Tensor Size Miss match on loss function - numpy

1:
when attempting to perfrom a pytorch training sequence using batch sizes, my loss function appears to error when the nn output and a batch are put through a MSEloss function.
2:
have tried to search about nn padding, however this is not a covnet but rather an autoencoder, similar stack over flow issues have not yielded results.
3:
the NN:
class Net(nn.Module):
def __init__(self, input_dim=10):
super().__init__()
self.fc1 = nn.Linear(input_dim, int(0.75 * input_dim))
self.fc2 = nn.Linear(int(0.75 * input_dim), int(0.5 * input_dim))
self.fc3 = nn.Linear(int(0.5 * input_dim), int(0.33 * input_dim))
self.fc4 = nn.Linear(int(0.33 * input_dim), int(0.25 * input_dim))
self.fc5 = nn.Linear(int(0.25 * input_dim), int(0.33 * input_dim))
self.fc6 = nn.Linear(int(0.33 * input_dim), int(0.5 * input_dim))
self.fc7 = nn.Linear(int(0.5 * input_dim), int(0.75 * input_dim))
self.fc8 = nn.Linear(int(0.75 * input_dim), input_dim)
def forward(self, x):
x = torch.tanh(self.fc1(x))
x = torch.tanh(self.fc2(x))
x = torch.tanh(self.fc3(x))
x = torch.tanh(self.fc4(x))
x = torch.tanh(self.fc5(x))
x = torch.tanh(self.fc6(x))
x = torch.tanh(self.fc7(x))
x = self.fc8(x)
return torch.softmax(x, dim=1)
the train method:
def train(net, x_train, x_opt, BATCH_SIZE, EPOCHS, input_dim):
outputs = 0
mse = 0
optimizer = optim.SGD(net.parameters(), lr=0.001)
loss_function = nn.MSELoss()
for epoch in range(EPOCHS):
for i in tqdm(range(0, len(x_train), BATCH_SIZE)):
batch_x = x_train[i:i + BATCH_SIZE]
# print("bx", batch_x.size())
batch_y = x_opt[i:i + BATCH_SIZE]
# print("by", batch_y.size())
net.zero_grad()
# batch_x.view(batch_y.shape[0])
outputs = net(batch_x)
# print('out', outputs)
loss = loss_function(outputs, batch_y)
loss.backward()
optimizer.step() # Does the update
print(f"Epoch: {epoch}. Loss: {loss}")
error:
99%|█████████▉| 1452/1466 [00:02<00:00, 718.09it/s]B:\tools and software\Anaconda\envs\pysyft-pytorch\lib\site-packages\torch\nn\modules\loss.py:431: UserWarning: Using a target size (torch.Size([39, 10])) that is different to the input size (torch.Size([38, 10])). This will likely lead to incorrect results due to broadcasting. Please ensure they have the same size.
return F.mse_loss(input, target, reduction=self.reduction)
100%|█████████▉| 1465/1466 [00:02<00:00, 718.36it/s]
Traceback (most recent call last):
File "<input>", line 1, in <module>
File "B:\tools and software\PyCharm 2020.1\plugins\python\helpers\pydev\_pydev_bundle\pydev_umd.py", line 197, in runfile
pydev_imports.execfile(filename, global_vars, local_vars) # execute the script
File "B:\tools and software\PyCharm 2020.1\plugins\python\helpers\pydev\_pydev_imps\_pydev_execfile.py", line 18, in execfile
exec(compile(contents+"\n", file, 'exec'), glob, loc)
File "B:/projects/openProjects/githubprojects/BotnetTrafficAnalysisFederaedLearning/anomaly-detection/pytorch_conversion.py", line 154, in <module>
input_dim=input_dim)
File "B:/projects/openProjects/githubprojects/BotnetTrafficAnalysisFederaedLearning/anomaly-detection/pytorch_conversion.py", line 64, in train
loss = loss_function(outputs, batch_y)
File "B:\tools and software\Anaconda\envs\pysyft-pytorch\lib\site-packages\torch\nn\modules\module.py", line 532, in __call__
result = self.forward(*input, **kwargs)
File "B:\tools and software\Anaconda\envs\pysyft-pytorch\lib\site-packages\torch\nn\modules\loss.py", line 431, in forward
return F.mse_loss(input, target, reduction=self.reduction)
File "B:\tools and software\Anaconda\envs\pysyft-pytorch\lib\site-packages\torch\nn\functional.py", line 2215, in mse_loss
expanded_input, expanded_target = torch.broadcast_tensors(input, target)
File "B:\tools and software\Anaconda\envs\pysyft-pytorch\lib\site-packages\torch\functional.py", line 52, in broadcast_tensors
return torch._C._VariableFunctions.broadcast_tensors(tensors)
RuntimeError: The size of tensor a (38) must match the size of tensor b (39) at non-singleton dimension 0

The error seems to say that the batch sizes of the target and the output are not the same have you tried printing the size of the target and output. If so what are the results. Also you might want to print the size of the input to the model to see if there is something off there. Sorry for posting this to an answer I can't comment yet.

