Related
TF 2.x - just for the experience I tried with a simple experimental dataset - to show the problem:
import numpy as np
import tensorflow as tf
import keras
from tensorflow.keras.callbacks import LambdaCallback
import tensorflow_datasets as tfds
data, info = tfds.load('iris', split='train[:80%]',
as_supervised=True, with_info=True)
print(info)
features, labels = tuple(zip(*data))
# NB: the generator should yield a dictionary for the inputs, and the output as is.
def gen(x_train, y_train):
print('generator initiated')
(x_train, y_train)= tfds.load('iris', shuffle_files=True, as_supervised=True, with_info=True)
idx = 0
while True:
yield tf.transpose([x_train[:32], tf.one_hot(y_train[:32])])
print('generator yielded a batch %d' % idx)
idx += 1
train_ds = tf.data.Dataset.from_generator(gen, args=(features, labels),
output_types=(tf.float32, tf.int32),
output_shapes=(tf.TensorShape([32,4]), tf.TensorShape([32,4 ])),
)
# OR
#output_signature=(
# tf.TensorSpec(shape=(4,), dtype=tf.float32),
# tf.TensorSpec(shape=(), dtype=tf.int32)),
#)
# datasetGen = iter(train_ds)
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.Dense(512, activation='relu', input_shape=(32,4,))) # 4 fields
model.add(tf.keras.layers.Dense(4, activation='softmax'))
model.compile(optimizer='rmsprop',
loss='categorical_crossentropy',
metrics=['accuracy'])
train_ds= train_ds.batch(32).prefetch(32)
# callbacks=[LambdaCallback(on_epoch_end=generator.on_epoch_end)],
history= model.fit(train_ds, epochs = 7, verbose = 1)
print(history.history['accuracy'])
& am getting :
In ln: yield tf.transpose([x_train[:32], tf.one_hot(y_train[:32])])
TypeError: unhashable type: 'slice'
problem seems to be here - x_train[:32] ?
Q ?? how to make corrections to the code (either to the generator-func? or to the output_signature? or to the input_shape=? or somewhere else) to be able to use Dataset in model.fit() method ?
(sorry for dummy example, but I'd like to test generator-func use in model.fit())
well, it was really a dummy example of generator use; & moreover tf.data always win in speed compared with generator use. Nevertheless, such works (code also needs refactoring - e.g. or organizing pipelines for BigData - e.g.)
import tensorflow as tf
import numpy as np
import pandas as pd
# LOAD DATA
df= pd.read_csv('https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv', dtype = 'float32', converters = {'variety' : str},
nrows=64, decimal='.')
# df.head()
_features=df.iloc[:,:4].copy()
_labels=df.iloc[:,-1:].copy()
_labels['variety1'] = pd.factorize(_labels['variety'])[0]
_target= _labels['variety1'].astype(np.int64).copy()
_targets= _target[:,np.newaxis]
#print(_features)
print(type(_targets))
# SPLIT for Train & Test
# https://www.kdnuggets.com/2020/07/getting-started-tensorflow2.html
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(_features,_targets, test_size=0.3)
# Typically, we normalize the data when we have a high amount of variance in it.
print(X_train.var())
print(X_test.var())
