Develop Reference

How to access all outputs from a single custom loss function in keras

I'm trying to reproduce the architecture of the network proposed in this publication in tensorFlow. Being a total beginner to this, I've been using this tutorial as a base to work on, using tensorflow==2.3.2.
To train this network, they use a loss which implies outputs from two branches of the network at the same time, which made me look towards custom losses function in keras. I've got that you can define your own, as long as the definition of the function looks like the following:
def custom_loss(y_true, y_pred):
I also understood that you could give other arguments like so:
def loss_function(margin=0.3):
def custom_loss(y_true, y_pred):
# And now you can use margin
You then just have to call these while compiling your model. When it comes to using multiple outputs, the most common approach seem to be the one proposed here, where you would give several losses functions, one being called for each of your output.
However, I could not find a solution to give several outputs to a loss function, which is what I need here.
To further explain it, here is a minimal working example showing what I've tried, which you can try for yourself in this collab.
import os
import tensorflow as tf
import keras.backend as K
from tensorflow.keras import datasets, layers, models, applications, losses
from tensorflow.keras.preprocessing import image_dataset_from_directory
_URL = 'https://storage.googleapis.com/mledu-datasets/cats_and_dogs_filtered.zip'
path_to_zip = tf.keras.utils.get_file('cats_and_dogs.zip', origin=_URL, extract=True)
PATH = os.path.join(os.path.dirname(path_to_zip), 'cats_and_dogs_filtered')
train_dir = os.path.join(PATH, 'train')
validation_dir = os.path.join(PATH, 'validation')
BATCH_SIZE = 32
IMG_SIZE = (160, 160)
IMG_SHAPE = IMG_SIZE + (3,)
train_dataset = image_dataset_from_directory(train_dir,
shuffle=True,
batch_size=BATCH_SIZE,
image_size=IMG_SIZE)
validation_dataset = image_dataset_from_directory(validation_dir,
shuffle=True,
batch_size=BATCH_SIZE,
image_size=IMG_SIZE)
data_augmentation = tf.keras.Sequential([
layers.experimental.preprocessing.RandomFlip('horizontal'),
layers.experimental.preprocessing.RandomRotation(0.2),
])
preprocess_input = applications.resnet50.preprocess_input
base_model = applications.ResNet50(input_shape=IMG_SHAPE,
include_top=False,
weights='imagenet')
base_model.trainable = True
conv = layers.Conv2D(filters=128, kernel_size=(1,1))
global_pooling = layers.GlobalAveragePooling2D()
horizontal_pooling = layers.AveragePooling2D(pool_size=(1, 5))
reshape = layers.Reshape((-1, 128))
def custom_loss(y_true, y_pred):
print(y_pred.shape)
# Do some stuffs involving both outputs
# Returning something trivial here for correct behavior
return K.mean(y_pred)
inputs = tf.keras.Input(shape=IMG_SHAPE)
x = data_augmentation(inputs)
x = preprocess_input(x)
x = base_model(x, training=True)
first_branch = global_pooling(x)
second_branch = conv(x)
second_branch = horizontal_pooling(second_branch)
second_branch = reshape(second_branch)
model = tf.keras.Model(inputs, [first_branch, second_branch])
base_learning_rate = 0.0001
model.compile(optimizer=tf.keras.optimizers.Adam(lr=base_learning_rate),
loss=custom_loss,
metrics=['accuracy'])
model.summary()
initial_epochs = 10
history = model.fit(train_dataset,
epochs=initial_epochs,
validation_data=validation_dataset)
while doing so, I thought that the y_pred given to loss function would be a list, containing both outputs. However, while running it, what I've got in stdout was this:
Epoch 1/10
(None, 2048)
(None, 5, 128)
What I understand from this is that the loss function is called with every output, one by one, instead of being called once with all the outputs, which means I can't define a loss that would use both the outputs at the same time. Is there any way to achieve this?
Please let me know if I'm unclear, or if you need further details.

