Reshaping tensor after max pooling ValueError: Shapes are not compatible - machine-learning

I am building CNN fitting my own data, based on this example
Basically, my data has 3640 features; I have a convolution layer followed by a pooling layer, that pools every other feature, so I end up with dimensions (?, 1, 1819, 1) because 3638 features after conv layer / 2 == 1819.
When I try to reshape my data after pooling to get it in the form [n_samples, n_fetures]
print("pool_shape", pool_shape) #pool (?, 1, 1819, 10)
print("y_shape", y_shape) #y (?,)
pool.set_shape([pool_shape[0], pool_shape[2]*pool_shape[3]])
y.set_shape([y_shape[0], 1])
I get an error:
ValueError: Shapes (?, 1, 1819, 10) and (?, 18190) are not compatible
My code:
N_FEATURES = 140*26
N_FILTERS = 1
WINDOW_SIZE = 3
def my_conv_model(x, y):
x = tf.cast(x, tf.float32)
y = tf.cast(y, tf.float32)
print("x ", x.get_shape())
print("y ", y.get_shape())
# to form a 4d tensor of shape batch_size x 1 x N_FEATURES x 1
x = tf.reshape(x, [-1, 1, N_FEATURES, 1])
# this will give you sliding window of 1 x WINDOW_SIZE convolution.
features = tf.contrib.layers.convolution2d(inputs=x,
num_outputs=N_FILTERS,
kernel_size=[1, WINDOW_SIZE],
padding='VALID')
print("features ", features.get_shape()) #features (?, 1, 3638, 10)
# Max pooling across output of Convolution+Relu.
pool = tf.nn.max_pool(features, ksize=[1, 1, 2, 1],
strides=[1, 1, 2, 1], padding='SAME')
pool_shape = pool.get_shape()
y_shape = y.get_shape()
print("pool_shape", pool_shape) #pool (?, 1, 1819, 10)
print("y_shape", y_shape) #y (?,)
### here comes the error ###
pool.set_shape([pool_shape[0], pool_shape[2]*pool_shape[3]])
y.set_shape([y_shape[0], 1])
pool_shape = pool.get_shape()
y_shape = y.get_shape()
print("pool_shape", pool_shape) #pool (?, 1, 1819, 10)
print("y_shape", y_shape) #y (?,)
prediction, loss = learn.models.logistic_regression(pool, y)
return prediction, loss
How to reshape the data to get any meaningful representation of it and to later pass it to logistic regression layer?

This looks like a confusion between the Tensor.set_shape() method and the tf.reshape() operator. In this case, you should use tf.reshape() because you are changing the shape of the pool and y tensors:
The tf.reshape(tensor, shape) operator takes a tensor of any shape, and returns a tensor with the given shape, as long as they have the same number of elements. This operator should be used to change the shape of the input tensor.
The tensor.set_shape(shape) method takes a tensor that might have a partially known or unknown shape, and asserts to TensorFlow that it actually has the given shape. This method should be used to provide more information about the shape of a particular tensor.
It can be used, e.g., when you take the output of an operator that has a data-dependent output shape (such as tf.image.decode_jpeg()) and assert that it has a static shape (e.g. based on knowledge about the sizes of images in your dataset).
In your program, you should replace the calls to set_shape() with something like the following:
pool_shape = tf.shape(pool)
pool = tf.reshape(pool, [pool_shape[0], pool_shape[2] * pool_shape[3]])
y_shape = tf.shape(y)
y = tf.reshape(y, [y_shape[0], 1])
# Or, more straightforwardly:
y = tf.expand_dims(y, 1)

