How to increase batch size in GPT2 training for translation task? - nlp

I am developing a code to use the pre-trained GPT2 model for a machine translation task. The length of my data's word-to-id is 91, and I developed the following code for my model:
import torch
from torch.utils.data import DataLoader
from transformers.models.gpt2.modeling_gpt2 import GPT2Model
# data preparation code
def batch_sequences(x, y, env):
"""
Take as input a list of n sequences (torch.LongTensor vectors) and return
a tensor of size (slen, n) where slen is the length of the longest
sentence, and a vector lengths containing the length of each sentence.
"""
lengths_x = torch.LongTensor([len(s) + 2 for s in x])
lengths_y = torch.LongTensor([len(s) + 2 for s in y])
max_length = max(lengths_x.max().item(), lengths_y.max().item())
sent_x = torch.LongTensor(
max_length, lengths_x.size(0)).fill_(env.pad_index)
sent_y = torch.LongTensor(
max_length, lengths_y.size(0)).fill_(env.pad_index)
assert lengths_x.min().item() > 2
assert lengths_y.min().item() > 2
sent_x[0] = env.eos_index
for i, s in enumerate(x):
sent_x[1:lengths_x[i] - 1, i].copy_(s)
sent_x[lengths_x[i] - 1, i] = env.eos_index
sent_y[0] = env.eos_index
for i, s in enumerate(y):
sent_y[1:lengths_y[i] - 1, i].copy_(s)
sent_y[lengths_y[i] - 1, i] = env.eos_index
return sent_x, sent_y, max_length
def collate_fn(elements):
"""
Collate samples into a batch.
"""
x, y = zip(*elements)
x = [torch.LongTensor([env.word2id[w]
for w in seq if w in env.word2id]) for seq in x]
y = [torch.LongTensor([env.word2id[w]
for w in seq if w in env.word2id]) for seq in y]
x, y, length = batch_sequences(x, y, env)
return (x, length), (y, length), torch.LongTensor(nb_ops)
loader = DataLoader(data, batch_size=1, shuffle=False, collate_fn=collate_fn)
gpt2 = GPT2Model.from_pretrained('gpt2')
in_layer = nn.Embedding(len(env.word2id), 768)
out_layer = nn.Linear(768, len(env.word2id))
parameters = list(gpt2.parameters()) + list(in_layer.parameters()) + list(out_layer.parameters())
optimizer = torch.optim.Adam(parameters)
loss_fn = nn.CrossEntropyLoss()
for layer in (gpt2, in_layer, out_layer):
layer.train()
accuracies = list()
n_epochs = 5
for i in range(n_epochs):
for (x, x_len), (y, y_len) in loader:
x = x.to(device=device)
y = y.to(device=device)
embeddings = in_layer(x.reshape(1, -1))
hidden_state = gpt2(inputs_embeds=embeddings).last_hidden_state[:, :]
logits = out_layer(hidden_state)[0]
loss = loss_fn(logits, y.reshape(-1))
accuracies.append(
(logits.argmax(dim=-1) == y.reshape(-1)).float().mean().item())
optimizer.zero_grad()
loss.backward()
optimizer.step()
if len(accuracies) % 500 == 0:
accuracy = sum(accuracies[-50:]) / len(accuracies[-50:])
print(f'Samples: {len(accuracies)}, Accuracy: {accuracy}')
This code works pretty well when the batch size is 1. But it is so slow. I wanted to increase the batch size from 1 to 32, but I get some dimension compatibility problems. How can I increase the batch size without errors?
My data consists of pair of sentences, the first one is a sentence in the first language and the second one is its translation in the second language.
For example, assume that x.shape is (batch_size, 12) (meaning we have 'batch_size' sentences of length 12 as input and y.shape is also (batch_size, 12) (the translations). And also we have a word-to-id dictionary of length 90 that matches each word in a sentence with its index)

This problem can be solved using padding. We need two special symbols:
code 0 in inputs (x) will denote "blank" tokens that should not be translated.
code -100 in outputs (y) will denote "blank" tokens that should not participate in the calculation of loss. nn.CrossEntropyLoss() is programmed to ignore this value (by the argument ignore_index).
