Conditional Constrained Graph Variational Autoencoders for Molecule Design

In recent years, deep generative models for graphs have been used to generate new molecules. These models have produced good results, leading to several proposals in the literature. However, these models may have troubles learning some of the complex laws governing the chemical world. In this work, we explore the usage of the histogram of atom valences to drive the generation of molecules in such models. We present Conditional Constrained Graph Variational Autoencoder (CCGVAE), a model that implements this key-idea in a state-of-the-art model, and shows improved results on several evaluation metrics on two commonly adopted datasets for molecule generation

Learning Multimodal Graph-to-Graph Translation for Molecular Optimization

We view molecular optimization as a graph-to-graph translation problem. The goal is to learn to map from one molecular graph to another with better properties based on an available corpus of paired molecules. Since molecules can be optimized in different ways, there are multiple viable translations for each input graph. A key challenge is therefore to model diverse translation outputs. Our primary contributions include a junction tree encoder-decoder for learning diverse graph translations along with a novel adversarial training method for aligning distributions of molecules. Diverse output distributions in our model are explicitly realized by low-dimensional latent vectors that modulate the translation process. We evaluate our model on multiple molecular optimization tasks and show that our model outperforms previous state-of-the-art baselines

Gravity-Inspired Graph Autoencoders for Directed Link Prediction

Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged as powerful node embedding methods. In particular, graph AE and VAE were successfully leveraged to tackle the challenging link prediction problem, aiming at figuring out whether some pairs of nodes from a graph are connected by unobserved edges. However, these models focus on undirected graphs and therefore ignore the potential direction of the link, which is limiting for numerous real-life applications. In this paper, we extend the graph AE and VAE frameworks to address link prediction in directed graphs. We present a new gravity-inspired decoder scheme that can effectively reconstruct directed graphs from a node embedding. We empirically evaluate our method on three different directed link prediction tasks, for which standard graph AE and VAE perform poorly. We achieve competitive results on three real-world graphs, outperforming several popular baselines.Comment: ACM International Conference on Information and Knowledge Management (CIKM 2019