I had the same problem trying to implement Triplet_Loss function.
I refered to Keras's implementation for Siamese Network with Triplet Loss Function but something didnt work out and I had to implement the network by myself.
def get_siamese_model(input_shape, conv2d_filters):
# Define the tensors for the input images
anchor_input = Input(input_shape, name="Anchor_Input")
positive_input = Input(input_shape, name="Positive_Input")
negative_input = Input(input_shape, name="Negative_Input")
body = build_body(input_shape, conv2d_filters)
# Generate the feature vectors for the images
encoded_a = body(anchor_input)
encoded_p = body(positive_input)
encoded_n = body(negative_input)
distance = DistanceLayer()(encoded_a, encoded_p, encoded_n)
# Connect the inputs with the outputs
siamese_net = Model(inputs=[anchor_input, positive_input, negative_input],
outputs=distance)
return siamese_net
and the "bug" was in DistanceLayer Implementation Keras posted (also in the same link above).
class DistanceLayer(tf.keras.layers.Layer):
"""
This layer is responsible for computing the distance between the anchor
embedding and the positive embedding, and the anchor embedding and the
negative embedding.
"""
def __init__(self, **kwargs):
super().__init__(**kwargs)
def call(self, anchor, positive, negative):
ap_distance = tf.math.reduce_sum(tf.math.square(anchor - positive), axis=1, keepdims=True, name='ap_distance')
an_distance = tf.math.reduce_sum(tf.math.square(anchor - negative), axis=1, keepdims=True, name='an_distance')
return (ap_distance, an_distance)
When I was training the model, the loss function took only one of the vectors ap_distance or an_distance.
FINALLY, THE FIX WAS to concatenate the vectors together (along axis=1 this case) and on the loss function, take them apart:
def call(self, anchor, positive, negative):
ap_distance = tf.math.reduce_sum(tf.math.square(anchor - positive), axis=1, keepdims=True, name='ap_distance')
an_distance = tf.math.reduce_sum(tf.math.square(anchor - negative), axis=1, keepdims=True, name='an_distance')
return tf.concat([ap_distance, an_distance], axis=1)
on my custom loss:
def get_loss(margin=1.0):
def triplet_loss(y_true, y_pred):
# The output of the network is NOT A tuple, but a matrix shape (batch_size, 2),
# containing the distances between the anchor and the positive example,
# and the anchor and the negative example.
ap_distance = y_pred[:, 0]
an_distance = y_pred[:, 1]
# Computing the Triplet Loss by subtracting both distances and
# making sure we don't get a negative value.
loss = tf.math.maximum(ap_distance - an_distance + margin, 0.0)
# tf.print("\n", ap_distance, an_distance)
# tf.print(f"\n{loss}\n")
return loss
return triplet_loss

Ok, here is an easy way to achieve this. We can achieve this by using the loss_weights parameter. We can weigh multiple outputs exactly the same so that we can get the combined loss results. So, for two output we can do
loss_weights = 1*output1 + 1*output2
In your case, your network has two outputs, by the name they are reshape, and global_average_pooling2d. You can do now as follows
# calculation of loss for one output, i.e. reshape
def reshape_loss(y_true, y_pred):
# do some math with these two
return K.mean(y_pred)
# calculation of loss for another output, i.e. global_average_pooling2d
def gap_loss(y_true, y_pred):
# do some math with these two
return K.mean(y_pred)
And while compiling now you need to do as this
model.compile(
optimizer=tf.keras.optimizers.Adam(lr=base_learning_rate),
loss = {
'reshape':reshape_loss,
'global_average_pooling2d':gap_loss
},
loss_weights = {
'reshape':1.,
'global_average_pooling2d':1.
}
)
Now, the loss is the result of 1.*reshape + 1.*global_average_pooling2d.

LSTM: Input 0 of layer sequential is incompatible with the layer

I know there are several questions about this here, but I haven't found one which fits exactly my problem.
I'm trying to fit an LSTM with data from Pandas DataFrames but getting confused about the format I have to provide them.
I created a small code snipped which shall show you what I try to do:
import pandas as pd, tensorflow as tf, random
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import LSTM, Dense
targets = pd.DataFrame(index=pd.date_range(start='2019-01-01', periods=300, freq='D'))
targets['A'] = [random.random() for _ in range(len(targets))]
targets['B'] = [random.random() for _ in range(len(targets))]
features = pd.DataFrame(index=targets.index)
for i in range(len(features)) :
features[str(i)] = [random.random() for _ in range(len(features))]
model = Sequential()
model.add(LSTM(units=targets.shape[1], input_shape=features.shape))
model.compile(optimizer='adam', loss='mae')
model.fit(features, targets, batch_size=10, epochs=10)
this results to:
ValueError: Input 0 of layer sequential is incompatible with the layer: expected ndim=3, found ndim=2. Full shape received: [10, 300]
which I expect relates to the dimensions of the features DataFrame provided. I guess that once fixed this the next error would mention the targets DataFrame.
As far as I understand, 'units' parameter of my first layer defines the output dimensionality of this model. The inputs have to have a 3D shape, but I don't know how to create them out of the 2D world of the Data Frames.
I hope you can help me understanding the reshape mechanism in Python and how to use them in combination with Pandas DataFrames. (I'm quite new to Python and came from R)
Thankls in advance

