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Accurately predicting molecular properties is a challenging but essential task in drug discovery. Recently, many mono-modal deep learning methods have been successfully applied to molecular property prediction. However, the inherent…

The integration of multi-omics single-cell data remains challenging due to high-dimensionality and complex inter-modality relationships. To address this, we introduce MoRE-GNN (Multi-omics Relational Edge Graph Neural Network), a…

Despite the impressive advances achieved using deep learning for functional brain activity analysis, the heterogeneity of functional patterns and the scarcity of imaging data still pose challenges in tasks such as identifying neurological…

We introduce GENomic Encoding REpresentation with Language Model (GENEREL), a framework designed to bridge genetic and biomedical knowledge bases. What sets GENEREL apart is its ability to fine-tune language models to infuse biological…

Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that…

In this paper, we propose MGNet, a simple and effective multiplex graph convolutional network (GCN) model for multimodal brain network analysis. The proposed method integrates tensor representation into the multiplex GCN model to extract…

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,…

Graph Neural Networks (GNNs) are well-suited for learning on homophilous graphs, i.e., graphs in which edges tend to connect nodes of the same type. Yet, achievement of consistent GNN performance on heterophilous graphs remains an open…

Graph neural networks for heterogeneous graph embedding is to project nodes into a low-dimensional space by exploring the heterogeneity and semantics of the heterogeneous graph. However, on the one hand, most of existing heterogeneous graph…

Multi-modal medical image segmentation plays an essential role in clinical diagnosis. It remains challenging as the input modalities are often not well-aligned spatially. Existing learning-based methods mainly consider sharing trainable…

Generative self-supervised learning on graphs, particularly graph masked autoencoders, has emerged as a popular learning paradigm and demonstrated its efficacy in handling non-Euclidean data. However, several remaining issues limit the…

Multi-modal neuroimaging technology has greatlly facilitated the efficiency and diagnosis accuracy, which provides complementary information in discovering objective disease biomarkers. Conventional deep learning methods, e.g. convolutional…

Graph Neural Networks (GNNs) are a framework for graph representation learning, where a model learns to generate low dimensional node embeddings that encapsulate structural and feature-related information. GNNs are usually trained in an…

Multimodal data provide complementary information of a natural phenomenon by integrating data from various domains with very different statistical properties. Capturing the intra-modality and cross-modality information of multimodal data is…

Recent years have witnessed the rapid development of heterogeneous graph neural networks (HGNNs) in information retrieval (IR) applications. Many existing HGNNs design a variety of tailor-made graph convolutions to capture structural and…

Learning effective embedding has been proved to be useful in many real-world problems, such as recommender systems, search ranking and online advertisement. However, one of the challenges is data sparsity in learning large-scale item…

Clinicians are increasingly looking towards machine learning to gain insights about patient evolutions. We propose a novel approach named Multi-Modal UMLS Graph Learning (MMUGL) for learning meaningful representations of medical concepts…

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Recent advances in multimodal single-cell technologies have enabled simultaneous acquisitions of multiple omics data from the same cell, providing deeper insights into cellular states and dynamics. However, it is challenging to learn the…

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…