Protocol

MFASS v1 (superseded)

MFASS v1 is a superseded historical protocol whose baseline used an incorrectly centred sequence window.

Sources

MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot

No reviewed evaluations are linked here in this release. See the sources and separately identified configurations below.

0 evaluations · 0 results

Overview

Datasets

Historical MFASS exon-recognition evaluation; the correction notice documents a sequence-orientation mismatch in the v1 baseline.

Metrics

Precision at a fixed review capacity, average precision and AUROC. Each method’s point estimates use its scored subset; paired comparisons use common scored variants.

Allowed inputs

Historical baseline uses the incorrectly centered sequence window; corrected assay-oriented pairs belong to v2.

Sources

Evaluation procedure diagram

How it worksComputational evaluation flow

Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.

Sources

limited source coverage · Automated source review, 2026-09-23. All specifications and missing details

Results

All evaluations

0 evaluations · 0 results. Different protocols are not a single leaderboard.

Applied filters: All linked evaluations

No evaluations linked in this release.

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

How it works

Evaluation methodology

Historical MFASS exon-recognition evaluation; the correction notice documents a sequence-orientation mismatch in the v1 baseline. The source distinguishes protocol versions from split versions. The earlier exon-only split-cost experiment requires a corrected rerun; its conclusions are withdrawn. Precision at a fixed review capacity, average precision and AUROC. Each method’s point estimates use its scored subset; paired comparisons use common scored variants. Historical baseline and specialist results are preserved for audit. The corrected v2 baseline and DNABERT-2 protocol must not be relabelled as v1. The v1 windowing defect invalidates its baseline comparisons as current evidence; this is separate from the grouped-split controls.

Sources

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Tasks

MFASS splice-variant prioritisation

These source-backed links do not make different protocols or scores interchangeable.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 0 active baseline roles have published Rewire measurements in this release. 1 historical protocols are retained separately. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

No reviewed evaluations with results linked in this release.

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Historical protocol

Training-set class prior where supervised fitting is permitted

Superseded protocol: retain history; do not start new runs.

Conventional reference

Historical protocol

Regularised classifier on simple permitted features, or protocol's conventional reference

Superseded protocol: retain history; do not start new runs.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

Limitations and conditions

Superseded baseline comparisons and split-cost claims must not be used as current evidence. This profile documents the correction and does not reproduce or rehabilitate the historical results.
Sources
MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot

Profile review details

Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied.

Stable record: rewire-mfass-v1

Specifications

Inputs, training, access and other details

Explanatory profile: limited source coverage · Automated source review, 2026-09-23. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.

Data, procedure and scoring
Property	Description and evidence
Datasets	Historical MFASS exon-recognition evaluation; the correction notice documents a sequence-orientation mismatch in the v1 baseline. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Splits	The source distinguishes protocol versions from split versions. The earlier exon-only split-cost experiment requires a corrected rerun; its conclusions are withdrawn. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Metrics	Precision at a fixed review capacity, average precision and AUROC. Each method’s point estimates use its scored subset; paired comparisons use common scored variants. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Baselines	Historical baseline and specialist results are preserved for audit. The corrected v2 baseline and DNABERT-2 protocol must not be relabelled as v1. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Leakage controls	The v1 windowing defect invalidates its baseline comparisons as current evidence; this is separate from the grouped-split controls. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Uncertainty	The archived SpliceAI comparison records 2,000 paired bootstrap draws, 454 independent groups and 95% interval bounds. These quantify sampling uncertainty in the historical run; they do not correct its sequence-window error and must not be reused as current baseline evidence. Sources (2) Archived MFASS v1 SpliceAI comparison; MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Archived JSON: independent_groups and paired.*.{draws,ci95_low,ci95_high}; README correction notice
Entity type	Superseded historical computational protocol. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Organisms	Human (Homo sapiens): naturally occurring ExAC variants in or beside human exons, measured in the MFASS minigene assay. Sources MFASS original assay accession GSE120695 · GSE120695 SOFT: Series_summary and Sample_organism_ch1 fields
Assays	MFASS functional exon-recognition labels. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Allowed inputs	Historical baseline uses the incorrectly centered sequence window; corrected assay-oriented pairs belong to v2. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Adaptation	Historical supervised baseline; its comparisons and split-cost claims are withdrawn pending corrected reruns. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot
Supersession cause	The archived v1 baseline combined raw sequence with assay-coordinate rel_position. For 7,770 of 27,733 eligible variants the raw field was the reverse complement of original_seq, placing the 21-base 3-mer window at the wrong base. The source withdraws v1 baseline comparisons and split-cost claims; preserved JSON remains historical evidence only. Sources MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · README.md correction notice lines 3–10 and cohort validation lines 59–64

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Papers and result coverage

Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.

