Related
I want to use the Segmentation_Models UNet (with ResNet34 Backbone) for uncertainty estimation, so i want to add some Dropout Layers into the upsampling part. The Model is not Sequential, so i think i have to reconnect some outputs to the new Dropout Layers and the following layer inputs to the output of Dropout.
I'm not sure, whats the right way to do this. I'm currently trying this:
# create model
model = sm.Unet('resnet34', classes=1, activation='sigmoid', encoder_weights='imagenet')
# define optimizer, loss and metrics
optim = tf.keras.optimizers.Adam(0.001)
total_loss = sm.losses.binary_focal_dice_loss # or sm.losses.categorical_focal_dice_loss
metrics = ['accuracy', sm.metrics.IOUScore(threshold=0.5), sm.metrics.FScore(threshold=0.5)]
# get input layer
updated_model_layers = model.layers[0]
# iterate over old model and add Dropout after given Convolutions
for layer in model.layers[1:]:
# take old layer and add to new Model
updated_model_layers = layer(updated_model_layers.output)
# after some convolutions, add Dropout
if layer.name in ['decoder_stage0b_conv', 'decoder_stage0a_conv', 'decoder_stage1a_conv', 'decoder_stage1b_conv', 'decoder_stage2a_conv',
'decoder_stage2b_conv', 'decoder_stage3a_conv', 'decoder_stage3b_conv', 'decoder_stage4a_conv']:
if (uncertain):
# activate dropout in predictions
next_layer = Dropout(0.1) (updated_model_layers, training=True)
else:
# add dropout layer
next_layer = Dropout(0.1) (updated_model_layers)
# add reconnected Droput Layer
updated_model_layers = next_layer
model = Model(model.layers[0], updated_model_layers)
This throws the following Error: AttributeError: 'KerasTensor' object has no attribute 'output'
But I think I'm doing something wrong. Does anybody have a Solution for this?
There is a problem with the Resnet model you are using. It is complex and has Add and Concatenate layers (residual layers, I guess), which take as input a list of tensors from several "subnetworks". In other words, the network is not linear, so you can't walk through the model with a simple loop.
Regarding your error, in the loop of your code: layer is a layer and updated_model_layers is a tensor (functional API). Therefore, updated_model_layers.output does not exist. You confuse the two a bit
I know we can access the hidden layer from each layer by the following code. However, each hidden output we obtains is the result mixed from 12 head by a fully connected layers. Is there a way to obtain the outputs before they enter the fully connected layers?
from transformers import BertModel, BertConfig
config = BertConfig.from_pretrained("xxx", output_hidden_states=True)
model = BertModel.from_pretrained("xxx", config=config)
outputs = model(inputs)
print(len(outputs)) # 3
hidden_states = outputs[2]
Thank you!
I have a Keras LSTM multitask model that performs two tasks. One is a sequence tagging task (so I predict a label per token). The other is a global classification task over the whole sequence using a CNN that is stacked on the hidden states of the LSTM.
In my setup (don't ask why) I only need the CNN task during training, but the labels it predicts have no use on the final product. So, on Keras, one can train a LSTM model without especifiying the input sequence lenght. like this:
l_input = Input(shape=(None,), dtype="int32", name=input_name)
However, if I add the CNN stacked on the LSTM hidden states I need to set a fixed sequence length for the model.
l_input = Input(shape=(timesteps_size,), dtype="int32", name=input_name)
The problem is that once I have trained the model with a fixed timestep_size I can no longer use it to predict longer sequences.
In other frameworks this is not a problem. But in Keras, I cannot get rid of the CNN and change the expected input shape of the model once it has been trained.
Here is a simplified version of the model
l_input = Input(shape=(timesteps_size,), dtype="int32")
l_embs = Embedding(len(input.keys()), 100)(l_input)
l_blstm = Bidirectional(GRU(300, return_sequences=True))(l_embs)
# Sequential output
l_out1 = TimeDistributed(Dense(len(labels.keys()),
activation="softmax"))(l_blstm)
# Global output
conv1 = Conv1D( filters=5 , kernel_size=10 )( l_embs )
conv1 = Flatten()(MaxPooling1D(pool_size=2)( conv1 ))
conv2 = Conv1D( filters=5 , kernel_size=8 )( l_embs )
conv2 = Flatten()(MaxPooling1D(pool_size=2)( conv2 ))
conv = Concatenate()( [conv1,conv2] )
conv = Dense(50, activation="relu")(conv)
l_out2 = Dense( len(global_labels.keys()) ,activation='softmax')(conv)
model = Model(input=input, output=[l_out1, l_out2])
optimizer = Adam()
model.compile(optimizer=optimizer,
loss="categorical_crossentropy",
metrics=["accuracy"])
I would like to know if anyone here has faced this issue, and if there are any solutions to delete layers from a model after training and, more important, how to reshape input layer sizes after training.
