Configuration

AMELIE-HPO default, singleton (Yuan et al. 2022)

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

Overview

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

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Evaluations and results

2 evaluations · 14 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AMELIE-HPO 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)	4.3% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 1(%)'
Configuration: AMELIE-HPO 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)	14.4% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 10(%)'
Configuration: AMELIE-HPO 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)	23.9% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 20(%)'
Configuration: AMELIE-HPO 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)	29.8% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 30(%)'
Configuration: AMELIE-HPO 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)	34.4% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 40(%)'
Configuration: AMELIE-HPO 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)	10.8% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 5(%)'
Configuration: AMELIE-HPO 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)	37.7% 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 AMELIE-HPO 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 11 (DDD, AMELIE-HPO), column 'TOP 50(%)'
Configuration: AMELIE-HPO 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)	2.4% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 1(%)'
Configuration: AMELIE-HPO 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)	16.3% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 10(%)'
Configuration: AMELIE-HPO 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)	23% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 20(%)'
Configuration: AMELIE-HPO 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)	25.4% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 30(%)'
Configuration: AMELIE-HPO 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-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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 40(%)'
Configuration: AMELIE-HPO 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)	9.6% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 5(%)'
Configuration: AMELIE-HPO 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)	30.6% 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 AMELIE-HPO 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 22 (KMCGD, AMELIE-HPO), column 'TOP 50(%)'

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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

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-yuan2022-amelie-hpo

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: AMELIE-HPO default, singleton (Yuan et al. 2022)
foundation model eligible: false
version: Oct 5, 2020 (as printed)
parameters: Default parameters; input HPO only; singleton proband analysis
source locator: Table 2 row 'AMELIE'; SM Table 3 row 'AMELIE-HPO'

Related records

configuration of: AMELIE
system: AMELIE-HPO default singleton on DDD 305
system: AMELIE-HPO default singleton on KMCGD 209

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