The batch of size 3 could look like this:
x:
[[1, 2, 3, 0, 0],
[ 4, 5, 6, 7, 8],
[ 9, 8, 0, 0, 0]]
y:
[[1, 2, 3, -100, -100],
[ 4, 5, 6, 7, 8],
[ 9, 8, -100, -100, -100]]
You could generate it with code such as:
def pad_sequences(batch, pad_value=0):
n = max(len(v) for v in batch)
return torch.tensor([v + [pad_value] * (n - len(v)) for v in batch])
However, I feel there is an issue with your problem statement. If you perform machine translation, then your inputs and outputs can have different lengths, but your architecture only allows x and y to have the same lengths. If you want to support x and y of different lengths, I would suggest to use a seq2seq architecture such as T5 instead.
Another issue is that GPT is autoregressive, so if y is completely aligned with x, then we cannot use the suffix of x while generating the left part of y. So if you wish your x and y to be perfectly aligned, but still would like to use the full information about x when generating y, I would recommend using a bidirectional encoder such as BERT.

Related

Applying a 2D function to a 4D tensor PyTorch

I got a 2D function that takes a matrix - 2D tensor with shape (28, 28)
and I got a tensor, lets say (64, 10, 28, 28) - it's a tensor that contains a batch of 64 images that passed through a (10 kernels) conv2d layer.
Now, I want to activate on the last two dimentions of the tensor, the (28,28) bit, a 2D function.
Now I did that in a very inefficient way:
def activation_func(input):
for batch_idx in range(input.shape[0]):
for channel_inx in range(input.shape[1]):
input[batch_idx][channel_inx] = 2D_function(input[batch_idx][channel_inx])
return input
which is highly inefficient as I noticed.
is there any way of doing this efficiently?
I can write the entire code If necessary
EDIT:
def 2D_function(input):
global indices # yes I know, I will remove this global stuff later
# indices = [(i, j) for i in range(1, 28, 4) for j in range(1, 28, 4)]
for x, y in indices:
relu_decision = relu(input[x, y]) # standard relu - relu(x)=(x>1)*x
if not relu_decision:
# zero out the patch
input[x - 1: x + 3, y - 1: y + 3] = 0
return input
In such cases, I use a Kronecker product trick:
import torch
torch.set_printoptions(linewidth=200) # you can better see how the mask is shaped
# simulating an input
input = torch.rand(1, 1, 28, 28) - 0.5
ids = torch.meshgrid((torch.arange(1, 28, 4), torch.arange(1, 28, 4)))
# note that relu(x) = (x > 0.) * x, so adjust it to your needs
relus = torch.nn.functional.relu(input[(slice(None), slice(None), *ids)]).to(bool)
A = torch.ones(4, 4)
# generate a block matrix with ones in positions where blocks are set to 0 in correspondence of relus = 0
mask = torch.kron(relus, A)
print(mask.shape)
output = input * mask
print(mask[0, 0])
print(output[0, 0])

CrossEntropyLoss on sequences

I need to compute the torch.nn.CrossEntropyLoss on sequences.
The output tensor y_est has shape: [batch_size, sequence_length, embedding_dim]. The values are embedded as one-hot vectors with embedding_dim dimensions (y_est is not binary however).
The target tensor y has shape: [batch_size, sequence_length] and contains the integer index of the correct class in the range [0, embedding_dim).
If I compute the loss on the two input data, with the shape described above, I get an error 1.
What I would like to do is described by the cycle at [2]. For each sequence in the batch, I would like the sum of the losses computed on each element in the sequence.
After reading the documentation of torch.nn.CrossEntropyLoss I came up with the solution [3], which seems to compute exactly what I want: the losses computed at point [2] and [3] are equale.
However, since .permute(.) returns a view of the original tensor, I am afraid it might mess up the backward propagation on the loss. Somewhere (I do not remember where, sorry) I have read that views should not be used in computing the loss.
Is my solution correct?
import torch
batch_size = 5
seq_len = 10
emb_dim = 100
y_est = torch.randn( (batch_size, seq_len, emb_dim))
y = torch.randint(0, emb_dim, (batch_size, seq_len) )
print("y_est, batch x seq x emb:", y_est.shape)
print("y, batch x seq", y.shape)
loss_fn = torch.nn.CrossEntropyLoss(reduction="none")
# [1]
# loss = loss_fn(y_est, y)
# error:
# RuntimeError: Expected target size [5, 100], got [5, 10]
[2]
loss = 0
for i in range(y_est.shape[1]):
loss += loss_fn ( y_est[:, i, :], y[:, i]).sum()
print(loss)
[3]
y_est_2 = torch.permute( y_est, (0, 2, 1))
print("y_est_2", y_est_2.shape)
loss2 = loss_fn(y_est_2, y).sum()
print(loss2)
whose output is:
y_est, batch x seq x emb: torch.Size([5, 10, 100])
y, batch x seq torch.Size([5, 10])
tensor(253.9994)
y_est_2 torch.Size([5, 100, 10])
tensor(253.9994)
Is the solution correct (also for what concerns the backward pass)? Is there a better way?
