Data-Driven Approach to Encoding and Decoding 3-D Crystal Structures

Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. However, many molecules require 3-D descriptors and exceed the chemical complexity of commonly used dataset. We present a method to encode and decode the position of atoms in 3-D molecules from a dataset of nearly 50,000 stable crystal unit cells that vary from containing 1 to over 100 atoms. We construct a smooth and continuous 3-D density representation of each crystal based on the positions of different atoms. Two different neural networks were trained on a dataset of over 120,000 three-dimensional samples of single and repeating crystal structures, made by rotating the single unit cells. The first, an Encoder-Decoder pair, constructs a compressed latent space representation of each molecule and then decodes this description into an accurate reconstruction of the input. The second network segments the resulting output into atoms and assigns each atom an atomic number. By generating compressed, continuous latent spaces representations of molecules we are able to decode random samples, interpolate between two molecules, and alter known molecules.

InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization

This paper studies learning the representations of whole graphs in both unsupervised and semi-supervised scenarios. Graph-level representations are critical in a variety of real-world applications such as predicting the properties of molecules and community analysis in social networks. Traditional graph kernel based methods are simple, yet effective for obtaining fixed-length representations for graphs but they suffer from poor generalization due to hand-crafted designs. There are also some recent methods based on language models (e.g. graph2vec) but they tend to only consider certain substructures (e.g. subtrees) as graph representatives. Inspired by recent progress of unsupervised representation learning, in this paper we proposed a novel method called InfoGraph for learning graph-level representations. We maximize the mutual information between the graph-level representation and the representations of substructures of different scales (e.g., nodes, edges, triangles). By doing so, the graph-level representations encode aspects of the data that are shared across different scales of substructures. Furthermore, we further propose InfoGraph*, an extension of InfoGraph for semi-supervised scenarios. InfoGraph* maximizes the mutual information between unsupervised graph representations learned by InfoGraph and the representations learned by existing supervised methods. As a result, the supervised encoder learns from unlabeled data while preserving the latent semantic space favored by the current supervised task. Experimental results on the tasks of graph classification and molecular property prediction show that InfoGraph is superior to state-of-the-art baselines and InfoGraph* can achieve performance competitive with state-of-the-art semi-supervised models.

vGraph: A Generative Model for Joint Community Detection and Node Representation Learning

This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are usually independently studied while they are actually highly correlated. We propose a probabilistic generative model called vGraph to learn community membership and node representation collaboratively. Specifically, we assume that each node can be represented as a mixture of communities, and each community is defined as a multinomial distribution over nodes. Both the mixing coefficients and the community distribution are parameterized by the low-dimensional representations of the nodes and communities. We designed an effective variational inference algorithm which regularizes the community membership of neighboring nodes to be similar in the latent space. Experimental results on multiple real-world graphs show that vGraph is very effective in both community detection and node representation learning, outperforming many competitive baselines in both tasks. We show that the framework of vGraph is quite flexible and can be easily extended to detect hierarchical communities.