Keras Neural Network Accuracy is always 0 While Training - python

I'm making a simple classification algo with a keras neural network. The goal is to take 3 data points on weather and decide whether or not there's a wildfire. Here's an image of the .csv dataset that I'm using to train the model(this image is only the top few lines and isn't the entire thing ):
wildfire weather dataset
As you can see, there are 4 columns with the fourth being either a "1" which means "fire", or a "0" which means "no fire". I want the algo to predict either a 1 or a 0. This is the code that I wrote:
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
import keras
from keras.models import Sequential
from keras.layers import Dense
from keras.layers import Dropout
from sklearn.preprocessing import StandardScaler
from sklearn.model_selection import train_test_split
import csv
#THIS IS USED TO TRAIN THE MODEL
# Importing the dataset
dataset = pd.read_csv('Fire_Weather.csv')
dataset.head()
X=dataset.iloc[:,0:3]
Y=dataset.iloc[:,3]
X.head()
obj=StandardScaler()
X=obj.fit_transform(X)
X_train,X_test,y_train,y_test=train_test_split(X, Y, test_size=0.25)
print(X_train.shape)
print(X_test.shape)
print(y_train.shape)
print(y_test.shape)
classifier = Sequential()
# Adding the input layer and the first hidden layer
classifier.add(Dense(units = 6, kernel_initializer = 'uniform', activation =
'relu', input_dim = 3))
# classifier.add(Dropout(p = 0.1))
# Adding the second hidden layer
classifier.add(Dense(units = 6, kernel_initializer = 'uniform', activation
= 'relu'))
# classifier.add(Dropout(p = 0.1))
# Adding the output layer
classifier.add(Dense(units = 1, kernel_initializer = 'uniform', activation
= 'sigmoid'))
# Compiling the ANN
classifier.compile(optimizer = 'adam', loss = 'binary_crossentropy', metrics
= ['accuracy'])
classifier.fit(X_train, y_train, batch_size = 3, epochs = 10)
y_pred = classifier.predict(X_test)
y_pred = (y_pred > 0.5)
print(y_pred)
classifier.save("weather_model.h5")
The problem is that whenever I run this, my accuracy is always "0.0000e+00" and my training output looks like this:
Epoch 1/10
2146/2146 [==============================] - 2s 758us/step - loss: nan - accuracy: 0.0238
Epoch 2/10
2146/2146 [==============================] - 1s 625us/step - loss: nan - accuracy: 0.0000e+00
Epoch 3/10
2146/2146 [==============================] - 1s 604us/step - loss: nan - accuracy: 0.0000e+00
Epoch 4/10
2146/2146 [==============================] - 1s 609us/step - loss: nan - accuracy: 0.0000e+00
Epoch 5/10
2146/2146 [==============================] - 1s 624us/step - loss: nan - accuracy: 0.0000e+00
Epoch 6/10
2146/2146 [==============================] - 1s 633us/step - loss: nan - accuracy: 0.0000e+00
Epoch 7/10
2146/2146 [==============================] - 1s 481us/step - loss: nan - accuracy: 0.0000e+00
Epoch 8/10
2146/2146 [==============================] - 1s 476us/step - loss: nan - accuracy: 0.0000e+00
Epoch 9/10
2146/2146 [==============================] - 1s 474us/step - loss: nan - accuracy: 0.0000e+00
Epoch 10/10
2146/2146 [==============================] - 1s 474us/step - loss: nan - accuracy: 0.0000e+00
Does anyone know why this is happening and what I could do to my code to fix this?
Thank You!

EDIT: I realized that my earlier response was highly misleading, which was thankfully pointed out by #xdurch0 and #Timbus Calin. Here is an edited answer.
Check that all your input values are valid. Are there any nan or inf values in your training data?
Try using different activation functions. ReLU is good, but it is prone to what is known as the dying ReLu problem, where the neural network basically learns nothing since no updates are made to its weight. One possibility is to use Leaky ReLu or PReLU.
Try using gradient clipping, which is a technique used to tackle vanishing or exploding gradients (which is likely what is happening in your case). Keras allows users to configure clipnorm clip value for optimizers.
There are posts on SO that report similar problems, such as this one, which might also be of interest to you.