# Here we can see that both X_train and X_test have very low variance, so no need to normalize the data.
# PREPROCESSING
#
# to_categorical
y_train = tf.keras.utils.to_categorical(y_train)
y_test = tf.keras.utils.to_categorical(y_test)
print(y_train[:5,:])
# convert our data to numpy arrays
X_train = X_train.values
X_test = X_test.values
#################################################
#################################################
def gen(_features, _labels):
x_train= _features
y_train= _labels
#print('gen:\n', list(x_train))
#print('gen:\n', list(y_train))
idx = 0
while idx<64:
yield x_train[:32], y_train[:32]
print('generator yielded a batch %d' % idx)
idx += 1
#################################################
# train_ds <<<<<<<<<<<<<<<<<<<<<<<
train_ds = tf.data.Dataset.from_generator(gen, args=(X_train, y_train),
output_types=(tf.float32, tf.int64),
output_shapes=(tf.TensorShape([32,4]), tf.TensorShape([32, 2 ])),
)
# OR
#output_signature=(
# tf.TensorSpec(shape=(4,), dtype=tf.float32),
# tf.TensorSpec(shape=(), dtype=tf.int32)),
#)
# datasetGen = iter(train_ds)
# print('train_ds:\n',list(train_ds.as_numpy_iterator()))
#################################################
# Model
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.Dense((512), activation='relu', input_shape=(32,4 ))) # 4 fields
model.add(tf.keras.layers.Dense((2), activation='softmax'))
# INSTEAD OF ONE-HOT CAN USE sparse_categorical_crossentropy HERE
model.compile(optimizer='rmsprop',
loss='categorical_crossentropy',
metrics=['accuracy'])
train_ds= train_ds.batch(32).prefetch(32)
# callbacks=[LambdaCallback(on_epoch_end=generator.on_epoch_end)],
history= model.fit(train_ds, epochs = 7, verbose = 1)
validation_ ds from source X_test, y_test formed with tf.data.Dataset.from_tensor_slices() have problems with shape (4,) instead of model's input shape (32,4,) - but it is of the inappropriate generator's task at all from the very beginningg, I think... though with train_ds evaluate() & predict() methods works (though that is not the task of ML)
##############################################
score = model.evaluate(train_ds, batch_size=32, verbose=1) # test_ds needed
print("Test Accuracy:", score[1])
y_pred = model.predict(train_ds)
print('PREDICTIONS:\n', y_pred)
##############################################
#https://medium.com/#nutanbhogendrasharma/tensorflow-deep-learning-model-with-iris-dataset-8ec344c49f91
#Print actual and predicted value
features, labels = tuple(zip(*train_ds)) # If you need the numpy array version, convert them using np.array(): # https://stackoverflow.com/a/65499385/15893581
actual = np.argmax(labels,axis=-1)
predicted = np.argmax(y_pred,axis=-1)
print(f"Actual: {actual}")
print(f"Predicted: {predicted}")
So, incoming test_ds e.g. still needs to be adopted (though better to adopt gen_func here, I think), but overall idea of using generator in TF 2.x is clear now (only if will be used for huge data)...
P.S.
and advice to improve the model here
I apologize for this dummy question, as I'm still a novice in ML, but needed to connect somehow generator & training for the experience
Finally I generated iris_dataset from function (really, not quick operation)... some attention stll needed else to repeat-fn, but code-design in general works (for really random data)
# Importing the tensorflow library
import tensorflow as tf
import numpy as np
import keras
#FeaturesDict({
# 'features': Tensor(shape=(4,), dtype=tf.float32),
# 'label': ClassLabel(shape=(), dtype=tf.int64, num_classes=3),
#})
BATCH_SIZE= 12
EPOCHS = 7
QTY_BATCHES= 10 # to be generated
# The Dataset.from_generator constructor converts the python generator to a fully functional tf.data.Dataset.
def gen():
for i in range(BATCH_SIZE):
# should yield a pair Features - Label
data= np.expand_dims(np.random.sample(4) , axis=0)
label= [np.random.randint(3)]
yield data, label
train_ds = tf.data.Dataset.from_generator(gen,
(tf.float32, tf.int32),
(tf.TensorShape([None,4]),
tf.TensorShape([ 1])))
# Applying the Dataset.repeat() transformation with no arguments will repeat the input indefinitely.
# The Dataset.repeat transformation concatenates its arguments without signaling the end of one epoch and the beginning of the next epoch. Because of this a Dataset.batch applied after Dataset.repeat will yield batches that straddle epoch boundaries:
train_ds= train_ds.repeat(count= EPOCHS*BATCH_SIZE*QTY_BATCHES).batch(BATCH_SIZE, drop_remainder=True).prefetch(BATCH_SIZE)
NUM_CLASSES= 3
train_ds = train_ds.map(lambda x, y: (x, tf.one_hot(y, depth=NUM_CLASSES)))
for x, y in train_ds:
print(x)
print(y)
# Build a simple linear model
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.Dense(64, activation='relu', input_shape=(None,4))) # unknown(variable) batch_size, 4 fields
model.add(tf.keras.layers.Dense(3, activation='softmax'))
model.compile(optimizer='rmsprop',
loss='categorical_crossentropy',
metrics=['accuracy'])
# steps_per_epoch = int( np.ceil(x_train.shape[0] / batch_size) )
# The Steps per epoch denote the number of batches to be selected for one epoch. If 500 steps are selected then the network will train for 500 batches to complete one epoch.
