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Search · four archives
30 papers · ranked by Valyu relevance
Huu Ngoc Tran Tran, J. Joshua Thomas, Nurul Hashimah Ahamed Hassain Malim, Yuriy Orlov
'Nurul Hashimah Ahamed Hassain Malim' 'Yuriy Orlov'] The exploration of drug-target interactions (DTI) is an essential stage in the drug development pipeline. Thanks to the assistance of computational models, notably in the deep learning approach, scientists have been able to shorten the time spent on this stage.…
Bin Wang, LvHang Cheng, JinFang Sheng, ZhengAng Hou + 1 more
With the advent of the wave of big data, the generation of more and more graph data brings great pressure to the traditional deep learning model. The birth of graph neural network fill the gap of deep learning in graph data. At present, graph convolutional networks (GCN) have surpassed traditional methods such as…
Qingju Jiao, Peige Zhao, Hanjin Zhang, Yahong Han + 2 more
'Toqir Rana'] Most current graph neural networks (GNNs) are designed from the view of methodology and rarely consider the inherent characters of graph. Although the inherent characters may impact the performance of GNNs, very few methods are proposed to resolve the issue. In this work, we mainly focus on improving the…
Yuchen Zhou, Hongtao Huo, Zhiwen Hou, Fanliang Bu + 1 more
Graph Convolutional Networks (GCNs) are powerful deep learning methods for non-Euclidean structure data and achieve impressive performance in many fields. But most of the state-of-the-art GCN models are shallow structures with depths of no more than 3 to 4 layers, which greatly limits the ability of GCN models to…
Zhao Chen, Danilo Comminiello, Tokunbo Ogunfunmi, Nithin V. George
Non-Euclidean data, such as social networks and citation relationships between documents, have node and structural information. The Graph Convolutional Network (GCN) can automatically learn node features and association information between nodes. The core ideology of the Graph Convolutional Network is to aggregate node…
Sanjay Ghosh, Eshan Bhargava, Chieh-Te Lin, Srikantan S. Nagarajan
The long term goal of this work is to develop powerful tools for brain network analysis in order to study structural and functional connectivity abnormalities in psychiatric disorders like schizophrenia. Graph convolutional neural networks (GCNN) are quite effective for learning complex discriminate features in…
Sukhdeep Singh, Anuj Sharma, Vinod Kumar Chauhan
Graph Neural Networks (GNN) has emerged as a popular and standard approach for learning from graph-structured data. The literature on GNN highlights the potential of this evolving research area and its widespread adoption in reallife applications. However, most of the approaches are either new in concept or derived…
Massimiliano Lupo Pasini, GS Jung, Stephan Irle
We developed a graph convolutional neural network (GCNN) to predict the formation energy and the bulk modulus for models of solid solution alloys for various atomic crystal structures and relaxed volumes. We trained the GCNN model on a dataset for nickel-niobium (NiNb) that was generated for simplicity with the…
M. Ravinder, Garima Saluja, Sarah Allabun, Mohammed S. Alqahtani + 3 more
The Brain Tumor presents a highly critical situation concerning the brain, characterized by the uncontrolled growth of an abnormal cell cluster. Early brain tumor detection is essential for accurate diagnosis and effective treatment planning. In this paper, a novel Convolutional Neural Network (CNN) based Graph Neural…
Yihe Deng, Ruochi Zhang, Pan Xu, Jian Ma + 1 more
Hypergraphs are powerful tools for modeling complex interactions across various domains, including biomedicine. However, learning meaningful node representations from hypergraphs remains a challenge. Existing supervised methods often lack generalizability, thereby limiting their real-world applications. We propose a…
Ragini Kihlman, Ilkka Launonen, Mikko J Sillanpää, Patrik Waldmann + 1 more
'D-J de Koning'] Title: Abstract In genomics, use of deep learning (DL) is rapidly growing and DL has successfully demonstrated its ability to uncover complex relationships in large biological and biomedical data sets. With the development of high-throughput sequencing techniques, genomic markers can now be allocated…
Srijani Bagchi, Anasua Sarkar, Ujjwal Maulik
In times like this, it is imperative to be cautious about the effects of drugs or vaccination doses on patients who are already suffering from other serious diseases. It’s not only the virus which can affect the body metabolisms, drugs to encounter the virus may also end up having unwanted negative effects. Therapeutic…
Zhonglin Ye, Zhuoran Li, Gege Li, Haixing Zhao
The dual-channel graph convolutional neural networks based on hybrid features jointly model the different features of networks, so that the features can learn each other and improve the performance of various subsequent machine learning tasks. However, current dual-channel graph convolutional neural networks are…
Xingyu Liu, Juan Chen, Quan Wen
Traditional convolutional neural networks are limited to handling Euclidean space data, overlooking the vast realm of real-life scenarios represented as graph data, including transportation networks, social networks, and reference networks. The pivotal step in transferring convolutional neural networks to graph data…
Artem Voytetskiy, Alan Herbert, Maria Poptsova
