We consider the problem of graph sparsification while preserving the test accuracy of Graph Neural Networks (GNNs). Prior work in this area is often motivated by the Lottery Ticket Hypothesis, which aims to prune redundant edges. However, these sparsification approaches typically operate as black boxes and provide no justification for which edges are removed. In contrast, edge importance scores obtained from GNN explanation methods provide a principled and interpretable basis for sparsification. In particular, we show that Shapley value–based explainers such as GNNShap enable effective sparsification, allowing up to 80% of edges to be removed without degrading model accuracy. We show that Shapley values are well-suited for this task due to their robustness in identifying less influential edges, resulting in sparse yet faithful subgraphs that are efficient for downstream applications.

Graph neural networks (GNNs) are popular machine learning models for graphs with many applications across scientific domains. However, GNNs are considered black box models, and it is challenging to understand how the model makes predictions. Game theoric Shapley value approaches are popular explanation methods in other domains but are not well-studied for graphs. Some studies have proposed Shapley value based GNN explanations, yet they have several limitations: they consider limited samples to approximate Shapley values; some mainly focus on small and large coalition sizes, and they are an order of magnitude slower than other explanation methods, making them inapplicable to even moderate-size graphs. In this work, we propose GNNShap, which provides explanations for edges since they provide more natural explanations for graphs and more fine-grained explanations. We overcome the limitations by sampling from all coalition sizes, parallelizing the sampling on GPUs, and speeding up model predictions by batching. GNNShap gives better fidelity scores and faster explanations than baselines on real-world datasets. The code is available at https://github.com/HipGraph/GNNShap.

The goal of the 22nd International Workshop on Data Mining in Bioinformatics (BIOKDD 2023) is to encourage KDD researchers to solve the numerous problems and challenges in Bioinformatics using Data Mining technologies. Based on the organizers' expertise and communities, BIOKDD 2023 features the theme ''Large-Scale Data-Driven Methods for Bioinformatics.'' This theme encourages the use of high-performance computing (HPC) to support the training of large machine learning models for problems in Bioinformatics and Computational Biology. The key goal is to accelerate the convergence between Data Mining and Bioinformatics communities to expedite discoveries in basic biology, medicine and healthcare.

A graph embedding algorithm embeds a graph into a low-dimensional space such that the embedding preserves the inherent properties of the graph. While graph embedding is fundamentally related to graph visualization, prior work did not exploit this connection explicitly. We develop Force2Vec that uses force-directed graph layout models in a graph embedding setting with an aim to excel in both machine learning (ML) and visualization tasks. We make Force2Vec highly parallel by mapping its core computations to linear algebra and utilizing multiple levels of parallelism available in modern processors. The resultant algorithm is an order of magnitude faster than existing methods (43× faster than DeepWalk, on average) and can generate embeddings from graphs with billions of edges in a few hours. In comparison to existing methods, Force2Vec is better in graph visualization and performs comparably or better in ML tasks such as link prediction, node classification, and clustering. Source code is available at https://github.com/HipGraph/Force2Vec.