Configuration

Caduceus-Ps (full fine-tuning, GFMBench-API)

Caduceus-Ps: About 7M parameters; Hugging Face checkpoint; full fine-tuning; full fine-tuning for 3 epochs.

Overview

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Evaluations and results

10 evaluations · 40 results. Different protocols are not a single leaderboard.

Sorted by Accuracy (test set) (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 configuration	Protocol and dataset	Accuracy (test set)	AUPRC (test set)	AUROC (test set)	MCC (test set)
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Promoter All, supervised, GUE Promoter All test set (GFMBench-API)	0.901 (best in column)	0.96 (best in column)	0.964 (best in column)	0.802
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Splice Site, supervised, GUE Splice Site test set (GFMBench-API)	0.896	0.917	0.955	0.821 (best in column)
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Non Coding Pathogenicity, supervised, Var Bench Non Coding Pathogenicity test set (GFMBench-API)	0.893	0.241	0.683	0
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API GUE Transcription Factor, supervised, GUE Transcription Factor test set (GFMBench-API)	0.806	0.887	0.891	0.614
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API LRB Variant Effect Causal eQTL, supervised, LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.629	0.686	0.679	0.284
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Expression, supervised, Var Bench Expression test set (GFMBench-API)	0.6	0.592	0.636	0.201
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Coding Pathogenicity, supervised, Var Bench Coding Pathogenicity test set (GFMBench-API)	0.575	0.507	0.606	0.0594
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench sQTL, supervised, Var Bench sQTL test set (GFMBench-API)	0.555	0.57	0.568	0.106
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench meQTL, supervised, Var Bench meQTL test set (GFMBench-API)	0.546	0.488	0.565	0.0078
Caduceus-Ps (full fine-tuning, GFMBench-API)Evaluation	GFMBench-API Var Bench Common Vs Rare, supervised, Var Bench Common Vs Rare test set (GFMBench-API)	0.5	0.5	0.5	0

All 40 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.901 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.96 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.964 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Promoter All, supervised Dataset: GUE Promoter All test set (GFMBench-API)	0.802 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Promoter All (supervised) lit-genomics-20261011-gfmbench-protocol-gue-promoter-all-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Promoter All', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.896 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.917 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.955 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Splice Site, supervised Dataset: GUE Splice Site test set (GFMBench-API)	0.821 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Splice Site (supervised) lit-genomics-20261011-gfmbench-protocol-gue-splice-site-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Splice Site', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.806 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.887 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.891 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API GUE Transcription Factor, supervised Dataset: GUE Transcription Factor test set (GFMBench-API)	0.614 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API GUE Transcription Factor (supervised) lit-genomics-20261011-gfmbench-protocol-gue-transcription-factor-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'GUE Transcription Factor', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.629 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.686 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.679 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API LRB Variant Effect Causal eQTL, supervised Dataset: LRB Variant Effect Causal eQTL test set (GFMBench-API)	0.284 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API LRB Variant Effect Causal eQTL (supervised) lit-genomics-20261011-gfmbench-protocol-lrb-variant-effect-causal-eqtl-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'LRB Variant Effect Causal eQTL', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.575 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.507 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.606 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Coding Pathogenicity, supervised Dataset: Var Bench Coding Pathogenicity test set (GFMBench-API)	0.0594 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Coding Pathogenicity (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-coding-pathogenicity-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Coding Pathogenicity', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'Caduceus-Ps', column 'Accuracy'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 AUPRC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'Caduceus-Ps', column 'AUPRC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0.5 AUROC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'Caduceus-Ps', column 'AUROC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Common Vs Rare, supervised Dataset: Var Bench Common Vs Rare test set (GFMBench-API)	0 MCC (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Common Vs Rare (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-common-vs-rare-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Common Vs Rare', row 'Caduceus-Ps', column 'MCC'
Configuration: Caduceus-Ps (full fine-tuning, GFMBench-API)	Protocol: GFMBench-API Var Bench Expression, supervised Dataset: Var Bench Expression test set (GFMBench-API)	0.6 Accuracy (test set) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source Caduceus-Ps on GFMBench-API Var Bench Expression (supervised) lit-genomics-20261011-gfmbench-protocol-var-bench-expression-supervised Aggregation: Not reported GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Table 1, task 'Var Bench Expression', row 'Caduceus-Ps', column 'Accuracy'

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GFMBench-API: A Standardized Interface for Benchmarking Genomic Foundation Models · Original source · bioRxiv preprint version 2, posted 2026-08-11

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-gfmbench-config-caduceus-ps-full-fine-tuning

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: Caduceus-Ps
foundation model eligible: true
parameters: About 7M parameters; Hugging Face checkpoint; full fine-tuning; full fine-tuning for 3 epochs
access reuse: Public checkpoint (Hugging Face; Evo2 via NVIDIA BioNeMo)
source locator: Benchmark Results sections A and B
missing metadata: version: reason: unreported; note: Checkpoint revision not printed; parameter count only
provenance note: Caduceus-Ps as evaluated in GFMBench-API, full fine-tuning.

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