Mohamed M. Ahmed

Rim Assouel, Mohamed Ahmed, Marwin H Segler et al.

Generating novel molecules with optimal properties is a crucial step in many industries such as drug discovery. Recently, deep generative models have shown a promising way of performing de-novo molecular design. Although graph generative models are currently available they either have a graph size dependency in their number of parameters, limiting their use to only very small graphs or are formulated as a sequence of discrete actions needed to construct a graph, making the output graph non-differentiable w.r.t the model parameters, therefore preventing them to be used in scenarios such as conditional graph generation. In this work we propose a model for conditional graph generation that is computationally efficient and enables direct optimisation of the graph. We demonstrate favourable performance of our model on prototype-based molecular graph conditional generation tasks.

Mathias Niepert, Mohamed Ahmed, Konstantin Kutzkov

Numerous important problems can be framed as learning from graph data. We propose a framework for learning convolutional neural networks for arbitrary graphs. These graphs may be undirected, directed, and with both discrete and continuous node and edge attributes. Analogous to image-based convolutional networks that operate on locally connected regions of the input, we present a general approach to extracting locally connected regions from graphs. Using established benchmark data sets, we demonstrate that the learned feature representations are competitive with state of the art graph kernels and that their computation is highly efficient.