Changes for compatibility with Keras 2.

MLP_plot_all.py

@@ -3,7 +3,7 @@
 from keras.layers import Activation, Dense, Dropout
 from keras.engine import Input, Model
 import keras.utils
-from keras.utils.visualize_util import plot
+from keras.utils.vis_utils import plot_model
 import numpy as np
 import datetime
 import random
@@ -28,7 +28,7 @@ def get_model(num_hid_layers, cells_per_layer, dropout_rate):
 	model.add(Dense(3, activation='softmax'))
 
 	model_name = models_directory + 'MLP.hidlay' + str(num_hid_layers) + '.cells' + str(cells_per_layer) + '.drop' + str(dropout_rate)
-	plot(model, to_file = model_name + '.png')
+	plot_model(model, to_file = model_name + '.png', show_shapes=True)
 
 	fp_model = open(model_name + '.json', 'w+')
 	fp_model.write(model.to_json())
@@ -61,7 +61,7 @@ def fit_and_eval(loss_function, optimizer, dropout_rate, dataset_name):
 		for cells_per_layer in [20,30,40,50,60]:
 			model = get_model(num_hid_layers, cells_per_layer, dropout_rate)
 			model.compile(optimizer=optimizer, loss=loss_function, metrics=['accuracy'])
-			model.fit(x_train, keras.utils.np_utils.to_categorical(y_train, num_classes), nb_epoch = nb_epoch, batch_size = 128, shuffle=True)
+			model.fit(x_train, keras.utils.np_utils.to_categorical(y_train, num_classes), epochs = nb_epoch, batch_size = 128, shuffle=True)
 			ev = model.evaluate(x = x_test, y = keras.utils.np_utils.to_categorical(y_test, num_classes), batch_size = 128)
 			results.append(ev[1])
 			#results.append(0.1*num_hid_layers + 0.001*cells_per_layer)		

MLPmodels/MLP.hidlay0.cells20.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_101", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 20, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_76", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_102", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"class_name": "Sequential", "backend": "theano", "keras_version": "2.0.3", "config": [{"class_name": "Dense", "config": {"kernel_regularizer": null, "dtype": "float32", "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "activation": "relu", "kernel_constraint": null, "batch_input_shape": [null, 79], "trainable": true, "bias_constraint": null, "bias_initializer": {"class_name": "Zeros", "config": {}}, "activity_regularizer": null, "units": 20, "use_bias": true, "name": "dense_1", "bias_regularizer": null}}, {"class_name": "Dropout", "config": {"rate": 0.4, "name": "dropout_1", "trainable": true}}, {"class_name": "Dense", "config": {"kernel_regularizer": null, "bias_regularizer": null, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "kernel_constraint": null, "activation": "softmax", "trainable": true, "bias_constraint": null, "bias_initializer": {"class_name": "Zeros", "config": {}}, "activity_regularizer": null, "units": 3, "use_bias": true, "name": "dense_2"}}]}

MLPmodels/MLP.hidlay0.cells30.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_103", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 30, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_77", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_104", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"class_name": "Sequential", "backend": "theano", "keras_version": "2.0.3", "config": [{"class_name": "Dense", "config": {"kernel_regularizer": null, "dtype": "float32", "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "activation": "relu", "kernel_constraint": null, "batch_input_shape": [null, 79], "trainable": true, "bias_constraint": null, "bias_initializer": {"class_name": "Zeros", "config": {}}, "activity_regularizer": null, "units": 30, "use_bias": true, "name": "dense_3", "bias_regularizer": null}}, {"class_name": "Dropout", "config": {"rate": 0.4, "name": "dropout_2", "trainable": true}}, {"class_name": "Dense", "config": {"kernel_regularizer": null, "bias_regularizer": null, "kernel_initializer": {"class_name": "VarianceScaling", "config": {"scale": 1.0, "mode": "fan_avg", "distribution": "uniform", "seed": null}}, "kernel_constraint": null, "activation": "softmax", "trainable": true, "bias_constraint": null, "bias_initializer": {"class_name": "Zeros", "config": {}}, "activity_regularizer": null, "units": 3, "use_bias": true, "name": "dense_4"}}]}

