rewirebio.iobenchmarks
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GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)

GPT-4o answering yes/no CRISPR screen questions by direct prompting, summarised over zero-shot, few-shot and chain-of-thought prompt variants.

2 evaluations · 10 results

Overview

An explanatory profile has not yet been reviewed for this record.

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

Evaluations and results

2 evaluations · 10 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (Difficult Benchmark) (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 configurationProtocol and datasetAUPRC (Difficult Benchmark)AUROC (Difficult Benchmark)F1 (Difficult Benchmark)F1 (Simple Benchmark)False positive rate (Difficult Benchmark)False positive rate (Simple Benchmark)Negative predictive value (Difficult Benchmark)Precision (Difficult Benchmark)Recall (Difficult Benchmark)Specificity (Difficult Benchmark)
GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)EvaluationVirtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes, Virtual CRISPR Difficult BenchmarkN/AN/A0.35Not reported0.79Not reported0.230.320.410.21
GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)EvaluationVirtual CRISPR Simple Benchmark: yes/no prediction of a screen hit, Virtual CRISPR Simple BenchmarkNot reportedNot reportedNot reported0.47 ± 0.06Not reported0.22 ± 0.06Not reportedNot reportedNot reportedNot reported
All 10 result rows with coverage, uncertainty and sources
Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
N/A AUPRC (Difficult Benchmark)
unitless · higher

Uncertainty: Not applicable

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "AUPRC"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
N/A AUROC (Difficult Benchmark)
unitless · higher

Uncertainty: Not applicable

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "AUROC"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.35 F1 (Difficult Benchmark)
fraction · higher

Uncertainty: ± 0.17 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "F1"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.79 False positive rate (Difficult Benchmark)
fraction · lower

Uncertainty: ± 0.19 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "FPR"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.23 Negative predictive value (Difficult Benchmark)
fraction · higher

Uncertainty: ± 0.13 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "NPV"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.32 Precision (Difficult Benchmark)
fraction · higher

Uncertainty: ± 0.14 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "PPV"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.41 Recall (Difficult Benchmark)
fraction · higher

Uncertainty: ± 0.22 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "Sens."
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Difficult Benchmark: hit prediction for complex phenotypes
Dataset: Virtual CRISPR Difficult Benchmark
0.21 Specificity (Difficult Benchmark)
fraction · higher

Uncertainty: ± 0.19 (type not stated). Printed on the line below the row; the caption says results are aggregated across prompting strategies but does not name the statistic. Table 1 uses mean and standard deviation for the same kind of aggregation.

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (prompting) on the Virtual CRISPR Difficult Benchmark

pheno-20261022-protocol-song2025-difficult-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 2, row "GPT-4o (prompting)", column "Spec."
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Simple Benchmark: yes/no prediction of a screen hit
Dataset: Virtual CRISPR Simple Benchmark
0.47 ± 0.06 F1 (Simple Benchmark)
fraction · higher

Uncertainty: SD 0.06. Caption: mean and std. dev. across up to 10 combinations of CoT and few-shot prompting; the number of combinations per model is not printed

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (direct prompting, mean over strategies) on the Virtual CRISPR Simple Benchmark

pheno-20261022-protocol-song2025-simple-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 1, row "GPT-4o", column "F1 Score"
Configuration: GPT-4o, direct prompting, mean over prompting strategies (Song et al. 2025)Protocol: Virtual CRISPR Simple Benchmark: yes/no prediction of a screen hit
Dataset: Virtual CRISPR Simple Benchmark
0.22 ± 0.06 False positive rate (Simple Benchmark)
fraction · lower

Uncertainty: SD 0.06. Caption: mean and std. dev. across up to 10 combinations of CoT and few-shot prompting; the number of combinations per model is not printed

Coverage: Not reported scored / Not reported eligible

Independent external evaluation · Source checked
Methods, coverage and source

GPT-4o (direct prompting, mean over strategies) on the Virtual CRISPR Simple Benchmark

pheno-20261022-protocol-song2025-simple-hit-classification

Aggregation: Not reported

Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? · Table 1, row "GPT-4o", column "FPR"

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: pheno-20261022-config-song2025-gpt-4o-prompting-mean

areas
cells-tissues
contexts
research
method types
foundation_model
reported name
GPT-4o
configuration type
paper_evaluation
foundation model eligible
true
version
gpt-4o-2024-11-20
model version
gpt-4o-2024-11-20
parameters
Direct prompting; up to 10 combinations of chain-of-thought and 0-, 1- or 2-shot examples
temperature note
Temperature 0 with a fixed random seed
access reuse
OpenAI API
source locator
Table 1, row "GPT-4o"; Appendix A.1 and Table 7
provenance note
Prompted by Song et al. 2025; the model is third-party.
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