorded runner configuration

How it worksEvaluated pipeline

Schematic of the pinned MFASS configuration; this does not generalise to every member of the model family.

Sources

MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e

Overview

Model type

Pretrained splice-usage specialist ensemble

Biological inputs

Variant genomic coordinates, GRCh38 reference and GENCODE annotation

Outputs

Maximum absolute predicted splice-usage change

Access

Public pinned runner with external reference, annotation and model dependencies.

Sources

MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure

limited source coverage · Automated source review, 2026-09-16. All specifications and missing details

Evaluations and results

1 evaluation · 3 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Pangolin · mask=False	Protocol: MFASS v2 Dataset: MFASS v2 eligible assay cohort	0.876 auroc fraction · higher Uncertainty: Not reported Coverage: 8301/8324	Rewire evaluation · Independently reproduced Methods, coverage and source Pangolin · mask=False on MFASS v2 Unchanged specialist run in genomic context with GENCODE v44; zero-shot on MFASS assay labels. Point metrics use the scored subset. Aggregation: Not reported MFASS v2 pinned rewire artifacts · benchmarks/mfass/results/pangolin-maskFalse.json :: auroc
Configuration: Pangolin · mask=False	Protocol: MFASS v2 Dataset: MFASS v2 eligible assay cohort	0.389 average_precision fraction · higher Uncertainty: Not reported Coverage: 8301/8324	Rewire evaluation · Independently reproduced Methods, coverage and source Pangolin · mask=False on MFASS v2 Unchanged specialist run in genomic context with GENCODE v44; zero-shot on MFASS assay labels. Point metrics use the scored subset. Aggregation: Not reported MFASS v2 pinned rewire artifacts · benchmarks/mfass/results/pangolin-maskFalse.json :: average_precision
Configuration: Pangolin · mask=False	Protocol: MFASS v2 Dataset: MFASS v2 eligible assay cohort	0.65 precision_at_100 fraction · higher Uncertainty: Not reported Coverage: 8301/8324	Rewire evaluation · Independently reproduced Methods, coverage and source Pangolin · mask=False on MFASS v2 Unchanged specialist run in genomic context with GENCODE v44; zero-shot on MFASS assay labels. Point metrics use the scored subset. Aggregation: Not reported MFASS v2 pinned rewire artifacts · benchmarks/mfass/results/pangolin-maskFalse.json :: precision_at_100

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

Use this model

How it works, versions and access

Related profile: Pangolin. This page retains the exact record and its evaluation context.

Underlying model: Pangolin. Results on this page belong to this configuration and its evaluated settings.

How it works

Evaluated procedure

The runner uses the specified reference and GENCODE annotation to predict changes in splice strength. The mask=False choice retains changes that annotation-based masking would remove. These specialist predictions were retained unchanged in the corrected v2 comparison.

Sources

MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

Tests a pretrained splice specialist without learning from MFASS assay labels.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e

Limitations and conditions

Results depend on annotation, masking and scored coverage. This configuration is not interchangeable with Pangolin’s masked default.
Sources
MFASS v2 pinned rewire artifacts · benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e

Profile review details

Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed.

Stable record: rewire-model-pangolin-maskfalse

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Inputs, outputs and configuration
Property	Description and evidence
Model type	Pretrained splice-usage specialist ensemble Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Architecture / procedure	Official 12-model Pangolin ensemble; use maximum absolute predicted splice-usage change with masking disabled. Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Biological inputs	Variant genomic coordinates, GRCh38 reference and GENCODE annotation Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Outputs	Maximum absolute predicted splice-usage change Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Parameters	An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. · Not reported in inspected sources Sources MFASS v2 run_pangolin.py · Pinned runner configuration and implementation; inspected for aggregate parameter count (component sizes are not added without an exact configuration)
Training data / fitting	No fitting on MFASS assay outcomes in this runner. Upstream training overlap at assayed exons remains unchecked. Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Context limits	10,000-bp genomic context and 50-base scoring distance in the recorded configuration. Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Known versions / configuration	Pangolin official final.{1,2,3}.{0,2,4,6}.3.v2 ensemble; mask=False Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Access	Public pinned runner with external reference, annotation and model dependencies. Sources MFASS v2 run_pangolin.py · run_pangolin.py; module documentation, main() configuration and scoring procedure
Code licence	MIT for the Rewire runner at the reviewed revision. Upstream Pangolin: GPLv3. These are separate component licences. Sources (2) Rewire benchmark runner licence; github.com/tkzeng/Pangolin LICENSE · LICENSE; complete MIT grant; upstream LICENSE
Weights licence	A separate grant specifically naming the Pangolin weight files is not stated in the inspected README or repository GPL licence; code and weight scope require clarification. · Not reported in inspected sources Sources github.com/tkzeng/Pangolin README.md · README.md; model installation and full repository LICENSE

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.

