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Description
Problem
When introducing the _DynamicDataset
in #39, we changed the meaning of raw
files. Previously, the labeled train.pkl
, validation.pkl
and test.pkl
file names were returned by raw_file_names_dict()
and raw_file_names()
. Now, the GO class has a raw_file_names_dict()
method that only the direct downloads (e.g., for GO, the go-basic.obo
and uniprot_sprot.dat
). It overwrites the method in _DynamicDataset
which returns data.pkl
. raw_file_names()
is missing completely.
Solution
- Introduce a third file names property for
data.pkl
- Link
raw_file_names
toraw_file_names_dict
- Add
chebi.obo
as raw file name for chebi classes - Use
data.pkl
in weighted BCE loss (for calculating weights) (@sfluegel05)
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