Table 2.

Comparison of approaches for extending Avocado to new cell types and assays

Test set	Retrain from scratch	Fine-tune	Freeze	Fivefold
ENCODE2018-Sparse	0.058	0.056	0.091	–
ENCODE2018-Sparse (w/o shRNA)	0.069	0.068	0.080	–
ENCODE2018-Core	0.049	0.050	0.051	0.050

The MSE of three approaches for adding new biosamples or assay on three test sets. The test sets are half of the experiments in the ENCODE2018-Sparse dataset, that same dataset with shRNA experiments removed, and the fifth fold from the ENCODE2018-Core dataset. The MSE from the fivefold cross-validation is shown for the ENCODE2018-Core test fold as a reference