Related

Loss for Multi-label Classification

I am working on a multi-label classification problem. My gt labels are of shape 14 x 10 x 128, where 14 is the batch_size, 10 is the sequence_length, and 128 is the vector with values 1 if the item in sequence belongs to the object and 0 otherwise.
My output is also of same shape: 14 x 10 x 128. Since, my input sequence was of varying length I had to pad it to make it of fixed length 10. I'm trying to find the loss of the model as follows:
total_loss = 0.0
unpadded_seq_lengths = [3, 4, 5, 7, 9, 3, 2, 8, 5, 3, 5, 7, 7, ...] # true lengths of sequences
optimizer = torch.optim.Adam(model.parameters(), lr=1e-3)
criterion = nn.BCEWithLogitsLoss()
for data in training_dataloader:
optimizer.zero_grad()
# shape of input 14 x 10 x 128
output = model(data)
batch_loss = 0.0
for batch_idx, sequence in enumerate(output):
# sequence shape is 10 x 128
true_seq_len = unpadded_seq_lengths[batch_idx]
# only keep unpadded gt and predicted labels since we don't want loss to be influenced by padded values
predicted_labels = sequence[:true_seq_len, :] # for example, 3 x 128
gt_labels = gt_labels_padded[batch_idx, :true_seq_len, :] # same shape as above, gt_labels_padded has shape 14 x 10 x 128
# loop through unpadded predicted and gt labels and calculate loss
for item_idx, predicted_labels_seq_item in enumerate(predicted_labels):
# predicted_labels_seq_item and gt_labels_seq_item are 1D vectors of length 128
gt_labels_seq_item = gt_labels[item_idx]
current_loss = criterion(predicted_labels_seq_item, gt_labels_seq_item)
total_loss += current_loss
batch_loss += current_loss
batch_loss.backward()
optimizer.step()
Can anybody please check to see if I'm calculating loss correctly. Thanks
Update:
Is this the correct approach for calculating accuracy metrics?
# batch size: 14
# seq length: 10
for epoch in range(10):
TP = FP = TN = FN = 0.
for x, y, mask in tr_dl:
# mask shape: (10,)
out = model(x) # out shape: (14, 10, 128)
y_pred = (torch.sigmoid(out) >= 0.5).float().type(torch.int64) # consider all predictions above 0.5 as 1, rest 0
y_pred = y_pred[mask] # y_pred shape: (14, 10, 10, 128)
y_labels = y[mask] # y_labels shape: (14, 10, 10, 128)
# do I flatten y_pred and y_labels?
y_pred = y_pred.flatten()
y_labels = y_labels.flatten()
for idx, prediction in enumerate(y_pred):
if prediction == 1 and y_labels[idx] == 1:
# calculate IOU (overlap of prediction and gt bounding box)
iou = 0.78 # assume we get this iou value for objects at idx
if iou >= 0.5:
TP += 1
else:
FP += 1
elif prediction == 1 and y_labels[idx] == 0:
FP += 1
elif prediction == 0 and y_labels[idx] == 1:
FN += 1
else:
TN += 1
EPOCH_ACC = (TP + TN) / (TP + TN + FP + FN)
It is usually recommended to stick with batch-wise operations and avoid going into single-element processing steps while in the main training loop. One way to handle this case is to make your dataset return padded inputs and labels with additionally a mask that will come useful for loss computation. In other words, to compute the loss term with sequences of varying sizes, we will use a mask instead of doing individual slices.
Dataset
The way to proceed is to make sure you build the mask in the dataset and not in the inference loop. Here I am showing a minimal implementation that you should be able to transfer to your dataset without much hassle:
class Dataset(data.Dataset):
def __init__(self):
super().__init__()
def __len__(self):
return 100
def __getitem__(self, index):
i = random.randint(5, SEQ_LEN) # for demo puporse, generate x with random length
x = torch.rand(i, EMB_SIZE)
y = torch.randint(0, N_CLASSES, (i, EMB_SIZE))
# pad data to fit in batch
pad = torch.zeros(SEQ_LEN-len(x), EMB_SIZE)
x_padded = torch.cat((pad, x))
y_padded = torch.cat((pad, y))
# construct tensor to mask loss
mask = torch.cat((torch.zeros(SEQ_LEN-len(x)), torch.ones(len(x))))
return x_padded, y_padded, mask
Essentially in the __getitem__, we not only pad the input x and target y with zero values, we also construct a simple mask containing the positions of the padded values in the currently processed element.
Notice how:
x_padded, shaped (SEQ_LEN, EMB_SIZE)
y_padded, shaped (SEQ_LEN, N_CLASSES)
mask, shaped (SEQ_LEN,)
are all three tensors which are shape invariant across the dataset, yet mask contains the padding information necessary for us to compute the loss function appropriately.
Inference
The loss you've used nn.BCEWithLogitsLoss, is the correct one since it's a multi-dimensional loss used for binary classification. In other words, you can use it here in this multi-label classification task, considering each one of the 128 logits as an individual binary prediction. Do not use nn.CrossEntropyLoss) as suggested elsewhere, since the softmax will push a single logit (i.e. class), which is the behaviour required for single-label classification tasks.
Therefore, in the training loop, we simply have to apply the mask to our loss.
for x, y, mask in dl:
y_pred = model(x)
loss = mask*bce(y_pred, y)
# backpropagation, loss postprocessing, logs, etc.
This is what you need for the first part of the question, there are already loss functions implemented in tensorflow: https://medium.com/#aadityaura_26777/the-loss-function-for-multi-label-and-multi-class-f68f95cae525. Yours is just tf.nn.weighted_cross_entropy_with_logits, but you need to set the weight.
The second part of the question is not straightforward, because there's conditioning on the IOU, generally, when you do machine learning, you should heavily depend on matrix multiplication, in your case, you probably need to pre-calculate the IOU -> 1 or 0 as a vector, then multiply with the y_pred , element-wise, this will give you the modified y_pred . After that, you can use any accuracy available function to calculate the final result.
if you can use the CROSSENTROPYLOSS instead of BCEWithLogitsLoss there is something called ignore_index. you can use it to exclude your padded sequences. the difference between the 2 losses is the activation function used (softmax vs sigmoid). but I think you can still use the CROSSENTROPYLOSSfor binary classification as well.