If y_est are probabilities you really want to compute the error/loss of a categorical output in each timestep/element of a sequence then y and y_est have to have the same shape. To do so, the categories/classes of y can be expanded to the same dim as y_est with one-hot encoding
import torch
batch_size = 5
seq_len = 10
emb_dim = 100
y_est = torch.randn( (batch_size, seq_len, emb_dim))
y = torch.randint(0, emb_dim, (batch_size, seq_len) )
y = torch.nn.functional.one_hot(y, num_classes=emb_dim).type(torch.float)
loss_fn = torch.nn.CrossEntropyLoss()
loss = loss_fn(y_est, y)
print(loss)

How to properly implement data reorganization using PyTorch?

It's going to be a long post, sorry in advance...
I'm working on a denoising algorithm and my goal is to:
Use PyTorch to design / train the model
Convert the PyTorch model into a CoreML model
The denoising algorithm consists in the following 3 parts:
A "down-sampling" + noise level map
A regular convnet
An "up-sampling"
The first part is quite simple in its idea, but not so easy to explain. Given for instance an input color image and a input value "sigma" that represents the standard deviation of the image noise.
The "down-sampling" part is in fact a space-to-depth. In short, for a given channel and for a subset of 2x2 pixels, the space-to-depth creates a single pixel composed of 4 channels. The number of channels is multiplied by 4 while the height and width are divided by 2. The data is simply reorganized.
The noise level map consists in creating 3 channels containing the standard deviation value so that the convnet knows how to properly denoise the input image.
This will be maybe more clear with some code:
def downsample_and_noise_map(input, sigma):
# Input tensor size (batch, channels, height, width)
in_n, in_c, in_h, in_w = input.size()
# Output tensor size
out_h = in_h // 2
out_w = in_w // 2
sigma_c = in_c # nb of channels of the standard deviation tensor
image_c = in_c * 4 # nb of channels of the image tensor
# Standard deviation tensor
output_sigma = sigma.view(1, 1, 1, 1).repeat(in_n, sigma_c, out_h, out_w)
# Image tensor
output_image = torch.zeros((in_n, image_c, out_h, out_w))
output_image[:, 0::4, :, :] = input[:, :, 0::2, 0::2]
output_image[:, 1::4, :, :] = input[:, :, 0::2, 1::2]
output_image[:, 2::4, :, :] = input[:, :, 1::2, 0::2]
output_image[:, 3::4, :, :] = input[:, :, 1::2, 1::2]
# Concatenate standard deviation and image tensors
return torch.cat((output_sigma, output_image), dim=1)
This function is then called as the first step in the model's forward function:
def forward(self, x, sigma):
x = downsample_and_noise_map(x, sigma)
x = self.convnet(x)
x = upsample(x)
return x
Let's consider an input tensor of size 1x3x100x100 (PyTorch standard: batch, channels, height, width) and a sigma value of 0.1. The output tensor has the following properties:
Tensor's shape is 1x15x50x50
Tensor's values for channels 0, 1 and 2 are all equal to sigma = 0.1
Tensor's values for channels 3, 4, 5, 6 are composed of the input image values of channel 0
Tensor's values for channels 7, 8, 9, 10 are composed of the input image values of channel 1
Tensor's values for channels 11, 12, 13, 14 are composed of the input image values of channel 2
If this code is not clear enough, I can post an even more naive version.
The up-sampling part is the reciprocal function of the downsampling one.
I was able to use this function for training and testing in PyTorch.
Then, I tried to convert the model to CoreML with ONNX as an intermediate step.
The conversion to ONNX generated "TracerWarning". Conversion from ONNX to CoreML failed (TypeError: 1.0 has type numpy.float64, but expected one of: int, long). The problem came from the down-sampling + noise level map (and from up-sampling too).