Related

InvalidArgumentError: Matrix size-incompatible: In[0]: [256,2048], In[1]: [256,1024]

I have been getting this error and i cant figure out the reason. if anyone could help would be great.
this is my code:
import numpy as np
import pickle
import os
import download
#from dataset import one_hot_encoded
#from sklearn.preprocessing import OneHotEncoder
import tensorflow as tf
from random import shuffle
data_path = "D:/Personal details/Internship/"
# Width and height of each image.
img_size = 32
# Number of channels in each image, 3 channels: Red, Green, Blue.
num_channels = 3
# Length of an image when flattened to a 1-dim array.
img_size_flat = img_size * img_size * num_channels
# Number of classes.
num_classes = 10
# Number of files for the training-set.
_num_files_train = 5
# Number of images for each batch-file in the training-set.
_images_per_file = 10000
def _get_file_path(filename=""):
return os.path.join(data_path, "cifar-10-batches-py/", filename)
def _unpickle(filename):
file_path = _get_file_path(filename)
print("Loading data: " + file_path)
with open(file_path, mode='rb') as file:
# In Python 3.X it is important to set the encoding,
# otherwise an exception is raised here.
data = pickle.load(file, encoding='bytes')
return data
def _convert_images(raw):
# Convert the raw images from the data-files to floating-points.
raw_float = np.array(raw, dtype=float) / 255.0
# Reshape the array to 4-dimensions.
images = raw_float.reshape([-1, num_channels, img_size, img_size])
# Reorder the indices of the array.
images = images.transpose([0, 2, 3, 1])
return images
def _load_data(filename):
# Load the pickled data-file.
data = _unpickle(filename)
# Get the raw images.
raw_images = data[b'data']
# Get the class-numbers for each image. Convert to numpy-array.
cls = np.array(data[b'labels'])
# Convert the images.
images = _convert_images(raw_images)
return images, cls
def load_class_names():
# Load the class-names from the pickled file.
raw = _unpickle(filename="batches.meta")[b'label_names']
# Convert from binary strings.
names = [x.decode('utf-8') for x in raw]
return names
def load_training_data():
images = np.zeros(shape=[_num_images_train, img_size, img_size, num_channels], dtype=float)
cls = np.zeros(shape=[_num_images_train], dtype=int)
# Begin-index for the current batch.
begin = 0
# For each data-file.
for i in range(_num_files_train):
# Load the images and class-numbers from the data-file.
images_batch, cls_batch = _load_data(filename="data_batch_" + str(i + 1))
# Number of images in this batch.
num_images = len(images_batch)
# End-index for the current batch.
end = begin + num_images
# Store the images into the array.
images[begin:end, :] = images_batch
# Store the class-numbers into the array.
cls[begin:end] = cls_batch
# The begin-index for the next batch is the current end-index.
begin = end
return images, cls, one_hot_encoded(class_numbers=cls, num_classes=num_classes)
def load_test_data():
images, cls = _load_data(filename="test_batch")
return images, cls, one_hot_encoded(class_numbers=cls, num_classes=num_classes)
########################################################################
def one_hot_encoded(class_numbers, num_classes=None):
if num_classes is None:
num_classes = np.max(class_numbers) + 1
return np.eye(num_classes, dtype=float)[class_numbers]
class_names = load_class_names()
images_train, cls_train, labels_train = load_training_data()
images_test, cls_test, labels_test = load_test_data()
images_train_train = images_train[0:45000]
validation_train = images_train[45000:50000]
labels_train_train = labels_train[0:45000]