Lets looks at the few popular ways in LSTMs are used.
Many to Many
Example: You have a sentence (composed of words in sequence). Give these sequence of words you would like to predict the Parts of speech (POS) of each word.
So you have n words and you feed each word per timestep to the LSTM. Each LSTM timestep (also called LSTM unwrapping) will produce and output. The word is represented by a a set of features normally word embeddings. So the input to LSTM is of size bath_size X time_steps X features
Keras code:
inputs = keras.Input(shape=(10,3))
lstm = keras.layers.LSTM(8, input_shape = (10, 3), return_sequences = True)(inputs)
outputs = keras.layers.TimeDistributed(keras.layers.Dense(5, activation='softmax'))(lstm)
model = keras.Model(inputs=inputs, outputs=outputs)
model.compile(loss='categorical_crossentropy', optimizer='adam')
X = np.random.randn(4,10,3)
y = np.random.randint(0,2, size=(4,10,5))
model.fit(X, y, epochs=2)
print (model.predict(X).shape)
Many to One
Example: Again you have a sentence (composed of words in sequence). Give these sequence of words you would like to predict sentiment of the sentence if it is positive or negative.
Keras code
inputs = keras.Input(shape=(10,3))
lstm = keras.layers.LSTM(8, input_shape = (10, 3), return_sequences = False)(inputs)
outputs =keras.layers.Dense(5, activation='softmax')(lstm)
model = keras.Model(inputs=inputs, outputs=outputs)
model.compile(loss='categorical_crossentropy', optimizer='adam')
X = np.random.randn(4,10,3)
y = np.random.randint(0,2, size=(4,5))
model.fit(X, y, epochs=2)
print (model.predict(X).shape)
Many to multi-headed
Example: You have a sentence (composed of words in sequence). Give these sequence of words you would like to predict sentiment of the sentence as well the author of the sentence.
This is multi-headed model where one head will predict the sentiment and another head will predict the author. Both the heads share the same LSTM backbone.
Keras code
inputs = keras.Input(shape=(10,3))
lstm = keras.layers.LSTM(8, input_shape = (10, 3), return_sequences = False)(inputs)
output_A = keras.layers.Dense(5, activation='softmax')(lstm)
output_B = keras.layers.Dense(5, activation='softmax')(lstm)
model = keras.Model(inputs=inputs, outputs=[output_A, output_B])
model.compile(loss='categorical_crossentropy', optimizer='adam')
X = np.random.randn(4,10,3)
y_A = np.random.randint(0,2, size=(4,5))
y_B = np.random.randint(0,2, size=(4,5))
model.fit(X, [y_A, y_B], epochs=2)
y_hat_A, y_hat_B = model.predict(X)
print (y_hat_A.shape, y_hat_B.shape)
What you are looking for is Many to Multi head model where your predictions for A will be made by one head and another head will make predictions for B

The input data for the LSTM has to be 3D.
If you print the shapes of your DataFrames you get:
targets : (300, 2)
features : (300, 300)
The input data has to be reshaped into (samples, time steps, features). This means that targets and features must have the same shape.
You need to set a number of time steps for your problem, in other words, how many samples will be used to make a prediction.
For example, if you have 300 days and 2 features the time step can be 3. So that three days will be used to make one prediction (you can choose this arbitrarily). Here is the code for reshaping your data (with a few more changes):
import pandas as pd
import numpy as np
import tensorflow as tf
import random
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import LSTM, Dense
data = pd.DataFrame(index=pd.date_range(start='2019-01-01', periods=300, freq='D'))
data['A'] = [random.random() for _ in range(len(data))]
data['B'] = [random.random() for _ in range(len(data))]
# Choose the time_step size.
time_steps = 3
# Use numpy for the 3D array as it is easier to handle.
data = np.array(data)
def make_x_y(ts, data):
"""
Parameters
ts : int
data : numpy array
This function creates two arrays, x and y.
x is the input data and y is the target data.
"""
x, y = [], []
offset = 0
for i in data:
if offset < len(data)-ts:
x.append(data[offset:ts+offset])
y.append(data[ts+offset])
offset += 1
return np.array(x), np.array(y)
x, y = make_x_y(time_steps, data)
print(x.shape, y.shape)
nodes = 100 # This is the width of the network.
out_size = 2 # Number of outputs produced by the network. Same size as features.
model = Sequential()
model.add(LSTM(units=nodes, input_shape=(x.shape[1], x.shape[2])))
model.add(Dense(out_size)) # For the output a Dense (fully connected) layer is used.
model.compile(optimizer='adam', loss='mae')
model.fit(x, y, batch_size=10, epochs=10)