When I removed the down-sampling + noise level map and up-sampling layers, I was able to convert to ONNX and to CoreML very easily since only a simple convnet remained. This means I have a solution to my problem: implement these 2 layers using 2 shaders on the mobile side. But I'm not satisfied with this solution as I want my model to contain all layers ^^
Before considering writing a post here, I crawled Internet to find an answer and I was able to write a better version of the previous function using reshape and permute. This version removed all ONNX warning, but the CoreML conversion still failed...
def downsample_and_noise_map(input, sigma):
# Input image size
in_n, in_c, in_h, in_w = input.size()
# Output tensor size
out_n = in_n
out_h = in_h // 2
out_w = in_w // 2
# Create standard deviation tensor
output_sigma = sigma.view(out_n, 1, 1, 1).repeat(out_n, in_c, out_h, out_w)
# Split RGB channels
channels_rgb = torch.split(input, 1, dim=1)
# Reshape (space-to-depth) each image channel
channels_reshaped = []
for channel in channels_rgb:
channel = channel.reshape(1, out_h, 2, out_w, 2)
channel = channel.permute(2, 4, 0, 1, 3)
channel = channel.reshape(1, 4, out_h, out_w)
channels_reshaped.append(channel)
# Concatenate all reshaped image channels together
output_image = torch.cat(channels_reshaped, dim=1)
# Concatenate standard deviation and image tensors
output = torch.cat([output_sigma, output_image], dim=1)
return output
So here are (some of) my questions:
What is the preferred PyTorch way to implement a function such as downsample_and_noise_map function within a model?
Same question but when the conversion to ONNX and then to CoreML is part of the equation?
Is the PyTorch -> ONNX -> CoreML still best path to deploy the model for iOS production?
Thanks for your help (and your patience) ^^
Disclaimer I'm not familiar with CoreML or deploying to iOS but I do have experience deploying PyTorch models in TensorRT and OpenVINO via ONNX.
The main issues I've faced when deploying to other frameworks is that operations like slicing and repeating tensors tend to have limited support in other frameworks. Often we can construct equivalent conv or transpose-conv operations which achieve the desired behavior.
In order to ensure we don't export the logic used to construct the conv weights I've separated the weight initialization from the application of the weights. This makes the ONNX export much more straightforward since all it sees is some constant tensors being applied.
class DownsampleAndNoiseMap():
def __init__(self):
self.initialized = False
self.weight = None
self.zeros = None
def init_weights(self, input):
with torch.no_grad():
in_n, in_c, in_h, in_w = input.size()
out_h = int(in_h // 2)
out_w = int(in_w // 2)
sigma_c = in_c
image_c = in_c * 4
# conv weights used for downsampling
self.weight = torch.zeros(image_c, in_c, 2, 2).to(input)
for c in range(in_c):
self.weight[4 * c, c, 0, 0] = 1
self.weight[4 * c + 1, c, 0, 1] = 1
self.weight[4 * c + 2, c, 1, 0] = 1
self.weight[4 * c + 3, c, 1, 1] = 1
# zeros used to replace repeat
self.zeros = torch.zeros(in_n, sigma_c, out_h, out_w).to(input)
self.initialized = True
def __call__(self, input, sigma):
assert self.initialized
output_sigma = self.zeros + sigma
output_image = torch.nn.functional.conv2d(input, self.weight, stride=2)
return torch.cat((output_sigma, output_image), dim=1)
class Upsample():
def __init__(self):
self.initialized = False
self.weight = None
def init_weights(self, input):
with torch.no_grad():
in_n, in_c, in_h, in_w = input.size()
image_c = in_c * 4
self.weight = torch.zeros(in_c + image_c, in_c, 2, 2).to(input)
for c in range(in_c):
self.weight[in_c + 4 * c, c, 0, 0] = 1
self.weight[in_c + 4 * c + 1, c, 0, 1] = 1
self.weight[in_c + 4 * c + 2, c, 1, 0] = 1
self.weight[in_c + 4 * c + 3, c, 1, 1] = 1
self.initialized = True
def __call__(self, input):
assert self.initialized
return torch.nn.functional.conv_transpose2d(input, self.weight, stride=2)
I made the assumption that upsample was the reciprocal of downsample in the sense that x == upsample(downsample_and_noise_map(x, sigma)) (correct me if I'm wrong in this assumption). I also verified that my version of downsample agrees with yours.