validation_labels = labels_train[45000:]
print(len(images_train_train))
print(len(validation_train))
##print(class_names)
##print(len(images_train))
##print(cls_train)
##print(labels_train)
##print(cls_test)
##print(labels_test)
n_classes = len(class_names)
batch_size = 128
x = tf.placeholder(tf.float32, shape=[None, 32, 32, 3], name='x')
y = tf.placeholder(tf.float32, shape=[None, n_classes], name='y_true')
def conv2d(x,W):
return tf.nn.conv2d(x, W, strides=[1,1,1,1], padding='SAME')
def maxpool2d(x):
return tf.nn.max_pool(x, ksize=[1,2,2,1], strides=[1,2,2,1], padding='SAME')
def convolutional_neural_network(x):
weights = {'W_conv1': tf.Variable(tf.random_normal([3,3,3,64])),
'W_conv2': tf.Variable(tf.random_normal([3,3,64,128])),
'W_conv3': tf.Variable(tf.random_normal([3,3,128,256])),
'W_conv4': tf.Variable(tf.random_normal([3,3,256,256])),
'W_fc1': tf.Variable(tf.random_normal([256,1024])),
'W_fc2': tf.Variable(tf.random_normal([1024,1024])),
'soft_max': tf.Variable(tf.random_normal([1024, n_classes]))}
biases = {'b_conv1': tf.Variable(tf.random_normal([64])),
'b_conv2': tf.Variable(tf.random_normal([128])),
'b_conv3': tf.Variable(tf.random_normal([256])),
'b_conv4': tf.Variable(tf.random_normal([256])),
'b_fc1': tf.Variable(tf.random_normal([1024])),
'b_fc2': tf.Variable(tf.random_normal([1024])),
'soft_max': tf.Variable(tf.random_normal([n_classes]))}
conv1 = tf.nn.relu(conv2d(x, weights['W_conv1']) + biases['b_conv1'])
conv1 = maxpool2d(conv1)
conv2 = tf.nn.relu(conv2d(conv1, weights['W_conv2']) + biases['b_conv2'])
conv2 = maxpool2d(conv2)
conv3 = tf.nn.relu(conv2d(conv2, weights['W_conv3']) + biases['b_conv3'])
conv4 = tf.nn.relu(conv2d(conv3, weights['W_conv4']) + biases['b_conv4'])
conv4 = maxpool2d(conv4)
fc1 = tf.reshape(conv4,[256,-1])
fc1 = tf.nn.relu(tf.matmul(fc1, weights['W_fc1']) + biases['b_fc1'])
fc2 = tf.nn.relu(tf.matmul(fc1, weights['W_fc2'] + biases['b_fc2']))
soft_max = tf.matmul(fc2, weights['soft_max']) + biases['soft_max']
return soft_max
def train_neural_network(x):
prediction = convolutional_neural_network(x)
cost = tf.reduce_mean( tf.nn.softmax_cross_entropy_with_logits(logits = prediction,labels = y) )
optimizer = tf.train.AdamOptimizer().minimize(cost)
hm_epochs = 3
with tf.Session() as sess:
sess.run(tf.initialize_all_variables())
for epoch in range(hm_epochs):
epoch_loss = 0
i = 0
while i < len(images_train_train):
start = i
end = i+batch_size
batch_x = np.array(images_train_train[start:end])
batch_y = np.array(labels_train_train[start:end])
_, c = sess.run([optimizer, cost], feed_dict={x: batch_x, y: batch_y})
epoch_loss += c
print('Epoch', epoch, 'completed out of',hm_epochs,'loss:',epoch_loss)
correct = tf.equal(tf.argmax(prediction, 1), tf.argmax(y, 1))
accuracy = tf.reduce_mean(tf.cast(correct, 'float'))
print('Accuracy:',accuracy.eval({x:validation_train, y:validation_labels}))
train_neural_network(x)
Ans this is the error i have been getting.
WARNING:tensorflow:From D:/Personal details/Internship/cifar-10v1.0.py:310: softmax_cross_entropy_with_logits (from tensorflow.python.ops.nn_ops) is deprecated and will be removed in a future version.
Instructions for updating:
Future major versions of TensorFlow will allow gradients to flow
into the labels input on backprop by default.
See #{tf.nn.softmax_cross_entropy_with_logits_v2}.
WARNING:tensorflow:From C:\Python35\lib\site-packages\tensorflow\python\util\tf_should_use.py:118: initialize_all_variables (from tensorflow.python.ops.variables) is deprecated and will be removed after 2017-03-02.
Instructions for updating:
Use `tf.global_variables_initializer` instead.