Thanks
Variable timesteps length makes a problem not because of using convolution layers (actually the good thing about convolution layers is that they do not depend on the input size). Rather, using Flatten layers cause the problem here since they need an input with specified size. Instead, you can use Global Pooling layers. Further, I think stacking convolution and pooling layers on top of each other might give a better result instead of using two separate convolution layers and merging them (although this depends on the specific problem and dataset you are working on). So considering these two points it might be better to write your model like this:
# Global output
conv1 = Conv1D(filters=16, kernel_size=5)(l_embs)
conv1 = MaxPooling1D(pool_size=2)(conv1)
conv2 = Conv1D(filters=32, kernel_size=5)(conv1)
conv2 = MaxPooling1D(pool_size=2)(conv2)
gpool = GlobalAveragePooling1D()(conv2)
x = Dense(50, activation="relu")(gpool)
l_out2 = Dense(len(global_labels.keys()), activation='softmax')(x)
model = Model(inputs=l_input, outputs=[l_out1, l_out2])
You may need to tune the number of conv+maxpool layers, number of filters, kernel size and even add dropout or batch normalization layers.
As a side note, using TimeDistributed on a Dense layer is redundant as the Dense layer is applied on the last axis.
I don't understand what's happening in this code:
def construct_model(use_imagenet=True):
# line 1: how do we keep all layers of this model ?
model = keras.applications.InceptionV3(include_top=False, input_shape=(IMG_SIZE, IMG_SIZE, 3),
weights='imagenet' if use_imagenet else None) # line 1: how do we keep all layers of this model ?
new_output = keras.layers.GlobalAveragePooling2D()(model.output)
new_output = keras.layers.Dense(N_CLASSES, activation='softmax')(new_output)
model = keras.engine.training.Model(model.inputs, new_output)
return model
Specifically, my confusion is, when we call the last constructor
model = keras.engine.training.Model(model.inputs, new_output)
we specify input layer and output layer, but how does it know we want all the other layers to stay?
In other words, we append the new_output layer to the pre-trained model we load in line 1, that is the new_output layer, and then in the final constructor (final line), we just create and return a model with a specified input and output layers, but how does it know what other layers we want in between?
Side question 1): What is the difference between keras.engine.training.Model and keras.models.Model?
Side question 2): What exactly happens when we do new_layer = keras.layers.Dense(...)(prev_layer)? Does the () operation return new layer, what does it do exactly?
This model was created using the Functional API Model
Basically it works like this (perhaps if you go to the "side question 2" below before reading this it may get clearer):
You have an input tensor (you can see it as "input data" too)
You create (or reuse) a layer
You pass the input tensor to a layer (you "call" a layer with an input)
You get an output tensor
You keep working with these tensors until you have created the entire graph.
But this hasn't created a "model" yet. (One you can train and use other things).
All you have is a graph telling which tensors go where.
To create a model, you define it's start end end points.
In the example.
They take an existing model: model = keras.applications.InceptionV3(...)
They want to expand this model, so they get its output tensor: model.output
They pass this tensor as the input of a GlobalAveragePooling2D layer
They get this layer's output tensor as new_output
They pass this as input to yet another layer: Dense(N_CLASSES, ....)
And get its output as new_output (this var was replaced as they are not interested in keeping its old value...)
But, as it works with the functional API, we don't have a model yet, only a graph. In order to create a model, we use Model defining the input tensor and the output tensor:
new_model = Model(old_model.inputs, new_output)
Now you have your model.
If you use it in another var, as I did (new_model), the old model will still exist in model. And these models are sharing the same layers, in a way that whenever you train one of them, the other gets updated as well.
Question: how does it know what other layers we want in between?