history= model.fit(train_ds, batch_size=BATCH_SIZE, epochs= EPOCHS, \
steps_per_epoch= (QTY_BATCHES*BATCH_SIZE)//BATCH_SIZE, \
verbose = 1)
print(history.history['accuracy'])
print(history.history['loss'])
# Keras - Plot training, validation and test set accuracy
# https://stackoverflow.com/questions/41908379/keras-plot-training-validation-and-test-set-accuracy
import keras
from matplotlib import pyplot as plt
plt.plot(history.history['accuracy'])
#plt.plot(history.history['val_acc'])
plt.title('model accuracy')
plt.ylabel('accuracy')
plt.xlabel('epoch')
#plt.legend(['train', 'val'], loc='upper left')
plt.legend(['train'], loc='upper left')
plt.show()
plt.plot(history.history['loss'])
# plt.plot(history.history['val_loss'])
plt.title('model loss')
plt.ylabel('loss')
plt.xlabel('epoch')
# plt.legend(['train', 'val'], loc='upper left')
plt.legend(['train'], loc='upper left')
plt.show()
ok, I'v got working case for the initial Dataset:
import numpy as np
import tensorflow as tf
import keras
from tensorflow.keras.callbacks import LambdaCallback
import tensorflow_datasets as tfds
data, info = tfds.load('iris', split='train[:100%]', batch_size=10, as_supervised=True, with_info=True)
print(info)
NUM_CLASSES= info.features["label"].num_classes
data = data.map(lambda x, y: (x, tf.one_hot(y, depth=NUM_CLASSES)))
features, labels = tuple(zip(*data))
print(features)
print(labels)
# NB: the generator should yield a dictionary for the inputs, and the output as is.
def gen(x_train, y_train):
print('generator initiated')
print(x_train.shape)
print(y_train.shape)
idx = 0
while True:
yield x_train, y_train
print('generator yielded a batch %d' % idx)
idx += 1
train_ds = tf.data.Dataset.from_generator(gen, args=(features, labels),
output_types=(tf.float32, tf.int32),
output_shapes=(tf.TensorShape([None,10,4]), tf.TensorShape([ None, 10, 3 ])),
)
# OR (better! because prev. is Deprecated)
#output_signature=(
# tf.TensorSpec(shape=(4,), dtype=tf.float32),
# tf.TensorSpec(shape=(), dtype=tf.int32)),
#)
#it = iter(train_ds)
#print(it.get_next())
for feature, label in train_ds:
print("shape of ds_generated: ", feature.shape,label.shape)
break
#num_val = len(train_ds) # TypeError: The dataset length is unknown. BECAUSE it is FLOW
#print(num_val)
model = tf.keras.models.Sequential()
model.add(tf.keras.layers.Dense(512, activation='relu', input_shape=(None,10,4))) # 4 fields
model.add(tf.keras.layers.Dense(3, activation='softmax'))
model.compile(optimizer='rmsprop',
loss='categorical_crossentropy',
metrics=['accuracy'])
train_ds= train_ds.batch(32).prefetch(32)
# callbacks=[LambdaCallback(on_epoch_end=generator.on_epoch_end)],
history= model.fit(train_ds, epochs = 2, steps_per_epoch= 120 // 10, verbose = 1)
print(history.history['accuracy'])
one-hot encoding I've moved out of gen_func-scope
divided DS for features & labels
! gave correct input_shape to model (& appropriate shape changes in gen_func) - according [variable_rows_count_in_batch, batch_size, columns_features]
verbose = 1 for readable Debug in MT env.
