How to deal with large layers in Keras - python

I'm trying to create a deep learning model with Keras, but when I'm trying make the model, keras uses too much memory.
I'm trying to make a model with a large amount of inputs (24,000) and it seems too much for my computer.
Here is my simple code:
N=20
M=5
n = 24310
nbclass = 4
X_train = np.random.rand(N,n)
X_test = np.random.rand(M,n)
Y_train = np_utils.to_categorical(np.random.randint(nbclass, size=N), nbclass)
Y_test = np_utils.to_categorical(np.random.randint(nbclass, size=M), nbclass)
model.add(Dense(n, input_dim=n, activation="relu", kernel_initializer="uniform"))
model.add(Dropout(0.25))
model.add(Dense(n//2, activation="relu", kernel_initializer="uniform"))
model.add(Dropout(0.25))
model.add(Dense(nbclass,activation="softmax", kernel_initializer="uniform"))
# Compiling the model
model.compile(loss='binary_crossentropy',
optimizer='adam', metrics=['accuracy'])
# Fitting the model
model.fit(X_train, Y_train, validation_data=(X_test, Y_test),epochs=100, batch_size=5,callbacks=[PlotLosses()])
My issue here is, when the fit is done, it consumes all my memory (20 Go), then it starting to swap and I cannot go further.
Somebody knows how can I modify the model to make it less memory consuming?

Related

How to train an unlabled data in machine learning?

I have the data of almost 9000 entities, I want to train my model and detect anomalies from data.
I tried few of things to did my work, and one thing I done is
def create_sequences(values, time_steps=TIME_STEPS):
output = []
for i in range(len(values) - time_steps):
output.append(values[i : (i + time_steps)])
return np.stack(output)
here I start splitting my training data
x_train = create_sequences(data['HR'].values)
x_train = np.expand_dims(x_train,axis=2)
x_train = create_sequences(data['PULSE'].values)
x_train = np.expand_dims(x_train,axis=2)
x_train = create_sequences(data['SpO2'].values)
x_train = np.expand_dims(x_train,axis=2)
x_train = create_sequences(data['ABPDias'].values)
x_train = np.expand_dims(x_train,axis=2)
x_train = create_sequences(data['ABPMean'].values)
x_train = np.expand_dims(x_train,axis=2)
x_train = create_sequences(data['RESP'].values)
x_train = np.expand_dims(x_train,axis=2)
and here is my model for training
model = Sequential()
model.add(Conv1D(filters=32, kernel_size=7, padding="same", strides=2, input_shape=(x_train.shape[1],x_train.shape[2])))
model.add(MaxPooling1D(pool_size=1,padding="valid"))
model.add(Dropout(0.2))
model.add(Conv1D(filters=16, kernel_size=7, padding="same", strides=2))
model.add(LSTM(units=20, return_sequences=True))
model.add(Dropout(0.2))
model.add(Conv1DTranspose(filters=16, kernel_size=7, padding="same",strides=2))
model.add(Conv1D(filters=32, kernel_size=7, padding="same"))
model.add(MaxPooling1D(pool_size=2,padding="valid"))
model.add(Conv1DTranspose(filters=32, kernel_size=7, padding="same",strides=4,activation="relu"))
model.add(Conv1DTranspose(filters=1, kernel_size=7, padding="same"))
model.compile(optimizer="adam", loss="mse")
model.summary()
history = model.fit(
x_train,
x_train,
epochs=150,
batch_size=128,
validation_split=0.1
)
But this took a lot of time. What I am missing?, Can anyone guide me?
And one thing more is, should I use train_test_split for unlabeled data?
You cannot make supervised learning without labeled data. It is not preferable to use features both as an input and label. What you are looking for is clustering-based anomaly detection, which falls under the category of unsupervised learning. DBSCAN might be a good choice for this task, which is available in scikit-learn.
You use some layer to encode and then decode the data. The technique you applied is supervised machine learning(ML). Since your dataset is unlabeled, you need to employ unsupervised ML approaches.
Clustering is a technique for finding patterns in unlabelled data with many dimensions.
There are two different approaches to clustering-based anomaly detection.
1- Unsupervised clustering where the anomaly detection model is trained using unlabelled data that consists of both normal as well as attack traffics.
2- Semi-supervised clustering where the model is trained using normal data only to build a profile of normal activity.

