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GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)

GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) as evaluated in the cited comparison.

3 evaluations · 60 results

Overview

GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025) as evaluated in the cited comparison.

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Evaluations and results

3 evaluations · 60 results. Different protocols are not a single leaderboard.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.668 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.929 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	70% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	89% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.856 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.982 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	85% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	97% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.972 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.991 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	97% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	100% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 5, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.786 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.977 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	87% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	97% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 50, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.742 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'AUPR', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	0.98 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'ROC AUC', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	74% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@1 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, ClinVar (Kafkas et al. 2025 Table 3) Dataset: ClinVar variants added 2 July to 7 October 2023, 100 genes (Kafkas et al. 2025)	96% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on ClinVar candidate gene sets rare-ranking-20261009-protocol-kafkas2025-clinvar-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 75, 'Hits@10 (%)', column 'ClinVar' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, GPCards (Kafkas et al. 2025 Table 3) Dataset: GPCards gene-phenotype cases (free-text phenotypes) (Kafkas et al. 2025)	0.559 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on GP-Cards candidate gene sets rare-ranking-20261009-protocol-kafkas2025-gpcards-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'AUPR', column 'GP-Cards' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, GPCards (Kafkas et al. 2025 Table 3) Dataset: GPCards gene-phenotype cases (free-text phenotypes) (Kafkas et al. 2025)	0.927 auroc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on GP-Cards candidate gene sets rare-ranking-20261009-protocol-kafkas2025-gpcards-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'ROC AUC', column 'GP-Cards' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, GPCards (Kafkas et al. 2025 Table 3) Dataset: GPCards gene-phenotype cases (free-text phenotypes) (Kafkas et al. 2025)	60% top-1-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on GP-Cards candidate gene sets rare-ranking-20261009-protocol-kafkas2025-gpcards-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@1 (%)', column 'GP-Cards' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, GPCards (Kafkas et al. 2025 Table 3) Dataset: GPCards gene-phenotype cases (free-text phenotypes) (Kafkas et al. 2025)	82% top-10-accuracy percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on GP-Cards candidate gene sets rare-ranking-20261009-protocol-kafkas2025-gpcards-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 100, 'Hits@10 (%)', column 'GP-Cards' 'GPT-4' 'One shot'
Configuration: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)	Protocol: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, GPCards (Kafkas et al. 2025 Table 3) Dataset: GPCards gene-phenotype cases (free-text phenotypes) (Kafkas et al. 2025)	0.756 auprc fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GPT-4 One shot on GP-Cards candidate gene sets rare-ranking-20261009-protocol-kafkas2025-gpcards-gene-sets Aggregation: Not reported The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Table 3 row Size 25, 'AUPR', column 'GP-Cards' 'GPT-4' 'One shot'

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The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients · Original source · Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML

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Technical metadata and extraction receipts

Stable ID: rare-ranking-20261009-config-kafkas2025-gpt-4-one-shot

areas: dna-genomes
contexts: clinical_research
method types: foundation_model
reported name: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)
foundation model eligible: true
version: gpt-4-1106-preview
parameters: One-shot chain-of-thought prompt (Q4)
source locator: Table 1; Table 3; Methods 'Prompt engineering'

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