advice from here
to define a variable batch size with None and setting the
steps_per_epoch
-- still not helps if taking split='train[:50%]' and steps_per_epoch= 60 // 10, -- as for unfully filled LAST batch -- the source of problem in my code IS in gen_func output_shapes -- that is clear here, because gen_func really was got dummy for testing purposes...
for real cases use Logical Output ! and appropriate Shapes
P.S.
though for 5 epochs I am getting:
Graph execution error: >> ZMQError: Too many open file
AttributeError: '_thread._local' object has no attribute 'event_pipe'
-- ! probably, NOT enough memory to finish training !... - decreasing output in Dense(512,..) HELPS (as well as decreasing number of epochs)
I am trying to solve one problem that resembles that of Fisher's irises classification. The problem is that I can train the model on my computer, but the given model has to predict class membership on a computer where it is impossible to install python and scikit learn. I want to understand how, having received the coefficients of the logistic regression model, I can predict the belonging to a certain class without using the predict method of the model.
Using the Fisher problem as an example, I do the following.
from sklearn.datasets import load_iris
from sklearn.model_selection import train_test_split
import pandas as pd
from sklearn.linear_model import LogisticRegression
from sklearn.preprocessing import StandardScaler
from sklearn.pipeline import make_pipeline
from sklearn.metrics import accuracy_score, f1_score
# data preparation
iris = load_iris()
data = pd.DataFrame(data=np.hstack([iris.data, iris.target[:, np.newaxis]]),
columns=iris.feature_names + ['target'])
names = data.columns
# split data
X_train, X_test, y_train, y_test = train_test_split(data[names[:-1]], data[names[-1]], random_state=42)
# train model
cls = make_pipeline(
StandardScaler(),
LogisticRegression(C=2, random_state=42)
)
cls = cls.fit(X_train.to_numpy(), y_train)
preds_train = cls.predict(X_train)
# prediction
preds_test = cls.predict(X_test)
# scores
train_score = accuracy_score(preds_train, y_train), f1_score(preds_train, y_train, average='macro') # on train data
# train_score = (0.9642857142857143, 0.9653621232568601)
test_score = accuracy_score(preds_test, y_test), f1_score(preds_test, y_test, average='macro') # on test data
# test_score = (1.0, 1.0)
# model coefficients
cls[1].coef_, cls[1].intercept_
>>> (array([[-1.13948079, 1.30623841, -2.21496793, -2.05617771],
[ 0.66515676, -0.2541143 , -0.55819748, -0.86441227],
[ 0.47432404, -1.05212411, 2.77316541, 2.92058998]]),
array([-0.35860337, 2.43929019, -2.08068682]))
Now I have the coefficients of the model. And I want to use them to make predictions.
First, I make a prediction using the predict method for the first five observations on the test sample.
preds_test = cls.predict_proba(X_test)
preds_test[0:5]
>>>array([[5.66019001e-03, 9.18455687e-01, 7.58841233e-02],
[9.75854479e-01, 2.41455095e-02, 1.10881450e-08],
[1.18780156e-09, 6.53295166e-04, 9.99346704e-01],
[6.71574900e-03, 8.14174200e-01, 1.79110051e-01],
[6.98756622e-04, 8.09096425e-01, 1.90204818e-01]])
Then I manually calculate the predictions of the class probabilities for the observations using the coefficients of the model.
# define two functions for making predictions
def logit(x, w):
return np.dot(x, w)
# from here: https://stackoverflow.com/questions/34968722/how-to-implement-the-softmax-function-in-python
def softmax(z):
assert len(z.shape) == 2
s = np.max(z, axis=1)
s = s[:, np.newaxis] # necessary step to do broadcasting
e_x = np.exp(z - s)
div = np.sum(e_x, axis=1)
div = div[:, np.newaxis] # dito
return e_x / div
n, k = X_test.shape
X_ = np.hstack((np.ones((n, 1)), X_test)) # add column with 1 for intercept
weights = np.hstack((cls[1].intercept_[:, np.newaxis], cls[1].coef_)) # create weights matrix
results = softmax(logit(X_, weights.T)) # calculate probabilities
results[0:5]
>>>array([[3.67343725e-14, 4.63938438e-06, 9.99995361e-01],
[2.81976786e-05, 8.63083152e-01, 1.36888650e-01],
[1.24572182e-22, 5.47800683e-11, 1.00000000e+00],
[3.32990060e-14, 3.08352323e-06, 9.99996916e-01],
[2.66415118e-15, 1.78252465e-06, 9.99998217e-01]])
If you compare the two results obtained (preds_test[0:5] and results[0:5]), you can see that they do not coincide at all. Please explain me what I am doing wrong and how I can use the model's coefficients to calculate predictions without using the predict method.