Paper or primary resource	Version	Reference
MFASS benchmark: corrected v2 protocol and reproducibility instructions	Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256	Read source

Search and extraction details

historical results preserved

Searches

Pangolin SpliceAI MFASS splice variant benchmark rewire

Evidence locations

Pinned README correction and archived v1 results links

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.

20 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 Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.caption` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram steps Input: Historical baseline uses the incorrectly centered sequence window; corrected assay-oriented pairs belong to v2. Evaluation: Historical supervised baseline; its comparisons and split-cost claims are withdrawn pending corrected reruns. Readout: Precision at a fixed review capacity, average precision and AUROC. Each method’s point estimates use its scored subset; paired comparisons use common scored variants. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.steps` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Diagram title Computational evaluation flow Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.diagram.title` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Datasets Historical MFASS exon-recognition evaluation; the correction notice documents a sequence-orientation mismatch in the v1 baseline. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.0.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Splits The source distinguishes protocol versions from split versions. The earlier exon-only split-cost experiment requires a corrected rerun; its conclusions are withdrawn. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.1.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Adaptation Historical supervised baseline; its comparisons and split-cost claims are withdrawn pending corrected reruns. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.10.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Supersession cause The archived v1 baseline combined raw sequence with assay-coordinate rel_position. For 7,770 of 27,733 eligible variants the raw field was the reverse complement of original_seq, placing the 21-base 3-mer window at the wrong base. The source withdraws v1 baseline comparisons and split-cost claims; preserved JSON remains historical evidence only. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ README.md correction notice lines 3–10 and cohort validation lines 59–64 Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.11.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Metrics Precision at a fixed review capacity, average precision and AUROC. Each method’s point estimates use its scored subset; paired comparisons use common scored variants. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.2.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Baselines Historical baseline and specialist results are preserved for audit. The corrected v2 baseline and DNABERT-2 protocol must not be relabelled as v1. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.3.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Leakage controls The v1 windowing defect invalidates its baseline comparisons as current evidence; this is separate from the grouped-split controls. Individual claims	MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e Original source ↗ Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot Version: bee9133b83f3aedaf2bbb9013f1875515845607e Retrieved: 2026-09-16T20:55:04.446365+00:00	source checked automated source review · 2026-09-23 Audit details Follow-up review of Supersession cause. Source locations and before/after decisions are recorded in the 23 September profile-evidence audit. Other explanatory content retains its earlier source scope. No human scientific review or independent reproduction is implied. Field: `attributes.profile.facts.4.value` Source artifact SHA-256: `62a9381484fd2360767e78b114d9aa6cd8a4fc6487a981881a4c4999f0ab1b23` 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: superseded

5 source records and release history

MFASS v2 pinned rewire artifacts · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
MFASS benchmark: corrected v2 protocol and reproducibility instructions · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
MFASS computational protocol README at bee9133b83f3aedaf2bbb9013f1875515845607e · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
Archived MFASS v1 SpliceAI comparison · Original source · bee9133b83f3aedaf2bbb9013f1875515845607e
MFASS original assay accession GSE120695 · Original source · GSE120695 SOFT retrieved 2026-09-16

Superseded by MFASS v2

Download this release

Technical metadata and extraction receipts

Stable ID: rewire-mfass-v1

areas: dna-genomes
entity level: protocol
version: v1
task: Splice-variant prioritisation
scope note: The mfass-v1 baseline used a mis-centred k-mer window for 7,770 assay variants whose raw sequence was reverse-complemented. mfass-v2 validates assay-oriented reference and mutant pairs and rebuilds the baseline; mfass-v1 remains a historical record.
benchmark research: review date: 2026-09-17; status: historical_results_preserved; primary sources: evidence-expansion-mfass-readme-62a93814; inspected locators: Pinned README correction and archived v1 results links; searched queries: Pangolin SpliceAI MFASS splice variant benchmark rewire; gaps: None recorded; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
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: benchmark
entity classification: review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: evidence-benchmark-mfass-pinned-readme; source locator: Pinned README: correction notice; Dataset; Cohort reconciliation; Split; MFASS-v2 results; Paired comparisons; Limits; Archived mfass-v1 snapshot; ambiguities: None recorded

Related records

evaluates task: MFASS splice-variant prioritisation
subject: MFASS v1 (superseded): evaluates task MFASS splice-variant prioritisation
supersedes: MFASS v2

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