Why am I getting horizontal line (almost zero) from neural network instead of the desired curve?

I am trying to use neural network for my regression problem in python but the output of the neural network is a straight horizontal line which is zero. I have one input and obviously one output.
Here is my code:
def baseline_model():
# create model
model = Sequential()
model.add(Dense(1, input_dim=1, kernel_initializer='normal', activation='relu'))
model.add(Dense(4, kernel_initializer='normal', activation='relu'))
model.add(Dense(1, kernel_initializer='normal'))
# Compile model
model.compile(loss='mean_squared_error',metrics=['mse'], optimizer='adam')
model.summary()
return model
# evaluate model
estimator = KerasRegressor(build_fn=baseline_model, epochs=50, batch_size=64,validation_split = 0.2, verbose=1)
kfold = KFold(n_splits=10)
results = cross_val_score(estimator, X_train, y_train, cv=kfold)
Here are the plots of NN prediction vs. target for both training and test data.
Training Data
Test Data
I have also tried different weight initializers (Xavier and He) with no luck!
I really appreciate your help
First of all correct your syntax while adding dense layers in model remove the double equal == with single equal = with kernal_initilizer like below
model.add(Dense(1, input_dim=1, kernel_initializer ='normal', activation='relu'))
Then to make the performance better do the followong
Increase the number of hidden neurons in the hidden layers
Increase the number of hidden layers.
If still you have same problem then try to change the optimizer and activation function. Tuning the hyperparameters may help you in converging to the solution
EDIT 1
You also have to fit the estimator after cross validation like below
estimator.fit(X_train, y_train)
and then you can test on the test data as follow
prediction = estimator.predict(X_test)
from sklearn.metrics import accuracy_score
accuracy_score(Y_test, prediction)

Overfitting in LSTM even after using regularizers

I am having a time series prediction problem and building an LSTM like below :
def create_model():
model = Sequential()
model.add(LSTM(50,kernel_regularizer=l2(0.01), recurrent_regularizer=l2(0.01), bias_regularizer=l2(0.01), input_shape=(train_X.shape[1], train_X.shape[2])))
model.add(Dropout(0.591))
model.add(Dense(1))
model.compile(loss='mean_squared_error', optimizer='adam')
return model
When I train the model on 5 splits like below :
tss = TimeSeriesSplit(n_splits = 5)
X = data.drop(labels=['target_prediction'], axis=1)
y = data['target_prediction']
for train_index, test_index in tss.split(X):
train_X, test_X = X.iloc[train_index, :].values, X.iloc[test_index,:].values
train_y, test_y = y.iloc[train_index].values, y.iloc[test_index].values
model=create_model()
history = model.fit(train_X, train_y, epochs=10, batch_size=64,validation_data=(test_X, test_y), verbose=0, shuffle=False)
I get an overfitting problem. The graph of loss is attached
I am not sure why there is overfitting when I use regularizers in my Keras model. Any help is appreciated .
EDIT:
Tried the architectures
def create_model():
model = Sequential()
model.add(LSTM(20, input_shape=(train_X.shape[1], train_X.shape[2])))
model.add(Dense(1))
model.compile(loss='mean_squared_error', optimizer='adam')
return model
def create_model(x,y):
# define LSTM
model = Sequential()
model.add(Bidirectional(LSTM(20, return_sequences=True), input_shape=(x,y)))
model.add(TimeDistributed(Dense(1, activation='sigmoid')))
model.compile(loss='mean_squared_error', optimizer='adam')
return model
but still it is overfitting.
First of all remove all your regularizers and dropout. You are literally spamming with all the tricks out there and 0.5 dropout is too high.
Reduce the number of units in your LSTM. Start from there. Reach a point where your model stops overfitting.
Then, add dropout if required.
After that, the next step is to add the tf.keras.Bidirectional. If still, you are not satfisfied then, increase number of layers. Remember to keep return_sequences True for every LSTM layer except the last one.
It is seldom I come across networks using layer regularization despite the availability because dropout and layer regularization have a same effect and people usually go with dropout (at maximum, I have seen 0.3 being used).

