Graph drawing techniques have been developed in the last few years with the purpose of producing esthetically pleasing node-link layouts. Recently, the employment of differentiable loss functions has paved the road to the massive usage of gradient descent and related optimization algorithms. In this article, we propose a novel framework for the development of Graph Neural Drawers (GNDs), machines that rely on neural computation for constructing efficient and complex maps. GND is Graph Neural Networks (GNNs) whose learning process can be driven by any provided loss function, such as the ones commonly employed in Graph Drawing. Moreover, we prove that this mechanism can be guided by loss functions computed by means of feedforward neural networks, on the basis of supervision hints that express beauty properties, like the minimization of crossing edges. In this context, we show that GNNs can nicely be enriched by positional features to deal also with unlabeled vertexes. We provide a proof-of-concept by constructing a loss function for the edge crossing and provide quantitative and qualitative comparisons among different GNN models working under the proposed framework.
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http://dx.doi.org/10.1109/TNNLS.2022.3184967 | DOI Listing |
Front Genet
December 2024
School of information engineering, Jingdezhen Ceramic University, Jingdezhen, China.
The early symptoms of hepatocellular carcinoma patients are often subtle and easily overlooked. By the time patients exhibit noticeable symptoms, the disease has typically progressed to middle or late stages, missing optimal treatment opportunities. Therefore, discovering biomarkers is essential for elucidating their functions for the early diagnosis and prevention.
View Article and Find Full Text PDFHealth Inf Sci Syst
December 2025
Division of Software, Yonsei University, Mirae Campus, Yeonsedae-gil 1, Wonju-si, 26493 Gangwon-do Korea.
Purpose: Drug repositioning, a strategy that repurposes already-approved drugs for novel therapeutic applications, provides a faster and more cost-effective alternative to traditional drug discovery. Network-based models have been adopted by many computational methodologies, especially those that use graph neural networks to predict drug-disease associations. However, these techniques frequently overlook the quality of the input network, which is a critical factor for achieving accurate predictions.
View Article and Find Full Text PDFFront Bioeng Biotechnol
December 2024
Department of Rehabilitation Medicine, University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
Introduction: Parkinson's disease (PD) is characterized by muscle stiffness, bradykinesia, and balance disorders, significantly impairing the quality of life for affected patients. While motion pose estimation and gait analysis can aid in early diagnosis and timely intervention, clinical practice currently lacks objective and accurate tools for gait analysis.
Methods: This study proposes a multi-level 3D pose estimation framework for PD patients, integrating monocular video with Transformer and Graph Convolutional Network (GCN) techniques.
Characterizing brain dynamic functional connectivity (dFC) patterns from functional Magnetic Resonance Imaging (fMRI) data is of paramount importance in neuroscience and medicine. Recently, many graph neural network (GNN) models, combined with transformers or recurrent neural networks (RNNs), have shown great potential for modeling the dFC patterns. However, these methods face challenges in effectively characterizing the modularity organization of brain networks and capturing varying dFC state patterns.
View Article and Find Full Text PDFThe human heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is a prototypical RNA-binding protein essential in regulating a wide range of post-transcriptional events in cells. As a multifunctional protein with a key role in RNA metabolism, deregulation of its functions has been linked to neurodegenerative diseases, tumour aggressiveness and chemoresistance, which has fuelled efforts to develop novel therapeutics that modulates its RNA binding activities. Here, using a combination of Molecular Dynamics (MD) simulations and graph neural network pockets predictions, we showed that hnRNPA1 N-terminal RNA binding domain (UP1) contains several cryptic pockets capable of binding small molecules.
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