I forgot that a scaler was applied. If you change the code a little, then the results are the same.
scaler = StandardScaler()
scaler.fit(X_train)
X_test_transf = scaler.transform(X_test)
def logit(x, w):
return np.dot(x, w)
def softmax(z):
assert len(z.shape) == 2
s = np.max(z, axis=1)
s = s[:, np.newaxis] # necessary step to do broadcasting
e_x = np.exp(z - s)
div = np.sum(e_x, axis=1)
div = div[:, np.newaxis] # dito
return e_x / div
n, k = X_test_transf.shape
X_ = np.hstack((np.ones((n, 1)), X_test_transf))
weights = np.hstack((cls[1].intercept_[:, np.newaxis], cls[1].coef_))
results = softmax(logit(X_, weights.T))
np.allclose(preds_test, results)
>>>True
There are two values for every predict_proba. The first value is the probability of the event not occurring and the probability of the event occurring. predict_proba(X)[:,1] to get the probability of the event occurring.
I need to calculate the gradient of the validation error w.r.t inputs x. I'm trying to see how much the validation error changes when I perturb one of the training samples.
The validation error (E) explicitly depends on the model weights (W).
The model weights explicitly depend on the inputs (x and y).
Therefore, the validation error implicitly depends on the inputs.
I'm trying to calculate the gradient of E w.r.t x directly.
An alternative approach would be to calculate the gradient of E w.r.t W (can easily be calculated) and the gradient of W w.r.t x (cannot do at the moment), which would allow the gradient of E w.r.t x to be calculated.
I have attached a toy example. Thanks in advance!
import numpy as np
import mnist
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense
from tensorflow.keras.utils import to_categorical
import tensorflow as tf
from autograd import grad
train_images = mnist.train_images()
train_labels = mnist.train_labels()
test_images = mnist.test_images()
test_labels = mnist.test_labels()
# Normalize the images.
train_images = (train_images / 255) - 0.5
test_images = (test_images / 255) - 0.5
# Flatten the images.
train_images = train_images.reshape((-1, 784))
test_images = test_images.reshape((-1, 784))
# Build the model.
model = Sequential([
Dense(64, activation='relu', input_shape=(784,)),
Dense(64, activation='relu'),
Dense(10, activation='softmax'),
])
# Compile the model.
model.compile(
optimizer='adam',
loss='categorical_crossentropy',
metrics=['accuracy'],
)
# Train the model.
model.fit(
train_images,
to_categorical(train_labels),
epochs=5,
batch_size=32,
)
model.save_weights('model.h5')
# Load the model's saved weights.
# model.load_weights('model.h5')
calculate_mse = tf.keras.losses.MeanSquaredError()
test_x = test_images[:5]
test_y = to_categorical(test_labels)[:5]
train_x = train_images[:1]
train_y = to_categorical(train_labels)[:1]
train_y = tf.convert_to_tensor(train_y, np.float32)
train_x = tf.convert_to_tensor(train_x, np.float64)
with tf.GradientTape() as tape:
tape.watch(train_x)
model.fit(train_x, train_y, epochs=1, verbose=0)
valid_y_hat = model(test_x, training=False)
mse = calculate_mse(test_y, valid_y_hat)
de_dx = tape.gradient(mse, train_x)
print(de_dx)
# approach 2 - does not run
def calculate_validation_mse(x):
model.fit(x, train_y, epochs=1, verbose=0)
valid_y_hat = model(test_x, training=False)
mse = calculate_mse(test_y, valid_y_hat)
return mse
train_x = train_images[:1]
train_y = to_categorical(train_labels)[:1]
validation_gradient = grad(calculate_validation_mse)
de_dx = validation_gradient(train_x)
print(de_dx)
Here's how you can do this. Derivation is as below.
