Probing-head-like (ab initio)

Overview

Baseline trained from scratch by the DART-Eval authors, evaluated ab initio.

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Evaluations and results

8 evaluations · 8 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: Probing-head-like (ab initio)	Task: DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.474 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-ACC: Cell-type-specific element classification, overall accuracy Classify which of five cell lines a accessible element belongs to. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-ACC)
Method: Probing-head-like (ab initio)	Task: DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.754 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 One-against-rest AUROC for GM12878 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-GM12878)
Method: Probing-head-like (ab initio)	Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.836 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC One-against-rest AUROC for H1ESC accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-H1ESC)
Method: Probing-head-like (ab initio)	Task: DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.757 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 One-against-rest AUROC for HEPG2 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-HEPG2)
Method: Probing-head-like (ab initio)	Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.807 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 One-against-rest AUROC for IMR90 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-IMR90)
Method: Probing-head-like (ab initio)	Task: DART-Eval CTS-K562: Cell-type-specific element classification, K562 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.741 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval CTS-K562: Cell-type-specific element classification, K562 One-against-rest AUROC for K562 accessible elements. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 4, row(Ab initio Probing-head-like), column(CTS-K562)
Method: Probing-head-like (ab initio)	Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.846 absolute_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(Ab initio Probing-head-like), column(ab initio absolute_accuracy)
Method: Probing-head-like (ab initio)	Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.932 paired_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Probing-head-like (ab initio) on DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Distinguish ENCODE cCREs from dinucleotide-shuffled background sequences. The setting the model was run in is part of the method name. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 3, row(Ab initio Probing-head-like), column(ab initio paired_accuracy)

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Sources and history

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Release 2026-09-29-06401fd5b220 · Record review: source checked

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DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Original source · 2412.05430v1

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Technical metadata and extraction receipts

Stable ID: dart-eval-method-probing-head-like-ab-initio

areas: dna-genomes
source locator: Table 1, row(Probing-head-like)
missing metadata: checkpoint revision: unreported; parameters: unextracted

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