Conv nets accuracy not changing while loss decreases - machine-learning

I'm training several CNNs to do image classification in TensorFlow. The training losses decrease normally. However the test accuracy never changed throughout the whole training procedure, plus the accuracy is very low (0.014) where the accuracy for randomly guessing would be 0.003 (There are around 300 classes). One thing I've noticed is that only those models that I applied batch norm to showed such a weird behavior. What can possibly be wrong to cause this issue? The training set has 80000 samples, in case you might figure this was caused by overfitting. Below is part of the code for evaluation:
Accuracy function:
correct_prediction = tf.equal(tf.argmax(Model(test_image), 1), tf.argmax(test_image_label, 0))
accuracy = tf.cast(correct_prediction, tf.float32)
the test_image is a batch with only one sample in it while the test_image_label is a scalar.
Session:
with tf.Session() as sess:
sess.run(tf.local_variables_initializer())
sess.run(tf.global_variables_initializer())
saver = tf.train.Saver()
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord, start=True)
print('variables initialized')
step = 0
for epoch in range(epochs):
sess.run(enqueue_train)
print('epoch: %d' %epoch)
if epoch % 5 == 0:
save_path = saver.save(sess, savedir + "/Model")
for batch in range(num_batch):
if step % 400 == 0:
summary_str = cost_summary.eval(feed_dict={phase: True})
file_writer.add_summary(summary_str, step)
else:
sess.run(train_step, feed_dict={phase: True})
step += 1
sess.run(train_close)
sess.run(enqueue_test)
accuracy_vector = []
for num in range(len(testnames)):
accuracy_vector.append(sess.run(accuracy, feed_dict={phase: False}))
mean_accuracy = sess.run(tf.divide(tf.add_n(accuracy_vector), len(testnames)))
print("test accuracy %g"%mean_accuracy)
sess.run(test_close)
save_path = saver.save(sess, savedir + "/Model_final")
coord.request_stop()
coord.join(threads)
file_writer.close()
The phase above is to indicate if it is training or testing for the batch norm layer.
Note that I tried to calculate the accuracy with the training set, which led to the minimal loss. However it gives the same poor accuracy. Please help me, I really appreciate it!

Related

LSTM regression model flat prediction

This is a time series regression problem for the battery capacity as output and a single input variable as voltage; the relation is non-linear.
LSTM Model prediction of the test data always returns a semi-flat line, probably the mean of the output variable in the training data.
This is an example of predicted vs test set output values, with the following model parameters:
(Window size: 10, batch site: 256, LSTM nodes: 16)
Prediction of the test data
Data had been normalized, down-sampled to 1 sec and later to 3 sec, original sampling was 10 Hz.
I was suspecting the voltage fluctuation is the problem, but sampling at 3 seconds hadn't resulted into noticeable improvement.
Here are the data after being down-sampled to 3 seconds:
Normalized Training Data ; Y:SOC, X: Voltage
Normalized Test Data ; Y:SOC, X: Voltage
I've tried many changes in the model and learning parameters as follows, but still the behavior is the same.
That's why i think it's not a parameter tuning issue, rather the model is not learning at all.
LSTM layer: always single, followed by Dense with no options.
LSTM nodes: [4,8,16,32]
Epoch: : [16,32,64,128]
window size (input vector depth): [8,32,64,128]
Batch size: [32,64,128,256]
learning rate: [.0005,.0001,.001]
optimizer : ADAM, options:[ none, clipnorm=1, clipvalue=0.5]
Model specification Code:
backend.clear_session()
model1 = Sequential()
model1.add(LSTM(16,input_shape=(win_sz, features_cnt) )) # stateless
model1.add(layers.Dense(1))
model1.summary()
Model training and validation Code:
n_epochs = 12
iterations = tr_samples_sh_cnt // batch_sz_tr
loss = tf.keras.losses.MeanAbsoluteError()
optimizer = tf.optimizers.Adam(learning_rate = 0.001)
loss_history = []
#tf.function
def train_model_on_batch():
start = epoch * batch_sz_tr
X_batch = df_feat_tr_3D[start:start+batch_sz_tr, :, :]
y_batch = df_SOC_tr_2D[start:start+batch_sz_tr, :]
with tf.GradientTape() as tape:
current_loss = loss(model1(X_batch), y_batch)
gradients = tape.gradient(current_loss, model1.trainable_variables)
optimizer.apply_gradients(zip(gradients, model1.trainable_variables))
return current_loss
for epoch in range(n_epochs+1):
for iteration in range(iterations):
current_loss = train_model_on_batch()
if epoch % 1 == 0:
loss_history.append(current_loss.numpy())
print("{}. \t\tLoss: {}".format(
epoch, loss_history[-1]))
print('\nTraining complete.')
P_test = model1.predict(df_feat_test_3D)
After adding sigmoid activation function in both LSTM and Dense layers, a very small change observed, but far from reasonable fit.
Prediction of the test data after adding activation function
The problem was the activation function as #Dr. Snoopy recommended

