Pytorch and batches - pytorch

I'm having trouble understanding how batches play a role into the Pytorch framework.
In this model:
class MyModel(nn.Module):
def __init__(self):
super(MyModel, self).__init__()
# 28x28x1 => 26x26x32
self.conv1 = nn.Conv2d(in_channels=1, out_channels=32, kernel_size=3)
self.d1 = nn.Linear(26 * 26 * 32, 128)
self.d2 = nn.Linear(128, 10)
def forward(self, x):
# 32x1x28x28 => 32x32x26x26
x = self.conv1(x)
x = F.relu(x)
# flatten => 32 x (32*26*26)
x = x.flatten(start_dim = 1)
#x = x.view(32, -1)
# 32 x (32*26*26) => 32x128
x = self.d1(x)
x = F.relu(x)
# logits => 32x10
logits = self.d2(x)
out = F.softmax(logits, dim=1)
return out
In the forward definition, we pass in some x, ie. aggregated images for a batch from a DataLoader. Here, the 32x1x28x28 dimension indicates that there are 32 images in a batch. Do we just ignore this fact and Pytorch handles applying Conv2d to each sample? The forward propagation seems to be just relative to a single image.

Indeed, the network is agnostic to batches: The model is designed to classify a single image.
So why do we need batches for?
Each model has weights (aka parameters) and one needs to optimize the weights using the training images so that the model will classify images as correctly as possible.
This optimization process is usually carried out using Stochastic Gradient Descent (SGD): we are using the current values of the weights to classify a batch of images. Using the prediction the current model made, and the expected predictions we know should be (the "labels") we can compute a gradient of the weights and improve the model.

Related

Question about input dimension for conv2D-LSTM implement

I am a PyTorch beginner and would like to get help applying the conv2d-LSTM model.
I have a 2D image (1 channel x Time x Frequency) that contains time and frequency information.
I’d like to extract features automatically using conv2D and then LSTM model because 2D image contains time information
According to PyTorch documents, the output shape of conv2D is (Batch size, Channel out, Height out, Width out) and the input shape of LSTM is (Batch size, sequence length, input size). From that, I thought before input features of the LSTM network there need to reshape the output features of conv2D.
I expected the cnn-lstm model to perform well because it could learn the characteristics and time information of the image, but it did not get the expected performance.
My question is when I insert data into the LSTM model, is there any idea that LSTM learns the data by each row without flattening? Should I always flatten the 2D output?
My networks code and input/output shape are as follows. (I maintained the width size in the conv layer to preserve time information.)
Thanks a lot
class CNN_LSTM(nn.Module):
def __init__(self, paramArr1, paramArr2):
super(CNN_LSTM, self).__init__()
self.input_dim = paramArr2[0]
self.hidden_dim = paramArr2[1]
self.n_layers = paramArr2[2]
self.batch_size = paramArr2[3]
self.conv = nn.Sequential(
nn.Conv2d(1, out_channels=paramArr1[0],
kernel_size=(paramArr1[1],1),
stride=(paramArr1[2],1)),
nn.BatchNorm2d(paramArr1[0]),
nn.ReLU(),
nn.MaxPool2d(kernel_size = (paramArr1[3],1),stride=(paramArr1[4],1))
)
self.lstm = nn.LSTM(input_size = paramArr2[0],
hidden_size=paramArr2[1],
num_layers=paramArr2[2],
batch_first=True)
self.linear = nn.Linear(in_features=paramArr2[1], out_features=1)
def reset_hidden_state(self):
self.hidden = (
torch.zeros(self.n_layers, self.batch_size, self.hidden_dim).to(device),
torch.zeros(self.n_layers, self.batch_size, self.hidden_dim).to(device)
)
def forward(self, x):
x = self.conv(x)
x = x.view(x.size(0), x.size(1),-1)
x = x.permute(0,2,1)
out, (hn, cn) = self.lstm(x, self.hidden)
out = out.squeeze()[-1, :]
out = self.linear(out)
return out
model input/output shape