Related

Neural network for adding two integer numbers

I want to create a neural network which can add two integer numbers. I have designed it as follows:
question I have really low accuracy of 0.002% . what can i do to increase it?
For creating data:
import numpy as np
import random
a=[]
b=[]
c=[]
for i in range(1, 1001):
a.append(random.randint(1,999))
b.append(random.randint(1,999))
c.append(a[i-1] + b[i-1])
X = np.array([a,b]).transpose()
y = np.array(c).transpose().reshape(-1, 1)
scaling my data :
from sklearn.preprocessing import MinMaxScaler
minmax = MinMaxScaler()
minmax2 = MinMaxScaler()
X = minmax.fit_transform(X)
y = minmax2.fit_transform(y)
The network :
from keras import Sequential
from keras.layers import Dense
from keras.optimizers import SGD
clfa = Sequential()
clfa.add(Dense(input_dim=2, output_dim=2, activation='sigmoid', kernel_initializer='he_uniform'))
clfa.add(Dense(output_dim=2, activation='sigmoid', kernel_initializer='uniform'))
clfa.add(Dense(output_dim=2, activation='sigmoid', kernel_initializer='uniform'))
clfa.add(Dense(output_dim=2, activation='sigmoid', kernel_initializer='uniform'))
clfa.add(Dense(output_dim=1, activation='relu'))
opt = SGD(lr=0.01)
clfa.compile(opt, loss='mean_squared_error', metrics=['acc'])
clfa.fit(X, y, epochs=140)
outputs :
Epoch 133/140
1000/1000 [==============================] - 0s 39us/step - loss: 0.0012 - acc: 0.0020
Epoch 134/140
1000/1000 [==============================] - 0s 40us/step - loss: 0.0012 - acc: 0.0020
Epoch 135/140
1000/1000 [==============================] - 0s 41us/step - loss: 0.0012 - acc: 0.0020
Epoch 136/140
1000/1000 [==============================] - 0s 40us/step - loss: 0.0012 - acc: 0.0020
Epoch 137/140
1000/1000 [==============================] - 0s 41us/step - loss: 0.0012 - acc: 0.0020
Epoch 138/140
1000/1000 [==============================] - 0s 42us/step - loss: 0.0012 - acc: 0.0020
Epoch 139/140
1000/1000 [==============================] - 0s 40us/step - loss: 0.0012 - acc: 0.0020
Epoch 140/140
1000/1000 [==============================] - 0s 42us/step - loss: 0.0012 - acc: 0.0020
That is my code with console outputs..
I have tried every different combinations of optimizers, losses, and activations, plus this data fits perfectly a Linear Regression.
Two mistakes, several issues.
The mistakes:
This is a regression problem, so the activation of the last layer should be linear, not relu (leaving it without specifying anything will work, since linear is the default activation in a Keras layer).
Accuracy is meaningless in regression; remove metrics=['acc'] from your model compilation - you should judge the performance of your model only with your loss.
The issues:
We don't use sigmoid activations for the intermediate layers; change all of them to relu.
Remove the kernel_initializer argument, thus leaving the default glorot_uniform, which is the recommended one.
A number of Dense layers each one only with two nodes is not a good idea; try reducing the number of layers and increasing the number of nodes. See here for a simple example network for the iris data.
You are trying to fit a linear function, but internally use sigmoid nodes, which map values to a range (0,1). Sigmoid is very useful for classification, but not really for regression if the values are outside (0,1). It could MAYBE work if you restricted your random number to floating point in the interval [0,1]. OR input into your nodes all the bits seperately, and have it learn an adder.