Well, just to finalize this issue I would like to provide one solution I have meanwhile worked on. The class TimeseriesGenerator in tf.keras.... enabled me quite easy to provide the data in the right shape to an LSTM model
from keras.preprocessing.sequence import TimeseriesGenerator
import numpy as np
window_size = 7
batch_size = 8
sampling_rate = 1
train_gen = TimeseriesGenerator(X_train.values, y_train.values,
length=window_size, sampling_rate=sampling_rate,
batch_size=batch_size)
valid_gen = TimeseriesGenerator(X_valid.values, y_valid.values,
length=window_size, sampling_rate=sampling_rate,
batch_size=batch_size)
test_gen = TimeseriesGenerator(X_test.values, y_test.values,
length=window_size, sampling_rate=sampling_rate,
batch_size=batch_size)
There are many other ways on implementing generators e.g. using the more_itertools which provides the function windowed, or making use of tensorflow.Dataset and its function window.
For me the TimeseriesGenerator was sufficient to feed the tests I did.
In case you would like to see an example modeling the DAX based on some stocks I'm sharing a notebook on Github.

Character-based Text Classification with Triplet Loss

Im trying to implement a text-classifier using triplet loss to classify different job descriptions into categories based on this paper. But whatever i do, the classifier yields very bad results.
For the embedding i followed this tutorial and the NN architecture is based on this article.
I create my encodings using:
max_char_len = 20
group_numbers = range(0, len(job_groups))
char_vocabulary = {'PAD':0}
X_char = []
y_temp = []
i = 1
for group, number in zip(job_groups, group_numbers):
for job in group:
job_cleaned = some_cleaning_function(job)
job_enc = []
for c in job_cleaned:
if c in char_vocabulary.keys():
job_enc.append(char_vocabulary[c])
else:
char_vocabulary[c] = i
job_enc.append(char_vocabulary[c])
i+=1
X_char.append(job_enc)
y_temp.append(number)
X_char = pad_sequences(X_char, maxlen = max_char_length, truncating='post')
My Neural Network is set up the following way:
def create_base_model():
char_in = Input(shape=(max_char_length,), name='Char_Input')
char_enc = Embedding(input_dim=len(char_vocabulary)+1, output_dim=20, mask_zero=True,name='Char_Embedding')(char_in)
x = Bidirectional(LSTM(64, return_sequences=True, recurrent_dropout=0.2, dropout=0.4))(char_enc)
x = Bidirectional(LSTM(64, return_sequences=True, recurrent_dropout=0.2, dropout=0.4))(x)
x = Bidirectional(LSTM(64, return_sequences=True, recurrent_dropout=0.2, dropout=0.4))(x)
x = Bidirectional(LSTM(64, return_sequences=False, recurrent_dropout=0.2, dropout=0.4))(x)
out = Dense(128, activation = "softmax")(x)
return Model(char_in, out)
def get_siamese_triplet_char():
anchor_input_c = Input(shape=(max_char_length,),name='Char_Input_Anchor')
pos_input_c = Input(shape=(max_char_length,),name='Char_Input_Positive')
neg_input_c = Input(shape=(max_char_length,),name='Char_Input_Negative')
base_model = create_base_model(encoding_generator)
encoded_anchor = base_model(anchor_input_c)
encoded_positive = base_model(pos_input_c)
encoded_negative = base_model(neg_input_c)
inputs = [anchor_input_c, pos_input_c, neg_input_c]
outputs = [encoded_anchor, encoded_positive, encoded_negative]
siamese_triplet = Model(inputs, outputs)
siamese_triplet.add_loss((triplet_loss(outputs)))
siamese_triplet.compile(loss=None, optimizer='adam')
return siamese_triplet, base_model
The triplet loss is defined as follows:
def triplet_loss(inputs):
anchor, positive, negative = inputs
positive_distance = K.square(anchor - positive)
negative_distance = K.square(anchor - negative)
positive_distance = K.sqrt(K.sum(positive_distance, axis=-1, keepdims = True))
negative_distance = K.sqrt(K.sum(negative_distance, axis=-1, keepdims = True))
loss = positive_distance - negative_distance
loss = K.maximum(0.0, 1 + loss)
return K.mean(loss)
The model is then trained with:
siamese_triplet_char.fit(x=
[Anchor_chars_train,
Positive_chars_train,
Negative_chars_train],
shuffle=True, batch_size=8, epochs=22, verbose=1)
My goal is to: First, train the network with no label data in order to minimize the space of the different phrases and second, add a classification layer and create the final classifier.
My general problem is that even the first phase shows sinking cost-values it overfits and the validation results jump around and the second phase fails badly as I'm not able to train the model to actually classify.
My questions are the following:
Could someone explain the Embedding Architecture? What is the output dimension refering to? The individual characters? Would that even make sense? Or is there a better way to encode the input data?
How can i add validation_data to a network that does not contain labeled data? I could use validation_split, but i would rather prefer passing specific data to validate as my data is stratified.
Is there a reason why the classification does not work? Applying a simple K-Nearest Neighbor algorithm achieves at best 0.5 accuracy! Is it because of the data? Or is there a systematic error in my system?
All ideas and suggestions are really appreciated!

