Index

B

batch_size (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.TrainingConfigs attribute) best_model_monitor (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute)

best_model_monitor_mode (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute)

C

calculate_loss() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method) compute_multi_class_weights() (in module epbd_bert.utility.data_utils) compute_predictions() (in module epbd_bert.dnabert2_epbd_crossattn.test)

Configs (class in epbd_bert.dnabert2_classifier.configs) (class in epbd_bert.dnabert2_epbd.configs) configure_optimizers() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method)

D

d_ff (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute) d_model (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute)

DNABERT2Classifier (class in epbd_bert.dnabert2_classifier.model) Dnabert2EPBDModel (class in epbd_bert.dnabert2_epbd.model)

E

epbd_bert module epbd_bert.datasets module epbd_bert.datasets.data_collators module epbd_bert.datasets.sequence_dataset module epbd_bert.datasets.sequence_epbd_dataset module epbd_bert.datasets.sequence_epbd_multimodal_dataset module epbd_bert.datasets.sequence_epbd_multimodal_labelspecific_dataset module epbd_bert.datasets.sequence_randepbd_dataset module epbd_bert.datasets.sequence_randepbd_multimodal_dataset module epbd_bert.dnabert2_classifier module epbd_bert.dnabert2_classifier.configs module epbd_bert.dnabert2_classifier.model module epbd_bert.dnabert2_classifier.test module epbd_bert.dnabert2_classifier.train_lightning module epbd_bert.dnabert2_epbd module epbd_bert.dnabert2_epbd.configs module epbd_bert.dnabert2_epbd.model module

epbd_bert.dnabert2_epbd.test module epbd_bert.dnabert2_epbd.train_lightning module epbd_bert.dnabert2_epbd_crossattn module epbd_bert.dnabert2_epbd_crossattn.configs module epbd_bert.dnabert2_epbd_crossattn.model module epbd_bert.dnabert2_epbd_crossattn.test module epbd_bert.dnabert2_epbd_crossattn.train_lightning module epbd_bert.models_factory module epbd_bert.path_configs module epbd_bert.utility module epbd_bert.utility.data_utils module epbd_bert.utility.dnabert2 module epbd_bert.utility.pickle_utils module epbd_bert.version module epbd_embedder_kernel_size (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute) epbd_feature_channels (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute) epbd_feature_input_dim (epbd_bert.dnabert2_epbd.configs.Configs attribute) epbd_features_type (epbd_bert.dnabert2_epbd.configs.Configs attribute) EPBDConfigs (class in epbd_bert.dnabert2_epbd_crossattn.configs) EPBDDnabert2Model (class in epbd_bert.dnabert2_epbd_crossattn.model) EPBDEmbedder (class in epbd_bert.dnabert2_epbd_crossattn.model)

F

forward() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDEmbedder method) (epbd_bert.dnabert2_epbd_crossattn.model.MultiModalLayer method) (epbd_bert.dnabert2_epbd_crossattn.model.PoolingLayer method) (epbd_bert.dnabert2_epbd_crossattn.model.PositionWiseFeedForward method)

G

get_dnabert2_pretrained_model() (in module epbd_bert.utility.dnabert2) get_dnabert2_tokenizer() (in module epbd_bert.utility.dnabert2)

get_model_and_dataloader() (in module epbd_bert.models_factory) get_uniform_peaks_metadata() (in module epbd_bert.utility.data_utils)

L

learning_rate (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.TrainingConfigs attribute)

load() (in module epbd_bert.utility.pickle_utils) load_dnabert2_for_classification() (in module epbd_bert.utility.dnabert2) load_pretrained_model() (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model class method)

M

max_epochs (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.TrainingConfigs attribute) module epbd_bert epbd_bert.datasets epbd_bert.datasets.data_collators epbd_bert.datasets.sequence_dataset epbd_bert.datasets.sequence_epbd_dataset epbd_bert.datasets.sequence_epbd_multimodal_dataset epbd_bert.datasets.sequence_epbd_multimodal_labelspecific_dataset epbd_bert.datasets.sequence_randepbd_dataset epbd_bert.datasets.sequence_randepbd_multimodal_dataset epbd_bert.dnabert2_classifier epbd_bert.dnabert2_classifier.configs epbd_bert.dnabert2_classifier.model epbd_bert.dnabert2_classifier.test epbd_bert.dnabert2_classifier.train_lightning epbd_bert.dnabert2_epbd epbd_bert.dnabert2_epbd.configs epbd_bert.dnabert2_epbd.model epbd_bert.dnabert2_epbd.test epbd_bert.dnabert2_epbd.train_lightning epbd_bert.dnabert2_epbd_crossattn epbd_bert.dnabert2_epbd_crossattn.configs epbd_bert.dnabert2_epbd_crossattn.model epbd_bert.dnabert2_epbd_crossattn.test epbd_bert.dnabert2_epbd_crossattn.train_lightning epbd_bert.models_factory epbd_bert.path_configs epbd_bert.utility epbd_bert.utility.data_utils epbd_bert.utility.dnabert2 epbd_bert.utility.pickle_utils epbd_bert.version

MultiModalLayer (class in epbd_bert.dnabert2_epbd_crossattn.model)

N

n_classes (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute) need_weights (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute)

num_heads (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute) num_workers (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.TrainingConfigs attribute)

O

on_validation_epoch_end() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method)

P

p_dropout (epbd_bert.dnabert2_epbd_crossattn.configs.EPBDConfigs attribute)

PoolingLayer (class in epbd_bert.dnabert2_epbd_crossattn.model) PositionWiseFeedForward (class in epbd_bert.dnabert2_epbd_crossattn.model)

S

save() (in module epbd_bert.utility.pickle_utils) SeqLabelDataCollator (class in epbd_bert.datasets.data_collators) SeqLabelEPBDDataCollator (class in epbd_bert.datasets.data_collators) SequenceDataset (class in epbd_bert.datasets.sequence_dataset)

SequenceEPBDDataset (class in epbd_bert.datasets.sequence_epbd_dataset) SequenceEPBDMultiModalDataset (class in epbd_bert.datasets.sequence_epbd_multimodal_dataset) SequenceEPBDMultiModalLabelSpecificDataset (class in epbd_bert.datasets.sequence_epbd_multimodal_labelspecific_dataset) SequenceRandEPBDDataset (class in epbd_bert.datasets.sequence_randepbd_dataset) SequenceRandEPBDMultiModalDataset (class in epbd_bert.datasets.sequence_randepbd_multimodal_dataset)

T

training_step() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method)

TrainingConfigs (class in epbd_bert.dnabert2_epbd_crossattn.configs)

V

validation_step() (epbd_bert.dnabert2_classifier.model.DNABERT2Classifier method) (epbd_bert.dnabert2_epbd.model.Dnabert2EPBDModel method) (epbd_bert.dnabert2_epbd_crossattn.model.EPBDDnabert2Model method)

W

weight_decay (epbd_bert.dnabert2_classifier.configs.Configs attribute) (epbd_bert.dnabert2_epbd.configs.Configs attribute) (epbd_bert.dnabert2_epbd_crossattn.configs.TrainingConfigs attribute)