python - returning nan when trying to predict with Keras

For a school project, I'm trying to predict data using the keras framework, but it's returning 'nan' loss and values when I try to get predicted data.
Source code :
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, random_state=5)
# create model
model = Sequential()
model.add(Dense(950, input_shape=(425,), activation='relu'))
model.add(Dense(425, activation='relu'))
model.add(Dense(200, activation='relu'))
model.add(Dense(50, activation='relu'))
model.add(Dense(1, activation='sigmoid'))
# Compile model
sgd = optimizers.SGD(lr=0.1, decay=1e-6, momentum=0.9, nesterov=True)
model.compile(loss='mean_squared_error', optimizer='sgd')
# Fit the model
model.fit(X_train, y_train, epochs=20, batch_size=1, verbose=1)
#evaluate the model
y_pred = model.predict(X_test)
score = model.evaluate(X_test, y_test,verbose=1)
print(score)
# calculate predictions
predictions = model.predict(X_pred)
Data :
X_train and X_test are (panda)dataframes of 5000 rows(nber of samples) * 425 columns (number of dimensions).
y_train and y_test look like :
array([ 1.17899644, 1.46080518, 0.9662137 , ..., 2.40157461,
0.53870386, 1.3192718 ])
Can you help me with that ?
Thank you for you help!
Usually, this means that something converges to infinity. As #desertnaut pointed out in the comment, reducing the learning rate might help.
But the root of the issue is your input data. What do these 425 data points mean? Are they from different sources, different features, different parameters? Finding outliners or normalizing the data, could help.
Your code looks fine otherwise.
Make sure your target output is in range (0, 1) as you have sigmoid in the last layer.
sigmoid has an output between zero and one so if the target output is not in this range then (a) change the activation function or (b) normalize outputs in the required range.
Make sure the purpose of this model is the regression.
After considering the above three points, play around with learning rate (decrease) and the optimiser (replace with any other).
Try changing your optimizer to 'Adam' instead of SGD
You initialized your SGD optimizer in variable sgd but you're not using it in compile

Don't know whats going wrong while training dataset. Keras Model Fit

I have just started using Keras and was trying to train a model using Keras deep learning kit. Works till the epochs are runned but crashes just after it.
np.random.seed(1778) # for reproducibility
need_normalise=True
need_validataion=True
nb_epoch=2#8
#Creating model
model = Sequential()
model.add(Dense(512, input_shape=(dims,)))
model.add(PReLU())
model.add(BatchNormalization())
model.add(Dropout(0.5))
model.add(Dense(nb_classes))
model.add(Activation('softmax'))
opt=Adadelta(lr=1,decay=0.995,epsilon=1e-5)
model.compile(loss='binary_crossentropy', optimizer=opt)
auc_scores=[]
best_score=-1
best_model=None
print('Training model...')
if need_validataion:
for i in range(nb_epoch):
#early_stopping=EarlyStopping(monitor='val_loss', patience=0, verbose=1)
#model.fit(X_train, y_train, nb_epoch=nb_epoch,batch_size=256,validation_split=0.01,callbacks=[early_stopping])
model.fit(X_train, y_train, nb_epoch=2,batch_size=256,validation_split=0.15)
y_pre = model.predict_proba(X_valid)
scores = roc_auc_score(y_valid,y_pre)
auc_scores.append(scores)
print (i,scores)
if scores>best_score:
best_score=scores
best_model=model
plt.plot(auc_scores)
plt.show()
else:
model.fit(X_train, y_train, nb_epoch=nb_epoch, batch_size=256)
y_pre = model.predict_proba(X_test)[:,1]
print roc_auc_score(y_test,y_pre)
Error Recieved:
I have pasted it over here. Please have a look at it.
http://pastebin.com/dSw9ckkk
It looks like you have two classes, a positive class and a negative class, so that the positive class labels are 1 minus the negative class labels. In that case, you can discard the negative class labels and make it a single-class problem:
model.add(Dense(1), activation='sigmoid') # instead of Dense(nb_classes) and Activation('softmax')
Alternatively, you can still train the model on both classes and just use the positive class in the AUC calculation:
roc_auc_score(y_test[:, 1],y_pre[:, 1])

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