epbd_bert package

Subpackages

• epbd_bert.datasets package
  • Submodules
  • epbd_bert.datasets.data_collators module
    • SeqLabelDataCollator
    • SeqLabelEPBDDataCollator
  • epbd_bert.datasets.sequence_dataset module
    • SequenceDataset
  • epbd_bert.datasets.sequence_epbd_dataset module
    • SequenceEPBDDataset
  • epbd_bert.datasets.sequence_epbd_multimodal_dataset module
    • SequenceEPBDMultiModalDataset
  • epbd_bert.datasets.sequence_epbd_multimodal_labelspecific_dataset module
    • SequenceEPBDMultiModalLabelSpecificDataset
  • epbd_bert.datasets.sequence_randepbd_dataset module
    • SequenceRandEPBDDataset
  • epbd_bert.datasets.sequence_randepbd_multimodal_dataset module
    • SequenceRandEPBDMultiModalDataset
  • Module contents
• epbd_bert.dnabert2_classifier package
  • Submodules
  • epbd_bert.dnabert2_classifier.configs module
    • Configs
      • Configs.batch_size
      • Configs.best_model_monitor
      • Configs.best_model_monitor_mode
      • Configs.learning_rate
      • Configs.max_epochs
      • Configs.n_classes
      • Configs.num_workers
      • Configs.weight_decay
  • epbd_bert.dnabert2_classifier.model module
    • DNABERT2Classifier
      • DNABERT2Classifier.calculate_loss()
      • DNABERT2Classifier.configure_optimizers()
      • DNABERT2Classifier.forward()
      • DNABERT2Classifier.on_validation_epoch_end()
      • DNABERT2Classifier.training_step()
      • DNABERT2Classifier.validation_step()
  • epbd_bert.dnabert2_classifier.test module
  • epbd_bert.dnabert2_classifier.train_lightning module
  • Module contents
• epbd_bert.dnabert2_epbd package
  • Submodules
  • epbd_bert.dnabert2_epbd.configs module
    • Configs
      • Configs.batch_size
      • Configs.best_model_monitor
      • Configs.best_model_monitor_mode
      • Configs.epbd_feature_input_dim
      • Configs.epbd_features_type
      • Configs.learning_rate
      • Configs.max_epochs
      • Configs.n_classes
      • Configs.num_workers
      • Configs.weight_decay
  • epbd_bert.dnabert2_epbd.model module
    • Dnabert2EPBDModel
      • Dnabert2EPBDModel.calculate_loss()
      • Dnabert2EPBDModel.configure_optimizers()
      • Dnabert2EPBDModel.forward()
      • Dnabert2EPBDModel.on_validation_epoch_end()
      • Dnabert2EPBDModel.training_step()
      • Dnabert2EPBDModel.validation_step()
  • epbd_bert.dnabert2_epbd.test module
  • epbd_bert.dnabert2_epbd.train_lightning module
  • Module contents
• epbd_bert.dnabert2_epbd_crossattn package
  • Submodules
  • epbd_bert.dnabert2_epbd_crossattn.configs module
    • EPBDConfigs
      • EPBDConfigs.best_model_monitor
      • EPBDConfigs.best_model_monitor_mode
      • EPBDConfigs.d_ff
      • EPBDConfigs.d_model
      • EPBDConfigs.epbd_embedder_kernel_size
      • EPBDConfigs.epbd_feature_channels
      • EPBDConfigs.n_classes
      • EPBDConfigs.need_weights
      • EPBDConfigs.num_heads
      • EPBDConfigs.p_dropout
    • TrainingConfigs
      • TrainingConfigs.batch_size
      • TrainingConfigs.learning_rate
      • TrainingConfigs.max_epochs
      • TrainingConfigs.num_workers
      • TrainingConfigs.weight_decay
  • epbd_bert.dnabert2_epbd_crossattn.model module
    • EPBDDnabert2Model
      • EPBDDnabert2Model.calculate_loss()
      • EPBDDnabert2Model.configure_optimizers()
      • EPBDDnabert2Model.forward()
      • EPBDDnabert2Model.load_pretrained_model()
      • EPBDDnabert2Model.on_validation_epoch_end()
      • EPBDDnabert2Model.training_step()
      • EPBDDnabert2Model.validation_step()
    • EPBDEmbedder
      • EPBDEmbedder.forward()
    • MultiModalLayer
      • MultiModalLayer.forward()
    • PoolingLayer
      • PoolingLayer.forward()
    • PositionWiseFeedForward
      • PositionWiseFeedForward.forward()
  • epbd_bert.dnabert2_epbd_crossattn.test module
    • compute_predictions()
  • epbd_bert.dnabert2_epbd_crossattn.train_lightning module
  • Module contents
• epbd_bert.utility package
  • Submodules
  • epbd_bert.utility.data_utils module
    • compute_multi_class_weights()
    • get_uniform_peaks_metadata()
  • epbd_bert.utility.dnabert2 module
    • get_dnabert2_pretrained_model()
    • get_dnabert2_tokenizer()
    • load_dnabert2_for_classification()
  • epbd_bert.utility.pickle_utils module
    • load()
    • save()
  • Module contents

Submodules

epbd_bert.models_factory module

epbd_bert.models_factory.get_model_and_dataloader(model_name, data_path, tokenizer: PreTrainedTokenizer, batch_size=64, num_workers=8)

epbd_bert.path_configs module

epbd_bert.version module

Module contents