Pytorch Multiclass Logistic Regression Type Errors

I'm new to ML and even more naive with Pytorch. Here's the problem. (I've skipped certain parts like the random_split() which seem to work just fine)
I've to predict wine quality (red) which from the dataset is the last column with 6 classes
That's what my dataset looks like
The link to the dataset (winequality-red.csv)
features = df.drop(['quality'], axis = 1)
targets = df.iloc[:, -1] # theres 6 classes
dataset = TensorDataset(torch.Tensor(np.array(features)).float(), torch.Tensor(targets).float())
# here's where I think the error might be, but I might be wrong
batch_size = 8
# Dataloader
train_loader = DataLoader(train_ds, batch_size, shuffle = True)
val_loader = DataLoader(val_ds, batch_size)
test_ds = DataLoader(test_ds, batch_size)
input_size = len(df.columns) - 1
output_size = 6
threshold = .5
class WineModel(nn.Module):
def __init__(self):
super().__init__()
self.linear = nn.Linear(input_size, output_size)
def forward(self, xb):
out = self.linear(xb)
return out
model = WineModel()
n_iters = 2000
num_epochs = n_iters / (len(train_ds) / batch_size)
num_epochs = int(num_epochs)
criterion = nn.CrossEntropyLoss()
optimizer = torch.optim.SGD(model.parameters(), lr=1e-2)
# the part below returns the error on running
iter = 0
for epoch in range(num_epochs):
for i, (x, y) in enumerate(train_loader):
optimizer.zero_grad()
outputs = model(x)
loss = criterion(outputs, y)
loss.backward()
optimizer.step()
RuntimeError: expected scalar type Long but found Float
Hopefully that is sufficient info
The targets for nn.CrossEntropyLoss are given as the class indices, which are required to be integers, to be precise they need to be of type torch.long, which is equivalent to torch.int64.
You converted the targets to floats, but you should convert them to longs:
dataset = TensorDataset(torch.Tensor(np.array(features)).float(), torch.Tensor(targets).long())
Since the targets are the indices of the classes, they must be in range [0, num_classes - 1]. As you have 6 classes that would be in range [0, 5]. Having a quick look at your data, the quality uses values in range [3, 8]. Even though you have 6 classes, the values cannot be used directly as the classes. If you list the classes as classes = [3, 4, 5, 6, 7, 8], you can see that the first class is 3, classes[0] == 3, up to the last class being classes[5] == 8.
You need to replace the class values with the indices, just like you would for named classes (e.g. if you had the classes dog and cat, dog would be 0 and cat would be 1), but you can avoid having to look them up, since the values are simply shifted by 3, i.e. index = classes[index] - 3. Therefore you can subtract 3 from the entire target tensor:
torch.Tensor(targets).long() - 3

