We Keep Coding

Adding Dropout Layers to Segmentation_Models Resnet34 with Keras

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

What is the most efficient way to modify a Keras Model?

Is there a way to add nodes to a layer in an existing Keras model? if so, what is the most efficient way to do so?
Also, is it possible to do the same but with layers? i.e. add a new layer to an existing Keras model (for example, right after the input layer).
One way I know of is to use Keras functional API by iterating and cloning each layer of the model in order to create a "copy" of the original model with the desired changes, but is it the most efficient way to accomplish this task?

You can take the output of a layer in a model and build another model starting from it:
import tensorflow as tf
# One simple model
inputs = tf.keras.Input(shape=(3,))
x = tf.keras.layers.Dense(4, activation='relu')(inputs)
outputs = tf.keras.layers.Dense(5, activation='softmax')(x)
model = tf.keras.Model(inputs=inputs, outputs=outputs)
# Make a second model starting from layer in previous model
x2 = tf.keras.layers.Dense(8, activation='relu')(model.layers[1].output)
outputs2 = tf.keras.layers.Dense(7, activation='softmax')(x2)
model2 = tf.keras.Model(inputs=model.input, outputs=outputs2)
Note that in this case model and model2 share the same input layer and first dense layer objects (model.layers[0] is model2.layers[0] and model.layers[1] is model2.layers[1]).

Delete last layer and insert three Conv2D layers in Keras

I have a model in Keras for classification that I trained on some dataset. Call that model "classification_model". That model is saved in "classification.h5". Model for detection is the same, except that we delete last convolutional layer, and add three Conv2D layers of size (3,3). So, our model for detection "detection_model" should look like this:
detection_model = classification_model[: last_conv_index] + Conv2d + Conv2d + Conv2d.
How can we implement that in Keras?

Well, load your classification model and use Keras functional API to construct your new model:
model = load_model("classification.h5")
last_conv_layer_output = model.layers[last_conv_index].output
conv = Conv2D(...)(last_conv_layer_output)
conv = Conv2D(...)(conv)
output = Conv2D(...)(conv)
new_model = Model(model.inputs, output)
# compile the new model and save it ...

Constructing a keras model

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.

Connecting Keras models / replacing input but keeping layers

This questions is similar to Keras replacing input layer.
I have a classifier network and an autoencoder network and I want to use the output of the autoencoder (i.e. encoding + decoding, as a preprocessing step) as the input to the classifier - but after the classifier was already trained on the regular data.
The classification network was built with the functional API like this (based on this example):
clf_input = Input(shape=(28,28,1))
clf_layer = Conv2D(...)(clf_input)
clf_layer = MaxPooling2D(...)(clf_layer)
...
clf_output = Dense(num_classes, activation='softmax')(clf_layer)
model = Model(clf_input, clf_output)
model.compile(...)
model.fit(...)
And the autoencoder like this (based on this example):
ae_input = Input(shape=(28,28,1))
x = Conv2D(...)(ae_input)
x = MaxPooling2D(...)(x)
...
encoded = MaxPooling2D(...)(x)
x = Conv2d(...)(encoded)
x = UpSampling2D(...)(x)
...
decoded = Conv2D(...)(x)
autoencoder = Model(ae_input, decoded)
autoencoder.compile(...)
autoencoder.fit(...)
I can concatenate the two models like this (I still need the original models, hence the copying):
model_copy = keras.models.clone_model(model)
model_copy.set_weights(model.get_weights())
# remove original input layer
model_copy.layers.pop(0)
# set the new input
new_clf_output = model_copy(decoded)
# get the stacked model
stacked_model = Model(ae_input, new_clf_output)
stacked_model.compile(...)
And this works great when all I want to do is apply the model to new test data, but it gives an error on something like this:
for layer in stacked_model.layers:
print layer.get_config()
where it gets to the end of the autoencoder but then fails with a KeyError at the point where the classifier model gets its input. Also when plotting the model with keras.utils.plot_model I get this:
where you can see the autoencoder layers but then at the end, instead of the individual layers from the classifier model, there is only the complete model in one block.
Is there a way to connect two models such the new stacked model is actually made up of all the individual layers?

Ok, what I could come up with is to really manually go through each layer of the model and reconnect them one by one again like this:
l = model.layers[1](decoded) # layer 0 is the input layer, which we're replacing
for i in range(2, len(model.layers)):
l = model.layers[i](l)
stacked_model = Model(ae_input, l)
stacked_model.compile(...)
while this works and produces the correct plot and no errors, this does not seem like the most elegant solution...
(btw, the copying of the model actually seems to be unnecessary as I'm not retraining anything.)