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Graph Convolution Network, molecule activity

Posted 2 years ago

I am trying to translate an example code for graph convolution network from Deep Learning for Physical Scientists: Accelerating Research with Machine Learning. Edward O. Pyzer-Knapp et. al. They have an example (Chapter 6, Section 6.3, Page 104-106) where they build a graph convolution network using Keras.

The model takes a 132*132 adjacency matrix built out of molecule connectivity, with a flag of 1 or 0 for active or inactive molecule.

from tensorflow.keras import datasets, layers, models 
 from sklearn.model_selection import train_test_split 
 model = models.Sequential() 
 model.add(layers.Conv2D(64, (3, 3), activation='relu', input_shape=(None, None, 1), padding='SAME')) 
 model.add(layers.MaxPooling2D((2, 2))) 
 model.add(layers.Conv2D(32, (3, 3), activation='relu')) 
 model.add(layers.GlobalMaxPooling2D()) 
 model.add(layers.Dense(2, activation='softmax')) 
 model.compile(optimizer='adam', 
               loss='sparse_categorical_crossentropy', 
               metrics=['accuracy']) 

I would like to build this model in WL. My attempt thus far is

net = NetChain[{ConvolutionLayer[64, {3, 3}], 
   ElementwiseLayer["ReLU"], PoolingLayer[{2, 2}, "Function" -> Max], 
   ConvolutionLayer[32, {2, 2}], 
   PoolingLayer[{2, 2}, "Function" -> Max], LinearLayer[2], 
   SoftmaxLayer[]}]

I can't find the GlobalMaxPooling option, and I am uncertain if my convolution layers are set up correctly. I appreciate if anyone could show how this could be done.

Thank you,

POSTED BY: Arun Sharma

What you are looking for seems to be AggregationLayer[Max] which will take [channels, height, width] and return [channels] using Max to aggregate the other dimensions.

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