Few things to note,
I have reduced the feature size from 784 to 256 as I was running out of memory in colab (line marked in the code) . Might have to do some mem profiling to find out why
Only computed grads for the first layer. Easily extendable to other layers
Disclaimer: this derivation is correct to best of my knowledge. Please do some research and verify that it is the case. You will run into memory issues for larger inputs and layer sizes.
import numpy as np
from tensorflow.keras.models import Sequential
from tensorflow.keras.layers import Dense
from tensorflow.keras.utils import to_categorical
import tensorflow as tf
f = 256
model = Sequential([
Dense(64, activation='relu', input_shape=(f,)),
Dense(64, activation='relu'),
Dense(10, activation='softmax'),
])
# Compile the model.
model.compile(
optimizer='adam',
loss='categorical_crossentropy',
metrics=['accuracy'],
)
w = model.weights[0]
# Inputs and labels
x_tr = tf.Variable(np.random.normal(size=(1,f)), shape=(1, f), dtype='float32')
y_tr = np.random.choice([0,1,2,3,4,5,6,7,8,9], size=(1,1))
y_tr_onehot = tf.keras.utils.to_categorical(y_tr, num_classes=10).astype('float32')
x_v = tf.Variable(np.random.normal(size=(1,f)), shape=(1, f), dtype='float32')
y_v = np.random.choice([0,1,2,3,4,5,6,7,8,9], size=(1,1))
y_v_onehot = tf.keras.utils.to_categorical(y_v, num_classes=10).astype('float32')
# In the context of GradientTape
with tf.GradientTape() as tape1:
with tf.GradientTape() as tape2:
y_tr_pred = model(x_tr)
tr_loss = tf.keras.losses.MeanSquaredError()(y_tr_onehot, y_tr_pred)
tmp_g = tape2.gradient(tr_loss, w)
print(tmp_g.shape)
# d(dE_tr/d(theta))/dx
# Warning this step consumes lot of memory for large layers
lr = 0.001
grads_1 = -lr * tape1.jacobian(tmp_g, x_tr)
with tf.GradientTape() as tape3:
y_v_pred = model(x_v)
v_loss = tf.keras.losses.MeanSquaredError()(y_v_onehot, y_v_pred)
# dE_val/d(theta)
grads_2 = tape3.gradient(v_loss, w)[tf.newaxis, :]
# Just crunching the dimension to get the final desired shape of (1,256)
grad = tf.matmul(tf.reshape(grads_2,[1, -1]), tf.reshape(tf.transpose(grads_1,[2,1,0,3]),[1, -1, 256]))
I want to implement Grad-CAM on my own network, should I save my model and load it, then treat my saved model like VGG-16, then do similar operations?
I tried to search on the internet, and I found that all methods are based on famous models, not their owns.
So I wonder, maybe I just need to treat my own model as VGG-16, then do similar things.