EarlyStopping TensorFlow 2.0

I am running a code using Python 3.7.5 with TensorFlow 2.0 for MNIST classification.
I am using EarlyStopping from TensorFlow 2.0 and the callback I have for it is:
callbacks = [
tf.keras.callbacks.EarlyStopping(
monitor='val_loss', patience = 3,
min_delta=0.001
)
]
According to EarlyStopping - TensorFlow 2.0 page, the definition of min_delta parameter is as follows:
min_delta: Minimum change in the monitored quantity to qualify as an
improvement, i.e. an absolute change of less than min_delta, will
count as no improvement.
Train on 60000 samples, validate on 10000 samples
Epoch 1/15 60000/60000 [==============================] - 10s
173us/sample - loss: 0.2040 - accuracy: 0.9391 - val_loss: 0.1117 -
val_accuracy: 0.9648
Epoch 2/15 60000/60000 [==============================] - 9s
150us/sample - loss: 0.0845 - accuracy: 0.9736 - val_loss: 0.0801 -
val_accuracy: 0.9748
Epoch 3/15 60000/60000 [==============================] - 9s
151us/sample - loss: 0.0574 - accuracy: 0.9817 - val_loss: 0.0709 -
val_accuracy: 0.9795
Epoch 4/15 60000/60000 [==============================] - 9s
149us/sample - loss: 0.0434 - accuracy: 0.9858 - val_loss: 0.0787 -
val_accuracy: 0.9761
Epoch 5/15 60000/60000 [==============================] - 9s
151us/sample - loss: 0.0331 - accuracy: 0.9893 - val_loss: 0.0644 -
val_accuracy: 0.9808
Epoch 6/15 60000/60000 [==============================] - 9s
150us/sample - loss: 0.0275 - accuracy: 0.9910 - val_loss: 0.0873 -
val_accuracy: 0.9779
Epoch 7/15 60000/60000 [==============================] - 9s
151us/sample - loss: 0.0232 - accuracy: 0.9921 - val_loss: 0.0746 -
val_accuracy: 0.9805
Epoch 8/15 60000/60000 [==============================] - 9s
151us/sample - loss: 0.0188 - accuracy: 0.9936 - val_loss: 0.1088 -
val_accuracy: 0.9748
Now if I look at the last three epochs viz., epochs 6, 7, and 8 and look at the validation loss ('val_loss'), their values are:
0.0688, 0.0843 and 0.0847.
And the differences between consecutive 3 terms are: 0.0155, 0.0004. But isn't the first difference greater than 'min_delta' as defined in the callback.
The code I came up with for EarlyStopping is as follows:
# numpy array to hold last 'patience = 3' values-
pv = [0.0688, 0.0843, 0.0847]
# numpy array to compute differences between consecutive elements in 'pv'-
differences = np.diff(pv, n=1)
differences
# array([0.0155, 0.0004])
# minimum change required for monitored metric's improvement-
min_delta = 0.001
# Check whether the consecutive differences is greater than 'min_delta' parameter-
check = differences > min_delta
check
# array([ True, False])
# Condition to see whether all 3 'val_loss' differences are less than 'min_delta'
# for training to stop since EarlyStopping is called-
if np.all(check == False):
print("Stop Training - EarlyStopping is called")
# stop training
But according to the 'val_loss', the differences between the not ALL of the 3 last epochs are greater than 'min_delta' of 0.001. For example, the first difference is greater than 0.001 (0.0843 - 0.0688) while the second difference is less than 0.001 (0.0847 - 0.0843).
Also, according to patience parameter definition of "EarlyStopping":
patience: Number of epochs with no improvement after which training will be stopped.
