SAF: Smart Aggregation Framework for Revealing Atoms Importance Rank and
  Improving Prediction Rates in Drug Discovery
Ronen Taub Yonatan Savir
Machine learning, and representation learning in particular, has the
potential to facilitate drug discovery by screening a large chemical space in
silico. A successful approach for representing molecules is to treat them as a
graph and utilize graph neural networks. One of the key limitations of such
methods is the necessity to represent compounds with different numbers of
atoms, which requires aggregating the atom's information. Common aggregation
operators, such as averaging, result in loss of information at the atom level.
In this work, we propose a novel aggregating approach where each atom is
weighted non-linearly using the Boltzmann distribution with a hyperparameter
analogous to temperature. We show that using this weighted aggregation improves
the ability of the gold standard message-passing neural network to predict
antibiotic activity. Moreover, by changing the temperature hyperparameter, our
approach can reveal the atoms that are important for activity prediction in a
smooth and consistent way, thus providing a novel, regulated attention
mechanism for graph neural networks. We further validate our method by showing
that it recapitulates the functional group in beta-Lactam antibiotics. The
ability of our approach to rank the atoms' importance for a desired function
can be used within any graph neural network to provide interpretability of the
results and predictions at the node level.