is binary cross entropy an additive function?

I am trying to train a machine learning model where the loss function is binary cross entropy, because of gpu limitations i can only do batch size of 4 and i'm having lot of spikes in the loss graph. So I'm thinking to back-propagate after some predefined batch size(>4). So it's like i'll do 10 iterations of batch size 4 store the losses, after 10th iteration add the losses and back-propagate. will it be similar to batch size of 40.
TL;DR
f(a+b) = f(a)+f(b) is it true for binary cross entropy?
f(a+b) = f(a) + f(b) doesn't seem to be what you're after. This would imply that BCELoss is additive which it clearly isn't. I think what you really care about is if for some index i
# false
f(x, y) == f(x[:i], y[:i]) + f([i:], y[i:])
is true?
The short answer is no, because you're missing some scale factors. What you probably want is the following identity
# true
f(x, y) == (i / b) * f(x[:i], y[:i]) + (1.0 - i / b) * f(x[i:], y[i:])
where b is the total batch size.
This identity is used as motivation for the gradient accumulation method (see below). Also, this identity applies to any objective function which returns an average loss across each batch element, not just BCE.
Caveat/Pitfall: Keep in mind that batch norm will not behave exactly the same when using this approach since it updates its internal statistics based on batch size during the forward pass.
We can actually do a little better memory-wise than just computing the loss as a sum followed by backpropagation. Instead we can compute the gradient of each component in the equivalent sum individually and allow the gradients to accumulate. To better explain I'll give some examples of equivalent operations
Consider the following model
import torch
import torch.nn as nn
import torch.nn.functional as F
class MyModel(nn.Module):
def __init__(self):
super().__init__()
num_outputs = 5
# assume input shape is 10x10
self.conv_layer = nn.Conv2d(3, 10, 3, 1, 1)
self.fc_layer = nn.Linear(10*5*5, num_outputs)
def forward(self, x):
x = self.conv_layer(x)
x = F.max_pool2d(x, 2, 2, 0, 1, False, False)
x = F.relu(x)
x = self.fc_layer(x.flatten(start_dim=1))
x = torch.sigmoid(x) # or omit this and use BCEWithLogitsLoss instead of BCELoss
return x
# to ensure same results for this example
torch.manual_seed(0)
model = MyModel()
# the examples will work as long as the objective averages across batch elements
objective = nn.BCELoss()
# doesn't matter what type of optimizer
optimizer = torch.optim.SGD(model.parameters(), lr=0.001)
and lets say our data and targets for a single batch are
torch.manual_seed(1) # to ensure same results for this example
batch_size = 32
input_data = torch.randn((batch_size, 3, 10, 10))
targets = torch.randint(0, 1, (batch_size, 20)).float()
Full batch
The body of our training loop for an entire batch may look something like this
# entire batch
output = model(input_data)
loss = objective(output, targets)
optimizer.zero_grad()
loss.backward()
optimizer.step()
loss_value = loss.item()
print("Loss value: ", loss_value)
print("Model checksum: ", sum([p.sum().item() for p in model.parameters()]))
