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Functions155 in github.com/Mew233/pairwise

⨍ Functions 155◇ Types & classes 31
↓ 10 callersFunctionget_model
(model_name,*args)
pairwise/get_model.py:14
↓ 10 callersFunctionsplit_it
(compound)
pairwise/utilitis.py:20
↓ 6 callersMethod__init__
(self, d_model, eps=1e-6)
pairwise/utilitis.py:362
↓ 5 callersFunctionsplit_it_cell
(compound)
pairwise/utilitis.py:24
↓ 4 callersFunctionSHAP
(model, model_weights,train_val_dataset, test_loader,args)
pairwise/dataloader.py:1083
↓ 4 callersFunctiondataloader
should be starting from X, and Y X_{}_trainval, X_{}_test, Y_{}_trainval, Y_{}_test
pairwise/dataloader.py:28
↓ 4 callersFunctiondataloader_graph
should be starting from X, and Y X_{}_trainval, X_{}_test, Y_{}_trainval, Y_{}_test
pairwise/dataloader.py:71
↓ 4 callersFunctiongetActivation
(name)
pairwise/dataloader.py:1110
↓ 4 callersFunctionk_fold_trainer
(dataset,model,args)
pairwise/dataloader.py:94
↓ 3 callersMethod__init__
(self, d_input, d_model, N, heads, dropout)
pairwise/models/transynergy_liu.py:19
↓ 3 callersMethod__init__
(self, input_dim: int, latent_dim: int, hidden_dims: list = None, \ dop: float = 0.1, noise_flag: bool
pairwise/models/pairwise.py:34
↓ 3 callersMethod_aggregation
(self, item_i_list)
pairwise/models/graphsynergy.py:128
↓ 3 callersMethod_get_neighbor_emb
(self, items, neighbors)
pairwise/models/graphsynergy.py:85
↓ 3 callersMethod_interaction_aggregation
(self, item_embeddings, neighbors_emb_list)
pairwise/models/graphsynergy.py:105
↓ 3 callersFunctionexplode_dpi
(targets)
pairwise/utilitis.py:48
↓ 3 callersFunctionget_neighbor_set
(items, item_target_dict, graph)
pairwise/models/graphsynergy.py:11
↓ 3 callersFunctionone_of_k_encoding_unk
Maps inputs not in the allowable set to the last element.
pairwise/utilitis.py:209
↓ 2 callersMethod__init__
(self, trainval_df)
pairwise/dataloader.py:261
↓ 2 callersMethod__init__
(self, layer_drug=3, dim_drug=128)
pairwise/models/TGSynergy.py:8
↓ 2 callersMethod__init__
(self, input_dim: int, latent_dim: int, hidden_dims: list = None, \ dop: float = 0.1, noise_f
pairwise/models/granuality.py:32
↓ 2 callersFunctionevaluate
(model, model_weights, test_loader, train_val_dataset, args)
pairwise/pipeline.py:548
↓ 2 callersFunctionfast_random_walk
(alpha, binary_mat, subgraph_norm, prop_data_prev)
pairwise/utilitis.py:261
↓ 2 callersFunctionget_clones
(module, N)
pairwise/models/transynergy_liu.py:14
↓ 2 callersFunctionk_fold_trainer_graph_pairwise
(temp_loader_trainval,model,args)
pairwise/dataloader.py:883
↓ 2 callersFunctionload_drug_features
()
pairwise/prepare_data.py:306
↓ 2 callersFunctionload_file
(postfix)
pairwise/prepare_data.py:190
↓ 2 callersFunctionnormalize_network
(network, symmetric_norm=False)
pairwise/utilitis.py:249
↓ 2 callersFunctionprocess_dpi
()
pairwise/prepare_data.py:356
↓ 2 callersFunctionsmile_to_graph
(smile)
pairwise/utilitis.py:216
↓ 1 callersMethod_emb_loss
(self, cell_embeddings, drug1_embeddings, drug2_embeddings, cell_neighbors_emb_list, drug1_
pairwise/models/graphsynergy.py:148
↓ 1 callersMethod_therapy
(self, drug1_embeddings, drug2_embeddings, cell_embeddings)
pairwise/models/graphsynergy.py:136