Pytorch - vanilla Gradient Visualization

I trained a neural network on MNIST using PyTorch:
class MnistCNN(nn.Module):
def __init__(self):
super().__init__()
self.conv1 = nn.Conv2d( 1, 16, 3, stride = 1, padding = 2)
self.pool1 = nn.MaxPool2d(kernel_size = 2)
self.conv2 = nn.Conv2d(16, 32, 3, stride = 1, padding = 2)
self.pool2 = nn.MaxPool2d(kernel_size = 2)
self.dropout = nn.Dropout(0.5)
self.lin = nn.Linear(32 * 8 * 8, 10)
def forward(self, x):
# conv block
x = F.relu(self.conv1(x))
x = self.pool1(x)
# conv block
x = F.relu(self.conv2(x))
x = self.pool2(x)
# dense block
x = x.view(x.size(0), -1)
x = self.dropout(x)
return self.lin(x)
I would like to implement vanilla Gradient Visualization (see reference below) on my model.
Simonyan, K., Vedaldi, A., Zisserman, A.
Deep inside convolutional networks: Visualising image classification models and saliency maps.
arXiv preprint arXiv:1312.6034 (2013)
Question: How can I implement this method in PyTorch?
If I understand correctly, vanilla gradient visualization consists in computing the partial derivatives of the loss of my model w.r.t all the pixels in my input image. So to make it short, I need to tweek my self.conv1 layer so that it computes the gradient over its input pixels instead of the gradient over its weights.
Please correct me if I'm wrong.
You do not need to change anything about your conv layer. Each layer computes gradients both w.r.t. parameters (for updates) and w.r.t. inputs (for "downstream" gradients by the chain rule). Therefore, all you need is to set your input image's x gradient property to true:
x, y = ... # get one image from MNIST
x.requires_grad_(True) # indicate to pytorch that you would like to look at these gradients
pred = model(x)
loss = criterion(pred, y)
loss.backward() # propagate gradients
x.grad # <- here you should have the gradients of the loss w.r.t pixels

Pytorch many-to-many time series LSTM always predicts the mean

I want to create an LSTM model using pytorch that takes multiple time series and creates predictions of all of them, a typical "many-to-many" LSTM network.
I am able to achieve what I want in keras. I create a set of data with three variables which are simply linearly spaced with some gaussian noise. Training the keras model I get a prediction 12 steps ahead that is reasonable.
When I try the same thing in pytorch the, model will always predict the mean of the input data. This is confirmed when looking at the loss during training I can see that the model never seems to perform better than just predicting the mean.
TL;DR; The question is: How can I achieve the same thing in pytorch as in the keras example in the gist below?
Full working examples are available here https://gist.github.com/jonlachmann/5cd68c9667a99e4f89edc0c307f94ddb
The keras network is defined as
model = Sequential()
model.add(LSTM(100, activation='relu', return_sequences=True, input_shape=(n_steps, n_features)))
model.add(LSTM(100, activation='relu'))
model.add(Dense(n_features))
model.compile(optimizer='adam', loss='mse')
and the pytorch network is
# Define the pytorch model
class torchLSTM(torch.nn.Module):
def __init__(self, n_features, seq_length):
super(torchLSTM, self).__init__()
self.n_features = n_features
self.seq_len = seq_length
self.n_hidden = 100 # number of hidden states
self.n_layers = 1 # number of LSTM layers (stacked)
self.l_lstm = torch.nn.LSTM(input_size=n_features,
hidden_size=self.n_hidden,
num_layers=self.n_layers,
batch_first=True)
# according to pytorch docs LSTM output is
# (batch_size,seq_len, num_directions * hidden_size)
# when considering batch_first = True
self.l_linear = torch.nn.Linear(self.n_hidden * self.seq_len, 3)
def init_hidden(self, batch_size):
# even with batch_first = True this remains same as docs
hidden_state = torch.zeros(self.n_layers, batch_size, self.n_hidden)
cell_state = torch.zeros(self.n_layers, batch_size, self.n_hidden)
self.hidden = (hidden_state, cell_state)
def forward(self, x):
batch_size, seq_len, _ = x.size()
lstm_out, self.hidden = self.l_lstm(x, self.hidden)
# lstm_out(with batch_first = True) is
# (batch_size,seq_len,num_directions * hidden_size)
# for following linear layer we want to keep batch_size dimension and merge rest
# .contiguous() -> solves tensor compatibility error
x = lstm_out.contiguous().view(batch_size, -1)
return self.l_linear(x)

