Guided Graph Compression for Quantum Graph Neural Networks

Graph Neural Networks (GNNs) are effective for processing graph-structured data but face challenges with large graphs due to high memory requirements and inefficient sparse matrix operations on GPUs. Quantum Computing (QC) offers a promising avenue to address these issues and inspires new algorithmic approaches. In particular, Quantum Graph Neural Networks (QGNNs) have been explored in recent literature. However, current quantum hardware limits the dimension of the data that can be effectively encoded. Existing approaches either simplify datasets manually or use artificial graph datasets. This work introduces the Guided Graph Compression (GGC) framework, which uses a graph autoencoder to reduce both the number of nodes and the dimensionality of node features. The compression is guided to enhance the performance of a downstream classification task, which can be applied either with a quantum or a classical classifier. The framework is evaluated on the Jet Tagging task, a classification problem of fundamental importance in high energy physics that involves distinguishing particle jets initiated by quarks from those by gluons. The GGC is compared against using the autoencoder as a standalone preprocessing step and against a baseline classical GNN classifier. Our numerical results demonstrate that GGC outperforms both alternatives, while also facilitating the testing of novel QGNN ansatzes on realistic datasets.

Towards a more inductive world for drug repurposing approaches

Drug-target interaction (DTI) prediction is a challenging, albeit essential task in drug repurposing. Learning on graph models have drawn special attention as they can significantly reduce drug repurposing costs and time commitment. However, many current approaches require high-demanding additional information besides DTIs that complicates their evaluation process and usability. Additionally, structural differences in the learning architecture of current models hinder their fair benchmarking. In this work, we first perform an in-depth evaluation of current DTI datasets and prediction models through a robust benchmarking process, and show that DTI prediction methods based on transductive models lack generalization and lead to inflated performance when evaluated as previously done in the literature, hence not being suited for drug repurposing approaches. We then propose a novel biologically-driven strategy for negative edge subsampling and show through in vitro validation that newly discovered interactions are indeed true. We envision this work as the underpinning for future fair benchmarking and robust model design. All generated resources and tools are publicly available as a python package.