Traceback (most recent call last):
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1322, in _do_call
return fn(*args)
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1307, in _run_fn
options, feed_dict, fetch_list, target_list, run_metadata)
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1409, in _call_tf_sessionrun
run_metadata)
tensorflow.python.framework.errors_impl.InvalidArgumentError: Matrix size-incompatible: In[0]: [256,2048], In[1]: [256,1024]
[[Node: MatMul = MatMul[T=DT_FLOAT, transpose_a=false, transpose_b=false, _device="/job:localhost/replica:0/task:0/device:CPU:0"](Reshape, Variable_4/read)]]
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:/Personal details/Internship/cifar-10v1.0.py", line 344, in <module>
train_neural_network(x)
File "D:/Personal details/Internship/cifar-10v1.0.py", line 327, in train_neural_network
_, c = sess.run([optimizer, cost], feed_dict={x: batch_x, y: batch_y})
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 900, in run
run_metadata_ptr)
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1135, in _run
feed_dict_tensor, options, run_metadata)
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1316, in _do_run
run_metadata)
File "C:\Python35\lib\site-packages\tensorflow\python\client\session.py", line 1335, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors_impl.InvalidArgumentError: Matrix size-incompatible: In[0]: [256,2048], In[1]: [256,1024]
[[Node: MatMul = MatMul[T=DT_FLOAT, transpose_a=false, transpose_b=false, _device="/job:localhost/replica:0/task:0/device:CPU:0"](Reshape, Variable_4/read)]]
Caused by op 'MatMul', defined at:
File "<string>", line 1, in <module>
File "C:\Python35\lib\idlelib\run.py", line 130, in main
ret = method(*args, **kwargs)
File "C:\Python35\lib\idlelib\run.py", line 357, in runcode
exec(code, self.locals)
File "D:/Personal details/Internship/cifar-10v1.0.py", line 344, in <module>
train_neural_network(x)
File "D:/Personal details/Internship/cifar-10v1.0.py", line 309, in train_neural_network
prediction = convolutional_neural_network(x)
File "D:/Personal details/Internship/cifar-10v1.0.py", line 300, in convolutional_neural_network
fc1 = tf.nn.relu(tf.matmul(fc1, weights['W_fc1']) + biases['b_fc1'])
File "C:\Python35\lib\site-packages\tensorflow\python\ops\math_ops.py", line 2122, in matmul
a, b, transpose_a=transpose_a, transpose_b=transpose_b, name=name)
File "C:\Python35\lib\site-packages\tensorflow\python\ops\gen_math_ops.py", line 4567, in mat_mul
name=name)
File "C:\Python35\lib\site-packages\tensorflow\python\framework\op_def_library.py", line 787, in _apply_op_helper
op_def=op_def)
File "C:\Python35\lib\site-packages\tensorflow\python\framework\ops.py", line 3392, in create_op
op_def=op_def)
File "C:\Python35\lib\site-packages\tensorflow\python\framework\ops.py", line 1718, in __init__
self._traceback = self._graph._extract_stack() # pylint: disable=protected-access
InvalidArgumentError (see above for traceback): Matrix size-incompatible: In[0]: [256,2048], In[1]: [256,1024]
[[Node: MatMul = MatMul[T=DT_FLOAT, transpose_a=false, transpose_b=false, _device="/job:localhost/replica:0/task:0/device:CPU:0"](Reshape, Variable_4/read)]]
It looks like the problem is in convolutional_neural_network layer() function wherein somehow it is mad at not being able to multiply the same dimension of the matrix. But it is not clear how to solve the issue
Thank you for the help in advance...
After reshaping conv4 at line fc1 = tf.reshape(conv4,[256,-1]), the shape of fc1 is (256, 2048) and the weight matrix W_fc1 has shape (256, 1024). Thus, you get a size incompatible error at the next line fc1 = tf.nn.relu(tf.matmul(fc1, weights['W_fc1']) + biases['b_fc1'])
in the matrix multiplication part. I suggest you to go through the dimensions at every step manually to find errors in future.

why dataset.output_shapes returns demension(none) after batching

I'm using the Dataset API for input pipelines in TensorFlow (version: r1.2). I built my dataset and batched it with a batch size of 128. The dataset fed into the RNN.
Unfortunately, the dataset.output_shape returns dimension(none) in the first dimension, so the RNN raises an error:
Traceback (most recent call last):
File "untitled1.py", line 188, in <module>
tf.app.run(main=main, argv=[sys.argv[0]] + unparsed)
File "/home/harold/anaconda2/envs/tensorflow_py2.7/lib/python2.7/site-packages/tensorflow/python/platform/app.py", line 48, in run
_sys.exit(main(_sys.argv[:1] + flags_passthrough))
File "untitled1.py", line 121, in main
run_training()
File "untitled1.py", line 57, in run_training
is_training=True)
File "/home/harold/huawei/ConvLSTM/ConvLSTM.py", line 216, in inference
initial_state=initial_state)
File "/home/harold/anaconda2/envs/tensorflow_py2.7/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 566, in dynamic_rnn
dtype=dtype)
File "/home/harold/anaconda2/envs/tensorflow_py2.7/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 636, in _dynamic_rnn_loop
"Input size (depth of inputs) must be accessible via shape inference,"
ValueError: Input size (depth of inputs) must be accessible via shape inference, but saw value None.
I think this error is caused by the shape of input, the first dimension should be batch size but not none.
here is the code:
origin_dataset = Dataset.BetweenS_Dataset(FLAGS.data_path)
train_dataset = origin_dataset.train_dataset
test_dataset = origin_dataset.test_dataset
shuffle_train_dataset = train_dataset.shuffle(buffer_size=10000)
shuffle_batch_train_dataset = shuffle_train_dataset.batch(128)
batch_test_dataset = test_dataset.batch(FLAGS.batch_size)
iterator = tf.contrib.data.Iterator.from_structure(
shuffle_batch_train_dataset.output_types,
shuffle_batch_train_dataset.output_shapes)
(images, labels) = iterator.get_next()
training_init_op = iterator.make_initializer(shuffle_batch_train_dataset)
test_init_op = iterator.make_initializer(batch_test_dataset)
print(shuffle_batch_train_dataset.output_shapes)
I print output_shapes and it gives:
(TensorShape([Dimension(None), Dimension(36), Dimension(100)]), TensorShape([Dimension(None)]))
I suppose that it should be 128, because I have batched dataset:
(TensorShape([Dimension(128), Dimension(36), Dimension(100)]), TensorShape([Dimension(128)]))
This feature has been added with the drop_remainder parameter used like the following:
batch_test_dataset = test_dataset.batch(FLAGS.batch_size, drop_remainder=True)
From the docs:
drop_remainder: (Optional.) A tf.bool scalar tf.Tensor, representing whether the last batch should be dropped in the case its has fewer than batch_size elements; the default behavior is not to drop the smaller batch.
