Graph Neural Networks (GNNs) have emerged as a powerful tool for data-driven learning on various graph domains. They are usually based on a message-passing mechanism and have gained increasing popularity for their intuitive formulation, which is closely linked to the Weisfeiler-Lehman (WL) test for graph isomorphism to which they have been proven equivalent in terms of expressive power. In this work, we establish new generalization properties and fundamental limits of GNNs in the context of learning so-called identity effects, i.e., the task of determining whether an object is composed of two identical components or not. Our study is motivated by the need to understand the capabilities of GNNs when performing simple cognitive tasks, with potential applications in computational linguistics and chemistry. We analyze two case studies: (i) two-letters words, for which we show that GNNs trained via stochastic gradient descent are unable to generalize to unseen letters when utilizing orthogonal encodings like one-hot representations; (ii) dicyclic graphs, i.e., graphs composed of two cycles, for which we present positive existence results leveraging the connection between GNNs and the WL test. Our theoretical analysis is supported by an extensive numerical study.
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http://dx.doi.org/10.1016/j.neunet.2024.106793 | DOI Listing |
J Cell Mol Med
January 2025
Postgraduate Training Base Alliance of Wenzhou Medical University, Wenzhou, Zhejiang, China.
Cancer is a complex disease driven by mutations in the genes that play critical roles in cellular processes. The identification of cancer driver genes is crucial for understanding tumorigenesis, developing targeted therapies and identifying rational drug targets. Experimental identification and validation of cancer driver genes are time-consuming and costly.
View Article and Find Full Text PDFEur J Neurosci
January 2025
National Institute of Education, Nanyang Technological University, Singapore.
Approximately 15%-20% of school-aged children suffer from mathematics learning difficulties (MLD). Most children with developmental dyscalculia (DD) or MLD also have comorbid cognitive deficits. Recent literature suggests that research should focus on uncovering the neural underpinnings of MLD across more inclusive samples, rather than limiting studies to pure cases of DD or MLD with highly stringent inclusion criteria.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Department of Organic Chemistry, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine.
Lipophilicity and acidity/basicity are fundamental physical properties that profoundly affect the compound's pharmacological activity, bioavailability, metabolism, and toxicity. Predicting lipophilicity, measured by (1-octanol-water distribution coefficient logarithm), and acidity/basicity, measured by (negative of acid ionization constant logarithm), is essential for early drug discovery success. However, the limited availability of experimental data and poor accuracy of standard and assessment methods for saturated fluorine-containing derivatives pose a significant challenge to achieving satisfactory results for this compound class.
View Article and Find Full Text PDFCNS Neurosci Ther
January 2025
Department of Neurology, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, China.
Objectives: Parkinson's disease (PD) is characterized by olfactory dysfunction (OD) and cognitive deficits at its early stages, yet the link between OD and cognitive deficits is also not well-understood. This study aims to examine the changes in the olfactory network associated with OD and their relationship with cognitive function in de novo PD patients.
Methods: A total of 116 drug-naïve PD patients and 51 healthy controls (HCs) were recruited for this study.
Chem Sci
December 2024
ByteDance Research Bellevue Washington 98004 USA
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges.
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