Trying to understand Pytorch's implementation of LSTM

I have a dataset containing 1000 examples where each example has 5 features (a,b,c,d,e). I want to feed 7 examples to an LSTM so it predicts the feature (a) of the 8th day.
Reading Pytorchs documentation of nn.LSTM() I came up with the following:
input_size = 5
hidden_size = 10
num_layers = 1
output_size = 1
lstm = nn.LSTM(input_size, hidden_size, num_layers)
fc = nn.Linear(hidden_size, output_size)
out, hidden = lstm(X) # Where X's shape is ([7,1,5])
output = fc(out[-1])
output # output's shape is ([7,1])
According to the docs:
The input of the nn.LSTM is "input of shape (seq_len, batch, input_size)" with "input_size – The number of expected features in the input x",
And the output is: "output of shape (seq_len, batch, num_directions * hidden_size): tensor containing the output features (h_t) from the last layer of the LSTM, for each t."
In this case, I thought seq_len would be the sequence of 7 examples, batchis 1 and input_size is 5. So the lstm would consume each example containing 5 features refeeding the hidden layer every iteration.
What am I missing?
When I extend your code to a full example -- I also added some comments to may help -- I get the following:
import torch
import torch.nn as nn
input_size = 5
hidden_size = 10
num_layers = 1
output_size = 1
lstm = nn.LSTM(input_size, hidden_size, num_layers)
fc = nn.Linear(hidden_size, output_size)
X = [
[[1,2,3,4,5]],
[[1,2,3,4,5]],
[[1,2,3,4,5]],
[[1,2,3,4,5]],
[[1,2,3,4,5]],
[[1,2,3,4,5]],
[[1,2,3,4,5]],
]
X = torch.tensor(X, dtype=torch.float32)
print(X.shape) # (seq_len, batch_size, input_size) = (7, 1, 5)
out, hidden = lstm(X) # Where X's shape is ([7,1,5])
print(out.shape) # (seq_len, batch_size, hidden_size) = (7, 1, 10)
out = out[-1] # Get output of last step
print(out.shape) # (batch, hidden_size) = (1, 10)
out = fc(out) # Push through linear layer
print(out.shape) # (batch_size, output_size) = (1, 1)
This makes sense to me, given your batch_size = 1 and output_size = 1 (I assume, you're doing regression). I don't know where your output.shape = (7, 1) come from.
Are you sure that your X has the correct dimensions? Did you create nn.LSTM maybe with batch_first=True? There are lot of little things that can sneak in.

Tensorflow dynamic_rnn TypeError: 'Tensor' object is not iterable

I'm trying to get a basic LSTM working in TensorFlow. I'm receiving the following error:
TypeError: 'Tensor' object is not iterable.
The offending line is:
rnn_outputs, final_state = tf.nn.dynamic_rnn(cell, x, sequence_length=seqlen,
initial_state=init_state,)`
I'm using version 1.0.1 on windows 7. My inputs and label have the following shapes
x_shape = (50, 40, 18), y_shape = (50, 40)
Where:
batch size = 50
sequence length = 40
input vector length at each step = 18
I'm building my graph as follows
def build_graph(learn_rate, seq_len, state_size=32, batch_size=5):
# use a fixed sequence length
seqlen = tf.constant(seq_len, shape=[batch_size],dtype=tf.int32)
# Placeholders
x = tf.placeholder(tf.float32, [batch_size, None, 18])
y = tf.placeholder(tf.float32, [batch_size, None])
keep_prob = tf.constant(1.0)
# RNN
cell = tf.contrib.rnn.LSTMCell(state_size)
init_state = tf.get_variable('init_state', [1, state_size],
initializer=tf.constant_initializer(0.0))
init_state = tf.tile(init_state, [batch_size, 1])
rnn_outputs, final_state = tf.nn.dynamic_rnn(cell, x, sequence_length=seqlen,
initial_state=init_state,)
# Add dropout, as the model otherwise quickly overfits
rnn_outputs = tf.nn.dropout(rnn_outputs, keep_prob)
# Prediction layer
with tf.variable_scope('prediction'):
W = tf.get_variable('W', [state_size, num_classes])
b = tf.get_variable('b', [num_classes], initializer=tf.constant_initializer(0.0))
preds = tf.tanh(tf.matmul(rnn_outputs, W) + b)
# MSE
loss = tf.square(tf.subtract(y, preds))
# loss = tf.reduce_mean(tf.nn.sparse_softmax_cross_entropy_with_logits(logits, y))
train_step = tf.train.AdamOptimizer(learn_rate).minimize(loss)
Can anyone tell me what I am missing?
Sequence length should be iterable e.g. a list or tensor, not a scalar. In your case specifically, you need to replace sequence length = 40 with a list of the lengths of each input. For instance, if your first sequence has 10 steps, the second 13 and the third 18, you would pass in [10, 13, 18]. This lets TensorFlow's dynamic RNN know how many steps to unroll for (I believe it uses a while loop internally).

