Reference

• cellmaps_vnn package
  • Submodules
  • cellmaps_vnn.annotate module
    • VNNAnnotate
      • VNNAnnotate.COMMAND
      • VNNAnnotate.DEFAULT_NDEX_SERVER
      • VNNAnnotate.DEFAULT_PASSWORD
      • VNNAnnotate.add_subparser()
      • VNNAnnotate.register_outputs()
      • VNNAnnotate.run()
  • cellmaps_vnn.ccc_loss module
    • CCCLoss
      • CCCLoss.forward()
  • cellmaps_vnn.cellmaps_vnncmd module
    • main()
    • set_arguments_from_config_and_defaults()
  • cellmaps_vnn.constants module
    • CRHO_SCORE
    • C_PVAL_SCORE
    • DEFAULT_CUDA
    • EDGE_IMPORTANCE_SCORE
    • GENE_IMPORTANCE_SCORE
    • GENE_RHO_FILE
    • GENE_SET_COLUMN_NAME
    • GENE_SET_WITH_DATA
    • HIERARCHY_FILENAME
    • IMPORTANCE_SCORE
    • ORIGINAL_HIERARCHY_FILENAME
    • PARENT_NETWORK_NAME
    • PRHO_SCORE
    • P_PVAL_SCORE
    • RLIPP_OUTPUT_FILE
    • RLIPP_SCORE
    • SCORE_FILE_NAME_SUFFIX
    • SYSTEM_INTERACTOME_FILE_SUFFIX
  • cellmaps_vnn.data_wrapper module
    • TrainingDataWrapper
  • cellmaps_vnn.exceptions module
    • CellmapsvnnError
  • cellmaps_vnn.predict module
    • VNNPredict
      • VNNPredict.COMMAND
      • VNNPredict.DEFAULT_CPU_COUNT
      • VNNPredict.DEFAULT_DRUG_COUNT
      • VNNPredict.add_subparser()
      • VNNPredict.predict()
      • VNNPredict.register_outputs()
      • VNNPredict.run()
  • cellmaps_vnn.rlipp_calculator module
    • RLIPPCalculator
      • RLIPPCalculator.calc_gene_rho()
      • RLIPPCalculator.calc_scores()
      • RLIPPCalculator.calc_term_rlipp()
      • RLIPPCalculator.create_child_feature_map()
      • RLIPPCalculator.create_drug_corr_map_sorted()
      • RLIPPCalculator.create_drug_pos_map()
      • RLIPPCalculator.exec_lm()
      • RLIPPCalculator.get_child_features()
      • RLIPPCalculator.load_all_features()
      • RLIPPCalculator.load_feature()
      • RLIPPCalculator.load_gene_features()
      • RLIPPCalculator.load_term_features()
  • cellmaps_vnn.runner module
    • CellmapsvnnRunner
      • CellmapsvnnRunner.run()
    • SLURMCellmapsvnnRunner
      • SLURMCellmapsvnnRunner.run()
    • VnnRunner
      • VnnRunner.run()
  • cellmaps_vnn.train module
    • VNNTrain
      • VNNTrain.COMMAND
      • VNNTrain.DEFAULT_ALPHA
      • VNNTrain.DEFAULT_DELTA
      • VNNTrain.DEFAULT_DROPOUT_FRACTION
      • VNNTrain.DEFAULT_EPOCH
      • VNNTrain.DEFAULT_LR
      • VNNTrain.DEFAULT_MIN_DROPOUT_LAYER
      • VNNTrain.DEFAULT_N_TRIALS
      • VNNTrain.DEFAULT_OPTIMIZE
      • VNNTrain.DEFAULT_PATIENCE
      • VNNTrain.DEFAULT_STD
      • VNNTrain.DEFAULT_WD
      • VNNTrain.add_subparser()
      • VNNTrain.register_outputs()
      • VNNTrain.run()
  • cellmaps_vnn.util module
    • build_input_vector()
    • calc_std_vals()
    • copy_and_register_gene2id_file()
    • create_term_mask()
    • get_grad_norm()
    • load_cell_features()
    • load_mapping()
    • load_numpy_data()
    • pearson_corr()
    • standardize_data()
  • cellmaps_vnn.vnn module
    • VNN
      • VNN.cal_term_dim()
      • VNN.construct_direct_gene_layer()
      • VNN.construct_nn_graph()
      • VNN.forward()
  • cellmaps_vnn.vnn_trainer module
    • VNNTrainer
      • VNNTrainer.TRAINING_PROGRESS_FILE
      • VNNTrainer.train_model()
  • Module contents