# consistency checking code
x = torch.randn(1, 3, 100, 100)
sigma = torch.randn(1)
# OP downsampling
y1 = downsample_and_noise_map(x, sigma)
ds = DownsampleAndNoiseMap()
ds.init_weights(x)
y2 = ds(x, sigma)
print('downsample diff:', torch.sum(torch.abs(y1 - y2)).item())
us = Upsample()
us.init_weights(x)
x_recov = us(ds(x, sigma))
print('recovery error:', torch.sum(torch.abs(x - x_recov)).item())
which results in
downsample diff: 0.0
recovery error: 0.0
Exporting to ONNX
When exporting we need to invoke init_weights for the new classes before using torch.onnx.export. For example
class Model(torch.nn.Module):
def __init__(self):
super().__init__()
self.downsample = DownsampleAndNoiseMap()
self.upsample = Upsample()
self.convnet = lambda x: x # placeholder
def init_weights(self, x):
self.downsample.init_weights(x)
self.upsample.init_weights(x)
def forward(self, x, sigma):
x = self.downsample(x, sigma)
x = self.convnet(x)
x = self.upsample(x)
return x
x = torch.randn(1, 3, 100, 100)
sigma = torch.randn(1)
model = Model()
# ... load state dict here
model.init_weights(x)
torch.onnx.export(model, (x, sigma), 'deploy.onnx', verbose=True, input_names=["input", "sigma"], output_names=["output"])
which gives the ONNX graph
graph(%input : Float(1, 3, 100, 100)
%sigma : Float(1)) {
%2 : Float(1, 3, 50, 50) = onnx::Constant[value=<Tensor>](), scope: Model
%3 : Float(1, 3, 50, 50) = onnx::Add(%2, %sigma), scope: Model
%4 : Float(12, 3, 2, 2) = onnx::Constant[value=<Tensor>](), scope: Model
%5 : Float(1, 12, 50, 50) = onnx::Conv[dilations=[1, 1], group=1, kernel_shape=[2, 2], pads=[0, 0, 0, 0], strides=[2, 2]](%input, %4), scope: Model
%6 : Float(1, 15, 50, 50) = onnx::Concat[axis=1](%3, %5), scope: Model
%7 : Float(15, 3, 2, 2) = onnx::Constant[value=<Tensor>](), scope: Model
%output : Float(1, 3, 100, 100) = onnx::ConvTranspose[dilations=[1, 1], group=1, kernel_shape=[2, 2], pads=[0, 0, 0, 0], strides=[2, 2]](%6, %7), scope: Model
return (%output);
}
As for the last question about the recommended way to deploy on iOS I can't answer that since I don't have experience in that area.

Numpy and tensorflow RNN shape representation mismatch

I'm building my first RNN in tensorflow. After understanding all the concepts regarding the 3D input shape, I came across with this issue.
In my numpy version (1.15.4), the shape representation of 3D arrays is the following: (panel, row, column). I will make each dimension different so that it is clearer:
In [1]: import numpy as np
In [2]: arr = np.arange(30).reshape((2,3,5))
In [3]: arr
Out[3]:
array([[[ 0, 1, 2, 3, 4],
[ 5, 6, 7, 8, 9],
[10, 11, 12, 13, 14]],
[[15, 16, 17, 18, 19],
[20, 21, 22, 23, 24],
[25, 26, 27, 28, 29]]])
In [4]: arr.shape
Out[4]: (2, 3, 5)
In [5]: np.__version__
Out[5]: '1.15.4'
Here my understanding is: I have two timesteps with each timestep having 3 observations with 5 features in each observation.
However, in tensorflow "theory" (which I believe it is strongly based in numpy) RNN cells expect tensors (i.e. just n-dimensional matrices) of shape [batch_size, timesteps, features], which could be translated to: (row, panel, column) in the numpy "jargon".
As can be seen, the representation doesn't match, leading to errors when feeding numpy data into a placeholder, which in most of the examples and theory is defined like:
x = tf.placeholder(tf.float32, shape=[None, N_TIMESTEPS_X, N_FEATURES], name='XPlaceholder')
np.reshape() doesn't solve the issue because it just rearranges the dimensions, but messes up with the data.
I'm using for the first time the Dataset API, but I encounter the problems once into the session, not in the Dataset API ops.
I'm using the static_rnn method, and everything works well until I have to feed the data into the placeholder, which obviously results in a shape error.
I have tried to change the placeholder shape to shape=[N_TIMESTEPS_X, None, N_FEATURES]. HOWEVER, I'm using the dataset API, and I get errors when making the initializer if I change the Xplaceholder to the shape=[N_TIMESTEPS_X, None, N_FEATURES].