They hardcoded batch size in implementation and it always will return None (tf 1.3).
def _padded_shape_to_batch_shape(s):
return tensor_shape.vector(None).concatenate(
tensor_util.constant_value_as_shape(s))
In this way, they can batch all elements (e.g. dataset_size=14, batch_size=5, last_batch_size=4).
You can use dataset.filter and dataset.map to fix this issue
d = contrib.data.Dataset.from_tensor_slices([[5] for x in range(14)])
batch_size = 5
d = d.batch(batch_size)
d = d.filter(lambda e: tf.equal(tf.shape(e)[0], batch_size))
def batch_reshape(e):
return tf.reshape(e, [args.batch_size] + [s if s is not None else -1 for s in e.shape[1:].as_list()])
d = d.map(batch_reshape)
r = d.make_one_shot_iterator().get_next()
print('dataset_output_shape = %s' % r.shape)
with tf.Session() as sess:
while True:
print(sess.run(r))
Output
dataset_output_shape = (5, 1)
[[5][5][5][5][5]]
[[5][5][5][5][5]]
OutOfRangeError

How to read next batch in tensorflow automatically?

I have 70 training sample, 10 testing samples, with every sample contains 11*99 elements. I want to use LSTM to classify the testing samples, here is the code:
import tensorflow as tf
import scipy.io as sc
# data read
feature_training = sc.loadmat("feature_training_reshaped.mat")
feature_training_reshaped = feature_training['feature_training_reshaped']
print (feature_training_reshaped.shape)
feature_testing = sc.loadmat("feature_testing_reshaped.mat")
feature_testing_reshaped = feature_testing['feature_testing_reshaped']
print (feature_testing_reshaped.shape)
label_training = sc.loadmat("label_training.mat")
label_training = label_training['aa']
print (label_training.shape)
label_testing = sc.loadmat("label_testing.mat")
label_testing = label_testing['label_testing']
print (label_testing.shape)
a=feature_training_reshaped.reshape([70, 11, 99])
b=feature_testing_reshaped.reshape([10, 11, 99])
print (a.shape)
# hyperparameters
lr = 0.001
training_iters = 1000
batch_size = 70
n_inputs = 99 # MNIST data input (img shape: 11*99)
n_steps = 11 # time steps
n_hidden_units = 128 # neurons in hidden layer
n_classes = 2 # MNIST classes (0-9 digits)
# tf Graph input
x = tf.placeholder(tf.float32, [None, n_steps, n_inputs])
y = tf.placeholder(tf.float32, [None, n_classes])
# Define weights
weights = {
# (28, 128)
'in': tf.Variable(tf.random_normal([n_inputs, n_hidden_units])),
# (128, 10)
'out': tf.Variable(tf.random_normal([n_hidden_units, n_classes]))
}
biases = {
# (128, )
'in': tf.Variable(tf.constant(0.1, shape=[n_hidden_units, ])),
# (10, )
'out': tf.Variable(tf.constant(0.1, shape=[n_classes, ]))
}
def RNN(X, weights, biases):
# hidden layer for input to cell
########################################
# all the data in this batch flow into this layer in one time
# transpose the inputs shape from 70batch, 11steps,99inputs
# X ==> (70 batch * 11 steps, 99 inputs)
X = tf.reshape(X, [-1, n_inputs])
# into hidden
# X_in = (70 batch * 11 steps, 99 inputs)
X_in = tf.matmul(X, weights['in']) + biases['in']
# another shape transpose X_in ==> (70 batch, 11 steps, 128 hidden),
X_in = tf.reshape(X_in, [-1, n_steps, n_hidden_units])
# cell
##########################################
# basic LSTM Cell.
lstm_cell = tf.nn.rnn_cell.BasicLSTMCell(n_hidden_units, forget_bias=1.0, state_is_tuple=True)
# lstm cell is divided into two parts (c_state, h_state)
##### TAKE Care, batch_size should be 10 when the testing dataset only has 10 data
_init_state = lstm_cell.zero_state(batch_size, dtype=tf.float32)
print ("_init_state:", _init_state)