Measuring uncertainty using MC Dropout on pytorch

I am trying to implement Bayesian CNN using Mc Dropout on Pytorch,
the main idea is that by applying dropout at test time and running over many forward passes , you get predictions from a variety of different models.
I’ve found an application of the Mc Dropout and I really did not get how they applied this method and how exactly they did choose the correct prediction from the list of predictions
here is the code
def mcdropout_test(model):
model.train()
test_loss = 0
correct = 0
T = 100
for data, target in test_loader:
if args.cuda:
data, target = data.cuda(), target.cuda()
data, target = Variable(data, volatile=True), Variable(target)
output_list = []
for i in xrange(T):
output_list.append(torch.unsqueeze(model(data), 0))
output_mean = torch.cat(output_list, 0).mean(0)
test_loss += F.nll_loss(F.log_softmax(output_mean), target, size_average=False).data[0] # sum up batch loss
pred = output_mean.data.max(1, keepdim=True)[1] # get the index of the max log-probability
correct += pred.eq(target.data.view_as(pred)).cpu().sum()
test_loss /= len(test_loader.dataset)
print('\nMC Dropout Test set: Average loss: {:.4f}, Accuracy: {}/{} ({:.2f}%)\n'.format(
test_loss, correct, len(test_loader.dataset),
100. * correct / len(test_loader.dataset)))
train()
mcdropout_test()
I have replaced
data, target = Variable(data, volatile=True), Variable(target)
by adding
with torch.no_grad(): at the beginning
And this is how I have defined my CNN
class Net(nn.Module):
def __init__(self):
super(Net, self).__init__()
self.conv1 = nn.Conv2d(3, 192, 5, padding=2)
self.pool = nn.MaxPool2d(2, 2)
self.conv2 = nn.Conv2d(192, 192, 5, padding=2)
self.fc1 = nn.Linear(192 * 8 * 8, 1024)
self.fc2 = nn.Linear(1024, 256)
self.fc3 = nn.Linear(256, 10)
self.dropout = nn.Dropout(p=0.3)
nn.init.xavier_uniform_(self.conv1.weight)
nn.init.constant_(self.conv1.bias, 0.0)
nn.init.xavier_uniform_(self.conv2.weight)
nn.init.constant_(self.conv2.bias, 0.0)
nn.init.xavier_uniform_(self.fc1.weight)
nn.init.constant_(self.fc1.bias, 0.0)
nn.init.xavier_uniform_(self.fc2.weight)
nn.init.constant_(self.fc2.bias, 0.0)
nn.init.xavier_uniform_(self.fc3.weight)
nn.init.constant_(self.fc3.bias, 0.0)
def forward(self, x):
x = self.pool(F.relu(self.dropout(self.conv1(x)))) # recommended to add the relu
x = self.pool(F.relu(self.dropout(self.conv2(x)))) # recommended to add the relu
x = x.view(-1, 192 * 8 * 8)
x = F.relu(self.fc1(x))
x = F.relu(self.fc2(self.dropout(x)))
x = self.fc3(self.dropout(x)) # no activation function needed for the last layer
return x
Can anyone help me to get the right implementation of the Monte Carlo Dropout method on CNN?