So, to summarize:
First problem: Shape errors with different shape representations.
Second problem: Dataset error when equating the shape representations (I think that either static_rnn or dynamic_rnn would function if this is resolved).
My question is:
¿Is there anything I'm missing in regard to this different representation logic which makes the practice confusing?
¿Could the solution be attained to switching to dynamic_rnn? (although the problems about the shape I encounter are related to the dataset API initializer being fed with shape [N_TIMESTEPS_X, None, N_FEATURES], not with the RNN cell itself.
Thank you very much for your time.
Full code:
'''The idea is to create xt, yt, xval and yval. My numpy arrays to
be fed are of the following shapes:
The 3D xt array has a shape of: (11, 69579, 74)
The 3D xval array has a shape of: (11, 7732, 74)
The yt array has a shape of: (69579, 3)
The yval array has a shape of: (7732, 3)
'''
N_TIMESTEPS_X = xt.shape[0] ## The stack number
BATCH_SIZE = 256
#N_OBSERVATIONS = xt.shape[1]
N_FEATURES = xt.shape[2]
N_OUTPUTS = yt.shape[1]
N_NEURONS_LSTM = 128 ## Number of units in the LSTMCell
N_NEURONS_DENSE = 64 ## Number of units in the Dense layer
N_EPOCHS = 600
LEARNING_RATE = 0.1
### Define the placeholders anda gather the data.
train_data = (xt, yt)
validation_data = (xval, yval)
## We define the placeholders as a trick so that we do not break into memory problems, associated with feeding the data directly.
'''As an alternative, you can define the Dataset in terms of tf.placeholder() tensors, and feed the NumPy arrays when you initialize an Iterator over the dataset.'''
batch_size = tf.placeholder(tf.int64)
x = tf.placeholder(tf.float32, shape=[None, N_TIMESTEPS_X, N_FEATURES], name='XPlaceholder')
y = tf.placeholder(tf.float32, shape=[None, N_OUTPUTS], name='YPlaceholder')
# Creating the two different dataset objects.
train_dataset = tf.data.Dataset.from_tensor_slices((x,y)).batch(BATCH_SIZE).repeat()
val_dataset = tf.data.Dataset.from_tensor_slices((x,y)).batch(BATCH_SIZE)
# Creating the Iterator type that permits to switch between datasets.
itr = tf.data.Iterator.from_structure(train_dataset.output_types, train_dataset.output_shapes)
train_init_op = itr.make_initializer(train_dataset)
validation_init_op = itr.make_initializer(val_dataset)
next_features, next_labels = itr.get_next()
### Create the graph
cellType = tf.nn.rnn_cell.LSTMCell(num_units=N_NEURONS_LSTM, name='LSTMCell')
inputs = tf.unstack(next_features, N_TIMESTEPS_X, axis=0)
'''inputs: A length T list of inputs, each a Tensor of shape [batch_size, input_size]'''
RNNOutputs, _ = tf.nn.static_rnn(cell=cellType, inputs=inputs, dtype=tf.float32)
predictionsLayer = tf.layers.dense(inputs=tf.layers.batch_normalization(RNNOutputs[-1]), units=N_NEURONS_DENSE, activation=None, name='Dense_Layer')
### Define the cost function, that will be optimized by the optimizer.
cost = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits_v2(logits=predictionsLayer, labels=next_labels, name='Softmax_plus_Cross_Entropy'))
optimizer_type = tf.train.AdamOptimizer(learning_rate=LEARNING_RATE, name='AdamOptimizer')
optimizer = optimizer_type.minimize(cost)
### Model evaluation
correctPrediction = tf.equal(tf.argmax(predictionsLayer,1), tf.argmax(y,1))
accuracy = tf.reduce_mean(tf.cast(correctPrediction,tf.float32))
#confusionMatrix = tf.confusion_matrix(next_labels, predictionsLayer, num_classes=3, name='ConfMatrix')
