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Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in…

Biomarker discovery from high-throughput transcriptomic data is crucial for advancing precision medicine. However, existing methods often neglect gene-gene regulatory relationships and lack stability across datasets, leading to conflation…

The intricate relationship between genetic variation and human diseases has been a focal point of medical research, evidenced by the identification of risk genes regarding specific diseases. The advent of advanced genome sequencing…

Target selection is crucial in pharmaceutical drug discovery, directly influencing clinical trial success. Despite its importance, drug development remains resource-intensive, often taking over a decade with significant financial costs.…

Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the protein-ligand interactions with graph neural networks (GNNs)…

Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as…

Since multidrug combination is widely applied, the accurate prediction of drug-drug interaction (DDI) is becoming more and more critical. In our method, we use graph to represent drug-drug interaction: nodes represent drug; edges represent…

Graph neural networks (GNNs) provide powerful insights for brain neuroimaging technology from the view of graphical networks. However, most existing GNN-based models assume that the neuroimaging-produced brain connectome network is a…

Decrypting intelligence from the human brain construct is vital in the detection of particular neurological disorders. Recently, functional brain connectomes have been used successfully to predict behavioral scores. However,…

Elucidating and accurately predicting the druggability and bioactivities of molecules plays a pivotal role in drug design and discovery and remains an open challenge. Recently, graph neural networks (GNN) have made remarkable advancements…

Several works based on Generative Adversarial Networks (GAN) have been recently proposed to predict a set of medical images from a single modality (e.g, FLAIR MRI from T1 MRI). However, such frameworks are primarily designed to operate on…

Graph Neural Networks (GNNs) is an architecture for structural data, and has been adopted in a mass of tasks and achieved fabulous results, such as link prediction, node classification, graph classification and so on. Generally, for a…

Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse…

Biomedical information graphs are crucial for interaction discovering of biomedical information in modern age, such as identification of multifarious molecular interactions and drug discovery, which attracts increasing interests in…

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

Identifying causative genes from patient phenotypes remains a significant challenge in precision medicine, with important implications for the diagnosis and treatment of genetic disorders. We propose a novel graph-based approach for…

Recently, Graph Neural Networks (GNNs) have significantly advanced the performance of machine learning tasks on graphs. However, this technological breakthrough makes people wonder: how does a GNN make such decisions, and can we trust its…

Imbalanced classification on graphs is ubiquitous yet challenging in many real-world applications, such as fraudulent node detection. Recently, graph neural networks (GNNs) have shown promising performance on many network analysis tasks.…

Graph deep learning has recently emerged as a powerful ML concept allowing to generalize successful deep neural architectures to non-Euclidean structured data. Such methods have shown promising results on a broad spectrum of applications…