# You have 2 options for following step.
# 1: tf.nn.rnn(cell, inputs);
# 2: tf.nn.dynamic_rnn(cell, inputs).
# If use option 1, you have to modified the shape of X_in, go and check out this:
# https://github.com/aymericdamien/TensorFlow-Examples/blob/master/examples/3_NeuralNetworks/recurrent_network.py
# In here, we go for option 2.
# dynamic_rnn receive Tensor (batch, steps, inputs) or (steps, batch, inputs) as X_in.
# Make sure the time_major is changed accordingly.
outputs, final_state = tf.nn.dynamic_rnn(lstm_cell, X_in, initial_state=_init_state, time_major=False)
# outputs size would be a tensor [70,11,128]; size of X_in is (70 batch, 11 steps, 128 hidden)
# final_state size would be [batch_size, outputs],which is [70,128]
print (outputs)
print (final_state)
# hidden layer for output as the final results
#############################################
results = tf.matmul(final_state[1], weights['out']) + biases['out']
# # or
# unpack to list [(batch, outputs)..] * steps
# outputs = tf.unpack(tf.transpose(outputs, [1, 0, 2])) # states is the last outputs
# results = tf.matmul(outputs[-1], weights['out']) + biases['out']
return results
pred = RNN(x, weights, biases)
cost = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(pred, y))
train_op = tf.train.AdamOptimizer(lr).minimize(cost)
correct_pred = tf.equal(tf.argmax(pred, 1), tf.argmax(y, 1))
accuracy = tf.reduce_mean(tf.cast(correct_pred, tf.float32))
init = tf.initialize_all_variables()
with tf.Session() as sess:
sess.run(init)
step = 0
while step * batch_size < training_iters:
# batch_xs, batch_ys = fea.next_batch(batch_size)
# batch_xs = batch_xs.reshape([batch_size, n_steps, n_inputs])
sess.run([train_op], feed_dict={
x: a,
y: label_training,
})
if step % 10 == 0:
print(sess.run(accuracy, feed_dict={
x: b,
y: label_testing,
}))
step += 1
At last, I got the result & error:
(770, 99)
(110, 99)
(70, 2)
(10, 2)
(70, 11, 99)
('_init_state:', LSTMStateTuple(c=<tf.Tensor 'zeros:0' shape=(70, 128) dtype=float32>, h=<tf.Tensor 'zeros_1:0' shape=(70, 128) dtype=float32>))
Tensor("RNN/transpose:0", shape=(70, 11, 128), dtype=float32)
LSTMStateTuple(c=<tf.Tensor 'RNN/while/Exit_2:0' shape=(70, 128) dtype=float32>, h=<tf.Tensor 'RNN/while/Exit_3:0' shape=(70, 128) dtype=float32>)
Traceback (most recent call last):
File "/home/xiangzhang/RNN.py", line 150, in <module>
y: label_testing,
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 717, in run
run_metadata_ptr)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 915, in _run
feed_dict_string, options, run_metadata)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 965, in _do_run
target_list, options, run_metadata)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/client/session.py", line 985, in _do_call
raise type(e)(node_def, op, message)
tensorflow.python.framework.errors.InvalidArgumentError: ConcatOp : Dimensions of inputs should match: shape[0] = [10,128] vs. shape[1] = [70,128]
[[Node: RNN/while/BasicLSTMCell/Linear/concat = Concat[N=2, T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/cpu:0"](RNN/while/BasicLSTMCell/Linear/concat/concat_dim, RNN/while/TensorArrayRead, RNN/while/Identity_3)]]
Caused by op u'RNN/while/BasicLSTMCell/Linear/concat', defined at:
File "/home/xiangzhang/RNN.py", line 128, in <module>
pred = RNN(x, weights, biases)
File "/home/xiangzhang/RNN.py", line 110, in RNN
outputs, final_state = tf.nn.dynamic_rnn(lstm_cell, X_in, initial_state=_init_state, time_major=False)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 836, in dynamic_rnn
dtype=dtype)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 1003, in _dynamic_rnn_loop
swap_memory=swap_memory)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2518, in while_loop
result = context.BuildLoop(cond, body, loop_vars, shape_invariants)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2356, in BuildLoop
pred, body, original_loop_vars, loop_vars, shape_invariants)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/control_flow_ops.py", line 2306, in _BuildLoop
body_result = body(*packed_vars_for_body)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 988, in _time_step
(output, new_state) = call_cell()
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn.py", line 974, in <lambda>
call_cell = lambda: cell(input_t, state)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn_cell.py", line 310, in __call__
concat = _linear([inputs, h], 4 * self._num_units, True)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/rnn_cell.py", line 907, in _linear
res = math_ops.matmul(array_ops.concat(1, args), matrix)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/array_ops.py", line 872, in concat
name=name)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/ops/gen_array_ops.py", line 436, in _concat
values=values, name=name)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/framework/op_def_library.py", line 749, in apply_op
op_def=op_def)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/framework/ops.py", line 2380, in create_op
original_op=self._default_original_op, op_def=op_def)
File "/home/xiangzhang/.local/lib/python2.7/site-packages/tensorflow/python/framework/ops.py", line 1298, in __init__
self._traceback = _extract_stack()
InvalidArgumentError (see above for traceback): ConcatOp : Dimensions of inputs should match: shape[0] = [10,128] vs. shape[1] = [70,128]
[[Node: RNN/while/BasicLSTMCell/Linear/concat = Concat[N=2, T=DT_FLOAT, _device="/job:localhost/replica:0/task:0/cpu:0"](RNN/while/BasicLSTMCell/Linear/concat/concat_dim, RNN/while/TensorArrayRead, RNN/while/Identity_3)]]
Process finished with exit code 1
I thought the reason maybe is the testing dataset is only 10, less than batch_size=70, so that when I run the testing dataset, the code _init_state = lstm_cell.zero_state(batch_size, dtype=tf.float32) would has the unmatch error.
