Related papers: Predicting Microbial Interactions Using Graph Neur…

Recommender systems play a crucial role in alleviating information overload by providing personalized recommendations tailored to users' preferences and interests. Recently, Graph Neural Networks (GNNs) have emerged as a promising approach…

We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only…

Graph neural networks (GNNs) are widely used for modeling complex interactions between entities represented as vertices of a graph. Despite recent efforts to theoretically analyze the expressive power of GNNs, a formal characterization of…

The recent focus on microbes in human medicine highlights their potential role in the genetic framework of diseases. To decode the complex interactions among genes, microbes, and diseases, computational predictions of gene-microbe-disease…

Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…

Graph Neural Networks have revolutionized many machine learning tasks in recent years, ranging from drug discovery, recommendation systems, image classification, social network analysis to natural language understanding. This paper shows…

Social networks have a vast range of applications with graphs. The available benchmark datasets are citation, co-occurrence, e-commerce networks, etc, with classes ranging from 3 to 15. However, there is no benchmark classification social…

When designing control strategies for an infectious disease it is critical to identify the key pathways of transmission. Data on infected hosts - when they were born, where they lived and with whom they interacted - can help infer sources…

Recent years have witnessed fast developments of graph neural networks (GNNs) that have benefited myriad graph analytic tasks and applications. Most GNNs rely on the homophily assumption that nodes belonging to the same class are more…

Predicting signed interactions in biological networks is crucial for understanding drug mechanisms and facilitating drug repurposing. While deep graph models have demonstrated success in modeling complex biological systems, existing…

A wide range of models have been proposed for Graph Generative Models, necessitating effective methods to evaluate their quality. So far, most techniques use either traditional metrics based on subgraph counting, or the representations of…

Large-eddy simulations (LES) require closures for filtered production rates because the resolved fields do not contain all correlations that govern chemical source terms. We develop a graph neural network (GNN) that predicts filtered…

Ecologists have long suspected that species are more likely to interact if their traits match in a particular way. For example, a pollination interaction may be more likely if the proportions of a bee's tongue fit a plant's flower shape.…

Graph Neural Network (GNN) is a powerful model to learn representations and make predictions on graph data. Existing efforts on GNN have largely defined the graph convolution as a weighted sum of the features of the connected nodes to form…

Although a number of studies have explored deep learning in neuroscience, the application of these algorithms to neural systems on a microscopic scale, i.e. parameters relevant to lower scales of organization, remains relatively novel.…

Recommender systems aim to provide personalized services to users and are playing an increasingly important role in our daily lives. The key of recommender systems is to predict how likely users will interact with items based on their…

Functional groups (FGs) are molecular substructures that are served as a foundation for analyzing and predicting chemical properties of molecules. Automatic discovery of FGs will impact various fields of research, including medicinal…

Graph-based collaborative filtering methods have prevailing performance for recommender systems since they can capture high-order information between users and items, in which the graphs are constructed from the observed user-item…

Graph Neural Networks (GNNs) achieve an impressive performance on structured graphs by recursively updating the representation vector of each node based on its neighbors, during which parameterized transformation matrices should be learned…

User and item attributes are essential side-information; their interactions (i.e., their co-occurrence in the sample data) can significantly enhance prediction accuracy in various recommender systems. We identify two different types of…