Weighted sum of loss on sub-batches
We could have computed this using the sum of multiple loss functions using
# This is simpler if the sub-batch size is a factor of batch_size
sub_batch_size = 4
assert (batch_size % sub_batch_size == 0)
# for this to work properly the batch_size must be divisible by sub_batch_size
num_sub_batches = batch_size // sub_batch_size
loss = 0
for sub_batch_idx in range(num_sub_batches):
start_idx = sub_batch_size * sub_batch_idx
end_idx = start_idx + sub_batch_size
sub_input = input_data[start_idx:end_idx]
sub_targets = targets[start_idx:end_idx]
sub_output = model(sub_input)
# add loss component for sub_batch
loss = loss + objective(sub_output, sub_targets) / num_sub_batches
optimizer.zero_grad()
loss.backward()
optimizer.step()
loss_value = loss.item()
print("Loss value: ", loss_value)
print("Model checksum: ", sum([p.sum().item() for p in model.parameters()]))
Gradient accumulation
The problem with the previous approach is that in order to apply back-propagation, pytorch needs to store intermediate results of layers in memory for every sub-batch. This ends up requiring a relatively large amount of memory and you may still run into memory consumption issues.
To alleviate this problem, instead of computing a single loss and performing back-propagation once, we could perform gradient accumulation. This gives equivalent results of the previous version. The difference here is that we instead perform a backward pass on each component of
the loss, only stepping the optimizer once all of them have been backpropagated. This way the computation graph is cleared after each sub-batch which will help with memory usage. Note that this works because .backward() actually accumulates (adds) the newly computed gradients to the existing .grad member of each model parameter. This is why optimizer.zero_grad() must be called only once, before the loop, and not during or after.
# This is simpler if the sub-batch size is a factor of batch_size
sub_batch_size = 4
assert (batch_size % sub_batch_size == 0)
# for this to work properly the batch_size must be divisible by sub_batch_size
num_sub_batches = batch_size // sub_batch_size
# Important! zero the gradients before the loop
optimizer.zero_grad()
loss_value = 0.0
for sub_batch_idx in range(num_sub_batches):
start_idx = sub_batch_size * sub_batch_idx
end_idx = start_idx + sub_batch_size
sub_input = input_data[start_idx:end_idx]
sub_targets = targets[start_idx:end_idx]
sub_output = model(sub_input)
# compute loss component for sub_batch
sub_loss = objective(sub_output, sub_targets) / num_sub_batches
# accumulate gradients
sub_loss.backward()
loss_value += sub_loss.item()
optimizer.step()
print("Loss value: ", loss_value)
print("Model checksum: ", sum([p.sum().item() for p in model.parameters()]))
I think 10 iterations of batch size 4 is same as one iteration of batch size 40, only here the time taken will be more. Across different training examples losses are added before backprop. But that doesn't make the function linear. BCELoss has a log component, and hence it is not a linear function. However what you said is correct. It will be similar to batch size 40.