Implementing MC Dropout in Pytorch is easy. All that is needed to be done is to set the dropout layers of your model to train mode. This allows for different dropout masks to be used during the different various forward passes. Below is an implementation of MC Dropout in Pytorch illustrating how multiple predictions from the various forward passes are stacked together and used for computing different uncertainty metrics.
import sys
import numpy as np
import torch
import torch.nn as nn
def enable_dropout(model):
""" Function to enable the dropout layers during test-time """
for m in model.modules():
if m.__class__.__name__.startswith('Dropout'):
m.train()
def get_monte_carlo_predictions(data_loader,
forward_passes,
model,
n_classes,
n_samples):
""" Function to get the monte-carlo samples and uncertainty estimates
through multiple forward passes
Parameters
----------
data_loader : object
data loader object from the data loader module
forward_passes : int
number of monte-carlo samples/forward passes
model : object
keras model
n_classes : int
number of classes in the dataset
n_samples : int
number of samples in the test set
"""
dropout_predictions = np.empty((0, n_samples, n_classes))
softmax = nn.Softmax(dim=1)
for i in range(forward_passes):
predictions = np.empty((0, n_classes))
model.eval()
enable_dropout(model)
for i, (image, label) in enumerate(data_loader):
image = image.to(torch.device('cuda'))
with torch.no_grad():
output = model(image)
output = softmax(output) # shape (n_samples, n_classes)
predictions = np.vstack((predictions, output.cpu().numpy()))
dropout_predictions = np.vstack((dropout_predictions,
predictions[np.newaxis, :, :]))
# dropout predictions - shape (forward_passes, n_samples, n_classes)
# Calculating mean across multiple MCD forward passes
mean = np.mean(dropout_predictions, axis=0) # shape (n_samples, n_classes)
# Calculating variance across multiple MCD forward passes
variance = np.var(dropout_predictions, axis=0) # shape (n_samples, n_classes)
epsilon = sys.float_info.min
# Calculating entropy across multiple MCD forward passes
entropy = -np.sum(mean*np.log(mean + epsilon), axis=-1) # shape (n_samples,)
# Calculating mutual information across multiple MCD forward passes
mutual_info = entropy - np.mean(np.sum(-dropout_predictions*np.log(dropout_predictions + epsilon),
axis=-1), axis=0) # shape (n_samples,)
Moving on to the implementation which is posted in the question above, multiple predictions from T different forward passes are obtained by first setting the model to train mode (model.train()). Note that this is not desirable because unwanted stochasticity will be introduced in the predictions if there are layers other than dropout such as batch-norm in the model. Hence the best way is to just set the dropout layers to train mode as shown in the snippet above.