N_BATCHES = train_data[0].shape[0] // BATCH_SIZE
## Saving variables so that we can restore them afterwards.
saver = tf.train.Saver()
save_dir = '/home/zmlaptop/Desktop/tfModels/{}_{}'.format(cellType.__class__.__name__, datetime.now().strftime("%Y%m%d%H%M%S"))
os.mkdir(save_dir)
varDict = {'nTimeSteps':N_TIMESTEPS_X, 'BatchSize': BATCH_SIZE, 'nFeatures':N_FEATURES,
'nNeuronsLSTM':N_NEURONS_LSTM, 'nNeuronsDense':N_NEURONS_DENSE, 'nEpochs':N_EPOCHS,
'learningRate':LEARNING_RATE, 'optimizerType': optimizer_type.__class__.__name__}
varDicSavingTxt = save_dir + '/varDict.txt'
modelFilesDir = save_dir + '/modelFiles'
os.mkdir(modelFilesDir)
logDir = save_dir + '/TBoardLogs'
os.mkdir(logDir)
acc_summary = tf.summary.scalar('Accuracy', accuracy)
loss_summary = tf.summary.scalar('Cost_CrossEntropy', cost)
summary_merged = tf.summary.merge_all()
with open(varDicSavingTxt, 'w') as outfile:
outfile.write(repr(varDict))
with tf.Session() as sess:
tf.set_random_seed(2)
sess.run(tf.global_variables_initializer())
train_writer = tf.summary.FileWriter(logDir + '/train', sess.graph)
validation_writer = tf.summary.FileWriter(logDir + '/validation')
# initialise iterator with train data
sess.run(train_init_op, feed_dict = {x : train_data[0], y: train_data[1], batch_size: BATCH_SIZE})
print('¡Training starts!')
for epoch in range(N_EPOCHS):
batchAccList = []
tot_loss = 0
for batch in range(N_BATCHES):
optimizer_output, loss_value, summary = sess.run([optimizer, cost, summary_merged])
accBatch = sess.run(accuracy)
tot_loss += loss_value
batchAccList.append(accBatch)
if batch % 10 == 0:
train_writer.add_summary(summary, batch)
epochAcc = tf.reduce_mean(batchAccList)
if epoch%10 == 0:
print("Epoch: {}, Loss: {:.4f}, Accuracy: {}".format(epoch, tot_loss / N_BATCHES, epochAcc))
#confM = sess.run(confusionMatrix)
#confDic = {'confMatrix': confM}
#confTxt = save_dir + '/confMDict.txt'
#with open(confTxt, 'w') as outfile:
# outfile.write(repr(confDic))
#print(confM)
# initialise iterator with validation data
sess.run(validation_init_op, feed_dict = {x : validation_data[0], y: validation_data[1], batch_size:len(validation_data[0])})
print('Validation Loss: {:4f}, Validation Accuracy: {}'.format(sess.run(cost), sess.run(accuracy)))
summary_val = sess.run(summary_merged)
validation_writer.add_summary(summary_val)
saver.save(sess, modelFilesDir)
Is there anything I'm missing in regard to this different
representation logic which makes the practice confusing?
In fact, you made a mistake about the input shapes of static_rnn and dynamic_rnn. The input shape of static_rnn is [timesteps,batch_size, features](link),which is a list of 2D tensors of shape [batch_size, features]. But The input shape of dynamic_rnn is either [timesteps,batch_size, features] or [batch_size,timesteps, features] depending on time_major is True or False(link).
Could the solution be attained to switching to dynamic_rnn?
The key is not that you use static_rnn or dynamic_rnn, but that your data shape matches the required shape. The general format of placeholder is like your code is [None, N_TIMESTEPS_X, N_FEATURES]. It's also convenient for you to use dataset API.
You can use transpose()(link) instead of reshape().transpose() will permute the dimensions of an array and won't messes up with the data.
So your code needs to be modified.
# permute the dimensions
xt = xt.transpose([1,0,2])
xval = xval.transpose([1,0,2])
# adjust shape,axis=1 represents timesteps
inputs = tf.unstack(next_features, axis=1)
Other errors should have nothing to do with rnn shape.

Embedding 3D data in Pytorch

I want to implement character-level embedding.
This is usual word embedding.
Word Embedding
Input: [ [‘who’, ‘is’, ‘this’] ]
-> [ [3, 8, 2] ] # (batch_size, sentence_len)
-> // Embedding(Input)
# (batch_size, seq_len, embedding_dim)
This is what i want to do.
Character Embedding
Input: [ [ [‘w’, ‘h’, ‘o’, 0], [‘i’, ‘s’, 0, 0], [‘t’, ‘h’, ‘i’, ‘s’] ] ]
-> [ [ [2, 3, 9, 0], [ 11, 4, 0, 0], [21, 10, 8, 9] ] ] # (batch_size, sentence_len, word_len)
-> // Embedding(Input) # (batch_size, sentence_len, word_len, embedding_dim)
-> // sum each character embeddings # (batch_size, sentence_len, embedding_dim)
The final output shape is same as Word embedding. Because I want to concat them later.
