Related papers: Graph-in-Graph Network for Automatic Gene Ontology…

Graph neural networks (GNNs) have been applied into a variety of graph tasks. Most existing work of GNNs is based on the assumption that the given graph data is optimal, while it is inevitable that there exists missing or incomplete edges…

Graph neural networks (GNNs) have gained prominence in recommendation systems in recent years. By representing the user-item matrix as a bipartite and undirected graph, GNNs have demonstrated their potential to capture short- and…

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified…

Existing Graph Neural Networks (GNNs) are limited to process graphs each of whose vertices is represented by a vector or a single value, limited their representing capability to describe complex objects. In this paper, we propose the first…

Graphs play an important role in many applications. Recently, Graph Neural Networks (GNNs) have achieved promising results in graph analysis tasks. Some state-of-the-art GNN models have been proposed, e.g., Graph Convolutional Networks…

Graph generation is a fundamental task with broad applications, such as drug discovery. Recently, discrete flow matching-based graph generation, \aka, graph flow model (GFM), has emerged due to its superior performance and flexible…

Graph Neural Networks (GNNs) are powerful models that can manage complex data sources and their interconnection links. One of GNNs' main drawbacks is their lack of interpretability, which limits their application in sensitive fields. In…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

Self-supervised protein language models have proved their effectiveness in learning the proteins representations. With the increasing computational power, current protein language models pre-trained with millions of diverse sequences can…

Graph neural networks can be effectively applied to find solutions for many real-world problems across widely diverse fields. The success of graph neural networks is linked to the message-passing mechanism on the graph, however, the…

Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…

This paper investigates the impact of hybridizing a multi-modal Genetic Algorithm with a Graph Neural Network for timetabling optimization. The Graph Neural Network is designed to encapsulate general domain knowledge to improve schedule…

Recently, Graph Neural Networks (GNNs) have gained popularity in a variety of real-world scenarios. Despite the great success, the architecture design of GNNs heavily relies on manual labor. Thus, automated graph neural network (AutoGNN)…

Graph learning algorithms have attained state-of-the-art performance on many graph analysis tasks such as node classification, link prediction, and clustering. It has, however, become hard to track the field's burgeoning progress. One…

Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data.…

This study aims to optimize the existing retrieval-augmented generation model (RAG) by introducing a graph structure to improve the performance of the model in dealing with complex knowledge reasoning tasks. The traditional RAG model has…

Research idea generation is the innovation-driving step of automated scientific research. Recently, large language models (LLMs) have shown potential for automating idea generation at scale. However, existing methods mainly condition LLMs…

In light of the recent success of Graph Neural Networks (GNNs) and their ability to perform inference on complex data structures, many studies apply GNNs to the task of text classification. In most previous methods, a heterogeneous graph,…

Discovery gene-disease links is important in biology and medicine areas, enabling disease identification and drug repurposing. Machine learning approaches accelerate this process by leveraging biological knowledge represented in ontologies…

Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…