Method

CNN

Two-layer convolutional network with 64 channels trained on one-hot encoded DNA for each task, without pretraining.

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Evaluations and results

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

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	Protocol and dataset	AUROC	AUPRC	MCC
CNNEvaluation	BEND CPG: CpG methylation, ENCODE CpG methylation (BEND split)	0.84 (best in column)	Not reported	Not reported
CNNEvaluation	BEND HISTONE: Histone modification, ENCODE histone modification (BEND split)	0.76	Not reported	Not reported
CNNEvaluation	BEND CHROMATIN: Chromatin accessibility, ENCODE chromatin accessibility (BEND split)	0.75	Not reported	Not reported
CNNEvaluation	BEND ENHANCER: Enhancer annotation, Fulco 2019, Gasperini 2019 and Enformer enhancer set (BEND split)	Not reported	0.03	Not reported
CNNEvaluation	BEND GENE-FINDING: Gene finding, GENCODE (BEND split)	Not reported	Not reported	0

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: CNN	Task: BEND CHROMATIN: Chromatin accessibility Dataset subset: ENCODE chromatin accessibility (BEND split)	0.75 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on BEND CHROMATIN: Chromatin accessibility A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(Chromatin accessibility)
Method: CNN	Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split)	0.84 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on BEND CPG: CpG methylation A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(CpG methylation)
Method: CNN	Task: BEND ENHANCER: Enhancer annotation Dataset subset: Fulco 2019, Gasperini 2019 and Enformer enhancer set (BEND split)	0.03 AUPRC fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on BEND ENHANCER: Enhancer annotation A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(Enhancer annotation)
Method: CNN	Task: BEND GENE-FINDING: Gene finding Dataset subset: GENCODE (BEND split)	0 MCC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on BEND GENE-FINDING: Gene finding A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(Gene finding)
Method: CNN	Task: BEND HISTONE: Histone modification Dataset subset: ENCODE histone modification (BEND split)	0.76 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CNN on BEND HISTONE: Histone modification A downstream head trained on frozen embeddings, except for the expert methods and the fully supervised baselines, which are trained end to end. Metric and splits are from Table 1. Aggregation: Not reported BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Table 3, row(CNN), column(Histone modification)

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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BEND: Benchmarking DNA Language Models on Biologically Meaningful Tasks · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256

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Technical metadata and extraction receipts

Stable ID: bend-method-cnn

areas: dna-genomes
source locator: Table 3, row(CNN)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Trained per task by the BEND authors as a supervised baseline.

Related records

system: CNN on BEND CHROMATIN: Chromatin accessibility
system: CNN on BEND CPG: CpG methylation
system: CNN on BEND ENHANCER: Enhancer annotation
system: CNN on BEND GENE-FINDING: Gene finding
system: CNN on BEND HISTONE: Histone modification

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