Index

A

add_subparser() (cellmaps_vnn.annotate.VNNAnnotate static method) (cellmaps_vnn.predict.VNNPredict static method) (cellmaps_vnn.train.VNNTrain static method)

B

build_input_vector() (in module cellmaps_vnn.util)

C

C_PVAL_SCORE (in module cellmaps_vnn.constants) cal_term_dim() (cellmaps_vnn.vnn.VNN method) calc_gene_rho() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) calc_scores() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) calc_std_vals() (in module cellmaps_vnn.util) calc_term_rlipp() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) CCCLoss (class in cellmaps_vnn.ccc_loss) cellmaps_vnn module cellmaps_vnn.annotate module cellmaps_vnn.ccc_loss module cellmaps_vnn.cellmaps_vnncmd module cellmaps_vnn.constants module cellmaps_vnn.data_wrapper module cellmaps_vnn.exceptions module cellmaps_vnn.predict module cellmaps_vnn.rlipp_calculator module

cellmaps_vnn.runner module cellmaps_vnn.train module cellmaps_vnn.util module cellmaps_vnn.vnn module cellmaps_vnn.vnn_trainer module CellmapsvnnError CellmapsvnnRunner (class in cellmaps_vnn.runner) COMMAND (cellmaps_vnn.annotate.VNNAnnotate attribute) (cellmaps_vnn.predict.VNNPredict attribute) (cellmaps_vnn.train.VNNTrain attribute) construct_direct_gene_layer() (cellmaps_vnn.vnn.VNN method) construct_nn_graph() (cellmaps_vnn.vnn.VNN method) copy_and_register_gene2id_file() (in module cellmaps_vnn.util) create_child_feature_map() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) create_drug_corr_map_sorted() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) create_drug_pos_map() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) create_term_mask() (in module cellmaps_vnn.util) CRHO_SCORE (in module cellmaps_vnn.constants)

D

DEFAULT_ALPHA (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_CPU_COUNT (cellmaps_vnn.predict.VNNPredict attribute) DEFAULT_CUDA (in module cellmaps_vnn.constants) DEFAULT_DELTA (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_DROPOUT_FRACTION (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_DRUG_COUNT (cellmaps_vnn.predict.VNNPredict attribute) DEFAULT_EPOCH (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_LR (cellmaps_vnn.train.VNNTrain attribute)

DEFAULT_MIN_DROPOUT_LAYER (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_N_TRIALS (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_NDEX_SERVER (cellmaps_vnn.annotate.VNNAnnotate attribute) DEFAULT_OPTIMIZE (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_PASSWORD (cellmaps_vnn.annotate.VNNAnnotate attribute) DEFAULT_PATIENCE (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_STD (cellmaps_vnn.train.VNNTrain attribute) DEFAULT_WD (cellmaps_vnn.train.VNNTrain attribute)

E

EDGE_IMPORTANCE_SCORE (in module cellmaps_vnn.constants)

exec_lm() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method)

F

forward() (cellmaps_vnn.ccc_loss.CCCLoss method) (cellmaps_vnn.vnn.VNN method)

G

GENE_IMPORTANCE_SCORE (in module cellmaps_vnn.constants) GENE_RHO_FILE (in module cellmaps_vnn.constants) GENE_SET_COLUMN_NAME (in module cellmaps_vnn.constants)

GENE_SET_WITH_DATA (in module cellmaps_vnn.constants) get_child_features() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator static method) get_grad_norm() (in module cellmaps_vnn.util)

H

HIERARCHY_FILENAME (in module cellmaps_vnn.constants)

I

IMPORTANCE_SCORE (in module cellmaps_vnn.constants)

L

load_all_features() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) load_cell_features() (in module cellmaps_vnn.util) load_feature() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method)

load_gene_features() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method) load_mapping() (in module cellmaps_vnn.util) load_numpy_data() (in module cellmaps_vnn.util) load_term_features() (cellmaps_vnn.rlipp_calculator.RLIPPCalculator method)

M

main() (in module cellmaps_vnn.cellmaps_vnncmd) module cellmaps_vnn cellmaps_vnn.annotate cellmaps_vnn.ccc_loss cellmaps_vnn.cellmaps_vnncmd cellmaps_vnn.constants cellmaps_vnn.data_wrapper cellmaps_vnn.exceptions cellmaps_vnn.predict cellmaps_vnn.rlipp_calculator cellmaps_vnn.runner cellmaps_vnn.train cellmaps_vnn.util cellmaps_vnn.vnn cellmaps_vnn.vnn_trainer

O

ORIGINAL_HIERARCHY_FILENAME (in module cellmaps_vnn.constants)

P

P_PVAL_SCORE (in module cellmaps_vnn.constants) PARENT_NETWORK_NAME (in module cellmaps_vnn.constants)

pearson_corr() (in module cellmaps_vnn.util) predict() (cellmaps_vnn.predict.VNNPredict method) PRHO_SCORE (in module cellmaps_vnn.constants)

R

register_outputs() (cellmaps_vnn.annotate.VNNAnnotate method) (cellmaps_vnn.predict.VNNPredict method) (cellmaps_vnn.train.VNNTrain method) RLIPP_OUTPUT_FILE (in module cellmaps_vnn.constants) RLIPP_SCORE (in module cellmaps_vnn.constants) RLIPPCalculator (class in cellmaps_vnn.rlipp_calculator)

run() (cellmaps_vnn.annotate.VNNAnnotate method) (cellmaps_vnn.predict.VNNPredict method) (cellmaps_vnn.runner.CellmapsvnnRunner method) (cellmaps_vnn.runner.SLURMCellmapsvnnRunner method) (cellmaps_vnn.runner.VnnRunner method) (cellmaps_vnn.train.VNNTrain method)

S

SCORE_FILE_NAME_SUFFIX (in module cellmaps_vnn.constants) set_arguments_from_config_and_defaults() (in module cellmaps_vnn.cellmaps_vnncmd)

SLURMCellmapsvnnRunner (class in cellmaps_vnn.runner) standardize_data() (in module cellmaps_vnn.util) SYSTEM_INTERACTOME_FILE_SUFFIX (in module cellmaps_vnn.constants)

T

train_model() (cellmaps_vnn.vnn_trainer.VNNTrainer method)

TRAINING_PROGRESS_FILE (cellmaps_vnn.vnn_trainer.VNNTrainer attribute) TrainingDataWrapper (class in cellmaps_vnn.data_wrapper)

V

VNN (class in cellmaps_vnn.vnn) VNNAnnotate (class in cellmaps_vnn.annotate) VNNPredict (class in cellmaps_vnn.predict)

VnnRunner (class in cellmaps_vnn.runner) VNNTrain (class in cellmaps_vnn.train) VNNTrainer (class in cellmaps_vnn.vnn_trainer)