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Caduceus-Ph (DNALONGBENCH)

Caduceus-Ph: Caduceus Ph; fine-tuned per task.

5 evaluations · 27 results 1 open disagreement between studies involves its model

Overview

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

Evaluations and results

5 evaluations · 27 results. Different protocols are not a single leaderboard.

Sorted by AUPRC (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	AUPRC	AUROC	AUROC (AS (Adipose_Subcutaneous))	AUROC (AT (Artery_Tibial))	AUROC (average over eQTLP conditions as printed)	AUROC (CCF (Cells_Cultured_fibroblasts))	AUROC (MS (Muscle Skeletal))	AUROC (NT (Nerve Tibial))	AUROC (SNSES (Skin_Not_Sun_Exposed_Suprapubic))	AUROC (SSELL (Skin_Sun_Exposed_Lower_leg))	AUROC (Thyroid)	AUROC (WB (Whole_Blood))	Pearson (average over RSAP conditions as printed)	Pearson (average over TISP conditions as printed)	Pearson (EC (ENCODE CAGE))	Pearson (ER (ENCODE RAMPAGE))	Pearson (FC (FANTOM CAGE))	Pearson (GC (GRO-cap))	Pearson (Human)	Pearson (Mouse)	Pearson (PC (PRO-cap))	Stratum adjusted correlation coefficient (average over CMP conditions as printed)	Stratum adjusted correlation coefficient (GM12878)	Stratum adjusted correlation coefficient (H1hESC)	Stratum adjusted correlation coefficient (HCT116)	Stratum adjusted correlation coefficient (HFF)	Stratum adjusted correlation coefficient (IMR90)
Caduceus-Ph (DNALONGBENCH)Evaluation	DNALONGBENCH Enhancer-target gene prediction (Table 3), DNALONGBENCH Enhancer-target gene prediction test set	0.38	0.826	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Caduceus-Ph (DNALONGBENCH)Evaluation	DNALONGBENCH Contact map prediction (Table 4), DNALONGBENCH Contact map prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.133	0.101	0.13	0.145	0.153	0.138
Caduceus-Ph (DNALONGBENCH)Evaluation	DNALONGBENCH Expression quantitative trait loci prediction (Table 7), DNALONGBENCH Expression quantitative trait loci prediction test set	Not reported	Not reported	0.541	0.547	0.565	0.597	0.538	0.588	0.586	0.574	0.527	0.594	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Caduceus-Ph (DNALONGBENCH)Evaluation	DNALONGBENCH Regulatory sequence activity prediction (Table 5), DNALONGBENCH Regulatory sequence activity prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.349	Not reported	Not reported	Not reported	Not reported	Not reported	0.301	0.4	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
Caduceus-Ph (DNALONGBENCH)Evaluation	DNALONGBENCH Transcription initiation signal prediction (Table 6), DNALONGBENCH Transcription initiation signal prediction test set	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	0.109	0.088	0.088	0.114	0.097	Not reported	Not reported	0.154	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.133 Stratum adjusted correlation coefficient (average over CMP conditions as printed) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'Avg'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.101 Stratum adjusted correlation coefficient (GM12878) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'GM12878'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.13 Stratum adjusted correlation coefficient (H1hESC) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'H1hESC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.145 Stratum adjusted correlation coefficient (HCT116) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'HCT116'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.153 Stratum adjusted correlation coefficient (HFF) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'HFF'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Contact map prediction (Table 4) Dataset: DNALONGBENCH Contact map prediction test set	0.138 Stratum adjusted correlation coefficient (IMR90) 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-Ph on DNALONGBENCH CMP lit-genomics-20261011-dnalongbench-protocol-cmp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 4, row 'Caduceus-Ph', column 'IMR90'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.541 AUROC (AS (Adipose_Subcutaneous)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'AS'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.547 AUROC (AT (Artery_Tibial)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'AT'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.565 AUROC (average over eQTLP conditions as printed) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'Avg'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.597 AUROC (CCF (Cells_Cultured_fibroblasts)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'CCF'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.538 AUROC (MS (Muscle Skeletal)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'MS'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.588 AUROC (NT (Nerve Tibial)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'NT'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.586 AUROC (SNSES (Skin_Not_Sun_Exposed_Suprapubic)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'SNSES'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.574 AUROC (SSELL (Skin_Sun_Exposed_Lower_leg)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'SSELL'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.527 AUROC (Thyroid) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'Thyroid'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Expression quantitative trait loci prediction (Table 7) Dataset: DNALONGBENCH Expression quantitative trait loci prediction test set	0.594 AUROC (WB (Whole_Blood)) 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-Ph on DNALONGBENCH eQTLP lit-genomics-20261011-dnalongbench-protocol-eqtlp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 7, row 'Caduceus-Ph', column 'WB'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.38 AUPRC 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-Ph on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-Ph', column 'AUPRC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Enhancer-target gene prediction (Table 3) Dataset: DNALONGBENCH Enhancer-target gene prediction test set	0.826 AUROC 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-Ph on DNALONGBENCH ETGP lit-genomics-20261011-dnalongbench-protocol-etgp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 3, row 'Caduceus-Ph', column 'AUROC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.349 Pearson (average over RSAP conditions as printed) 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-Ph on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'Caduceus-Ph', column 'Avg'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.301 Pearson (Human) 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-Ph on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'Caduceus-Ph', column 'Human'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Regulatory sequence activity prediction (Table 5) Dataset: DNALONGBENCH Regulatory sequence activity prediction test set	0.4 Pearson (Mouse) 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-Ph on DNALONGBENCH RSAP lit-genomics-20261011-dnalongbench-protocol-rsap Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 5, row 'Caduceus-Ph', column 'Mouse'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.109 Pearson (average over TISP conditions as printed) 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-Ph on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'Caduceus-Ph', column 'Avg'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.088 Pearson (EC (ENCODE CAGE)) 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-Ph on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'Caduceus-Ph', column 'EC'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.088 Pearson (ER (ENCODE RAMPAGE)) 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-Ph on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'Caduceus-Ph', column 'ER'
Configuration: Caduceus-Ph (DNALONGBENCH)	Protocol: DNALONGBENCH Transcription initiation signal prediction (Table 6) Dataset: DNALONGBENCH Transcription initiation signal prediction test set	0.114 Pearson (FC (FANTOM CAGE)) 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-Ph on DNALONGBENCH TISP lit-genomics-20261011-dnalongbench-protocol-tisp Aggregation: Not reported DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Table 6, row 'Caduceus-Ph', column 'FC'

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

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DNALONGBENCH: a benchmark suite for long-range DNA prediction tasks · Original source · Nature Communications 16, published 2025-11-18; PMC12627797 full-text XML

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-dnalongbench-config-caduceus-ph

areas: dna-genomes
contexts: research
method types: foundation_model
reported name: Caduceus-Ph
foundation model eligible: true
parameters: Caduceus Ph; fine-tuned per task
access reuse: Public model code and weights
source locator: Methods 'Expert model', 'CNN' and 'DNA Foundation Model'
missing metadata: version: reason: unreported; note: Checkpoint or release not printed beyond the model name
provenance note: Caduceus-Ph as evaluated in DNALONGBENCH.

Related records

configuration of: Caduceus
system: Caduceus-Ph on DNALONGBENCH CMP
system: Caduceus-Ph on DNALONGBENCH eQTLP
system: Caduceus-Ph on DNALONGBENCH ETGP
system: Caduceus-Ph on DNALONGBENCH RSAP
system: Caduceus-Ph on DNALONGBENCH TISP

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