Hi i have one solution in pytorch
import torch
import torch.nn as nn
from torch.utils import data
from torchvision import transforms
from torchvision import datasets
import matplotlib.pyplot as plt
import numpy as np
# use the ImageNet transformation
transform = transforms.Compose([transforms.Resize((224, 224)),
transforms.ToTensor(),
transforms.Normalize(mean=[0.485, 0.456, 0.406], std=[0.229, 0.224, 0.225])])
# define a 1 image dataset
dataset = datasets.ImageFolder(root='./data/Elephant/', transform=transform)
# define the dataloader to load that single image
dataloader = data.DataLoader(dataset=dataset, shuffle=False, batch_size=1)
vgg19 = Mymodel() ## create an object of your model
vgg19.load_state_dict(torch.load("your_vgg19_weights"))
class VGG(nn.Module):
def __init__(self):
super(VGG, self).__init__()
# get the pretrained VGG19 network
self.vgg = vgg19
# disect the network to access its last convolutional layer
self.features_conv = self.vgg.features[:36] # 36th layer was my last conv layer
# get the max pool of the features stem
self.max_pool = nn.MaxPool2d(kernel_size=2, stride=2, padding=0, dilation=1, ceil_mode=False)
# get the classifier of the vgg19
self.classifier = self.vgg.classifier
# placeholder for the gradients
self.gradients = None
# hook for the gradients of the activations
def activations_hook(self, grad):
self.gradients = grad
def forward(self, x):
x = self.features_conv(x)
# register the hook
h = x.register_hook(self.activations_hook)
# apply the remaining pooling
x = self.max_pool(x)
x = x.view((1, -1))
x = self.classifier(x)
return x
# method for the gradient extraction
def get_activations_gradient(self):
return self.gradients
# method for the activation exctraction
def get_activations(self, x):
return self.features_conv(x)
vgg = VGG()
# set the evaluation mode
vgg.eval()
# get the image from the dataloader
img, _ = next(iter(dataloader))
# get the most likely prediction of the model
pred_class = vgg(img).argmax(dim=1).numpy()[0]
pred = vgg(img)
pred[:, pred_class].backward()
# pull the gradients out of the model
gradients = vgg.get_activations_gradient()
# pool the gradients across the channels
pooled_gradients = torch.mean(gradients, dim=[0, 2, 3])
# get the activations of the last convolutional layer
activations = vgg.get_activations(img).detach()
# weight the channels by corresponding gradients
for i in range(512):
activations[:, i, :, :] *= pooled_gradients[i]
# average the channels of the activations
heatmap = torch.mean(activations, dim=1).squeeze()
# relu on top of the heatmap
# expression (2) in https://arxiv.org/pdf/1610.02391.pdf
heatmap = np.maximum(heatmap, 0)
# normalize the heatmap
heatmap /= torch.max(heatmap)
heatmap = heatmap.numpy()
import cv2
img = cv2.imread('./data/Elephant/data/05fig34.jpg')
heatmap = cv2.resize(heatmap, (img.shape[1], img.shape[0]))
heatmap = np.uint8(255 * heatmap)
heatmap = cv2.applyColorMap(heatmap, cv2.COLORMAP_JET)
superimposed_img = heatmap * 0.4 + img
cv2.imwrite('./map.jpg', superimposed_img) ###saves gradcam visualization image
I am trying to use 20 news groups data set available in sklearn to train a LSTM to do incremental learning (classification). I used the sklearn's TfidfVectorizer to pre-process the data. Then I turned the resulting sparse matrix into a numpy array before feeding it. After that when coding the below line:
outputs, final_state = tf.nn.dynamic_rnn(cell, inputs_, initial_state=initial_state)
It gave an error saying that the 'inputs_' should have 3 dimensions. so I used:
inputs_ = tf.expand_dims(inputs_, 0)
To expand the dimension. But when I do that i get the error:
ValueError: Input size (depth of inputs) must be accessible via shape
inference, but saw value None.
The shape of 'input_' is:
(1, 134410)
I already went through this post, but it did not help.
I cannot seem to understand how to solve this issue. Any help is much appreciated. Thank you in advance!
