GenBench Long-range splice site prediction (Splice acceptor); arXiv v2

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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.

Protocol: GenBench Long-range splice site prediction (Splice acceptor) · Dataset: GenBench Long-range splice site prediction (Splice acceptor)

Sorted by AUROC (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	AUROC
Caduceus (GenBench)Evaluation	0.74 (best in column)
GENA-LM (GenBench)Evaluation	0.73
HyenaDNA (GenBench)Evaluation	0.723
NT (GenBench)Evaluation	0.722
DNABERT2 (GenBench)Evaluation	0.707
SpliceAI (GenBench)Evaluation	0.691

All 6 result rows with coverage, uncertainty and sources

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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: Caduceus (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.74 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 on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'Caduceus'
Configuration: DNABERT2 (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.707 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 DNABERT2 on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'DNABERT2'
Configuration: GENA-LM (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.73 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 GENA-LM on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'GENA-LM'
Configuration: HyenaDNA (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.723 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 HyenaDNA on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'HyenaDNA'
Configuration: NT (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.722 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 Nucleotide Transformer on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'Nucleotide Transformer'
Configuration: SpliceAI (GenBench)	Protocol: GenBench Long-range splice site prediction (Splice acceptor) Dataset: GenBench Long-range splice site prediction (Splice acceptor)	0.691 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 SpliceAI on GenBench Long-range splice site prediction (Splice acceptor) lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor Aggregation: Not reported GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Table 5, row 'Long-range splice site prediction (Splice acceptor)', column 'SpliceAI'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

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

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

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Evidence table

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models · Original source · arXiv 2406.01627 version 2

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Technical metadata and extraction receipts

Stable ID: lit-genomics-20261011-genbench-protocol-long-splice-splice-acceptor

areas: dna-genomes
contexts: research
protocol: Fine-tuning per dataset; 'Top-1' score as printed (not defined in the source).
version: arXiv v2
metric: auroc
metric direction: higher
unit: unitless
limitations: 'Top-1' is not defined in the source; no uncertainty printed.
source locator: Table 5

Related records

part of: GenBench
uses data: GenBench Long-range splice site prediction (Splice acceptor)
assessment: Caduceus on GenBench Long-range splice site prediction (Splice acceptor)
assessment: DNABERT2 on GenBench Long-range splice site prediction (Splice acceptor)
assessment: GENA-LM on GenBench Long-range splice site prediction (Splice acceptor)
assessment: HyenaDNA on GenBench Long-range splice site prediction (Splice acceptor)
assessment: Nucleotide Transformer on GenBench Long-range splice site prediction (Splice acceptor)
assessment: SpliceAI on GenBench Long-range splice site prediction (Splice acceptor)