model.fit() Keras Classification Multiple Inputs-Single Output gives error: AttributeError: 'NoneType' object has no attribute 'fit'

I am constructing a Keras Classification model with Multiple Inputs (3 actually) to predict one single output. Specifically, my 3 inputs are:
Actors
Plot Summary
Relevant Movie Features
Output:
Genre tags
All the above inputs and the single output are related to 10,000 IMDB Movies.
Even though the creation of the model is successful, when I try to fit the model on my three different X_train's I get an Attribute error. I have one X_train and X_test for actors, a different one X_train and X_test for plot summary and a different one X_train and X_test for movie features. My y_train and y_test are the same for all the inputs.
Python Code (create the multiple input keras)
def kera_multy_classification_model():
sentenceLength_actors = 15
vocab_size_frequent_words_actors = 20001
sentenceLength_plot = 23
vocab_size_frequent_words_plot = 17501
sentenceLength_features = 69
vocab_size_frequent_words_features = 20001
model = keras.Sequential(name='Multy-Input Keras Classification model')
actors = keras.Input(shape=(sentenceLength_actors,), name='actors_input')
plot = keras.Input(shape=(sentenceLength_plot,), name='plot_input')
features = keras.Input(shape=(sentenceLength_features,), name='features_input')
emb1 = layers.Embedding(input_dim = vocab_size_frequent_words_actors + 1,
# based on keras documentation input_dim: int > 0. Size of the vocabulary, i.e. maximum integer index + 1.
output_dim = Keras_Configurations_model1.EMB_DIMENSIONS,
# int >= 0. Dimension of the dense embedding
embeddings_initializer = 'uniform',
# Initializer for the embeddings matrix.
mask_zero = False,
input_length = sentenceLength_actors,
name="actors_embedding_layer")(actors)
encoded_layer1 = layers.LSTM(100)(emb1)
emb2 = layers.Embedding(input_dim = vocab_size_frequent_words_plot + 1,
output_dim = Keras_Configurations_model2.EMB_DIMENSIONS,
embeddings_initializer = 'uniform',
mask_zero = False,
input_length = sentenceLength_plot,
name="plot_embedding_layer")(plot)
encoded_layer2 = layers.LSTM(100)(emb2)
emb3 = layers.Embedding(input_dim = vocab_size_frequent_words_features + 1,
output_dim = Keras_Configurations_model3.EMB_DIMENSIONS,
embeddings_initializer = 'uniform',
mask_zero = False,
input_length = sentenceLength_features,
name="features_embedding_layer")(features)
encoded_layer3 = layers.LSTM(100)(emb3)
merged = layers.concatenate([encoded_layer1, encoded_layer2, encoded_layer3])
layer_1 = layers.Dense(Keras_Configurations_model1.BATCH_SIZE, activation='relu')(merged)
output_layer = layers.Dense(Keras_Configurations_model1.TARGET_LABELS, activation='softmax')(layer_1)
model = keras.Model(inputs=[actors, plot, features], outputs=output_layer)
print(model.output_shape)
print(model.summary())
model.compile(optimizer='adam',
loss='sparse_categorical_crossentropy',
metrics=['sparse_categorical_accuracy'])
Python Code (fit the multiple input keras on my inputs)
def fit_keras_multy_input(model, x_train_seq_actors, x_train_seq_plot, x_train_seq_features, x_test_seq_actors, x_test_seq_plot, x_test_seq_features, y_train, y_test):
s = time()
fit_model = model.fit([x_train_seq_actors, x_train_seq_plot, x_train_seq_features], y_train,
epochs=Keras_Configurations_model1.NB_EPOCHS,
verbose = Keras_Configurations_model1.VERBOSE,
batch_size=Keras_Configurations_model1.BATCH_SIZE,
validation_data=([x_test_seq_actors, x_test_seq_plot, x_test_seq_features], y_test),
callbacks=callbacks)
duration = time() - s
print("\nTraining time finished. Duration {} secs".format(duration))
Model's Structure
Error produced
Note: Please not that each of the X_train and X_test are sequences of numbers. (Text that have been tokenized)
Having done a little research, the problem starts in the model.compile() function. Although, I am not sure what should be changed in my model's compile function so as to fix this.
Thank you in advance for any advice or help on this matter. Feel free to ask on the comments any additional information that I may have missed, to make this question more complete.

