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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 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

  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