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Gene regulatory relationships can be abstracted as a gene regulatory network (GRN), which plays a key role in characterizing complex cellular processes and pathways. Recently, graph neural networks (GNNs), as a class of deep learning…

Molecular Networks · Quantitative Biology 2023-11-07 Hui Zhang , Xuexin An , Qiang He , Yudong Yao , Yudong Zhang , Feng-Lei Fan , Yueyang Teng

Existing Graph Neural Networks (GNNs) compute the message exchange between nodes by either aggregating uniformly (convolving) the features of all the neighboring nodes, or by applying a non-uniform score (attending) to the features. Recent…

Machine Learning · Computer Science 2023-03-02 Adrián Javaloy , Pablo Sanchez-Martin , Amit Levi , Isabel Valera

We present an attention mechanism inspired from definition of screened Coulomb potential. This attention mechanism was used to interpret the Graph Attention (GAT) model layers and training dataset by using a flexible and scalable framework…

Machine Learning · Computer Science 2019-12-19 Burc Gokden

Representing and learning from graphs is essential for developing effective machine learning models tailored to non-Euclidean data. While Graph Neural Networks (GNNs) strive to address the challenges posed by complex, high-dimensional graph…

Quantum Physics · Physics 2025-01-15 Wenxuan Wang

Knowledge graphs offer a structured representation of real-world entities and their relationships, enabling a wide range of applications from information retrieval to automated reasoning. In this paper, we conduct a systematic comparison…

Machine Learning · Computer Science 2025-07-31 Thanh Hoang-Minh

Quantum Graph Neural Networks (QGNNs) represent a novel fusion of quantum computing and Graph Neural Networks (GNNs), aimed at overcoming the computational and scalability challenges inherent in classical GNNs that are powerful tools for…

Graphs are a fundamental representation of complex, nonlinear structured data across various domains, including social networks and quantum systems. Quantum Graph Recurrent Neural Networks (QGRNNs) have been proposed to model quantum…

Quantum Physics · Physics 2025-07-01 Jawaher Kaldari , Saif Al-Kuwari

Transformers serve as the backbone architectures of Foundational Models, where domain-specific tokenizers allow them to adapt to various domains. Graph Transformers (GTs) have recently emerged as leading models in geometric deep learning,…

Neural and Evolutionary Computing · Computer Science 2025-04-03 Limei Wang , Kaveh Hassani , Si Zhang , Dongqi Fu , Baichuan Yuan , Weilin Cong , Zhigang Hua , Hao Wu , Ning Yao , Bo Long

Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…

Machine Learning · Computer Science 2022-03-03 Tuan Le , Frank Noé , Djork-Arné Clevert

Auto-encoders have emerged as a successful framework for unsupervised learning. However, conventional auto-encoders are incapable of utilizing explicit relations in structured data. To take advantage of relations in graph-structured data,…

Machine Learning · Computer Science 2019-05-28 Amin Salehi , Hasan Davulcu

In this paper, we present Conjoint Attentions (CAs), a class of novel learning-to-attend strategies for graph neural networks (GNNs). Besides considering the layer-wise node features propagated within the GNN, CAs can additionally…

Machine Learning · Computer Science 2021-12-14 Tiantian He , Yew-Soon Ong , Lu Bai

Graphs can facilitate modeling various complex systems such as gene networks and power grids, as well as analyzing the underlying relations within them. Learning over graphs has recently attracted increasing attention, particularly graph…

Machine Learning · Computer Science 2023-03-28 O. Deniz Kose , Yanning Shen

Quantum computing (QC) is a new computational paradigm whose foundations relate to quantum physics. Notable progress has been made, driving the birth of a series of quantum-based algorithms that take advantage of quantum computational…

Quantum Physics · Physics 2022-02-22 Yehui Tang , Junchi Yan , Hancock Edwin

Graph neural networks (GNN) have recently been applied to exploit knowledge graph (KG) for recommendation. Existing GNN-based methods explicitly model the dependency between an entity and its local graph context in KG (i.e., the set of its…

Information Retrieval · Computer Science 2020-04-27 Susen Yang , Yong Liu , Yonghui Xu , Chunyan Miao , Min Wu , Juyong Zhang

This paper proposes a new Quantum Spatial Graph Convolutional Neural Network (QSGCNN) model that can directly learn a classification function for graphs of arbitrary sizes. Unlike state-of-the-art Graph Convolutional Neural Network (GCNN)…

Machine Learning · Computer Science 2023-04-04 Lu Bai , Yuhang Jiao , Luca Rossi , Lixin Cui , Jian Cheng , Edwin R. Hancock

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the…

Machine Learning · Computer Science 2023-12-19 Vijay Prakash Dwivedi , Yozen Liu , Anh Tuan Luu , Xavier Bresson , Neil Shah , Tong Zhao

Graph or network data is ubiquitous in the real world, including social networks, information networks, traffic networks, biological networks and various technical networks. The non-Euclidean nature of graph data poses the challenge for…

Social and Information Networks · Computer Science 2019-09-06 Junjie Huang , Huawei Shen , Liang Hou , Xueqi Cheng

We investigate quantum circuits for graph representation learning, and propose equivariant quantum graph circuits (EQGCs), as a class of parameterized quantum circuits with strong relational inductive bias for learning over graph-structured…

Machine Learning · Computer Science 2022-06-15 Péter Mernyei , Konstantinos Meichanetzidis , İsmail İlkan Ceylan

In this work, we introduce the Quantum Adaptive Excitation Network (QAE-Net), a hybrid quantum-classical framework designed to enhance channel attention mechanisms in Convolutional Neural Networks (CNNs). QAE-Net replaces the classical…

Quantum Physics · Physics 2025-07-16 Yu-Chao Hsu , Kuan-Cheng Chen , Tai-Yue Li , Nan-Yow Chen

Graph Attention Networks (GATs) are one of the most popular GNN architectures and are considered as the state-of-the-art architecture for representation learning with graphs. In GAT, every node attends to its neighbors given its own…

Machine Learning · Computer Science 2022-02-01 Shaked Brody , Uri Alon , Eran Yahav