Changing input dimension for AlexNet

I am beginner and I am trying to implement AlexNet for image classification. The pytorch implementation of AlexNet is as follows:
class AlexNet(nn.Module):
def __init__(self, num_classes=1000):
super(AlexNet, self).__init__()
self.features = nn.Sequential(
nn.Conv2d(3, 64, kernel_size=11, stride=4, padding=2),
nn.ReLU(inplace=True),
nn.MaxPool2d(kernel_size=3, stride=2),
nn.Conv2d(64, 192, kernel_size=5, padding=2),
nn.ReLU(inplace=True),
nn.MaxPool2d(kernel_size=3, stride=2),
nn.Conv2d(192, 384, kernel_size=3, padding=1),
nn.ReLU(inplace=True),
nn.Conv2d(384, 256, kernel_size=3, padding=1),
nn.ReLU(inplace=True),
nn.Conv2d(256, 256, kernel_size=3, padding=1),
nn.ReLU(inplace=True),
nn.MaxPool2d(kernel_size=3, stride=2),
)
self.avgpool = nn.AdaptiveAvgPool2d((6, 6))
self.classifier = nn.Sequential(
nn.Dropout(),
nn.Linear(256 * 6 * 6, 4096),
nn.ReLU(inplace=True),
nn.Dropout(),
nn.Linear(4096, 4096),
nn.ReLU(inplace=True),
nn.Linear(4096, num_classes),
)
def forward(self, x):
x = self.features(x)
x = self.avgpool(x)
x = x.view(x.size(0), 256 * 6 * 6)
x = self.classifier(x)
return x
However I am trying to implement the network for a input size of (3,448,224) with num of classes = 8.
I have no idea on how to change x.view in the forward method and how many layers I should drop to get optimum performance. Please help.
As stated in https://github.com/pytorch/vision/releases:
Since, most of the pretrained models provided in torchvision (the newest version) already added self.avgpool = nn.AdaptiveAvgPool2d((size, size)) to resolve the incompatibility with input size. So you don't have to care about it so much.
Below is the code, very short.
import torchvision
import torch.nn as nn
num_classes = 8
model = torchvision.models.alexnet(pretrained=True)
# replace the last classifier
model.classifier[6] = nn.Linear(4096, num_classes)
# now you can trained it with your dataset of size (3, 448, 224)
Transfer learning
There are two popular ways to do transfer learning. Suppose that we trained a model M in very large dataset D_large, now we would like to transfer the "knowledge" learned by the model M to our new model, M', on other datasets such as D_other (which has a smaller size than that of D_large).
Use (most) parts of M as the architecture of our new M' and initialize those parts with the weights trained on D_large. We can start training the model M' on the dataset D_other and let it learn the weights of those above parts from M to find the optimal weights on our new dataset. This is usually referred as fine-tuning the model M'.
Same as the above method except that before training M' we freeze all the parameters of those parts and start training M' on our dataset D_other. In both cases, those parts from M are mostly the first components in the model M' (the base). However, in this case, we refer those parts of M as the model to extract the features from the input dataset (or feature extractor). The accuracy obtained from the two methods may differ a little to some extent. However, this method guarantees the model doesn't overfit on the small dataset. It's a good point in terms of accuracy. On the other hands, when we freeze the weights of M, we don't need to store some intermediate values (the hidden outputs from each hidden layer) in the forward pass and also don't need to compute the gradients during the backward pass. This improves the speed of training and reduces the memory required during training.
The implementation
Along with Alexnet, a lot of pretrained models on ImageNet is already provided by Facebook team such as ResNet, VGG.
To fit your requirements the most in the aspect of model size, it would be nice to use VGG11, and ResNet which have fewest parameters in their model family.
I just pick VGG11 as an example:
Obtain a pretrained model from torchvision.
Freeze the all the parameters of this model.
Replace the last layer in the model by your new Linear layer to perform your classification. This means that you can reuse all most everything of M to M'.
import torchvision
# obtain the pretrained model
model = torchvision.models.vgg11(pretrained=True)
# freeze the params
for param in net.parameters():
param.requires_grad = False
# replace with your classifier
num_classes = 8
net.classifier[6] = nn.Linear(in_features=4096, out_features=num_classes)
# start training with your dataset
Warnings
In the old torchvision package version, there is no self.avgpool = nn.AdaptiveAvgPool2d((size, size)) which makes harder to train on our input size which is different from [3, 224, 224] used in training ImageNet. You can do a little effort as below:
class OurVGG11(nn.Module):
def __init__(self, num_classes=8):
super(OurVGG11, self).__init__()
self.vgg11 = torchvision.models.vgg11(pretrained=True)
for param in self.vgg11.parameters():
param.requires_grad = False
# Add a avgpool here
self.avgpool = nn.AdaptiveAvgPool2d((7, 7))
# Replace the classifier layer
self.vgg11.classifier[-1] = nn.Linear(4096, num_classes)
def forward(self, x):
x = self.vgg11.features(x)
x = self.avgpool(x)
x = x.view(x.size(0), 512 * 7 * 7)
x = self.vgg11.classifier(x)
return x
model = OurVGG11()
# now start training `model` on our dataset.
Try out with different models in torchvision.models.

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