So, EarlyStopping should be called when there is no improvement for 'val_loss' for 3 consecutive epochs where the absolute change of less than 'min_delta' does not count as improvement.
Then why is EarlyStopping called?
Code for model definition and 'fit()' are:
import tensorflow_model_optimization as tfmot
from tensorflow_model_optimization.sparsity import keras as sparsity
import matplotlib.pyplot as plt from tensorflow.keras.layers import AveragePooling2D, Conv2D
from tensorflow.keras import models, layers, datasets
from tensorflow.keras.layers import Dense, Flatten, Reshape, Input, InputLayer
from tensorflow.keras.models import Sequential, Model
# Specify the parameters to be used for layer-wise pruning, NO PRUNING is done here:
pruning_params_unpruned = {
'pruning_schedule': sparsity.PolynomialDecay(
initial_sparsity=0.0, final_sparsity=0.0,
begin_step = 0, end_step=0, frequency=100) }
def pruned_nn(pruning_params):
"""
Function to define the architecture of a neural network model
following 300 100 architecture for MNIST dataset and using
provided parameter which are used to prune the model.
Input: 'pruning_params' Python 3 dictionary containing parameters which are used for pruning
Output: Returns designed and compiled neural network model
"""
pruned_model = Sequential()
pruned_model.add(l.InputLayer(input_shape=(784, )))
pruned_model.add(Flatten())
pruned_model.add(sparsity.prune_low_magnitude(
Dense(units = 300, activation='relu', kernel_initializer=tf.initializers.GlorotUniform()),
**pruning_params))
# pruned_model.add(l.Dropout(0.2))
pruned_model.add(sparsity.prune_low_magnitude(
Dense(units = 100, activation='relu', kernel_initializer=tf.initializers.GlorotUniform()),
**pruning_params))
# pruned_model.add(l.Dropout(0.1))
pruned_model.add(sparsity.prune_low_magnitude(
Dense(units = num_classes, activation='softmax'),
**pruning_params))
# Compile pruned CNN-
pruned_model.compile(
loss=tf.keras.losses.categorical_crossentropy,
# optimizer='adam',
optimizer=tf.keras.optimizers.Adam(lr = 0.001),
metrics=['accuracy'])
return pruned_model
batch_size = 32
epochs = 50
# Instantiate NN-
orig_model = pruned_nn(pruning_params_unpruned)
# Train unpruned Neural Network-
history_orig = orig_model.fit(
x = X_train, y = y_train,
batch_size = batch_size,
epochs = epochs,
verbose = 1,
callbacks = callbacks,
validation_data = (X_test, y_test),
shuffle = True )
The behaviour of the Early Stopping callback is related to:
Metric or Loss to be monitored
min_delta which is the minimum quantity to be considered an improvement, between the performance of the monitored quantity in the current epoch and the best result in that metric.
patience which is the number of epochs without improvements (taking into consideration that improvements have to be of a greater change than min_delta) before stopping the algorithm.
In your case, the best val_lossis 0.0644 and should have a value of lower than 0.0634 to be registered as improvement:
Epoch 6/15 val_loss: 0.0873 | Difference is: + 0.0229
Epoch 7/15 val_loss: 0.0746 | Difference is: + 0.0102
Epoch 8/15 val_loss: 0.1088 | Difference is: + 0.0444
Be aware that the quantities that are printed in the "training log", are approximated and you shouldn't base your assumptions on these values. You should rather take into consideration the true values from callbacks or the history of the training.
Reference