23 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
Diagram caption Schematic of the pinned MFASS configuration; this does not generalise to every member of the model family. Individual claims	MFASS v2 pinned rewire artifacts Original source ↗ benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T10:50:02Z	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `a3af693afc070b39b334e359beed7f9affd76f7456a4f9264e2d1e9dab26111d` Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash
Diagram steps Variant and genomic context Pangolin predictor Splice-strength changes mask=False aggregation Variant ranking Individual claims	MFASS v2 pinned rewire artifacts Original source ↗ benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T10:50:02Z	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `a3af693afc070b39b334e359beed7f9affd76f7456a4f9264e2d1e9dab26111d` Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash
Diagram title Evaluated pipeline Individual claims	MFASS v2 pinned rewire artifacts Original source ↗ benchmarks/mfass/README.md, MFASS-v2 results; results/pangolin-maskFalse.json, config and notes at bee9133b83f3aedaf2bbb9013f1875515845607e Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T10:50:02Z	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `a3af693afc070b39b334e359beed7f9affd76f7456a4f9264e2d1e9dab26111d` Hash scope: Local imported data/benchmark-runs/mfass-v2.json; not the upstream repository or result-file hash
Model type Pretrained splice-usage specialist ensemble Individual claims	MFASS v2 run_pangolin.py Original source ↗ run_pangolin.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Architecture / procedure Official 12-model Pangolin ensemble; use maximum absolute predicted splice-usage change with masking disabled. Individual claims	MFASS v2 run_pangolin.py Original source ↗ run_pangolin.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Weights licence A separate grant specifically naming the Pangolin weight files is not stated in the inspected README or repository GPL licence; code and weight scope require clarification. Individual claims	github.com/tkzeng/Pangolin README.md Original source ↗ README.md; model installation and full repository LICENSE Version: 5cf94b8db938c658391b4305cd7ce33297d44ff7 Retrieved: 2026-09-16T19:46:20.582143+00:00	unreported automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `9117f9d255d6b6e810d224a600d381192bccccd3f0cd417fed9559d49ca8fffd` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Biological inputs Variant genomic coordinates, GRCh38 reference and GENCODE annotation Individual claims	MFASS v2 run_pangolin.py Original source ↗ run_pangolin.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Outputs Maximum absolute predicted splice-usage change Individual claims	MFASS v2 run_pangolin.py Original source ↗ run_pangolin.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Parameters An aggregate parameter total for this exact evaluated configuration is not established by the inspected sources. Individual claims	MFASS v2 run_pangolin.py Original source ↗ Pinned runner configuration and implementation; inspected for aggregate parameter count (component sizes are not added without an exact configuration) Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	unreported automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Training data / fitting No fitting on MFASS assay outcomes in this runner. Upstream training overlap at assayed exons remains unchecked. Individual claims	MFASS v2 run_pangolin.py Original source ↗ run_pangolin.py; module documentation, main() configuration and scoring procedure Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:47:15.959417+00:00	source checked automated source review · 2026-09-16 Audit details Pinned MFASS runner source rechecked at bee9133b83f3aedaf2bbb9013f1875515845607e. Existing numerical records and historical artifacts remain unchanged; no new run was performed. Field: `attributes.profile.facts.5.value` Source artifact SHA-256: `83e5b71d7265c63fb0874d7b493ac2c8d205f645c079b09f350d69b44e5c921b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

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

5 source records and release history

MFASS v2 pinned rewire artifacts · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
MFASS v2 run_pangolin.py · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
Rewire benchmark runner licence · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
github.com/tkzeng/Pangolin LICENSE · Original source · 5cf94b8db938c658391b4305cd7ce33297d44ff7
github.com/tkzeng/Pangolin README.md · Original source · 5cf94b8db938c658391b4305cd7ce33297d44ff7

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Technical metadata and extraction receipts

Stable ID: rewire-model-pangolin-maskfalse

areas: dna-genomes
entity level: method
version: bee9133b83f3aedaf2bbb9013f1875515845607e
reported name: Pangolin · mask=False
historical missing metadata: None recorded
metadata review scope: historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: evidence-reported-rewire-run-pangolin; source locator: run_pangolin.py; module documentation, main() configuration and scoring procedure | run_pangolin.py module documentation and recorded runner configuration; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

Related records

uses model: Pangolin
family: Pangolin
subject: Pangolin · mask=False: family Pangolin
subject: Pangolin · mask=False: uses model Pangolin
model: Pangolin · mask=False on MFASS v2

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