In this paper we study the practicality and usefulness of incorporating distributed representations of graphs into models within the context of drug pair scoring. We argue that the real world growth and update cycles of drug pair scoring datasets subvert the limitations of transductive learning associated with distributed representations. Furthermore, we argue that the vocabulary of discrete substructure patterns induced over drug sets is not dramatically large due to the limited set of atom types and constraints on bonding patterns enforced by chemistry. Under this pretext, we explore the effectiveness of distributed representations of the molecular graphs of drugs in drug pair scoring tasks such as drug synergy, polypharmacy, and drug-drug interaction prediction. To achieve this, we present a methodology for learning and incorporating distributed representations of graphs within a unified framework for drug pair scoring. Subsequently, we augment a number of recent and state-of-the-art models to utilise our embeddings. We empirically show that the incorporation of these embeddings improves downstream performance of almost every model across different drug pair scoring tasks, even those the original model was not designed for. We publicly release all of our drug embeddings for the DrugCombDB, DrugComb, DrugbankDDI, and TwoSides datasets.

We present Geo2DR, a Python library for unsupervised learning on graph-structured data using discrete substructure patterns and neural language models. It contains efficient implementations of popular graph decomposition algorithms and neural language models in PyTorch which are combined to learn representations using the distributive hypothesis. Furthermore, Geo2DR comes with general data processing and loading methods which can bring substantial speed-up in the training of the neural language models. Through this we provide a unified set of tools and design methodology to quickly construct systems capable of learning distributed representations of graphs. This is useful for replication of existing methods, modification, or even creation of novel systems. This work serves to present the Geo2DR library and perform a comprehensive comparative analysis of existing methods re-implemented using Geo2DR across several widely used graph classification benchmarks. We show a high reproducibility of results in published methods and interoperability with other libraries useful for distributive language modelling.