Self-supervised learning holds promise to revolutionize molecule property prediction -a central task to drug discovery and many more industries -by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a wide range of molecule property prediction tasks.

Recently there has been increasing interest in developing and deploying deep graph learning algorithms for many graph analysis tasks such as node and edge classification, link prediction, and clustering with numerous practical applications such as fraud detection, drug discovery, or recommender systems. Allbeit there is a limited number of publicly available graph-structured datasets, most of which are tiny compared to production-sized applications with trillions of edges and billions of nodes. Further, new algorithms and models are benchmarked across similar datasets with similar properties. In this work, we tackle this shortcoming by proposing a scalable synthetic graph generation tool that can mimic the original data distribution of real-world graphs and scale them to arbitrary sizes. This tool can be used then to learn a set of parametric models from proprietary datasets that can subsequently be released to researchers to study various graph methods on the synthetic data increasing prototype development and novel applications. Finally, the performance of the graph learning algorithms depends not only on the size but also on the dataset's structure. We show how our framework generalizes across a set of datasets, mimicking both structural and feature distributions as well as its scalability across varying dataset sizes. * equal contribution Preprint. Under review.