Keras Multi-layer Neural Network Accuracy

I've built a simplistic multi-layer NN using Keras with precipitation data in Australia. The code takes 4 input columns: ['MinTemp', 'MaxTemp', 'Rainfall', 'WindGustSpeed'] and trains against the RainTomorrow output.
I've partitioned the data into training/test buckets, transformed all values into 0 <= n <= 1. When I trying to run model.fit, my loss values steady at ~13.2, but my accuracy is always 0.0. An example of logged fitting intervals are:
...
Epoch 37/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.1274 - acc: 0.0000e+00 - val_loss: -16.1168 - val_acc: 0.0000e+00
Epoch 38/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.1457 - acc: 0.0000e+00 - val_loss: -16.1168 - val_acc: 0.0000e+00
Epoch 39/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.1315 - acc: 0.0000e+00 - val_loss: -16.1168 - val_acc: 0.0000e+00
Epoch 40/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.1797 - acc: 0.0000e+00 - val_loss: -16.1168 - val_acc: 0.0000e+00
Epoch 41/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.1844 - acc: 0.0000e+00 - val_loss: -16.1169 - val_acc: 0.0000e+00
Epoch 42/200
113754/113754 [==============================] - 0s 2us/step - loss: -13.2205 - acc: 0.0000e+00 - val_loss: -16.1169 - val_acc: 0.0000e+00
Epoch 43/200
...
How can I amend the following script, so my accuracy grows, and my predication output returns a value between 0 and 1 (0: no rain, 1: rain)?
import keras
import sklearn.model_selection
import numpy as np
import pandas as pd
from sklearn.preprocessing import LabelEncoder
from sklearn.preprocessing import MinMaxScaler
labelencoder = LabelEncoder()
# read data, replace NaN with 0.0
csv_data = pd.read_csv('weatherAUS.csv', header=0)
csv_data = csv_data.replace(np.nan, 0.0, regex=True)
# Input/output columns scaled to 0<=n<=1
x = csv_data.loc[:, ['MinTemp', 'MaxTemp', 'Rainfall', 'WindGustSpeed']]
y = labelencoder.fit_transform(csv_data['RainTomorrow'])
scaler_x = MinMaxScaler(feature_range =(-1, 1))
x = scaler_x.fit_transform(x)
scaler_y = MinMaxScaler(feature_range =(-1, 1))
y = scaler_y.fit_transform([y])[0]
# Partitioned data for training/testing
x_train, x_test, y_train, y_test = sklearn.model_selection.train_test_split(x, y, test_size=0.2)
# model
model = keras.models.Sequential()
model.add( keras.layers.normalization.BatchNormalization(input_shape=tuple([x_train.shape[1]])))
model.add(keras.layers.core.Dense(4, activation='relu'))
model.add(keras.layers.core.Dropout(rate=0.5))
model.add(keras.layers.normalization.BatchNormalization())
model.add(keras.layers.core.Dense(4, activation='relu'))
model.add(keras.layers.core.Dropout(rate=0.5))
model.add(keras.layers.normalization.BatchNormalization())
model.add(keras.layers.core.Dense(4, activation='relu'))
model.add(keras.layers.core.Dropout(rate=0.5))
model.add(keras.layers.core.Dense(1, activation='sigmoid'))
model.compile(loss='binary_crossentropy', optimizer='rmsprop', metrics=["accuracy"])
callback_early_stopping = keras.callbacks.EarlyStopping(monitor='val_loss', patience=10, verbose=0, mode='auto')
model.fit(x_train, y_train, batch_size=1024, epochs=200, validation_data=(x_test, y_test), verbose=1, callbacks=[callback_early_stopping])
y_test = model.predict(x_test.values)
As you can see, the sigmoid activation function that you are using in your neural network output (the last layer) range from 0 to 1.
Note that your label (y) is rescaled to -1 to 1.
I suggest you change the y range to 0 to 1 and keep the sigmoid output.
So the sigmoid Ranges from 0 to 1.
Your MinMaxscaler scales data from -1 to 1.
You can fix it by replacing 'sigmoid' in the output layer with 'tanh', as tanh has output ranging from -1 to 1
Both the other answers can be used to address the fact that your network ouput is not in the same range as your y vector values. Either adjust your final layer to a tanh activation, or change the y-vector range to [0,1].
However, your network loss function and metric is defined for classification purposes, where as you are attempting regression (continuous values between [-1, 1]). The most common loss function and accuracy metric to use is the mean sqaured error, or mean absolute errtr. So I suggest you change the following:
model.compile(loss='mse', optimizer='rmsprop', metrics=['mse, 'mae'])