MLPmodels/MLP.hidlay0.cells40.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_105", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 40, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_78", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_106", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"config": [{"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "batch_input_shape": [null, 79], "kernel_regularizer": null, "use_bias": true, "activation": "relu", "trainable": true, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "units": 40, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "name": "dense_5", "dtype": "float32", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_3", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "softmax", "units": 3, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_6", "kernel_constraint": null}, "class_name": "Dense"}], "class_name": "Sequential", "keras_version": "2.0.3", "backend": "theano"}

MLPmodels/MLP.hidlay0.cells50.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_107", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 50, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_79", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_108", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"config": [{"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "batch_input_shape": [null, 79], "kernel_regularizer": null, "use_bias": true, "activation": "relu", "trainable": true, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "units": 50, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "name": "dense_7", "dtype": "float32", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_4", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "softmax", "units": 3, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_8", "kernel_constraint": null}, "class_name": "Dense"}], "class_name": "Sequential", "keras_version": "2.0.3", "backend": "theano"}

MLPmodels/MLP.hidlay0.cells60.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_109", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 60, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_80", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_110", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"config": [{"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "batch_input_shape": [null, 79], "kernel_regularizer": null, "use_bias": true, "activation": "relu", "trainable": true, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "units": 60, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "name": "dense_9", "dtype": "float32", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_5", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "softmax", "units": 3, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_10", "kernel_constraint": null}, "class_name": "Dense"}], "class_name": "Sequential", "keras_version": "2.0.3", "backend": "theano"}

MLPmodels/MLP.hidlay1.cells20.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_111", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 20, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_81", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_112", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 20, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_82", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_113", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"config": [{"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "batch_input_shape": [null, 79], "kernel_regularizer": null, "use_bias": true, "activation": "relu", "trainable": true, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "units": 20, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "name": "dense_11", "dtype": "float32", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_6", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "relu", "units": 20, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_12", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_7", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "softmax", "units": 3, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_13", "kernel_constraint": null}, "class_name": "Dense"}], "class_name": "Sequential", "keras_version": "2.0.3", "backend": "theano"}

MLPmodels/MLP.hidlay1.cells30.drop0.4.json

@@ -1 +1 @@
-{"keras_version": "1.1.1", "class_name": "Sequential", "config": [{"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_114", "init": "glorot_uniform", "b_regularizer": null, "batch_input_shape": [null, 79], "input_dtype": "float32", "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 30, "bias": true, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_83", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_115", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "relu", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 30, "W_regularizer": null}}, {"class_name": "Dropout", "config": {"name": "dropout_84", "p": 0.4, "trainable": true}}, {"class_name": "Dense", "config": {"W_constraint": null, "name": "dense_116", "init": "glorot_uniform", "b_regularizer": null, "bias": true, "b_constraint": null, "activation": "softmax", "input_dim": null, "trainable": true, "activity_regularizer": null, "output_dim": 3, "W_regularizer": null}}]}
+{"config": [{"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "batch_input_shape": [null, 79], "kernel_regularizer": null, "use_bias": true, "activation": "relu", "trainable": true, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "units": 30, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "name": "dense_14", "dtype": "float32", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_8", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "relu", "units": 30, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_15", "kernel_constraint": null}, "class_name": "Dense"}, {"config": {"rate": 0.4, "name": "dropout_9", "trainable": true}, "class_name": "Dropout"}, {"config": {"bias_regularizer": null, "bias_constraint": null, "activity_regularizer": null, "kernel_initializer": {"config": {"mode": "fan_avg", "scale": 1.0, "seed": null, "distribution": "uniform"}, "class_name": "VarianceScaling"}, "kernel_regularizer": null, "use_bias": true, "activation": "softmax", "units": 3, "bias_initializer": {"config": {}, "class_name": "Zeros"}, "trainable": true, "name": "dense_16", "kernel_constraint": null}, "class_name": "Dense"}], "class_name": "Sequential", "keras_version": "2.0.3", "backend": "theano"}