↓ 1 callersMethod_toxic
(self, drug1_embeddings, drug2_embeddings)
pairwise/models/graphsynergy.py:145
↓ 1 callersFunctionarg_parse
()
pairwise/main.py:10
↓ 1 callersFunctionatom_features
(atom)
pairwise/utilitis.py:191
↓ 1 callersFunctionatom_to_feature_vector
Converts rdkit atom object to feature list of indices :param mol: rdkit atom object :return: list 8 features are canonical, 2 feature
pairwise/utilitis.py:98
↓ 1 callersFunctionattention
(q, k, v, d_k, mask=None, dropout=None)
pairwise/utilitis.py:445
↓ 1 callersFunctionbond_to_feature_vector
Converts rdkit bond object to feature list of indices :param mol: rdkit bond object :return: list
pairwise/utilitis.py:120
↓ 1 callersFunctionconfiguration_from_json
(args)
pairwise/utilitis.py:69
↓ 1 callersMethodencode
(self, input)
pairwise/models/granuality.py:108
↓ 1 callersMethodencode
(self, input)
pairwise/models/pairwise.py:110
↓ 1 callersFunctionevaluator
_summary_ Args: model (_type_): _description_ test_loader (_type_): _description_ Returns: _type_: _description_
pairwise/dataloader.py:1363
↓ 1 callersFunctionevaluator_graph
(model,model_weights,temp_loader_test,args)
pairwise/dataloader.py:1412
↓ 1 callersFunctionevaluator_graph_TGSynergy
(model,model_weights,train_val_dataset, temp_loader_test,args)
pairwise/dataloader.py:1469
↓ 1 callersFunctionevaluator_graph_pairwise
(model,model_weights,train_val_dataset, temp_loader_test,args)
pairwise/dataloader.py:1585
↓ 1 callersFunctionevaluator_graph_trans
(model,model_weights,train_val_dataset, temp_loader_test,args)
pairwise/dataloader.py:1525
↓ 1 callersFunctionget_GNNCell
(cellFeatures_dicts, cellset)
pairwise/select_features.py:30
↓ 1 callersFunctionget_cell
(cellFeature_dicts, synergy_cellset, cell_omics, cell_filtered_by, matrix=False)
pairwise/select_features.py:44
↓ 1 callersFunctionget_cell_target_dict
(cpi_df)
pairwise/prepare_data.py:509
↓ 1 callersFunctionget_clones
(module, N)
pairwise/models/granuality.py:12
↓ 1 callersFunctionget_clones
(module, N)
pairwise/models/pairwise.py:15
↓ 1 callersFunctionget_drug
(drugFeature_dicts, original_list)
pairwise/select_features.py:9
↓ 1 callersFunctionget_fps
(mol)
pairwise/prepare_data.py:338
↓ 1 callersFunctionget_target_dict
(dpi_df)
pairwise/prepare_data.py:484
↓ 1 callersFunctionk_fold_trainer_graph
(temp_loader_trainval,model,args)
pairwise/dataloader.py:274
↓ 1 callersFunctionk_fold_trainer_graph_TGSynergy
(temp_loader_trainval,model,args)
pairwise/dataloader.py:467
↓ 1 callersFunctionk_fold_trainer_graph_trans
(temp_loader_trainval,model,args)
pairwise/dataloader.py:662
↓ 1 callersFunctionload_cellline_features
Load cell line features. load all data in the specified dataset and revise into the same format. Store all kinds of cell lines features in a
pairwise/prepare_data.py:177
↓ 1 callersFunctionload_synergy
Load synergy datasets. Load multi-omics dataset and revise into the specified format. param: dataset: str
pairwise/prepare_data.py:16
↓ 1 callersFunctionmain
()
pairwise/main.py:57
↓ 1 callersFunctionnetwork_kernel_propagation
(network, network_kernel, binary_matrix, verbose=False, **save_args)
pairwise/utilitis.py:312
↓ 1 callersFunctionnetwork_propagation