Keras model.predict always predicts 1

I'm working on some Artificial Intelligence project and I want to predict the bitcoin trend but while using the model.predict function from Keras with my test_set, the prediction is always equal to 1 and the line in my diagram is therefor always straight.
import csv
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from cryptory import Cryptory
from keras.models import Sequential, Model, InputLayer
from keras.layers import LSTM, Dropout, Dense
from sklearn.preprocessing import MinMaxScaler
def format_to_3d(df_to_reshape):
reshaped_df = np.array(df_to_reshape)
return np.reshape(reshaped_df, (reshaped_df.shape[0], 1, reshaped_df.shape[1]))
crypto_data = Cryptory(from_date = "2014-01-01")
bitcoin_data = crypto_data.extract_coinmarketcap("bitcoin")
sc = MinMaxScaler()
for col in bitcoin_data.columns:
if col != "open":
del bitcoin_data[col]
training_set = bitcoin_data;
training_set = sc.fit_transform(training_set)
# Split the data into train, validate and test
train_data = training_set[365:]
# Split the data into x and y
x_train, y_train = train_data[:len(train_data)-1], train_data[1:]
model = Sequential()
model.add(LSTM(units=4, input_shape=(None, 1))) # 128 -- neurons**?
# model.add(Dropout(0.2))
model.add(Dense(units=1, activation="softmax")) # activation function could be different
model.compile(optimizer="adam", loss="mean_squared_error") # mse could be used for loss, look into optimiser
model.fit(format_to_3d(x_train), y_train, batch_size=32, epochs=15)
test_set = bitcoin_data
test_set = sc.transform(test_set)
test_data = test_set[:364]
input = test_data
input = sc.inverse_transform(input)
input = np.reshape(input, (364, 1, 1))
predicted_result = model.predict(input)
print(predicted_result)
real_value = sc.inverse_transform(input)
plt.plot(real_value, color='pink', label='Real Price')
plt.plot(predicted_result, color='blue', label='Predicted Price')
plt.title('Bitcoin Prediction')
plt.xlabel('Time')
plt.ylabel('Prices')
plt.legend()
plt.show()
The training set performance looks like this:
1566/1566 [==============================] - 3s 2ms/step - loss: 0.8572
Epoch 2/15
1566/1566 [==============================] - 1s 406us/step - loss: 0.8572
Epoch 3/15
1566/1566 [==============================] - 1s 388us/step - loss: 0.8572
Epoch 4/15
1566/1566 [==============================] - 1s 388us/step - loss: 0.8572
Epoch 5/15
1566/1566 [==============================] - 1s 389us/step - loss: 0.8572
Epoch 6/15
1566/1566 [==============================] - 1s 392us/step - loss: 0.8572
Epoch 7/15
1566/1566 [==============================] - 1s 408us/step - loss: 0.8572
Epoch 8/15
1566/1566 [==============================] - 1s 459us/step - loss: 0.8572
Epoch 9/15
1566/1566 [==============================] - 1s 400us/step - loss: 0.8572
Epoch 10/15
1566/1566 [==============================] - 1s 410us/step - loss: 0.8572
Epoch 11/15
1566/1566 [==============================] - 1s 395us/step - loss: 0.8572
Epoch 12/15
1566/1566 [==============================] - 1s 386us/step - loss: 0.8572
Epoch 13/15
1566/1566 [==============================] - 1s 385us/step - loss: 0.8572
Epoch 14/15
1566/1566 [==============================] - 1s 393us/step - loss: 0.8572
Epoch 15/15
1566/1566 [==============================] - 1s 397us/step - loss: 0.8572
I'm supposed to print a plot with the Real Price and the Predicted Price, the Real Price is displayed properly but the Predicted price is only a straight line because of that model.predict that only contains the value 1.
Thanks in advance!
You're trying to predict a price value, that is, you're aiming at solving a regression problem and not a classification problem.
However, in your last layer of the network (model.add(Dense(units=1, activation="softmax"))), you have a single neuron (which would be adequate for a regression problem), but you've chosen to use a softmax activation function. The softmax function is used in multi-class classification problems, to normalize the outputs into a probability distribution. If you have a single output neuron and you apply softmax, the final result will always 1.0, as it is the only parameter of the probability distribution.
In summary, for regression problems you do not use an activation function, as the network is intended to already output the predicted value.

Keras network fit: loss is 'nan', accuracy doesn't change

I try to fit keras network, but in each epoch loss is 'nan' and accuracy doesn't change... I tried to change epoch, layers count, neurons count, learning rate, optimizers, I checked nan data in datasets, normalize data by different ways, but problem was not solved. Thanks for your help.
np.random.seed(1337)
# example of input vector: [-1.459746, 0.2694708, ... 0.90043]
# example of output vector: [1, 0] or [0, 1]
model = Sequential()
model.add(Dense(1000, activation='tanh', init='normal', input_dim=503))
model.add(Dense(2, init='normal', activation='softmax'))
opt = optimizers.sgd(lr=0.01)
model.compile(loss="categorical_crossentropy", optimizer=opt, metrics=['accuracy'])
print(model.summary())
model.fit(x_train, y_train, batch_size=1000, nb_epoch=100, verbose=1)
99804/99804 [==============================] - 5s 52us/step - loss: nan - acc: 0.4938
Epoch 1/100
99804/99804 [==============================] - 5s 49us/step - loss: nan - acc: 0.4938
Epoch 2/100
99804/99804 [==============================] - 5s 51us/step - loss: nan - acc: 0.4938
Epoch 3/100
99804/99804 [==============================] - 5s 52us/step - loss: nan - acc: 0.4938
Epoch 4/100
99804/99804 [==============================] - 5s 52us/step - loss: nan - acc: 0.4938
Epoch 5/100
99804/99804 [==============================] - 5s 51us/step - loss: nan - acc: 0.4938
...
Oh, problem has been found! After normalization, one nan neuron appeared in the input vector
First convert your output to categorical, as described in Keras documentation:
Note: when using the categorical_crossentropy loss, your targets should be in categorical format. In order to convert integer targets into categorical targets, you can use the Keras utility to_categorical:
from keras.utils import to_categorical
categorical_labels = to_categorical(int_labels, num_classes=None)

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