(self, hidden_size = 64,
num_go_gnn_layers = 1,
num_gene_gnn_layers = 1,
decoder_hidden_size = 16,
num_similar_genes_go_graph = 20,
num_similar_genes_co_express_graph = 20,
coexpress_threshold = 0.4,
uncertainty = False,
uncertainty_reg = 1,
direction_lambda = 1e-1,
G_go = None,
G_go_weight = None,
G_coexpress = None,
G_coexpress_weight = None,
no_perturb = False,
**kwargs
)
| 281 | enumerate(self.pert_list) if pert in self.gene_list} |
| 282 | |
| 283 | def model_initialize(self, hidden_size = 64, |
| 284 | num_go_gnn_layers = 1, |
| 285 | num_gene_gnn_layers = 1, |
| 286 | decoder_hidden_size = 16, |
| 287 | num_similar_genes_go_graph = 20, |
| 288 | num_similar_genes_co_express_graph = 20, |
| 289 | coexpress_threshold = 0.4, |
| 290 | uncertainty = False, |
| 291 | uncertainty_reg = 1, |
| 292 | direction_lambda = 1e-1, |
| 293 | G_go = None, |
| 294 | G_go_weight = None, |
| 295 | G_coexpress = None, |
| 296 | G_coexpress_weight = None, |
| 297 | no_perturb = False, |
| 298 | **kwargs |
| 299 | ): |
| 300 | |
| 301 | self.config = {'hidden_size': hidden_size, |
| 302 | 'num_go_gnn_layers' : num_go_gnn_layers, |
| 303 | 'num_gene_gnn_layers' : num_gene_gnn_layers, |
| 304 | 'decoder_hidden_size' : decoder_hidden_size, |
| 305 | 'num_similar_genes_go_graph' : num_similar_genes_go_graph, |
| 306 | 'num_similar_genes_co_express_graph' : num_similar_genes_co_express_graph, |
| 307 | 'coexpress_threshold': coexpress_threshold, |
| 308 | 'uncertainty' : uncertainty, |
| 309 | 'uncertainty_reg' : uncertainty_reg, |
| 310 | 'direction_lambda' : direction_lambda, |
| 311 | 'G_go': G_go, |
| 312 | 'G_go_weight': G_go_weight, |
| 313 | 'G_coexpress': G_coexpress, |
| 314 | 'G_coexpress_weight': G_coexpress_weight, |
| 315 | 'device': self.device, |
| 316 | 'num_genes': self.num_genes, |
| 317 | 'num_perts': self.num_perts, |
| 318 | 'no_perturb': no_perturb |
| 319 | } |
| 320 | |
| 321 | if self.wandb: |
| 322 | self.wandb.config.update(self.config) |
| 323 | |
| 324 | if self.config['G_coexpress'] is None: |
| 325 | ## calculating co expression similarity graph |
| 326 | edge_list = get_similarity_network(network_type='co-express', |
| 327 | adata=self.adata, |
| 328 | threshold=coexpress_threshold, |
| 329 | k=num_similar_genes_co_express_graph, |
| 330 | data_path=self.data_path, |
| 331 | data_name=self.dataset_name, |
| 332 | split=self.split, seed=self.seed, |
| 333 | train_gene_set_size=self.train_gene_set_size, |
| 334 | set2conditions=self.set2conditions) |
| 335 | |
| 336 | sim_network = GeneSimNetwork(edge_list, self.gene_list, node_map = self.node_map) |
| 337 | self.config['G_coexpress'] = sim_network.edge_index |
| 338 | self.config['G_coexpress_weight'] = sim_network.edge_weight |
| 339 | |
| 340 | if self.config['G_go'] is None: |
no test coverage detected