Related papers: Gene Regulatory Network Inference from Pre-trained…

Biological foundation models have shown strong performance in single-cell representation learning by applying transformer architectures directly to gene-expression matrices. However, these approaches predominantly operate in static settings…

Graph Neural Networks (GNNs) are a promising deep learning approach for circumventing many real-world problems on graph-structured data. However, these models usually have at least one of four fundamental limitations: over-smoothing,…

Graph neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…

Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based…

Session-based recommendation systems suggest relevant items to users by modeling user behavior and preferences using short-term anonymous sessions. Existing methods leverage Graph Neural Networks (GNNs) that propagate and aggregate…

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…

Graph neural networks (GNNs) have attracted much attention due to their ability to leverage the intrinsic geometries of the underlying data. Although many different types of GNN models have been developed, with many benchmarking procedures…

Graph Neural Networks (GNNs) have been widely applied to various fields due to their powerful representations of graph-structured data. Despite the success of GNNs, most existing GNNs are designed to learn node representations on the fixed…

The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale…

Graph neural networks (GNNs) have been widely used in representation learning on graphs and achieved state-of-the-art performance in tasks such as node classification and link prediction. However, most existing GNNs are designed to learn…

Graph Convolutional Neural Networks (GCNNs) are generalizations of CNNs to graph-structured data, in which convolution is guided by the graph topology. In many cases where graphs are unavailable, existing methods manually construct graphs…

Recent studies have highlighted the limitations of message-passing based graph neural networks (GNNs), e.g., limited model expressiveness, over-smoothing, over-squashing, etc. To alleviate these issues, Graph Transformers (GTs) have been…

Inferring genetic networks from gene expression data is one of the most challenging work in the post-genomic era, partly due to the vast space of possible networks and the relatively small amount of data available. In this field, Gaussian…

Graph Neural Networks (GNNs) have achieved great success among various domains. Nevertheless, most GNN methods are sensitive to the quality of graph structures. To tackle this problem, some studies exploit different graph structure learning…

Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies. No existing simulator jointly models gene-gene and cell-cell…

Graph neural networks (GNNs) have become a powerful tool for processing graph-structured data but still face challenges in effectively aggregating and propagating information between layers, which limits their performance. We tackle this…

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…

Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…

The two most fundamental processes describing change in biology, development and evolu-tion, occur over drastically different timescales, difficult to reconcile within a unified framework. Development involves temporal sequences of cell…

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…