https://github.com/Bayer-Group/MotherML/blob/main/src/mother/feature_generation/core.py https://github.com/Bayer-Group/MotherML/blob/main/src/mother/feature_generation/config.py currently the Morgan Fingeprint setting in Mother is to not use counts. Binary fingerprints are usually not a good choice for ML, so should make sure that the standard setting is to use counts. Especially as they allow for better handling of bit collisions, as they at least increase the count by +1 instead od just ignoring. And maybe increase fpsize to 2048 in core.py too as is already in the config. Most users will not change on their own, and for some tasks using binary FP can make models perform substantially worse, which is also backed by literature: Count-Based Morgan Fingerprint: A More Efficient and Interpretable Molecular Representation in Deve… Count your bits: fingerprint benchmarking to assess broad chemical space representation | Journal o…
def init(
self, radius: int = 2, fpSize=1024 -> 2048, include_chirality: bool = False, use_counts: bool = False -> True, **kwargs
) -> None:
super().init(
https://github.com/Bayer-Group/MotherML/blob/main/src/mother/feature_generation/core.py https://github.com/Bayer-Group/MotherML/blob/main/src/mother/feature_generation/config.py currently the Morgan Fingeprint setting in Mother is to not use counts. Binary fingerprints are usually not a good choice for ML, so should make sure that the standard setting is to use counts. Especially as they allow for better handling of bit collisions, as they at least increase the count by +1 instead od just ignoring. And maybe increase fpsize to 2048 in core.py too as is already in the config. Most users will not change on their own, and for some tasks using binary FP can make models perform substantially worse, which is also backed by literature: Count-Based Morgan Fingerprint: A More Efficient and Interpretable Molecular Representation in Deve… Count your bits: fingerprint benchmarking to assess broad chemical space representation | Journal o…
def init(
self, radius: int = 2, fpSize=1024 -> 2048, include_chirality: bool = False, use_counts: bool = False -> True, **kwargs
) -> None:
super().init(