Although I tried it, I am not sure how to implement 3-D embedding. Do you know how to implement such a data?
def forward(self, x):
print('x', x.size()) # (N, seq_len, word_len)
bs = x.size(0)
seq_len = x.size(1)
word_len = x.size(2)
embd_list = []
for i, elm in enumerate(x):
tmp = torch.zeros(1, word_len, self.embd_size)
for chars in elm:
tmp = torch.add(tmp, 1.0, self.embedding(chars.unsqueeze(0)))
Above code got an error because output of self.embedding is Variable.
TypeError: torch.add received an invalid combination of arguments - got (torch.FloatTensor, float, Variable), but expected one of:
* (torch.FloatTensor source, float value)
* (torch.FloatTensor source, torch.FloatTensor other)
* (torch.FloatTensor source, torch.SparseFloatTensor other)
* (torch.FloatTensor source, float value, torch.FloatTensor other)
didn't match because some of the arguments have invalid types: (torch.FloatTensor, float, Variable)
* (torch.FloatTensor source, float value, torch.SparseFloatTensor other)
didn't match because some of the arguments have invalid types: (torch.FloatTensor, float, Variable)
Update
I could do this. But for is not effective for batch. Do you guys know more efficient way?
def forward(self, x):
print('x', x.size()) # (N, seq_len, word_len)
bs = x.size(0)
seq_len = x.size(1)
word_len = x.size(2)
embd = Variable(torch.zeros(bs, seq_len, self.embd_size))
for i, elm in enumerate(x): # every sample
for j, chars in enumerate(elm): # every sentence. [ [‘w’, ‘h’, ‘o’, 0], [‘i’, ‘s’, 0, 0], [‘t’, ‘h’, ‘i’, ‘s’] ]
chars_embd = self.embedding(chars.unsqueeze(0)) # (N, word_len, embd_size) [‘w’,‘h’,‘o’,0]
chars_embd = torch.sum(chars_embd, 1) # (N, embd_size). sum each char's embedding
embd[i,j] = chars_embd[0] # set char_embd as word-like embedding
x = embd # (N, seq_len, embd_dim)
Update2
This is my final code. Thank you, Wasi Ahmad!
def forward(self, x):
# x: (N, seq_len, word_len)
input_shape = x.size()
bs = x.size(0)
seq_len = x.size(1)
word_len = x.size(2)
x = x.view(-1, word_len) # (N*seq_len, word_len)
x = self.embedding(x) # (N*seq_len, word_len, embd_size)
x = x.view(*input_shape, -1) # (N, seq_len, word_len, embd_size)
x = x.sum(2) # (N, seq_len, embd_size)
return x
I am assuming you have a 3d tensor of shape BxSxW where:
B = Batch size
S = Sentence length
W = Word length
And you have declared embedding layer as follows.
self.embedding = nn.Embedding(dict_size, emsize)
Where:
dict_size = No. of unique characters in the training corpus
emsize = Expected size of embeddings
So, now you need to convert the 3d tensor of shape BxSxW to a 2d tensor of shape BSxW and give it to the embedding layer.
emb = self.embedding(input_rep.view(-1, input_rep.size(2)))
The shape of emb will be BSxWxE where E is the embedding size. You can convert the resulting 3d tensor to a 4d tensor as follows.
emb = emb.view(*input_rep.size(), -1)
The final shape of emb will be BxSxWxE which is what you are expecting.
What you are looking for is implemented in allennlp TimeDistributed layer
Here is a demonstration:
from allennlp.modules.time_distributed import TimeDistributed
batch_size = 16
sent_len = 30
word_len = 5
Consider a sentence in input:
sentence = torch.randn(batch_size, sent_len, word_len) # suppose is your data
Define a char embedding layer (suppose you have also the input padded):
char_embedding = torch.nn.Embedding(char_vocab_size, char_emd_dim, padding_idx=char_pad_idx)
Wrap it!
embedding_sentence = TimeDistributed(char_embedding)(sentence) # shape: batch_size, sent_len, word_len, char_emb_dim
embedding_sentence has shape batch_size, sent_len, word_len, char_emb_dim
Actually, you can easily redefine a module in PyTorch to do this.

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