Configuration

GENA-LM (probed)

DNA language model evaluated by the DART-Eval authors in the probed setting.

Overview

DNA language model evaluated by the DART-Eval authors in the probed setting.

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

Evaluations and results

22 evaluations · 22 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: GENA-LM (probed)	Task: DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.784 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-AUROC-GM12878: Chromatin activity prediction, GM12878, positives against negatives Separating positive GM12878 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-AUROC-GM12878)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.809 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-AUROC-H1ESC: Chromatin activity prediction, H1ESC, positives against negatives Separating positive H1ESC peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-AUROC-H1ESC)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.771 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-AUROC-HEPG2: Chromatin activity prediction, HEPG2, positives against negatives Separating positive HEPG2 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-AUROC-HEPG2)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.799 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-AUROC-IMR90: Chromatin activity prediction, IMR90, positives against negatives Separating positive IMR90 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-AUROC-IMR90)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.761 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-AUROC-K562: Chromatin activity prediction, K562, positives against negatives Separating positive K562 peaks from matched negatives. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-AUROC-K562)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.49 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-SPEARMAN-GM12878: Chromatin activity prediction, GM12878, positives only Rank correlation with measured accessibility among positive GM12878 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-SPEARMAN-GM12878)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.678 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-SPEARMAN-H1ESC: Chromatin activity prediction, H1ESC, positives only Rank correlation with measured accessibility among positive H1ESC peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-SPEARMAN-H1ESC)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.401 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-SPEARMAN-HEPG2: Chromatin activity prediction, HEPG2, positives only Rank correlation with measured accessibility among positive HEPG2 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-SPEARMAN-HEPG2)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.329 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-SPEARMAN-IMR90: Chromatin activity prediction, IMR90, positives only Rank correlation with measured accessibility among positive IMR90 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-SPEARMAN-IMR90)
Configuration: GENA-LM (probed)	Task: DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.461 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval CA-SPEARMAN-K562: Chromatin activity prediction, K562, positives only Rank correlation with measured accessibility among positive K562 peaks. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 5, row(Probed GENA-LM), column(CA-SPEARMAN-K562)
Configuration: GENA-LM (probed)	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)	0.383 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-ACC)
Configuration: GENA-LM (probed)	Task: DART-Eval CTS-GM12878: Cell-type-specific element classification, GM12878 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.627 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-GM12878)
Configuration: GENA-LM (probed)	Task: DART-Eval CTS-H1ESC: Cell-type-specific element classification, H1ESC Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.787 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-H1ESC)
Configuration: GENA-LM (probed)	Task: DART-Eval CTS-HEPG2: Cell-type-specific element classification, HEPG2 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.773 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-HEPG2)
Configuration: GENA-LM (probed)	Task: DART-Eval CTS-IMR90: Cell-type-specific element classification, IMR90 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.714 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-IMR90)
Configuration: GENA-LM (probed)	Task: DART-Eval CTS-K562: Cell-type-specific element classification, K562 Dataset subset: ENCODE chromatin accessibility peaks in five cell lines (DART-Eval split)	0.693 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(Probed GENA-LM), column(CTS-K562)
Configuration: GENA-LM (probed)	Task: DART-Eval REI-ABS: Regulatory element identification, absolute accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.887 absolute_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(GENA-LM), column(probed absolute_accuracy)
Configuration: GENA-LM (probed)	Task: DART-Eval REI-PAIR: Regulatory element identification, paired accuracy Dataset subset: ENCODE cCREs against dinucleotide-shuffled backgrounds (DART-Eval split)	0.959 paired_accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) 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(GENA-LM), column(probed paired_accuracy)
Configuration: GENA-LM (probed)	Task: DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	0.515 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval VS-AFRICAN-AUROC: Variant scoring on Chromatin QTLs in African LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African GENA-LM), column(probed auroc)
Configuration: GENA-LM (probed)	Task: DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Dataset subset: Chromatin QTLs in African LCLs (DART-Eval split)	-0.007 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval VS-AFRICAN-PEARSON_R: Variant scoring on Chromatin QTLs in African LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(African GENA-LM), column(probed pearson_r)
Configuration: GENA-LM (probed)	Task: DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.466 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval VS-YORUBAN-AUROC: Variant scoring on DNase QTLs in Yoruban LCLs, AUROC Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban GENA-LM), column(probed auroc)
Configuration: GENA-LM (probed)	Task: DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Dataset subset: DNase QTLs in Yoruban LCLs (DART-Eval split)	0.059 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GENA-LM (probed) on DART-Eval VS-YORUBAN-PEARSON_R: Variant scoring on DNase QTLs in Yoruban LCLs, Pearson r Score the effect of a variant on chromatin accessibility, against the measured QTL call. Aggregation: Not reported DART-Eval: A Comprehensive DNA Language Model Evaluation Benchmark on Regulatory DNA · Table 6, row(Yoruban GENA-LM), column(probed pearson_r)

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