Dropout Tensorflow: Weight scaling at test time

Do I need to scale weights at test time in tensorflow i.e weights*keep_prob at testing or tensorflow does it itself? if so then how?
At training my keep_prob is 0.5. and at test time its 1.
Although network is regularized but accuracy is not good as before regularization.
P.S i'm classifying CIFAR10
n_nodes_h1=1000
n_nodes_h2=1000
n_nodes_h3=400
n_nodes_h4=100
classes=10
x=tf.placeholder('float',[None,3073])
y=tf.placeholder('float')
keep_prob=tf.placeholder('tf.float32')
batch_size=100
def neural_net(data):
hidden_layer1= {'weight':tf.Variable(tf.random_normal([3073,n_nodes_h1])),
'biases':tf.Variable(tf.random_normal([n_nodes_h1]))}
hidden_layer2={'weight':tf.Variable(tf.random_normal([n_nodes_h1,n_nodes_h2])),
'biases':tf.Variable(tf.random_normal([n_nodes_h2]))}
out_layer={'weight':tf.Variable(tf.random_normal([n_nodes_h2,classes])),
'biases':tf.Variable(tf.random_normal([classes]))}
l1= tf.add(tf.matmul(data,hidden_layer1['weight']), hidden_layer1['biases'])
l1=tf.nn.relu(l1)
#************DROPOUT*******************
l1=tf.nn.dropout(l1,keep_prob)
l2= tf.add(tf.matmul(l1,hidden_layer2['weight']), hidden_layer2['biases'])
l2=tf.nn.relu(l2)
out= tf.matmul(l2,out_layer['weight'])+ out_layer['biases']
return out
This was network
iterations=20
Train_loss=[]
Test_loss=[]
def train_nn(x):
prediction=neural_net(x)
cost=tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=prediction,labels=y))
optimizer=tf.train.AdamOptimizer().minimize(cost)
epochs=iterations
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
for epoch in range (epochs):
e_loss=0
i=0
for _ in range(int(X_train.shape[0]/batch_size)):
e_x=X_train[i:i+batch_size]
e_y=y_hot_train[i:i+batch_size]
i+=batch_size
_,c=sess.run([optimizer,cost],feed_dict={x:e_x,y:e_y, keep_prob:0.5})
e_loss+=c
print "Epoch: ",epoch," Train loss= ",e_loss
Train_loss.append(e_loss)
correct=tf.equal(tf.argmax(prediction,1),tf.argmax(y,1))
accuracy=tf.reduce_mean(tf.cast(correct,'float'))
print "Accuracy on test: " ,accuracy.eval({x:X_test,y:y_hot_test , keep_prob:1.})
print "Accuracy on train:" ,accuracy.eval({x:X_train[0:2600],y:y_hot_train[0:2600], keep_prob=1.})
train_nn(x)
Do I need something like
hidden_layer1['weight']*=keep_prob
#testing time
Tensorflow does it itself:
With probability keep_prob, outputs the input element scaled up by 1 /
keep_prob, otherwise outputs 0. The scaling is so that the expected
sum is unchanged.
(from this page)

Tensorflow: loss becomes 'NaN'

I was doing CIFAR-10 training on CPU with Tensorflow. During the first few rounds, the loss seemed alright. But after the step 10210 the loss varies and ends up becoming NaN.
My network model the CIFAR-10 CNN model from their website. Here is my setting,
image_size = 32
num_channels = 3
num_classes = 10
num_batches_to_run = 50000
batch_size = 128
eval_batch_size = 64
initial_learning_rate = 0.1
learning_rate_decay_factor = 0.1
num_epochs_per_decay = 350.0
moving_average_decay = 0.9999
and the result is shown as below.
2017-05-12 21:53:05.125242: step 10210, loss = 4.99 (124.9 examples/sec; 1.025 sec/batch)
2017-05-12 21:53:13.960001: step 10220, loss = 7.55 (139.5 examples/sec; 0.918 sec/batch)
2017-05-12 21:53:23.491228: step 10230, loss = 6.63 (149.5 examples/sec; 0.856 sec/batch)
2017-05-12 21:53:33.355805: step 10240, loss = 8.08 (113.3 examples/sec; 1.129 sec/batch)
2017-05-12 21:53:43.007007: step 10250, loss = 7.18 (126.7 examples/sec; 1.010 sec/batch)
2017-05-12 21:53:52.650118: step 10260, loss = 16.61 (138.0 examples/sec; 0.928 sec/batch)
2017-05-12 21:54:02.537279: step 10270, loss = 9.60 (137.6 examples/sec; 0.930 sec/batch)
2017-05-12 21:54:12.390117: step 10280, loss = 46526.25 (145.5 examples/sec; 0.880 sec/batch)
2017-05-12 21:54:22.060741: step 10290, loss = 133479743509972411931057146822656.00 (130.4 examples/sec; 0.982 sec/batch)
2017-05-12 21:54:31.691058: step 10300, loss = nan (115.8 examples/sec; 1.105 sec/batch)
Any idea about the NaN loss?
This happens a lot in practice when your learning rate is too high, I tend to start at 0.001 and move from there, 0.1 is on the very high side on most datasets, especially if you aren't dividing your loss by your batch size.
You can clip the gradients, if you are using Keras with Tensorflow backend, you could do as follows,
The parameters clipnorm and clipvalue can be used with all optimizers to control gradient clipping:
from keras import optimizers
# All parameter gradients will be clipped to
# a maximum norm of 1.
sgd = optimizers.SGD(lr=0.01, clipnorm=1.)
or
from keras import optimizers
# All parameter gradients will be clipped to
# a maximum value of 0.5 and
# a minimum value of -0.5.
sgd = optimizers.SGD(lr=0.01, clipvalue=0.5)
You might have the cross entropy loss and take log(0). Just add a small constant within the log.
(you might also want to look into gradient clipping)

