Related papers: GLaDiGAtor: Language-Model-Augmented Multi-Relatio…

Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target…

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic…

Many rare genetic diseases exhibit recognizable facial phenotypes, which are often used as diagnostic clues. However, current facial phenotype diagnostic models, which are trained on image datasets, have high accuracy but often suffer from…

The gut microbiome, crucial for human health, presents challenges in analyzing its complex metaomic data due to high dimensionality and sparsity. Traditional methods struggle to capture its intricate relationships. We investigate graph…

A large number of real-world networks include multiple types of nodes and edges. Graph Neural Network (GNN) emerged as a deep learning framework to generate node and graph embeddings for downstream machine learning tasks. However, popular…

One of the notable fields in studying the genetics of cancer is disease gene identification which affects disease treatment and drug discovery. Many researches have been done in this field. Genome-wide association studies (GWAS) are one of…

Explainability is necessary for many tasks in biomedical research. Recent explainability methods have focused on attention, gradient, and Shapley value. These do not handle data with strong associated prior knowledge and fail to constrain…

Graph neural networks (GNNs) have witnessed an unprecedented proliferation in tackling several problems in computer vision, computer-aided diagnosis, and related fields. While prior studies have focused on boosting the model accuracy,…

Combination therapy has shown to improve therapeutic efficacy while reducing side effects. Importantly, it has become an indispensable strategy to overcome resistance in antibiotics, anti-microbials, and anti-cancer drugs. Facing enormous…

Graph Neural Networks (GNNs) excel in graph-based learning tasks, but their complex, non-linear operations often render them as opaque "black boxes". This opacity hinders user trust, complicates debugging, bias detection, and adoption in…

This work presents a novel approach to tabular data prediction leveraging graph structure learning and graph neural networks. Despite the prevalence of tabular data in real-world applications, traditional deep learning methods often…

The era of data deluge has sparked the interest in graph-based learning methods in a number of disciplines such as sociology, biology, neuroscience, or engineering. In this paper, we introduce a graph recurrent neural network (GRNN) for…

Graph Neural Networks (GNNs) and their message passing framework that leverages both structural and feature information, have become a standard method for solving graph-based machine learning problems. However, these approaches still…

Graph neural networks (GNNs) have brought revolutionary advancements to the field of link prediction (LP), providing powerful tools for mining potential relationships in graphs. However, existing methods face challenges when dealing with…

With the increasing use of graph-structured data, there is also increasing interest in investigating graph data dependencies and their applications, e.g., in graph data profiling. Graph Generating Dependencies (GGDs) are a class of…

Graph Neural Networks (GNNs) are an emerging research field. This specialized Deep Neural Network (DNN) architecture is capable of processing graph structured data and bridges the gap between graph processing and Deep Learning (DL). As…

Predictive tasks on relational databases are critical in real-world applications spanning e-commerce, healthcare, and social media. To address these tasks effectively, Relational Deep Learning (RDL) encodes relational data as graphs,…

Knowledge graphs offer a structured representation of real-world entities and their relationships, enabling a wide range of applications from information retrieval to automated reasoning. In this paper, we conduct a systematic comparison…

The challenge of effectively learning inter-series correlations for multivariate time series forecasting remains a substantial and unresolved problem. Traditional deep learning models, which are largely dependent on the Transformer paradigm…

Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…