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GPT-4 (gpt-4-1106-preview), zero-shot prompt (Kafkas et al. 2025)

GPT-4 (gpt-4-1106-preview), zero-shot prompt (Kafkas et al. 2025) as evaluated in the cited comparison.

Overview

GPT-4 (gpt-4-1106-preview), zero-shot prompt (Kafkas et al. 2025) 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

3 evaluations · 60 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: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.622 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.911 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	68% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	81% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.802 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.964 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	82% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	94% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.944 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	93% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.806 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.971 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	81% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.663 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.925 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	71% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.343 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.928 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	86% 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 Zero 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' 'Zero shot'
Configuration: GPT-4 (gpt-4-1106-preview), zero-shot prompt (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)	0.77 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 Zero 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' 'Zero 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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Stable ID: rare-ranking-20261009-config-kafkas2025-gpt-4-zero-shot

areas: dna-genomes
contexts: clinical_research
method types: foundation_model
reported name: GPT-4 (gpt-4-1106-preview), zero-shot prompt (Kafkas et al. 2025)
foundation model eligible: true
version: gpt-4-1106-preview
parameters: Zero-shot gene-ranking prompt; the specific zero-shot prompt (Q1-Q3 or Q2Q3) used in Table 3 is not stated
source locator: Table 1; Table 3; Methods 'Prompt engineering'

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