Protocol

Lin et al. 2025 OncoKB level-of-evidence assignment

LLM evidence-level classification task from Lin et al. 2025.

Overview

LLM evidence-level classification task from Lin et al. 2025.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

6 recorded evaluations, 6 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

6 evaluations · 6 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-4o, basic prompt, temperature 1.0 (default) (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.339 top-1-accuracy fraction · higher Uncertainty: 95% CI 0.3369 to 0.3417 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source gpt-4o-basic on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 1 (Tab1), row 'OncoKB', column 'GPT-4o' Mean accuracy; 95% CI in the next column
Configuration: Llama 3.1 70B, basic prompt, temperature 0.4 (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.318 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source llama-basic-t0-4 on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 2 (Tab2), row 10 ('Llama 3.1', 'Basic prompt + temperature (0.4)', 'OncoKB'), column 'Accuracy'
Configuration: Llama 3.1 70B, basic prompt, temperature 0.8 (default) (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.307 top-1-accuracy fraction · higher Uncertainty: 95% CI 0.3041 to 0.309 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source llama-basic-t0-8 on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 1 (Tab1), row 'OncoKB', column 'Llama 3' Mean accuracy; 95% CI in the next column
Configuration: Llama 3.1 70B, basic prompt, temperature 0 (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.331 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source llama-basic-t0 on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 2 (Tab2), row 11 ('Llama 3.1', 'Basic prompt + temperature (0)', 'OncoKB'), column 'Accuracy'
Configuration: Qwen 2.5 72B, basic prompt, temperature 0.8 (default) (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.333 top-1-accuracy fraction · higher Uncertainty: 95% CI 0.3316 to 0.334 Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source qwen-basic on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 1 (Tab1), row 'OncoKB', column 'Qwen 2.5' Mean accuracy; 95% CI in the next column
Configuration: Qwen 2.5 72B, refined prompt, temperature 0.8 (default) (Lin et al. 2025)	Protocol: Lin et al. 2025 OncoKB level-of-evidence assignment Dataset: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)	0.299 top-1-accuracy fraction · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source qwen-refined on oncokb (Lin et al. 2025) egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment Aggregation: Not reported Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Table 2 (Tab2), row 6 ('Qwen2.5', 'Refined prompt + Default temperature (0.8)', 'OncoKB'), column 'Accuracy'

Source checking is not independent reproduction. Release 2026-10-09-ba02f2f4a36e.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

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External evaluations: 6

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Training-set class prior where supervised fitting is permitted

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

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Regularised classifier on simple permitted features, or protocol's conventional reference

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

Coverage is derived from release 2026-10-09-ba02f2f4a36e. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

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Strengths, limitations and unresolved questions

Evidence

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Evidence table

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Sources and history

Release 2026-10-09-ba02f2f4a36e · Record review: source checked

1 source records and release history

Benchmarking large language models GPT-4o, llama 3.1, and qwen 2.5 for cancer genetic variant classification · Original source · npj Precision Oncology 9:141, published 2025-05-15; PMC12078457 full-text XML

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Technical metadata and extraction receipts

Stable ID: egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment

areas: dna-genomes
contexts: clinical_research
protocol: Ask each LLM to assign the OncoKB level (1, 2, 3, 4, R1, R2 or VUS) for each gene, alteration and cancer type of the OncoKB actionable-genes table. Reference: OncoKB level in the actionable-genes table. Score the top-1 answer (up to three levels may be returned); repeat each query 100 times for basic prompts and 10 times for other settings; report mean accuracy.
version: Lin et al. 2025 Methods
metric: top-1-accuracy
metric direction: higher
limitations: Pan-cancer variant set; no EGFR- or NSCLC-specific score is reported.; The model assigns an evidence level from gene, alteration and tumour type alone; no prior therapy, line or evidence date is given and no source is cited.; Public OncoKB and CIViC tables may be in the models' training data (Discussion P33).; Queries name the gene, alteration and tumour type but no drug, while the reference table assigns levels per drug or evidence item; the paper does not say how a query with several reference levels was scored, so sensitivity and resistance levels for the same variant cannot be told apart.; The 95% confidence intervals span 0.0004 to 0.0049 in width and appear to describe variation between repeated runs of the same queries, not uncertainty from the choice of variants.
source locator: Lin et al. 2025 Methods 'Dataset' (P35-P38), 'Model selection' (P39-P40), 'System prompts' (P41-P43), 'Testing framework design' (P44-P47); Tables 1-2

Related records

uses data: OncoKB actionable-genes table, 625 variant-cancer-drug associations (accessed 2024-11-20)
subject: query_format: egfrnsclc-20261009-protocol-lin2025-oncokb-level-assignment
assessment: gpt-4o-basic on oncokb (Lin et al. 2025)
assessment: llama-basic-t0-4 on oncokb (Lin et al. 2025)
assessment: llama-basic-t0-8 on oncokb (Lin et al. 2025)
assessment: llama-basic-t0 on oncokb (Lin et al. 2025)
assessment: qwen-basic on oncokb (Lin et al. 2025)
assessment: qwen-refined on oncokb (Lin et al. 2025)
assessed by: Review EGFR lung-cancer actionability evidence

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