Table 1.

Comparison of evaluation criteria used to evaluate models in candidate enhancer activity conservation prediction papers

Evaluation Criterium	Chen et al. 2018 [57]	Huh et al. 2018 [58]	Kelley 2020 [59]	Minnoye et al. 2020 [60]	This Paper
Evaluation on Genomic Regions not Used in Training	✓	✓	✓	✓	✓
Evaluation on Species not Used in Training	✓	✓	✓	✘	✓
Comparison of Model Trained on One Species to Model Trained on Multiple Species	✘	✓	✓	✘	✓
Evaluation of Lineage-Specific Enhancer Accuracy	✘	✘	✘	✘	✓
Evaluation of Tissue-Specific Enhancer Accuracy	✘	✘	✘	✘	✓
Evaluation of Phylogeny-Matching Correlations	✘	✘	✘	✘	✓
Comparison to Conservation Scores	✘	✘	✘	✘	✓
Identification of Biologically Relevant Enhancers with Correctly Predicted Lineage-Specificity	✘	✘	✘	✓	✓