Knowledge Graph Completion has been increasingly adopted as a useful method for several tasks in biomedical research, like drug repurposing or drug-target identification. To that end, a variety of datasets and Knowledge Graph Embedding models has been proposed over the years. However, little is known about the properties that render a dataset useful for a given task and, even though theoretical properties of Knowledge Graph Embedding models are well understood, their practical utility in this field remains controversial. We conduct a comprehensive investigation into the topological properties of publicly available biomedical Knowledge Graphs and establish links to the accuracy observed in real-world applications. By releasing all model predictions and a new suite of analysis tools we invite the community to build upon our work and continue improving the understanding of these crucial applications.

In this paper, we propose XG-BoT, an explainable deep graph neural network model for botnet node detection. The proposed model comprises a botnet detector and an explainer for automatic forensics. The XG-BoT detector can effectively detect malicious botnet nodes in large-scale networks. Specifically, it utilizes a grouped reversible residual connection with a graph isomorphism network to learn expressive node representations from botnet communication graphs. The explainer, based on the GNNExplainer and saliency map in XG-BoT, can perform automatic network forensics by highlighting suspicious network flows and related botnet nodes. We evaluated XG-BoT using real-world, large-scale botnet network graph datasets. Overall, XG-BoT outperforms state-of-the-art approaches in terms of key evaluation metrics. Additionally, we demonstrate that the XG-BoT explainers can generate useful explanations for automatic network forensics.

Recently, graph neural networks (GNNs) have been successfully applied to predicting molecular properties, which is one of the most classical cheminformatics tasks with various applications. Despite their effectiveness, we empirically observe that training a single GNN model for diverse molecules with distinct structural patterns limits its prediction performance. In this paper, motivated by this observation, we propose TopExpert to leverage topology-specific prediction models (referred to as experts), each of which is responsible for each molecular group sharing similar topological semantics. That is, each expert learns topology-specific discriminative features while being trained with its corresponding topological group. To tackle the key challenge of grouping molecules by their topological patterns, we introduce a clustering-based gating module that assigns an input molecule into one of the clusters and further optimizes the gating module with two different types of self-supervision: topological semantics induced by GNNs and molecular scaffolds, respectively. Extensive experiments demonstrate that TopExpert has boosted the performance for molecular property prediction and also achieved better generalization for new molecules with unseen scaffolds than baselines. The code is available at https://github.com/kimsu55/ToxExpert.

Joint network topology inference represents a canonical problem of jointly learning multiple graph Laplacian matrices from heterogeneous graph signals. In such a problem, a widely employed assumption is that of a simple common component shared among multiple networks. However, in practice, a more intricate topological pattern, comprising simultaneously of sparse, homogeneity and heterogeneity components, would exhibit in multiple networks. In this paper, we propose a general graph estimator based on a novel structured fusion regularization that enables us to jointly learn multiple graph Laplacian matrices with such complex topological patterns, and enjoys both high computational efficiency and rigorous theoretical guarantee. Moreover, in the proposed regularization term, the topological pattern among networks is characterized by a Gram matrix, endowing our graph estimator with the ability of flexible modelling different types of topological patterns by different choices of the Gram matrix. Computationally, the regularization term, coupling the parameters together, makes the formulated optimization problem intractable and thus, we develop a computationally-scalable algorithm based on the alternating direction method of multipliers (ADMM) to solve it efficiently. Theoretically, we provide a theoretical analysis of the proposed graph estimator, which establishes a non-asymptotic bound of the estimation error under the high-dimensional setting and reflects the effect of several key factors on the convergence rate of our algorithm. Finally, the superior performance of the proposed method is illustrated through simulated and real data examples.