Related papers: Graph-Based Multi-Omics Integration Improves Subty…

Motivation: Multi-omics integration can improve cancer subtyping, but modality informativeness and noise vary across cancer types and patients. Existing graph-based methods optimize modality weights jointly with the classification objective…

Clustering cancer patients into subgroups and identifying cancer subtypes is an important task in cancer genomics. Clustering based on comprehensive multi-omic molecular profiling can often achieve better results than those using a single…

The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating…

Cancer is a highly heterogeneous disease with significant variability in molecular features and clinical outcomes, making diagnosis and treatment challenging. In recent years, high-throughput omic technologies have facilitated the discovery…

Defining subtypes of complex diseases such as cancer and stratifying patient groups with the same disease but different subtypes for targeted treatments is important for personalized and precision medicine. Approaches that incorporate…

Integrating multi-omics datasets through data-driven analysis offers a comprehensive understanding of the complex biological processes underlying various diseases, particularly cancer. Graph Neural Networks (GNNs) have recently demonstrated…

Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely…

Multi-omics data integration is crucial for understanding complex diseases, yet limited sample sizes, noise, and heterogeneity often reduce predictive power. To address these challenges, we introduce Omics-GAN, a Generative Adversarial…

Multi-omics data is increasingly being utilized to advance computational methods for cancer classification. However, multi-omics data integration poses significant challenges due to the high dimensionality, data complexity, and distinct…

Network biology has been successfully used to help reveal complex mechanisms of disease, especially cancer. On the other hand, network biology requires in-depth knowledge to construct disease-specific networks, but our current knowledge is…

The integration of quantum machine learning with classical deep learning offers promising avenues for medical image analysis by mapping data into high-dimensional Hilbert spaces. However, effectively unifying these distinct paradigms…

The task of data integration for multi-omics data has emerged as a powerful strategy to unravel the complex biological underpinnings of cancer. Recent advancements in graph neural networks (GNNs) offer an effective framework to model…

The integration of multi-omics data has emerged as a promising approach for gaining comprehensive insights into complex diseases such as cancer. This paper proposes a novel approach to identify cancer subtypes through the integration of…

There exists unexplained diverse variation within the predefined colon cancer stages using only features either from genomics or histopathological whole slide images as prognostic factors. Unraveling this variation will bring about improved…

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…

Network topology excels at structural predictions but fails to capture functional semantics encoded in biomedical literature. We present RAG-GNN, an end-to-end trainable retrieval-augmented graph neural network framework that integrates GNN…

Cancer cell response to targeted therapy arises from complex molecular interactions, making single omics insufficient for accurate prediction. This study develops a model to predict Dabrafenib sensitivity by integrating multiple omics…

In this study, we present the Graph Sub-Graph Network (GSN), a novel hybrid image classification model merging the strengths of Convolutional Neural Networks (CNNs) for feature extraction and Graph Neural Networks (GNNs) for structural…

Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is…

Multi-omics research has enhanced our understanding of cancer heterogeneity and progression. Investigating molecular data through multi-omics approaches is crucial for unraveling the complex biological mechanisms underlying cancer, thereby…