Evaluation

GPT-4 One shot on PAVS candidate gene sets

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Evaluation results

1 evaluation · 20 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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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), 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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.539 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.937 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	57.8% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	84.8% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.784 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.979 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	77.8% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	99% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.956 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	94.8% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.677 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.973 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	68.4% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	95.2% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.595 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	0.96 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	61.8% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' '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, PAVS (Kafkas et al. 2025 Table 3) Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)	91.4% 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 PAVS candidate gene sets rare-ranking-20261009-protocol-kafkas2025-pavs-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 'PAVS' 'GPT-4' 'One shot'

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

Evaluation procedure

rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets

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, PAVS (Kafkas et al. 2025 Table 3)
Dataset: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)

origin: Author-reported evaluation
configuration: Primary source as retrieved 2026-10-09
dataset version: As published
split: No split
population: PAVS genotype-phenotype pairs
inputs: HPO-coded phenotypes and a candidate gene list
adaptation: One shot
metric implementation: Hits@k, ROC AUC and AUPR over candidate sets
aggregation: Per candidate-set size
budget: Candidate sets of 5, 25, 50, 75 and 100 genes
protocol id: rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split: No split
Adaptation: One shot
Scoring implementation: Hits@k, ROC AUC and AUPR over candidate sets

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

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Inspect claims, sources and review details

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19 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
attributes.comparison.adaptation One shot Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.adaptation` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.aggregation Per candidate-set size Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.aggregation` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.budget Candidate sets of 5, 25, 50, 75 and 100 genes Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.budget` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.dataset_version As published Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.dataset_version` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.inputs HPO-coded phenotypes and a candidate gene list Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.inputs` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.metric_implementation Hits@k, ROC AUC and AUPR over candidate sets Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.metric_implementation` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.population PAVS genotype-phenotype pairs Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.population` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.protocol_id rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.protocol_id` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.comparison.split No split Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.comparison.split` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
attributes.limitations 1 values The authors designed the GPT-4 prompts, including the one-shot chain-of-thought prompt Q4 (Table 1; Methods 'Prompt engineering'; Author contributions), so these rows are author_reported. Context-only references	The application of Large Language Models to the phenotype-based prioritization of causative genes in rare disease patients Original source ↗ Table 3 column 'PAVS', 'GPT-4' 'One shot' Version: Scientific Reports 15, published 2025-04-29; PMC12041562 full-text XML Retrieved: 2026-10-09T21:20:27Z	not individually reviewed No individual claim review recorded author reported Audit details Field: `attributes.limitations` Source artifact SHA-256: `75851f55d59fb0f194ca8bbcf10f47b6f593e8658239dc0fb85f5d2844236a3b` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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

1 source records and release history

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-eval-kafkas2025-pavs-gpt-4-one-shot

areas: dna-genomes
contexts: clinical_research
origin: author_reported
protocol: rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets
version: Primary source as retrieved 2026-10-09
comparison: dataset version: As published; split: No split; population: PAVS genotype-phenotype pairs; inputs: HPO-coded phenotypes and a candidate gene list; adaptation: One shot; metric implementation: Hits@k, ROC AUC and AUPR over candidate sets; aggregation: Per candidate-set size; budget: Candidate sets of 5, 25, 50, 75 and 100 genes; protocol id: rare-ranking-20261009-protocol-kafkas2025-pavs-gene-sets
source locator: Table 3 column 'PAVS', 'GPT-4' 'One shot'
limitations: The authors designed the GPT-4 prompts, including the one-shot chain-of-thought prompt Q4 (Table 1; Methods 'Prompt engineering'; Author contributions), so these rows are author_reported.

Related records

system: GPT-4 (gpt-4-1106-preview), one-shot chain-of-thought prompt Q4 (Kafkas et al. 2025)
assessment: Ranking the causative gene within synthetic candidate sets of 5 to 100 genes, PAVS (Kafkas et al. 2025 Table 3)
data: PAVS Saudi phenotype-associated variants, 500 genes (Kafkas et al. 2025)
evaluation: kafkas2025-pavs-gpt-4-one-shot-size100-auprc auprc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size100-auroc auroc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size100-hits1 top-1-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size100-hits10 top-10-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size25-auprc auprc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size25-auroc auroc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size25-hits1 top-1-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size25-hits10 top-10-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size5-auprc auprc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size5-auroc auroc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size5-hits1 top-1-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size5-hits10 top-10-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size50-auprc auprc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size50-auroc auroc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size50-hits1 top-1-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size50-hits10 top-10-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size75-auprc auprc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size75-auroc auroc
evaluation: kafkas2025-pavs-gpt-4-one-shot-size75-hits1 top-1-accuracy
evaluation: kafkas2025-pavs-gpt-4-one-shot-size75-hits10 top-10-accuracy

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