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AMELIE 3.1.0, Protocol D (Yuan et al. 2024)

AMELIE 3.1.0, Protocol D: filterByCount on, alfqCutoff 2.0%; singleton; AMELIE trio mode was unavailable and LIRICAL trio mode was under development.

2 evaluations · 14 results

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Evaluations and results

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

Sorted by Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)	Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes)
AMELIE 3.1.0, Protocol D (Yuan et al. 2024)Evaluation	Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	55.9% (best in column)	86.8%	87.5%	88.2%	88.2%	81.6%	88.2%
AMELIE 3.1.0, Protocol D (Yuan et al. 2024)Evaluation	Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1), DDD 305 solved probands (Yuan et al. selection)	50.5%	90.5% (best in column)	91.8% (best in column)	92.8% (best in column)	92.8% (best in column)	83% (best in column)	93.1% (best in column)

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	50.5% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	90.5% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	91.8% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	92.8% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	92.8% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	83% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 305 DDD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: DDD 305 solved probands (Yuan et al. selection)	93.1% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on DDD rare-ranking-20261009-protocol-yuan2024-ddd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (DDD, AMELIE, PROT D), column 'Top50 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	55.9% Top-1 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top1 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	86.8% Top-10 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top10 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	87.5% Top-20 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top20 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	88.2% Top-30 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top30 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	88.2% Top-40 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top40 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	81.6% Top-5 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top5 (%)'
Configuration: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)	Protocol: Causal-gene rank in 152 KGD trio-family exomes across parameter protocols (Yuan et al. 2024 Table 1) Dataset: KingMed in-house trio cohort, 152 families (Yuan et al. 2024)	88.2% Top-50 accuracy (proportion of solved cases with the causal gene within the tool's top-ranked genes) 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 Protocol D on KGD rare-ranking-20261009-protocol-yuan2024-kgd-parameter-protocols Aggregation: Not reported Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Table 1 row (KGD, AMELIE, PROT D), column 'Top50 (%)'

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Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases · Original source · Scientific Reports 14:2845, published 2024-02-03; PMC10838329 full-text XML

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Stable ID: rare-ranking-20261009-config-yuan2024-amelie-protocol-d

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: AMELIE 3.1.0, Protocol D (Yuan et al. 2024)
foundation model eligible: false
version: 3.1.0
parameters: filterByCount on, alfqCutoff 2.0%; singleton; AMELIE trio mode was unavailable and LIRICAL trio mode was under development (Discussion paragraph 1, item 4)
source locator: Table 1 rows 'AMELIE', PROT 'D'; Results 'Performance improvement assessment'; Discussion paragraph 1, item 4
provenance note: AMELIE 3.1.0, Protocol D (Yuan et al. 2024) as evaluated in the cited comparison.

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