add saving history #92

GooglingTheCancerGenome · Jul 21, 2021 · 21697db · 21697db
1 parent 687bd94
commit 21697db
Showing 1 changed file with 21 additions and 3 deletions.
diff --git a/scripts/utils/optimize.py b/scripts/utils/optimize.py
@@ -95,11 +95,19 @@ def fitness(cnn_filters, cnn_layers, cnn_kernel_size, cnn_fc_nodes,
     print('cnn_regularization_rate: ', cnn_regularization_rate)
     print()
 
+    #if path_input_model is None:
+
     model = create_model(train_X, 2,
                          learning_rate=cnn_init_learning_rate, regularization_rate=cnn_regularization_rate,
                          filters=cnn_filters, layers=cnn_layers, kernel_size=cnn_kernel_size, fc_nodes=cnn_fc_nodes)
     print(model.summary())
 
+    # else:
+    #
+    #     model = load_model(path_input_model)
+    #     model.trainable = False
+    #     model.summary()
+
     callback_log = TensorBoard(
         log_dir='log_dir',
         histogram_freq=0,
@@ -130,22 +138,26 @@ def fitness(cnn_filters, cnn_layers, cnn_kernel_size, cnn_fc_nodes,
 
     hist_df = pd.DataFrame(history.history)
     hist_csv_file = 'history.csv'
-    with open(hist_csv_file, mode='w') as f:
-        hist_df.to_csv(f)
 
     print()
     print('Accuracy: {0:.2%}'.format(accuracy))
     if accuracy > best_accuracy:
+
+        with open(hist_csv_file, mode='w') as f:
+            hist_df.to_csv(f)
+
         model.save(path_best_model)
         best_accuracy = accuracy
+
     del model
     tf.keras.backend.clear_session()
     return -accuracy
 
 
 def optimize(args):
 
-    global train_X, val_X, train_y, val_y, class_weights, batch_size, max_epoch, path_best_model
+    global train_X, val_X, train_y, val_y, class_weights, batch_size,\
+        max_epoch, path_best_model, path_input_model
 
     randomState = 46
     np.random.seed(randomState)
@@ -154,6 +166,7 @@ def optimize(args):
     batch_size = args.batch_size
     max_epoch = args.epochs
     path_best_model = args.model
+    path_input_model = args.input_model
 
     # training data
     windows = args.windows.split(',')
@@ -238,6 +251,11 @@ def main():
                         type=str,
                         default='DEL',
                         help="Type of SV")
+    parser.add_argument('-im',
+                        '--input_model',
+                        type=str,
+                        default='~/Documents/Projects/GTCG/sv-channels/sv-channels_manuscript/1KG_trios/results/manta_loocv/HG01053/manta_model.keras',
+                        help="Input model")
     parser.add_argument('-m',
                         '--model',
                         type=str,