Related papers: netgwas: An R Package for Network-Based Genome-Wid…
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…
Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…
High-dimensional networks play a key role in understanding complex relationships. These relationships are often dynamic in nature and can change with multiple external factors (e.g., time and groups). Methods for estimating graphical models…
This paper introduces the \proglang{R} package \pkg{meta4diag} for implementing Bayesian bivariate meta-analyses of diagnostic test studies. Our package \pkg{meta4diag} is a purpose-built front end of the \proglang{R} package \pkg{INLA}.…
This paper explores the applications and challenges of graph neural networks (GNNs) in processing complex graph data brought about by the rapid development of the Internet. Given the heterogeneity and redundancy problems that graph data…
In this paper, we introduce a novel method for merging the weights of multiple pre-trained neural networks using a genetic algorithm called MeGA. Traditional techniques, such as weight averaging and ensemble methods, often fail to fully…
We developed DyGETViz, a novel framework for effectively visualizing dynamic graphs (DGs) that are ubiquitous across diverse real-world systems. This framework leverages recent advancements in discrete-time dynamic graph (DTDG) models to…
Free and open source software package ecosystems have existed for a long time and are among the most sophisticated human-made systems. One of the oldest and most popular software package ecosystems is CRAN, the repository of packages of the…
Identifying critical nodes and links in graphs is a crucial task. These nodes/links typically represent critical elements/communication links that play a key role in a system's performance. However, a majority of the methods available in…
Networks are useful for representing phenomena in a broad range of domains. Although their ability to represent complexity can be a virtue, it is sometimes useful to focus on a simplified network that contains only the most important edges:…
GeneVis is a web-based tool to visualize complementary data sets of different disciplines within the field of genetics. It overlays gene-cluster information, gene-interaction data and gene-disease association data by means of web-based…
To understand how genetic variants in human genomes manifest in phenotypes -- traits like height or diseases like asthma -- geneticists have sequenced and measured hundreds of thousands of individuals. Geneticists use this data to build…
\pkg{multiplex} is a computer program that provides algebraic tools for the analysis of multiple network structures within the \proglang{R} environment. Apart from the possibility to create and manipulate multivariate data representing…
Reverse-phase protein array (RPPA) analysis is a powerful, relatively new platform that allows for high-throughput, quantitative analysis of protein networks. One of the challenges that currently limit the potential of this technology is…
Graph Neural Networks (GNNs) are popular machine learning methods for modeling graph data. A lot of GNNs perform well on homophily graphs while having unsatisfactory performance on heterophily graphs. Recently, some researchers turn their…
Ising models are a simple generative approach to describing interacting binary variables. They have proven useful in a number of biological settings because they enable one to represent observed many-body correlations as the separable…
Circuit representation learning has shown promise in advancing Electronic Design Automation (EDA) by capturing structural and functional circuit properties for various tasks. Existing pre-trained solutions rely on graph learning with…
In this study, we present a collection of local models, termed geographically weighted (GW) models, that can be found within the GWmodel R package. A GW model suits situations when spatial data are poorly described by the global form, and…
Graphical Gaussian models are popular tools for the estimation of (undirected) gene association networks from microarray data. A key issue when the number of variables greatly exceeds the number of samples is the estimation of the matrix of…
Large language models (LLMs) commonly struggle with specialized or emerging topics which are rarely seen in the training corpus. Graph-based retrieval-augmented generation (GraphRAG) addresses this by structuring domain knowledge as a graph…