PHACTboost
Gradient-boosted tree classifier that combines PHACT phylogeny-aware scores with features from multiple sequence alignments and phylogenetic trees.
Results are recorded on linked configurations and versions of this method. Their settings and evaluations are kept separate below.
Results on linked records
This method has no results of its own in this release. 2 linked records have results. They are not assigned to the underlying method: each record keeps its own settings and evaluations, and its scores are on its own page.
- PHACTboost rank score, dbNSFP 5.3.1a (Lee 2026) Configuration · configuration · 3 evaluations · 6 results
- PHACTboost (Livesey and Marsh 2025) Configuration · configuration · 6 evaluations · 7 results
Overview
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Evidence
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Evidence table
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1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Description Gradient-boosted tree classifier that combines PHACT phylogeny-aware scores with features from multiple sequence alignments and phylogenetic trees. Individual claims | PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting qa-descriptions-20261011-e-source-phactboost: Abstract Version: Europe PMC full-text XML for PMC11251492, Molecular Biology and Evolution 2024 | source checked ["automated-source-review","ai-assisted-source-review"] · 2026-10-11 Audit detailsApproved with two corrections, both applied: the MutFormer source licence is CC BY 4.0 per the arXiv abstract page, and the MetaRNN source locator now names the Background passage. Checked the 27 Chen 2020 descriptions row by row against Table 1 (PMC7033911) and spot-checked AlphaMissense, MisFit, popEVE, VARITY, MetaRNN, MutFormer and gMVP against their abstracts; accurate. Licences on the other new sources match Europe PMC. Field: Claim: metadata-correction-60681ea382c13d3db9f4 Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the Europe PMC full-text XML. These renderings are not always byte-stable; the article text is the evidence. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
2 source records and release history
- An openly licensed benchmark and per-gene calibration map for missense pathogenicity predictors on activating cancer drivers · Original source · bioRxiv 2026.07.16.739080 v1, posted 2026-07-23; full-text HTML page
- PHACTboost: A Phylogeny-Aware Pathogenicity Predictor for Missense Mutations via Boosting · Original source · Europe PMC full-text XML for PMC11251492, Molecular Biology and Evolution 2024
Technical metadata and extraction receipts
Stable ID: somatic-oncogenicity-20261009-method-phactboost
- areas
- dna-genomes
- contexts
- clinical_research
- method types
- supervised_machine_learning
- reported name
- PHACTboost
- entity level
- method
- source locator
- Algorithm lists of the cited sources
- missing metadata
- version: reason: inapplicable; note: Family record; score sources are on configurations
Related records
- subject: PHACTboost: description
- configuration of: PHACTboost rank score, dbNSFP 5.3.1a (Lee 2026)
- configuration of: PHACTboost (Livesey and Marsh 2025)