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Table 2 Comparison of approaches for extending Avocado to new cell types and assays

From: Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples

Test setRetrain from scratchFine-tuneFreezeFivefold
ENCODE2018-Sparse0.0580.0560.091
ENCODE2018-Sparse (w/o shRNA)0.0690.0680.080
ENCODE2018-Core0.0490.0500.0510.050
  1. 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