Index

A

add_features() (TreeFeatureEngineer method)

B

BaseGATNet (built-in class) BasePhyloGNN (built-in class) built-in function create_default_trainer() create_trainer_from_config() dendropy_tree_to_ete3() get_max_meta_time() load_training_config() read_tree_as_ete3() read_tree_with_dendropy()

C

ConfiguredTrainingSetup (built-in class) convert() (TreeToGraphConverter method) convert_and_save() (TreeToGraphConverter method)

create_default_trainer() built-in function create_trainer_from_config() built-in function

D

DatasetSplit (built-in class)

dendropy_tree_to_ete3() built-in function

F

fit() (Trainer method) freeze_encoder() (BasePhyloGNN method)

from_dict() (DatasetSplit class method) from_manifest_dir() (DatasetSplit class method) from_ratios() (DatasetSplit class method)

G

GATBiLSTMNet (built-in class) get_available_features() (TreeFeatureEngineer method)

get_max_meta_time() built-in function get_num_parameters() (BasePhyloGNN method)

L

load_checkpoint() (Trainer method) load_data() (TreeToGraphConverter static method)

load_training_config() built-in function

P

predict() (Trainer method)

R

read_tree_as_ete3() built-in function

read_tree_with_dendropy() built-in function rescale_tree() (TreeFeatureEngineer method)

S

save_checkpoint() (Trainer method) save_data() (TreeToGraphConverter method) save_history() (Trainer method)

SplitDatasetView (built-in class) SplitPhyloDataset (built-in class) SplitPhyloDiskDataset (built-in class)

T

TemporalBiLSTMEncoder (built-in class) TrackingConfig (built-in class) TrackingError TrackingRunInfo (built-in class) Trainer (built-in class)

TrainingConfig (built-in class) TrainingConfigError TreeFeatureEngineer (built-in class) TreeReadConfig (built-in class) TreeToGraphConverter (built-in class)

U

unfreeze_all() (BasePhyloGNN method)

V

validate() (TrainingConfig method)

validate_data() (BasePhyloGNN method)

W

WandbTracker (built-in class)