There are two ways to solve it but I don't know how to implement any of it neither:
change the batch_size value, set it as 70 when training, 10 when testing. But, I don't know how to code it, please tell me how to do?
Or, I can set the batch_size=10 , and automatically read the training dataset ten by ten. Also, I don't know how to read next batch in tensorflow automatically, and the command next_batch in MNIST dataset can not work.
The second solution is particular important, please kindly to help me, thanks very much.

Cannot convert partially known tensor in TensorFlow/TFLearn

I'm a beginner to TensorFlow and still trying to figure out how it works, so I'm not sure if the error is a problem with my architecture or something more basic -- here I'm trying to train a siamese neural network (we feed a left and right input into left and right NN with identical weights, and try to map it to feature vectors that have small distance if the inputs are similar and large distance if the inputs are different).
The error I get occurs at the regression step:
File "siamese.py", line 59, in <module>
network = regression(y_pred, optimizer='adam',
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tflearn/models/dnn.py", line 63, in __init__
best_val_accuracy=best_val_accuracy)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tflearn/helpers/trainer.py", line 120, in __init__
clip_gradients)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tflearn/helpers/trainer.py", line 646, in initialize_training_ops
ema_num_updates=self.training_steps)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tflearn/summaries.py", line 236, in add_loss_summaries
loss_averages_op = loss_averages.apply([loss] + other_losses)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tensorflow/python/training/moving_averages.py", line 292, in apply
colocate_with_primary=(var.op.type == "Variable"))
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tensorflow/python/training/slot_creator.py", line 106, in create_zeros_slot
val = array_ops.zeros(primary.get_shape().as_list(), dtype=dtype)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tensorflow/python/ops/array_ops.py", line 1071, in zeros
shape = ops.convert_to_tensor(shape, dtype=dtypes.int32, name="shape")
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tensorflow/python/framework/ops.py", line 628, in convert_to_tensor
ret = conversion_func(value, dtype=dtype, name=name, as_ref=as_ref)
File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/tensorflow/python/framework/constant_op.py", line 198, in _tensor_shape_tensor_conversion_function
"Cannot convert a partially known TensorShape to a Tensor: %s" % s)
ValueError: Cannot convert a partially known TensorShape to a Tensor: (?,)
I don't know how to resolve this problem if the first dimension needs to be None for the batch size (correct me if I'm wrong).
Relevant parts of the code are below:
BATCH_SIZE=100
def contrastive_loss(y_pred, y_true, margin=1.0):
return tf.mul(1-y_true, tf.square(y_pred)) + tf.mul(y_true, tf.square(tf.maximum((margin-y_pred),0)))
## Load dataset
f = h5py.File('./data/paired_training_data.hdf','r')
X1 = f["train_X1"]
X2 = f["train_X2"]
Y = f["train_Y_paired"]
## Inputs: 1 example (phoneme pair), dropout probability
inp_sound1 = input_data(shape=[None, 1, N_MFCC_CHANNELS, N_IN_CHANNELS])
networkL = conv_1d(inp_sound1, reuse=None, scope="conv1d")
networkL = max_pool_1x6(networkL)
networkL = fully_connected(networkL, n_units=N_FULLY_CONN, activation='relu', scope="fc1")
networkL = dropout(networkL, .5) # unshared?
networkL = fully_connected(networkL, n_units=N_FULLY_CONN, activation='relu', scope="fc2")
inp_sound2 = input_data(shape=[None, 1, N_MFCC_CHANNELS, N_IN_CHANNELS])
networkR = conv_1d(inp_sound2, reuse=True, scope="conv1d")
networkR = max_pool_1x6(networkR)
networkR = fully_connected(networkR, n_units=N_FULLY_CONN, activation='relu', reuse=True, scope="fc1")
networkR = dropout(networkR, .5)
networkR = fully_connected(networkR, n_units=N_FULLY_CONN, activation='relu', reuse=True, scope="fc2")
l2_loss = tf.reduce_sum(tf.square(tf.sub(networkL, networkR)), 1)
y_pred = tf.sqrt(l2_loss)
#y_true = input_data(shape=[None])
## Training
network = regression(y_pred, optimizer='adam',
loss=contrastive_loss, learning_rate=0.0001, to_one_hot=False)
model = tflearn.DNN(network, tensorboard_verbose=0)
model.fit([X1, X2], Y, n_epoch=10, batch_size=BATCH_SIZE, show_metric=True, validation_set=0.1)
Any help -- especially with understanding how to debug these issues on my own in the future -- would be greatly appreciated!