Neural network blind guessing

I'm trying to train simple neural network
that consists of:
Convolution layer filter (5x5) x 8, stride 2.
Max pooling 25x25 (the image has kinda low amount of details)
Flatting output into (2x2x8) vector
Classifier with logistic regression
Altogether network has < 1000 weights.
File: nn.py
#!/bin/python
import tensorflow as tf
import create_batch
# Prepare data
batch = create_batch.batch
x = tf.reshape(batch[0], [-1,100,100,3])
y_ = batch[1]
# CONVOLUTION NETWORK
# For initialization
def weight_variable(shape):
initial = tf.truncated_normal(shape, stddev=0.3)
return tf.Variable(initial)
def bias_variable(shape):
initial = tf.constant(0.2, shape=shape)
return tf.Variable(initial)
# Convolution with stride 1
def conv2d(x, W):
return tf.nn.conv2d(x, W, strides=[1, 2, 2, 1], padding='SAME')
def max_pool_25x25(x):
return tf.nn.max_pool(x, ksize=[1, 25, 25, 1],
strides=[1, 25, 25, 1], padding='SAME')
# First layer
W_conv1 = weight_variable([5, 5, 3, 8])
b_conv1 = bias_variable([8])
x_image = tf.reshape(x, [-1,100,100,3])
# First conv1
h_conv1 = tf.nn.relu(conv2d(x_image, W_conv1) + b_conv1)
h_pool1 = max_pool_25x25(h_conv1)
# Dense connection layer
# make data flat
W_fc1 = weight_variable([2 * 2 * 8, 2])
b_fc1 = bias_variable([2])
h_pool1_flat = tf.reshape(h_pool1, [-1, 2*2*8])
y_conv = tf.nn.softmax(tf.matmul(h_pool1_flat, W_fc1) + b_fc1)
#Learning
cross_entropy = tf.reduce_mean(-tf.reduce_sum(y_ * tf.log(y_conv), reduction_indices=[1]))
train_step = tf.train.GradientDescentOptimizer(0.001).minimize(cross_entropy)
correct_prediction = tf.equal(tf.argmax(y_conv, 1), tf.argmax(y_, 1))
accuracy = tf.reduce_mean(tf.cast(correct_prediction, tf.float32))
# Session
sess = tf.Session()
sess.run(tf.initialize_all_variables())
# Start input enqueue threads.
coord = tf.train.Coordinator()
threads = tf.train.start_queue_runners(sess=sess, coord=coord)
for i in range(200):
if i%10 == 0:
train_accuracy = accuracy.eval(session=sess)
print("step %d, training accuracy %g"%(i, train_accuracy))
train_step.run(session=sess)
File: create_batch.py
#!/bin/python
import tensorflow as tf
PATH1 = "../dane/trening/NK/"
PATH2 = "../dane/trening/K/"
def create_labeled_image_list():
filenames = [(PATH1 + "nk_%d.png" % i) for i in range(300)]
labels = [[1,0] for i in range(300)]
filenames += [(PATH2 + "kulki_%d.png" % i) for i in range(300)]
labels += [[0,1] for i in range(300)]
return filenames, labels
def read_images_from_disk(input_queue):
label = input_queue[1]
file_contents = tf.read_file(input_queue[0])
example = tf.image.decode_png(file_contents, channels=3)
example.set_shape([100, 100, 3])
example = tf.to_float(example)
print ("READ, label:")
print(label)
return example, label
# Start
image_list, label_list = create_labeled_image_list()
# Create appropriate tensors for naming
images = tf.convert_to_tensor(image_list, dtype=tf.string)
labels = tf.convert_to_tensor(label_list, dtype=tf.float32)
input_queue = tf.train.slice_input_producer([images, labels],
shuffle=True)
image, label = read_images_from_disk(input_queue)
batch = tf.train.batch([image, label], batch_size=600)
I'm feeding 100x100 images i have two classess 300 images each.
Basically randomly initialzied network at step 0 has better accuracy than trained one.
Network stops learning after it reaches 0.5 accuracy (basically coin flip). Images contain blue blooby thing (class 1) or grass (class 2).
I'm traning network using whole imageset at once (600 images), the loss function is cross entropy.
What I'm doing wrong?
OK, I've find a fix there were two errors, now the network is learning.
Images were RGBA despite the fact I declared them as RGB in tf
I did not perform normalization of Images to [-1,1] float32.
In tensorflow it should be done with something like this:
# i use "im" for image
tf.image.convert_image_dtype(im, dtype=float32)
im = tf.sub(im, -0.5)
im = tf.mul(im, 2.0)
To all newbies to ML - prepare your data with caution!
Thanks.

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