Index

B

beam_decode() (TransformerNetwork method), [1]

bin_spectrum() (H5Dataset method), [1]

C

calculate_accuracy() (RandomForest method), [1] calculate_fc1_size() (ConvolutionalNetwork method), [1] check_classification_accuracy() (RandomForest method), [1] check_parameter_for_tuning() (Trainer method), [1] check_regression_accuracy() (RandomForest method), [1]

config (H5Dataset attribute), [1] configure_optimizers() (LightningModule method) ConvolutionalNetwork (class in lipidetective) (class in lipidetective.models.convolutional_network) custom_accuracy_scoring() (LipidLibrary method)

D

dataset_len (H5Dataset attribute), [1]

dataset_names (H5Dataset attribute), [1] decimal_accuracy (H5Dataset attribute), [1]

E

evaluate_custom_transformer_accuracy() (Evaluator method) evaluate_regression_accuracy() (Evaluator method) Evaluator (class in lipidetective.helpers.logging)

extract_features_and_labels() (RandomForest method), [1] extract_info_dataset() (RandomForest method), [1] extract_info_dataset_no_split() (RandomForest method), [1]

F

FeedForwardNetwork (class in lipidetective) (class in lipidetective.models.feedforward_network) file_path (H5Dataset attribute), [1] find_nearest_headgroup() (Evaluator method)

find_nearest_side_chain() (Evaluator method) forward() (ConvolutionalNetwork method), [1] (FeedForwardNetwork method), [1] (TransformerNetwork method), [1]

G

generate_mask() (TransformerNetwork method), [1] generate_prediction_info() (Evaluator method) get_attention_layers() (TransformerNetwork method), [1] get_lipid_species_components() (LipidLibrary method) get_n_highest_peaks() (H5Dataset method), [1] (PredictionDataset method), [1] get_neural_network() (LightningModule method) get_pred_files() (Trainer method), [1]

get_preds_vs_labels() (LightningModule method) get_project_root() (in module lipidetective) get_regression_label() (LipidLibrary method) get_spectrum_data() (RandomForest method), [1] get_test_preds_vs_labels() (LightningModule method) get_transformer_label() (LipidLibrary method) get_unique_lipids() (Trainer method), [1] greedy_decode() (TransformerNetwork method), [1]

H

H5Dataset (class in lipidetective) (class in lipidetective.workflow.h5_dataset)

hdf5_file (H5Dataset attribute), [1]

L

LightningModule (class in lipidetective)

lipid_librarian (H5Dataset attribute), [1] LipidLibrary (class in lipidetective)

N

network_type (H5Dataset attribute), [1]

normalize_precursor_mass() (LipidLibrary method)

P

parse_lipid_dataset_name() (Trainer method), [1] parse_lipid_species_components() (LipidLibrary method) perform_data_split() (Trainer method), [1] plot_decision_tree() (RandomForest method), [1] predict() (Trainer method), [1] (TransformerNetwork method), [1] predict_beam_decode() (TransformerNetwork method), [1] predict_greedy() (TransformerNetwork method), [1]

predict_step() (LightningModule method) predict_top_3() (TransformerNetwork method), [1] PredictionDataset (class in lipidetective) (class in lipidetective.workflow.prediction_dataset) prepare_data() (RandomForest method), [1] prepare_tune_config() (Trainer method), [1] process_input() (PredictionDataset method), [1] process_json() (PredictionDataset method), [1] process_mzml() (PredictionDataset method), [1]

R

RandomForest (class in lipidetective) (class in lipidetective.models.random_forest) read_yaml() (in module lipidetective) resolve_config_path() (in module lipidetective) resolve_config_paths() (in module lipidetective)

resolve_data_path() (in module lipidetective) resolve_model_path() (in module lipidetective) resolve_output_path() (in module lipidetective) return_encoder_embedding() (TransformerNetwork method), [1] run() (RandomForest method), [1] run_random_forest() (Trainer method), [1]

S

save_model() (LightningModule method) schedule_tuning() (Trainer method), [1]

set_seeds() (in module lipidetective) split_data_by_lipid_species() (Trainer method), [1] split_data_via_instructions() (Trainer method), [1]

T

test() (Trainer method), [1] test_step() (LightningModule method) train_with_validation() (Trainer method), [1] train_without_validation() (Trainer method), [1] Trainer (class in lipidetective) (class in lipidetective.workflow.trainer)

training_step() (LightningModule method) TransformerNetwork (class in lipidetective) (class in lipidetective.models.transformer_network) translate_tokens_to_name() (LipidLibrary method) tune_model() (Trainer method), [1]

U

use_single_classifier() (RandomForest method), [1]

use_triple_classifier() (RandomForest method), [1] use_triple_regressor() (RandomForest method), [1]

V

validation_step() (LightningModule method)

W

write_output_to_file() (RandomForest method), [1]

write_yaml() (in module lipidetective)