Deep learning methods have been successfully applied to the tasks of predicting functional genomic elements such as histone marks, transcriptions factor binding sites, non-B DNA structures, and regulatory variants. Initially convolutional neural networks (CNN) and recurrent neural networks (RNN) or hybrid CNN-RNN…
Mohamed Radwan, Pedro G. Lind, Anis Yazidi
In this study, we investigate the use of temporal dynamics in brain connectivity for the classification of electroencephalography (EEG) signals using dynamic Graph Neural Networks (GNNs). Our methods are applied to several large-scale EEG datasets focused on abnormality and epilepsy detection. The implemented models…
Chunya Zou, Andi Han, Lequan Lin, Junbin Gao
In this paper, we will present a simple yet effective way for directed Graph (digraph) Convolutional Neural Networks based on the classic Singular Value Decomposition (SVD), named SVD-GCN for digraphs. Through empirical experiments on node classification datasets, we have found that SVD-GCN has remarkable improvements…
Sebastian Lutz, Florian Auer, Dennis Hartmann, Hryhorii Chereda + 2 more
Colorectal Cancer has the second-highest mortality rate worldwide, which requires advanced diagnostics and individualized therapies to be developed. Information about the interactions between molecular entities provides valuable information to detect the responsible genes driving cancer progression. Graph Convolutional…
Adil Mudasir Malla, Asif Ali Banka
— In recent years, tasks of machine learning ranging from image processing & audio/video analysis to natural language understanding have been transformed by deep learning. The data content in all these scenarios are expressed via Euclidean space. However, a considerable amount of application data is structured in…
Zhuo Xu, Lixin Cui, Yue Wang, Hangyuan Du + 2 more
'Edwin R. Hancock'] Abstract—In this paper, we develop a novel local graph pooling method, namely the Separated Subgraph-based Hierarchical Pooling (SSHPool), for graph classification. To this end, we commence by assigning the nodes of a sample graph into different clusters, resulting in a family of separated…
Authors not listed
Accurate prediction of redox potentials of iron (Fe) complexes, in tandem with uncertainty quantification, is essential to advance technologies related to electro-deposition and energy storage by enabling reliable modeling, guiding experimental design, and improving the efficiency of material discovery. Since…
Nedra Mekni, Hosein Fooladi, Ugo Perricone, Thierry Langer
Machine learning models are employed to enhance the speed and provide novel insights in drug discovery due to their demonstrated effectiveness in predicting properties of small molecules like pKa, solubility, and binding affinity. These approaches accelerate drug discovery by helping researchers efficiently identify…
Authors not listed
Pharmacophores are widely used to describe protein-ligand interactions, and the Grids of Pharmacophore Interaction Fields (GRAIL) method extends this concept by representing binding pockets as interpretable sets of interaction type-specific pharmacophoric maps. In this work, we propose a hybrid framework for binding…
Om Roy, Yashar Moshfeghi, Keith Smith
Modelling dynamically evolving spatio-temporal signals is a prominent challenge in the Graph Neural Network (GNN) literature. Notably, GNNs assume an existing underlying graph structure. While this underlying structure may not always exist or is derived independently from the signal, a temporally evolving functional…
David Buterez, Jon Paul Janet, Steven Kiddle, Pietro Liò
We investigate the potential of graph neural networks for transfer learning and improving molecular property prediction on sparse and expensive to acquire high-fidelity data by leveraging low-fidelity measurements as an inexpensive proxy for a targeted property ofinterest. This problem arises in discovery processes…
Zachary Humphreys, Xenophon Evangelopoulos, Stavros Gerolymatos, Edward O. Pyzer-Knapp + 1 more
Graph neural networks have recently met huge success in various inference tasks including materials property prediction amongst many others. Nevertheless, having an inherently locally-based representation capacity as they do, global representation of materials' structures can only only be achieved by expanding the…
Xun Liu, Alex Hay‐Man Ng, Fangyuan Lei, Yikuan Zhang + 1 more
Xun Liu1,2 , Alex Hay-Man Ng1,3∗ , Fangyuan Lei4,5∗ , Member, IEEE, Yikuan Zhang2 , Zhengmin Li5 1School of Information Engineering, Guangdong University of Technology 2Department of Electronics, Software Engineering Institute of Guangzhou 3School of Civil and Transportation Engineering, Guangdong University of…
Yongze Wang, Haimin Zhang, Qiang Wu, Min Xu
Graph neural networks (GNNs) have shown great success in learning from graph-based data. The key mechanism of current GNNs is message passing, where a node's feature is updated based on the information passing from its local neighbourhood. A limitation of this mechanism is that node features become increasingly…
Tom Brenner
Graph neural networks were used to model protein isoelectric points. Predictions contained markedly fewer outliers (predicted with errors > 0.5 pH units) compared to tools published in the literature, despite slightly higher root-mean-squared errors. This result was reproduced for graph convolutional and graph…
Authors not listed
Predicting protein-ligand binding affinity from three-dimensional (3D) structural data is a central task in structure-based drug discovery, yet it remains challenging due to limited data availability, structural complexity, and the sparse nature of 3D molecular representations. In this study, we investigate the…