MGATAF: multi-channel graph attention network with adaptive fusion for cancer-drug response prediction.

Background: Drug response prediction is critical in precision medicine to determine the most effective and safe treatments for individual patients. Traditional prediction methods relying on demographic and genetic data often fall short in accuracy and robustness. Recent graph-based models, while promising, frequently neglect the critical role of atomic interactions and fail to integrate drug fingerprints with SMILES for comprehensive molecular graph construction.

AutoAMS: Automated attention-based multi-modal graph learning architecture search.

Multi-modal attention mechanisms have been successfully used in multi-modal graph learning for various tasks. However, existing attention-based multi-modal graph learning (AMGL) architectures heavily rely on manual design, requiring huge effort and expert experience. Meanwhile, graph neural architecture search (GNAS) has made great progress toward automatically designing graph-based learning architectures.

AutoDDI: Drug-Drug Interaction Prediction With Automated Graph Neural Network.

Drug-drug interaction (DDI) has attracted widespread attention because when incompatible drugs are taken together, DDI will lead to adverse effects on the body, such as drug poisoning or reduced drug efficacy. The adverse effects of DDI are closely determined by the molecular structures of the drugs involved. To represent drug data effectively, researchers usually treat the molecular structure of drugs as a molecule graph.

Cancer drug response prediction with surrogate modeling-based graph neural architecture search.

Motivation: Understanding drug-response differences in cancer treatments is one of the most challenging aspects of personalized medicine. Recently, graph neural networks (GNNs) have become state-of-the-art methods in many graph representation learning scenarios in bioinformatics. However, building an optimal handcrafted GNN model for a particular drug sensitivity dataset requires manual design and fine-tuning of the hyperparameters for the GNN model, which is time-consuming and requires expert knowledge.

Multi-View Graph Neural Architecture Search for Biomedical Entity and Relation Extraction.

Recently, graph neural architecture search (GNAS) frameworks have been successfully used to automatically design the optimal neural architectures for many problems such as node classification and graph classification. In the existing GNAS frameworks, the designed graph neural network (GNN) architectures learn the representation of homogenous graphs with one type of relationship connecting two nodes. However, multi-view graphs, where each view represents a type of relationship among nodes, are ubiquitous in the real world.

A Principal Neighborhood Aggregation-Based Graph Convolutional Network for Pneumonia Detection.

Pneumonia is one of the main causes of child mortality in the world and has been reported by the World Health Organization (WHO) to be the cause of one-third of child deaths in India. Designing an automated classification system to detect pneumonia has become a worthwhile research topic. Numerous deep learning models have attempted to detect pneumonia by applying convolutional neural networks (CNNs) to X-ray radiographs, as they are essentially images and have achieved great performances.