(network, binary_matrix, alpha=0.7, symmetric_norm=False, verbose=True, **save_args)
pairwise/utilitis.py:271
↓ 1 callersFunctionone_hot
(mu,clean_cells_ALL,clean_genes_ALL)
pairwise/utilitis.py:31
↓ 1 callersFunctionone_of_k_encoding
(x, allowable_set)
pairwise/utilitis.py:203
↓ 1 callersFunctionprepare_data
(args)
pairwise/pipeline.py:31
↓ 1 callersFunctionprocess_ChemicalDescrpitor
()
pairwise/prepare_data.py:336
↓ 1 callersFunctionprocess_dpi_RWR
()
pairwise/prepare_data.py:400
↓ 1 callersFunctionprocess_drugcomb
()
pairwise/prepare_data.py:28
↓ 1 callersFunctionprocess_fingerprint
()
pairwise/prepare_data.py:311
↓ 1 callersFunctionprocess_smiles
()
pairwise/prepare_data.py:546
↓ 1 callersFunctionprocess_smiles2graph
()
pairwise/prepare_data.py:568
↓ 1 callersFunctionprocess_smiles2graph_TGSynergy
()
pairwise/prepare_data.py:583
↓ 1 callersFunctionprocess_smilesGrover
()
pairwise/prepare_data.py:599
↓ 1 callersFunctionsmiles2graph
Converts SMILES string or rdkit's mol object to graph Data object without remove salt :input: SMILES string (str) :return: graph object
pairwise/utilitis.py:136
↓ 1 callersFunctionsplit_it_cellName
(compound)
pairwise/utilitis.py:28
↓ 1 callersFunctiontraining
(X_cell, X_drug, Y, Y_ic1, Y_ic2, args)
pairwise/pipeline.py:245
↓ 1 callersFunctiontraining_baselines
(X_cell, X_drug, Y, args)
pairwise/pipeline.py:205
↓ 1 callersFunctionwrite_config
(args)
pairwise/utilitis.py:76
FunctionALL
()
pairwise/select_features.py:80
MethodERT
(self)
pairwise/models/baselines.py:16
MethodLR
(self)
pairwise/models/baselines.py:20
MethodRF
(self)
pairwise/models/baselines.py:8
MethodXGBOOST
(self)
pairwise/models/baselines.py:12
Method__getitem__
(self, index)
pairwise/dataloader.py:269
Method__getitem__
(self, index)
pairwise/dataloader.py:656
Method__getitem__
(self, index)
pairwise/dataloader.py:878
Method__init__
(self, trainval_df)
pairwise/dataloader.py:649
Method__init__
(self, trainval_df)
pairwise/dataloader.py:871
Method__init__
(self, d_model, heads, dropout=0.1)
pairwise/utilitis.py:379
Method__init__
(self, d_input, d_model, heads, dropout=0.1)
pairwise/utilitis.py:396
Method__init__
(self, d_input, d_model, heads, dropout=0.1)
pairwise/utilitis.py:417
Method__init__
(self, heads, d_model, dropout=0.1)
pairwise/utilitis.py:462
Method__init__
(self, d_model, d_ff=256, dropout=0.1)
pairwise/utilitis.py:500
Method__init__
(self, H, W, d_layers = None, dropout=0.2)
pairwise/utilitis.py:515
Method__init__
(self, items)
pairwise/utilitis.py:572
Method__init__
(self, num_feature=1, layer_cell=3, dim_cell=8, cluster_predefine=None)
pairwise/models/TGSynergy.py:42
Method__init__
(self, cluster_predefine)
pairwise/models/TGSynergy.py:93
Method__init__
(self, cell_channels: int, drug_fp_channels: int, drug_tg_channels: int, dropo
pairwise/models/multitaskdnn_kim.py:9
Method__init__
(self, d_input, d_model, N, heads, dropout)
pairwise/models/transynergy_liu.py:33
Method__init__
(self, max_drug_sm_len=244, num_comp_char=60)
pairwise/models/transynergy_liu.py:47
Method__init__
(self, d_input, d_model, n_feature_type, N, heads, dropout)
pairwise/models/transynergy_liu.py:68
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