ResNet-LM | method

Overview

Baseline trained end to end from one-hot sequence by the BEND authors.

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

Evaluations and results

7 evaluations · 7 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: ResNet-LM	Task: BEND CHROMATIN: Chromatin accessibility Dataset subset: ENCODE chromatin accessibility (BEND split)	0.82 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM 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(ResNet-LM), column(Chromatin accessibility)
Method: ResNet-LM	Task: BEND CPG: CpG methylation Dataset subset: ENCODE CpG methylation (BEND split)	0.87 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM 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(ResNet-LM), column(CpG methylation)
Method: ResNet-LM	Task: BEND ENHANCER: Enhancer annotation Dataset subset: Fulco 2019, Gasperini 2019 and Enformer enhancer set (BEND split)	0.02 auprc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM 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(ResNet-LM), column(Enhancer annotation)
Method: ResNet-LM	Task: BEND GENE-FINDING: Gene finding Dataset subset: GENCODE (BEND split)	0.36 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM 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(ResNet-LM), column(Gene finding)
Method: ResNet-LM	Task: BEND HISTONE: Histone modification Dataset subset: ENCODE histone modification (BEND split)	0.77 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM 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(ResNet-LM), column(Histone modification)
Method: ResNet-LM	Task: BEND VARIANT-DISEASE: Noncoding variant effects on disease Dataset subset: ClinVar disease variants (BEND split)	0.55 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM on BEND VARIANT-DISEASE: Noncoding variant effects on disease 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(ResNet-LM), column(Noncoding variant effects on disease)
Method: ResNet-LM	Task: BEND VARIANT-EXPRESSION: Noncoding variant effects on expression Dataset subset: DeepSEA expression variants (BEND split)	0.55 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ResNet-LM on BEND VARIANT-EXPRESSION: Noncoding variant effects on expression 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(ResNet-LM), column(Noncoding variant effects on expression)

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Evidence

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