It looks like TensorFlow cannot infer the shape of your contrastive_loss. Try to call set_shape in your contrastive_loss function if you know its output shape in advance:
def contrastive_loss(y_pred, y_true, margin=1.0):
loss = tf.mul(1-y_true, tf.square(y_pred)) + tf.mul(y_true, tf.square(tf.maximum((margin-y_pred),0)))
loss.set_shape([...])
return loss

Preserving tensor values between session runs

Consider the following example:
import tensorflow as tf
import math
import numpy as np
INPUTS = 10
HIDDEN_1 = 20
BATCH_SIZE = 3
def create_graph(inputs):
with tf.name_scope('h1'):
weights = tf.Variable(
tf.truncated_normal([INPUTS, HIDDEN_1],
stddev=1.0 / math.sqrt(float(INPUTS))),
name='weights')
biases = tf.Variable(tf.zeros([HIDDEN_1]),
name='biases')
state = tf.Variable(tf.zeros([HIDDEN_1]), name='inner_state')
state = tf.Print(state, [state], message=" this is state before: ")
state = 0.9*state + 0.1*( tf.matmul(inputs, weights) + biases )
state = tf.Print(state, [state], message=" this is state after: ")
output = tf.nn.relu(state)
return output
def data_iter():
while True:
idxs = np.random.rand(BATCH_SIZE, INPUTS)
yield idxs
with tf.Graph().as_default():
inputs = tf.placeholder(tf.float32, shape=(BATCH_SIZE, INPUTS))
output = create_graph(inputs)
sess = tf.Session()
# Run the Op to initialize the variables.
init = tf.initialize_all_variables()
sess.run(init)
iter_ = data_iter()
for i in xrange(0, 2):
print ("iteration: ",i)
input_data = iter_.next()
out = sess.run(output, feed_dict={ inputs: input_data})
I was hoping to have the tensor state to preserve its intermediate and to change slowly on each iteration. However, What I am seeing is that on each sess.run invocation, the state begins on zero values:
('iteration: ', 0)
I tensorflow/core/kernels/logging_ops.cc:79] this is state before: [0 0 0...]
I tensorflow/core/kernels/logging_ops.cc:79] this is state after: [0.007762237 0.044753391 0.049343754...]
('iteration: ', 1)
I tensorflow/core/kernels/logging_ops.cc:79] this is state before: [0 0 0...]
I tensorflow/core/kernels/logging_ops.cc:79] this is state after: [0.040079735 0.074709542 0.078258425...]
I would appreciate any clarification how to address this behavior
Edit
after commenting the tf.Print lines and replacing the incorrect assignment with
state = state.assign(0.9*state + 0.1*( tf.matmul(inputs, weights) + biases ))
I get these errors:
Traceback (most recent call last):
File "cycles_in_graphs.py", line 33, in <module>
output = create_graph(inputs)
File "cycles_in_graphs.py", line 21, in create_graph
state = state.assign(0.9*state + 0.1*( tf.matmul(inputs, weights) + biases ))
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/variables.py", line 453, in assign
return state_ops.assign(self._variable, value, use_locking=use_locking)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/gen_state_ops.py", line 40, in assign
use_locking=use_locking, name=name)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/op_def_library.py", line 655, in apply_op
op_def=op_def)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 2156, in create_op
set_shapes_for_outputs(ret)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/ops.py", line 1612, in set_shapes_for_outputs
shapes = shape_func(op)
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/ops/state_ops.py", line 197, in _AssignShape
return [op.inputs[0].get_shape().merge_with(op.inputs[1].get_shape())]
File "/usr/local/lib/python2.7/dist-packages/tensorflow/python/framework/tensor_shape.py", line 554, in merge_with
(self, other))
ValueError: Shapes (20,) and (3, 20) are not compatible
When you write state = 0.9 * state + 0.1 * (tf.matmul(inputs, weights) + biases), you do not update the value of the variable state.
You only compute the value of 0.9 * state + 0.1 * ..., but the value of the Variable stays the same.
To update your tf.Variable, you should use the function assign or assign_add on your variable state:
state = state.assign(0.9 * state + 0.1 * (tf.matmul(inputs, weights) + biases))
Everything is explained in the TensorFlow tutorial on Variables.