When you do:
outputTensor = SomeLayer(...)(inputTensor)
you have a connection between the input and output. (Keras will use the inner tensorflow mechanism and add these tensors and nodes to the graph). The output tensor cannot exist without the input. The entire InceptionV3 model is connected from start to end. Its input tensor goes through all the layers to yield an ouptut tensor. There is only one possible way for the data to follow, and the graph is the way.
When you get the output of this model and use it to get further outputs, all your new outputs are connected to this, and thus to the first input of the model.
Probably the attribute _keras_history that is added to the tensors is closely related to how it tracks the graph.
So, doing Model(old_model.inputs, new_output) will naturally follow the only way possible: the graph.
If you try doing this with tensors that are not connected, you will get an error.
Side question 1
Prefer to import from "keras.models". Basically, this module will import from the other module:
https://github.com/keras-team/keras/blob/master/keras/models.py
Notice that the file keras/models.py imports Model from keras.engine.training. So, it's the same thing.
Side question 2
It's not new_layer = keras.layers.Dense(...)(prev_layer).
It is output_tensor = keras.layers.Dense(...)(input_tensor).
You're doing two things in the same line:
Creating a layer - with keras.layers.Dense(...)
Calling the layer with an input tensor to get an output tensor
If you wanted to use the same layer with different inputs:
denseLayer = keras.layers.Dense(...) #creating a layer
output1 = denseLayer(input1) #calling a layer with an input and getting an output
output2 = denseLayer(input2) #calling the same layer on another input
output3 = denseLayer(input3) #again
Bonus - Creating a functional model that is equal to a sequential model
If you create this sequential model:
model = Sequential()
model.add(Layer1(...., input_shape=some_shape))
model.add(Layer2(...))
model.add(Layer3(...))
You're doing exactly the same as:
inputTensor = Input(some_shape)
outputTensor = Layer1(...)(inputTensor)
outputTensor = Layer2(...)(outputTensor)
outputTensor = Layer3(...)(outputTensor)
model = Model(inputTensor,outputTensor)
What is the difference?
Well, functional API models are totally free to be build anyway you want. You can create branches:
out1 = Layer1(..)(inputTensor)
out2 = Layer2(..)(inputTensor)
You can join tensors:
joinedOut = Concatenate()([out1,out2])
With this, you can create anything you want with all kinds of fancy stuff, branches, gates, concatenations, additions, etc., which you can't do with a sequential model.
In fact, a Sequential model is also a Model, but created for a quick use in models without branches.
There's this way of building a model from a pretrained one that you may build upon.
See https://keras.io/applications/#fine-tune-inceptionv3-on-a-new-set-of-classes:
base_model = InceptionV3(weights='imagenet', include_top=False)
x = base_model.output
x = GlobalAveragePooling2D()(x)
x = Dense(1024, activation='relu')(x)
predictions = Dense(200, activation='softmax')(x)
model = Model(inputs=base_model.input, outputs=predictions)
for layer in base_model.layers:
layer.trainable = False
model.compile(optimizer='rmsprop', loss='categorical_crossentropy')
Each time a layer is added by an op like "x=Dense(...", information about the computational graph is updated. You can type this interactively to see what it contains:
x.graph.__dict__
You can see there's all kinds of attributes, including about previous and next layers. These are internal implementation details and possibly change over time.
Imagine a fully-connected neural network with its last two layers of the following structure:
[Dense]
units = 612
activation = softplus
[Dense]
units = 1
activation = sigmoid
The output value of the net is 1, but I'd like to know what the input x to the sigmoidal function was (must be some high number, since sigm(x) is 1 here).
Folllowing indraforyou's answer I managed to retrieve the output and weights of Keras layers:
outputs = [layer.output for layer in model.layers[-2:]]
functors = [K.function( [model.input]+[K.learning_phase()], [out] ) for out in outputs]
test_input = np.array(...)
layer_outs = [func([test_input, 0.]) for func in functors]
print layer_outs[-1][0] # -> array([[ 1.]])
dense_0_out = layer_outs[-2][0] # shape (612, 1)
dense_1_weights = model.layers[-1].weights[0].get_value() # shape (1, 612)
dense_1_bias = model.layers[-1].weights[1].get_value()
x = np.dot(dense_0_out, dense_1_weights) + dense_1_bias
print x # -> -11.7
How can x be a negative number? In that case the last layers output should be a number closer to 0.0 than 1.0. Are dense_0_out or dense_1_weights the wrong outputs or weights?
