Configuration

Phenolyzer default, singleton (Yuan et al. 2022)

Phenolyzer default, singleton (Yuan et al. 2022) as evaluated in the cited comparison.

Overview

Phenolyzer default, singleton (Yuan et al. 2022) as evaluated in the cited comparison.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

2 evaluations · 14 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: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	1.3% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 1(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	7.9% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 10(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	13.4% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 20(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	18.4% top-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 30(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	20.7% top-40-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 40(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	5.2% top-5-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 5(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 305 DDD exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: DDD 305 solved probands (Yuan et al. selection)	23.3% top-50-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on DDD 305 rare-ranking-20261009-protocol-yuan2022-ddd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 7 (DDD, Phenolyzer), column 'TOP 50(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	3.8% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 1(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	20.6% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 10(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	29.2% top-20-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 20(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	37.8% top-30-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 30(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	42.1% top-40-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 40(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	13.4% top-5-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 5(%)'
Configuration: Phenolyzer default, singleton (Yuan et al. 2022)	Protocol: Causal-gene rank in 209 in-house exomes, default singleton runs (Yuan et al. 2022 SM Table 3) Dataset: KingMed Changsha in-house cohort, 209 solved cases (Yuan et al. 2022)	44.5% top-50-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Phenolyzer default singleton on KMCGD 209 rare-ranking-20261009-protocol-yuan2022-kmcgd-singleton-default Aggregation: Not reported Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases; Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · SM Table 3 row 18 (KMCGD, Phenolyzer), column 'TOP 50(%)'

Source checking is not independent reproduction. Release 2026-10-10-6e93f504adfc.

Use this model

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-10-6e93f504adfc
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

All evidence (JSONL) (gzip)How to read the evidence

Sources and history

Release 2026-10-10-6e93f504adfc · Record review: source checked

2 source records and release history

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases · Original source · Briefings in Bioinformatics 23(2):bbac019, published 2022-02-04; PMC8921623 full-text XML
Yuan et al. 2022, SM Table 3 (accuracy in each top level experiment) · Original source · sm_table_3_r1_bbac019.docx inside the Europe PMC supplementaryFiles zip for PMC8921623

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-yuan2022-phenolyzer

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: Phenolyzer default, singleton (Yuan et al. 2022)
foundation model eligible: false
version: 0.4.0
parameters: Default parameters; input HPO only; singleton proband analysis
source locator: Table 2 row 'Phenolyzer'; SM Table 3 row 'Phenolyzer'

Related records

configuration of: Phenolyzer
system: Phenolyzer default singleton on DDD 305
system: Phenolyzer default singleton on KMCGD 209

Suggest a correction