Learning Multimodal Graph-to-Graph Translation for Molecule Optimization

Wengong Jin, Kevin Yang, Regina Barzilay, Tommi Jaakkola

Abstract: We view molecule 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 molecule optimization tasks and show that our model outperforms previous state-of-the-art baselines by a significant margin.

Keywords: graph-to-graph translation, graph generation, molecular optimization

TL;DR: We introduce a graph-to-graph encoder-decoder framework for learning diverse graph translations.