Sep 2026· ACM Transactions on Knowledge Discovery from Data· 0 citations· 57 references
Advanced Graph Neural Networks
Abstract
Existing research on robust Graph Neural Networks (GNNs) focuses predominantly on undirected graphs, overlooking the trustworthiness inherent in the link directions of directed graphs. In this work, we analyze the limitations of current approaches from both the attack and defense perspectives and redefine the robustness of GNNs in directed graphs. From the attack side, we introduce a more realistic directed graph attack setting that addresses the shortcomings of existing attacks. From the defense side, we propose a simple yet effective message-passing framework that serves as a plug-in layer to strengthen GNN robustness while avoiding a false sense of robustness. Our findings show that the trust signals encoded in directed graphs can be harnessed to substantially improve the robustness of GNNs. When combined with existing defense strategies, the framework achieves state-of-the-art robust performance alongside strong clean accuracy against both transfer and adaptive attacks. These results point to a novel and promising direction for strengthening the robustness of graph deep learning.
Agile methods continue to gain popularity. In particular, the Scrum method appears to be on the verge of becoming a de-facto standard in the industry, leading the so called Agile movement. While there are success stories and recommendations, there is little scientifically valid evidence of the challenges in the adoptio...
A. Marchenko, P. Abrahamsson· Agile Conference· 59 citations· ⚡11
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MCGLPPI, a novel geometric representation learning framework that combines graph neural networks (GNNs) with the MARTINI molecular coarse-grained (CG) model to predict overall PPI properties accurately and efficiently, offers an effective and efficient solution for PPI overall property predictions.
Yang Yue, Shu Li, Yihua Cheng et al.· bioRxiv· 15 citations
PepPCBench enables a robust evaluation of PFNN-based methods and supports their continued development for peptide-protein structure prediction, and highlights the influence of peptide length, conformational flexibility, and training set similarity on prediction accuracy.
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Abstract Predicting properties from coordinate–category data—sets of vectors paired with categorical information—is fundamental to computational science, manifesting in materials science as predicting formation energies or elastic moduli from crystal structures. While large language models (LLMs) have increasingly been...
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