How to use a fixed validation set (not K-fold cross validation) in Scikit-learn for a decision tree classifier/random forest classifier?

I am new to machine learning and data science. Sorry, if it is a very stupid question.
I see there is an inbuilt function for cross-validation but not for a fixed validation set. I have a dataset with 50,000 samples labeled with years from 1990 to 2010. I need to train different classifiers on 1990-2008 samples, then validate on 2009 samples, and test on 2010 samples.
EDIT:
After #Quan Tran's answer, I tried this. This is how it should be?
# Fit a decision tree
estimator1 = DecisionTreeClassifier( max_depth = 9, max_leaf_nodes=9)
estimator1.fit(X_train, y_train)
print estimator1
# validate using validation set
acc = np.zeros((20,20)) # store accuracy
for i in range(20):
for j in range(20):
estimator1 = DecisionTreeClassifier(max_depth = i+1, max_leaf_nodes=j+2)
estimator1.fit(X_valid, y_valid)
y_pred = estimator1.predict(X_valid)
acc[i,j] = accuracy_score(y_valid, y_pred)
best_mod = np.where(acc == acc.max())
print best_mod
print acc[best_mod]
# Predict target values
estimator1 = DecisionTreeClassifier(max_depth = int(best_mod[0]) + 1, max_leaf_nodes= int(best_mod[1]) + 2)
estimator1.fit(X_valid, y_valid)
y_pred = estimator1.predict(X_test)
confusion = metrics.confusion_matrix(y_test, y_pred)
TP = confusion[1, 1]
TN = confusion[0, 0]
FP = confusion[0, 1]
FN = confusion[1, 0]
# Classification Accuracy
print "======= ACCURACY ========"
print((TP + TN) / float(TP + TN + FP + FN))
print accuracy_score(y_valid, y_pred)
# store the predicted probabilities for class
y_pred_prob = estimator1.predict_proba(X_test)[:, 1]
# plot a ROC curve for y_test and y_pred_prob
fpr, tpr, thresholds = metrics.roc_curve(y_test, y_pred_prob)
plt.plot(fpr, tpr)
plt.xlim([0.0, 1.0])
plt.ylim([0.0, 1.0])
plt.title('ROC curve for DecisionTreeClassifier')
plt.xlabel('False Positive Rate (1 - Specificity)')
plt.ylabel('True Positive Rate (Sensitivity)')
plt.grid(True)
print("======= AUC ========")
print(metrics.roc_auc_score(y_test, y_pred_prob))
I get this answer, which is not the best accuracy.
DecisionTreeClassifier(class_weight=None, criterion='gini', max_depth=9,
max_features=None, max_leaf_nodes=9, min_samples_leaf=1,
min_samples_split=2, min_weight_fraction_leaf=0.0,
presort=False, random_state=None, splitter='best')
(array([5]), array([19]))
[ 0.8489011]
======= ACCURACY ========
0.574175824176
0.538461538462
======= AUC ========
0.547632099893
In this case, there are three separate sets. The train set, the test set and the validation set.
The train set is used to fit the parameters of the classifier. For example:
clf = DecisionTreeClassifier(max_depth=2)
clf.fit(trainfeatures, labels)
The validation set is used to tune the hyper parameters of the classifier or find the cutoff point for the training procedure. For example, in the case of Decision tree, max_depth is a hyper parameter. You will need to find a good set of hyper parameters by experimenting with different values of hyper parameters (tuning) and compare the performance measures (accuracy/precision,..) on the validation set.
The test set is used to estimate the error rate on unseen data. After having the performance measures on the test set, the model must not be trained/tuned any further.

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