Since you're using get_value(), I'll assume that you're using Theano backend. To get the value of the node before the sigmoid activation, you can traverse the computation graph.
The graph can be traversed starting from outputs (the result of some computation) down to its inputs using the owner field.
In your case, what you want is the input x of the sigmoid activation op. The output of the sigmoid op is model.output. Putting these together, the variable x is model.output.owner.inputs[0].
If you print out this value, you'll see Elemwise{add,no_inplace}.0, which is an element-wise addition op. It can be verified from the source code of Dense.call():
def call(self, inputs):
output = K.dot(inputs, self.kernel)
if self.use_bias:
output = K.bias_add(output, self.bias)
if self.activation is not None:
output = self.activation(output)
return output
The input to the activation function is the output of K.bias_add().
With a small modification of your code, you can get the value of the node before activation:
x = model.output.owner.inputs[0]
func = K.function([model.input] + [K.learning_phase()], [x])
print func([test_input, 0.])
For anyone using TensorFlow backend: use x = model.output.op.inputs[0] instead.
I can see a simple way just changing a little the model structure. (See at the end how to use the existing model and change only the ending).
The advantages of this method are:
You don't have to guess if you're doing the right calculations
You don't need to care about the dropout layers and how to implement a dropout calculation
This is a pure Keras solution (applies to any backend, either Theano or Tensorflow).
There are two possible solutions below:
Option 1 - Create a new model from start with the proposed structure
Option 2 - Reuse an existing model changing only its ending
Model structure
You could just have the last dense separated in two layers at the end:
[Dense]
units = 612
activation = softplus
[Dense]
units = 1
#no activation
[Activation]
activation = sigmoid
Then you simply get the output of the last dense layer.
I'd say you should create two models, one for training, the other for checking this value.
Option 1 - Building the models from the beginning:
from keras.models import Model
#build the initial part of the model the same way you would
#add the Dense layer without an activation:
#if using the functional Model API
denseOut = Dense(1)(outputFromThePreviousLayer)
sigmoidOut = Activation('sigmoid')(denseOut)
#if using the sequential model - will need the functional API
model.add(Dense(1))
sigmoidOut = Activation('sigmoid')(model.output)
Create two models from that, one for training, one for checking the output of dense:
#if using the functional API
checkingModel = Model(yourInputs, denseOut)
#if using the sequential model:
checkingModel = model
trainingModel = Model(checkingModel.inputs, sigmoidOut)
Use trianingModel for training normally. The two models share weights, so training one is training the other.
Use checkingModel just to see the outputs of the Dense layer, using checkingModel.predict(X)
Option 2 - Building this from an existing model:
from keras.models import Model
#find the softplus dense layer and get its output:
softplusOut = oldModel.layers[indexForSoftplusLayer].output
#or should this be the output from the dropout? Whichever comes immediately after the last Dense(1)
#recreate the dense layer
outDense = Dense(1, name='newDense', ...)(softPlusOut)
#create the new model
checkingModel = Model(oldModel.inputs,outDense)
It's important, since you created a new Dense layer, to get the weights from the old one:
wgts = oldModel.layers[indexForDense].get_weights()
checkingModel.get_layer('newDense').set_weights(wgts)
In this case, training the old model will not update the last dense layer in the new model, so, let's create a trainingModel:
outSigmoid = Activation('sigmoid')(checkingModel.output)
trainingModel = Model(checkingModel.inputs,outSigmoid)
Use checkingModel for checking the values you want with checkingModel.predict(X). And train the trainingModel.
So this is for fellow googlers, the working of the keras API has changed significantly since the accepted answer was posted. The working code for extracting a layer's output before activation (for tensorflow backend) is:
model = Your_Keras_Model()
the_tensor_you_need = model.output.op.inputs[0] #<- this is indexable, if there are multiple inputs to this node then you can find it with indexing.
In my case, the final layer was a dense layer with activation softmax, so the tensor output I needed was <tf.Tensor 'predictions/BiasAdd:0' shape=(?, 1000) dtype=float32>.
(TF backend)
Solution for Conv layers.
I had the same question, and to rewrite a model's configuration was not an option.
The simple hack would be to perform the call function manually. It gives control over the activation.
