Autoencoding Undirected Molecular Graphs With Neural Networks

Abstract: Discrete structure rules for validating molecular structures are usually limited to fulfillment of the octet rule or similar simple deterministic heuristics. We propose a model, inspired by language modeling from natural language processing, with the ability to learn from a collection of undirected molecular graphs, enabling fitting of any underlying structure rule present in the collection. We introduce an adaption to the popular Transformer model, which can learn relationships between atoms and bonds. To our knowledge, the Transformer adaption is the first model that is trained to solve the unsupervised task of recovering partially observed molecules. In this work, we assess how different degrees of information impact performance w.r.t. to fitting the QM9 dataset, which conforms to the octet rule, and to fitting the ZINC dataset, which contains hypervalent molecules and ions requiring the model to learn a more complex structure rule. More specifically, we test a full discrete graph with bond order information, a full discrete graph with only connectivity, a bag-of-neighbors, a bag-of-atoms, and a count-based unigram statistics. These results provide encouraging evidence that neural networks, even when only connectivity is available, can learn arbitrary molecular structure rules specific to a dataset, as the Transformer adaption surpasses a strong octet rule baseline on the ZINC dataset.