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A generalization of Convolutional Neural Networks to Graph-Structured Data

This is supplementary code to "A generalization of Convolutional Neural Networks to Graph-Structured Data", by Yotam Hechtlinger, Purvasha Chakravarti and Jining Qin.

Basic example

The graph convolution is implemented as a Keras layer, receiving as an argument an index matrix denoting the nodes proximity according to the expected number of visits. The implementation details are discussed in the paper.

from kears.models import Sequential
from graph_convolution import GraphConv

g_model = Sequential()
g_model.add(GraphConv(filters=filters, neighbors_ix_mat=neighbors_ix_mat, 
                      num_neighbors=num_neighbors, input_shape=(1000,1)))

Merck Dataset

The DPP4 dataset is part of the Merck Molecular Activity Challenge, a previous Kaggle competition. The data used here was downloaded from the supplementary material of the paper "Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships" by Ma et al.

Dependencies

Requires Keras version 2.0.0 or higher running the Theano backend.