Copy-paste from the Keras source, with self changed to layer. You can do the same with any other layer.
def conv_no_activation(layer, inputs, activation=False):
if layer.rank == 1:
outputs = K.conv1d(
inputs,
layer.kernel,
strides=layer.strides[0],
padding=layer.padding,
data_format=layer.data_format,
dilation_rate=layer.dilation_rate[0])
if layer.rank == 2:
outputs = K.conv2d(
inputs,
layer.kernel,
strides=layer.strides,
padding=layer.padding,
data_format=layer.data_format,
dilation_rate=layer.dilation_rate)
if layer.rank == 3:
outputs = K.conv3d(
inputs,
layer.kernel,
strides=layer.strides,
padding=layer.padding,
data_format=layer.data_format,
dilation_rate=layer.dilation_rate)
if layer.use_bias:
outputs = K.bias_add(
outputs,
layer.bias,
data_format=layer.data_format)
if activation and layer.activation is not None:
outputs = layer.activation(outputs)
return outputs
Now we need to modify the main function a little. First, identify the layer by its name. Then retrieve activations from the previous layer. And at last, compute the output from the target layer.
def get_output_activation_control(model, images, layername, activation=False):
"""Get activations for the input from specified layer"""
inp = model.input
layer_id, layer = [(n, l) for n, l in enumerate(model.layers) if l.name == layername][0]
prev_layer = model.layers[layer_id - 1]
conv_out = conv_no_activation(layer, prev_layer.output, activation=activation)
functor = K.function([inp] + [K.learning_phase()], [conv_out])
return functor([images])
Here is a tiny test. I'm using VGG16 model.
a_relu = get_output_activation_control(vgg_model, img, 'block4_conv1', activation=True)[0]
a_no_relu = get_output_activation_control(vgg_model, img, 'block4_conv1', activation=False)[0]
print(np.sum(a_no_relu < 0))
> 245293
Set all negatives to zero to compare with the results retrieved after an embedded in VGG16 ReLu operation.
a_no_relu[a_no_relu < 0] = 0
print(np.allclose(a_relu, a_no_relu))
> True
easy way to define new layer with new activation function:
def change_layer_activation(layer):
if isinstance(layer, keras.layers.Conv2D):
config = layer.get_config()
config["activation"] = "linear"
new = keras.layers.Conv2D.from_config(config)
elif isinstance(layer, keras.layers.Dense):
config = layer.get_config()
config["activation"] = "linear"
new = keras.layers.Dense.from_config(config)
weights = [x.numpy() for x in layer.weights]
return new, weights
I had the same problem but none of the other answers worked for me. Im using a newer version of Keras with Tensorflow so some answers dont work now. Also the structure of the model is given so i can't change it easely. The general idea is to create a copy of the original model that will work exactly like the original one but spliting the activation from the outputs layers. Once this is done we can easely access the outputs values before the activation is applied.
First we will create a copy of the original model but with no activation on the outputs layers. This will be done using Keras clone_model function (See Docs).
from tensorflow.keras.models import clone_model
from tensorflow.keras.layers import Activation
original_model = get_model()
def f(layer):
config = layer.get_config()
if not isinstance(layer, Activation) and layer.name in original_model.output_names:
config.pop('activation', None)
layer_copy = layer.__class__.from_config(config)
return layer_copy
copy_model = clone_model(model, clone_function=f)
This alone will only make a clone with new weights so we must copy the original_model weights to the new one:
copy_model.build(original_model.input_shape)
copy_model.set_weights(original_model.get_weights())
Now we will add the activations layers:
from tensorflow.keras.models import Model
old_outputs = [ original_model.get_layer(name=name) for name in copy_model.output_names ]
new_outputs = [ Activation(old_output.activation)(output) if old_output.activation else output
for output, old_output in zip(copy_model.outputs, old_outputs) ]
copy_model = Model(copy_model.inputs, new_outputs)
Finally we could create a new model whose evaluation will be the outputs with no activation applied:
no_activation_outputs = [ copy_model.get_layer(name=name).output for name in original_model.output_names ]
no_activation_model = Model(copy.inputs, no_activation_outputs)
Now we could use copy_model like the original_model and no_activation_model to access pre-activation outputs. Actually you could even modify the code to split a custom set of layers instead of the outputs.