show below is my complete code:
import os
from collections import Counter
import tensorflow as tf
import numpy as np
from sklearn.feature_extraction.text import TfidfVectorizer
from sklearn.datasets import fetch_20newsgroups
import matplotlib as mplt
from matplotlib import cm
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
from sklearn.metrics import f1_score, recall_score, precision_score
from string import punctuation
from sklearn.model_selection import train_test_split
from sklearn.preprocessing import LabelBinarizer
def pre_process():
newsgroups_data = fetch_20newsgroups(subset='all', remove=('headers', 'footers', 'quotes'))
vectorizer = TfidfVectorizer()
features = vectorizer.fit_transform(newsgroups_data.data)
lb = LabelBinarizer()
labels = np.reshape(newsgroups_data.target, [-1])
labels = lb.fit_transform(labels)
return features, labels
def get_batches(x, y, batch_size=1):
for ii in range(0, len(y), batch_size):
yield x[ii:ii + batch_size], y[ii:ii + batch_size]
def plot_error(errorplot, datapoint, numberOfWrongPreds):
errorplot.set_xdata(np.append(errorplot.get_xdata(), datapoint))
errorplot.set_ydata(np.append(errorplot.get_ydata(), numberOfWrongPreds))
errorplot.autoscale(enable=True, axis='both', tight=None)
plt.draw()
def train_test():
features, labels = pre_process()
#Defining Hyperparameters
epochs = 1
lstm_layers = 1
batch_size = 1
lstm_size = 30
learning_rate = 0.003
print(lstm_size)
print(batch_size)
print(epochs)
#--------------placeholders-------------------------------------
# Create the graph object
graph = tf.Graph()
# Add nodes to the graph
with graph.as_default():
tf.set_random_seed(1)
inputs_ = tf.placeholder(tf.float32, [None,None], name = "inputs")
# labels_ = tf.placeholder(dtype= tf.int32)
labels_ = tf.placeholder(tf.int32, [None,None], name = "labels")
#getting dynamic batch size according to the input tensor size
# dynamic_batch_size = tf.shape(inputs_)[0]
#output_keep_prob is the dropout added to the RNN's outputs, the dropout will have no effect on the calculation of the subsequent states.
keep_prob = tf.placeholder(tf.float32, name = "keep_prob")
# Your basic LSTM cell
lstm = tf.contrib.rnn.BasicLSTMCell(lstm_size)
# Add dropout to the cell
drop = tf.contrib.rnn.DropoutWrapper(lstm, output_keep_prob=keep_prob)
#Stack up multiple LSTM layers, for deep learning
cell = tf.contrib.rnn.MultiRNNCell([drop] * lstm_layers)
# Getting an initial state of all zeros
initial_state = cell.zero_state(batch_size, tf.float32)
inputs_ = tf.expand_dims(inputs_, 0)
outputs, final_state = tf.nn.dynamic_rnn(cell, inputs_, initial_state=initial_state)
#hidden layer
hidden = tf.layers.dense(outputs[:, -1], units=25, activation=tf.nn.relu)
logit = tf.contrib.layers.fully_connected(hidden, 1, activation_fn=None)
cost = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(logits=logit, labels=labels_))
optimizer = tf.train.AdamOptimizer(learning_rate).minimize(cost)
saver = tf.train.Saver()
# ----------------------------online training-----------------------------------------
with tf.Session(graph=graph) as sess:
tf.set_random_seed(1)
sess.run(tf.global_variables_initializer())
iteration = 1
state = sess.run(initial_state)
wrongPred = 0
errorplot, = plt.plot([], [])
for ii, (x, y) in enumerate(get_batches(features, labels, batch_size), 1):
feed = {inputs_: x.toarray(),
labels_: y,
keep_prob: 0.5,
initial_state: state}
predictions = tf.round(tf.nn.softmax(logit)).eval(feed_dict=feed)
print("----------------------------------------------------------")
print("Iteration: {}".format(iteration))
print("Prediction: ", predictions)
print("Actual: ",y)
pred = np.array(predictions)
print(pred)
print(y)
if not ((pred==y).all()):
wrongPred += 1
if ii % 27 == 0:
plot_error(errorplot,ii,wrongPred)
loss, states, _ = sess.run([cost, final_state, optimizer], feed_dict=feed)
print("Train loss: {:.3f}".format(loss))
iteration += 1
saver.save(sess, "checkpoints/sentiment.ckpt")
errorRate = wrongPred/len(labels)
print("ERROR RATE: ", errorRate )
if __name__ == '__main__':
train_test()
ValueError: Input size (depth of inputs) must be accessible via shape inference, but saw value None.
This error is given because you don't specify the size nor the amount of inputs.
I got the script working like this:
inputs_ = tf.placeholder(tf.float32, [1,None], name = "inputs")
inputs_withextradim = tf.expand_dims(inputs_, 2)
outputs, final_state = tf.nn.dynamic_rnn(cell, inputs_withextradim, initial_state=initial_state)