Your function kera_multy_classification_model() doesn't return anything, so after model = kera_multy_classification_model(), you get model == None as your function returns nothing. And None's type is NoneType and it really doesn't have a method called fit().
Just add return model in the end of kera_multy_classification_model().

How do I get the predicted labels from a model.predict function from Keras?

I have built a LSTM model using Keras library to predict duplicate questions on the Quora official dataset. The test labels are 0 or 1. 1 indicates the question pair is duplicate. After building the model using model.fit, I test the model using model.predict on the test data. The output is an array of values(probabilities) like below:
[ 0.00514298]
[ 0.15161049]
[ 0.27588326]
[ 0.00236167]
[ 1.80067325]
[ 0.01048524]
[ 1.43425131]
[ 1.99202418]
[ 0.54853892]
[ 0.02514757]
I am only showing the first 10 values in the array. I don't understand what do these values mean and how do I compare it against the test labels to calculate the test accuracy. I want the model to output the binary predicted values as 0 or 1 rather than the probabilities. Please refer the last section of my code below:
sequence_1_input = Input(shape=(MAX_SEQUENCE_LENGTH,), dtype='int32')
embedded_sequences_1 = embedding_layer(sequence_1_input)
x1 = lstm_layer(embedded_sequences_1)
sequence_2_input = Input(shape=(MAX_SEQUENCE_LENGTH,), dtype='int32')
embedded_sequences_2 = embedding_layer(sequence_2_input)
y1 = lstm_layer(embedded_sequences_2)
merged = concatenate([x1, y1])
merged = Dropout(rate_drop_dense)(merged)
merged = BatchNormalization()(merged)
merged = Dense(num_dense, activation=act)(merged)
merged = Dropout(rate_drop_dense)(merged)
merged = BatchNormalization()(merged)
preds = Dense(1, activation='sigmoid')(merged)
########################################
## train the model
########################################
model = Model(inputs=[sequence_1_input, sequence_2_input], \
outputs=preds)
model.compile(loss='binary_crossentropy',
optimizer='nadam',
metrics=['acc'])
hist = model.fit([data_1_train, data_2_train], labels_train, \
validation_data=([data_1_val, data_2_val], labels_val, weight_val), \
epochs=200, batch_size=2048, shuffle=True, \
class_weight=class_weight, callbacks=[early_stopping, model_checkpoint])
preds = model.predict([test_data_1, test_data_2], batch_size=8192,
verbose=1)
preds += model.predict([test_data_2, test_data_1], batch_size=8192,
verbose=1)
preds /= 2
print(type(preds))
print(preds[:20])
print('preds.ravel')
print(preds.ravel())

As you say, your output is a np array with probabilities. You can convert it to binary labels by doing for example (model.predict(X) > 0.5).astype(int)

Artificial neural networks are probablisitc classfiiers, so your output is absolutly fine. It´s just the probability to belong to your target label.
In addition one interesting fact is that 0.5 is maybe not the offet you want to use. It depends on, how important true-positives and false-positives are in your task. You can take a look at the ROC Curves to find the optimal offset.

You can try changing your activation function to softmax in your last layer or you can make your own softmax function and pass your output to that function. Here's an example for a custom softmax function
def softmax(x):
return np.exp(x) / np.sum(np.exp(x), axis=0)