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 due to the branch properties of the molecular structure of drugs. Then, previous studies can use the handcrafted graph neural network (GNN) model to learn the molecular graph representations of drugs for DDI prediction. However, in the field of bioinformatics, manually designing GNN architectures for specific molecular structure datasets is time-consuming and depends on expert experience. To address this problem, we propose an automatic drug–drug interaction prediction method named AutoDDI that can efficiently and automatically design the GNN architecture for drug–drug interaction prediction without manual intervention. To this end, we first design an effective search space for drug–drug interaction prediction by revisiting various handcrafted GNN architectures. Then, to efficiently and automatically design the optimal GNN architecture for each drug dataset from the search space, a reinforcement learning search algorithm is adopted. We test the performance of our proposed AutoDDI method on two real-world datasets. The experiment results show that AutoDDI can outperform baseline methods and achieve the best performance. Moreover, the visual interpretation results of the case study show that AutoDDI can effectively capture drug substructure for drug–drug interaction prediction. The code is available at: https://github.com/Zhen-Peng-Wu/AutoDDI .

Graph neural networks (GNNs) have received much attention as GNNs have recently been successfully applied on non-euclidean data. However, artificially designed graph neural networks often fail to get satisfactory model performance for a given graph data. Graph neural architecture search effectively constructs the GNNs that achieve the expected model performance with the rise of automatic machine learning. The challenge is efficiently and automatically getting the optimal GNN architecture in a vast search space. Existing search methods serially evaluate the GNN architectures, severely limiting system efficiency. To solve these problems, we develop an Auto matic G raph N eural A rchitecture S earch framework (Auto-GNAS) with parallel estimation to implement an automatic graph neural search process that requires almost no manual intervention. In Auto-GNAS, we design the search algorithm with multiple genetic searchers. Each searcher can simultaneously use evaluation feedback information, information entropy, and search results from other searchers based on sharing mechanism to improve the search efficiency. As far as we know, this is the first work using parallel computing to improve the system efficiency of graph neural architecture search. According to the experiment on the real datasets, Auto-GNAS obtain competitive model performance and better search efficiency than other search algorithms. Since the parallel estimation ability of Auto-GNAS is independent of search algorithms, we expand different search algorithms based on Auto-GNAS for scalability experiments. The results show that Auto-GNAS with varying search algorithms can achieve nearly linear acceleration with the increase of computing resources.

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. The traditional GNAS frameworks learn the graph representation without considering the interactions between nodes and multiple relationships, so they fail to solve multi-view graph-based problems, such as multi-view graphs modelling the biomedical entity and relation extraction tasks. In this paper, we propose MVGNAS, a multi-view graph neural network automatic modelling framework for biomedical entity and relation extraction, to resolve this challenge. In MVGNAS, we propose an automatic multi-view representation learning to learn low-dimensional representations of nodes that capture multiple relationships in a multi-view graph, representing the first research work in literature to solve the problem of multi-view graph representation learning architecture search for biomedical entity and relation extraction tasks. The experimental results demonstrate that MVGNAS can achieve the best performance in biomedical entity and relation extraction tasks against the state-of-the-art baseline methods.

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. Results: In this work, we propose AutoCDRP, a novel framework for automated cancer drug–response predictor using GNNs. Our approach leverages surrogate modeling to efficiently search for the most effective GNN architecture. AutoCDRP uses a surrogate model to predict the performance of GNN architectures sampled from a search space, allowing it to select the optimal architecture based on evaluation performance. Hence, AutoCDRP can efficiently identify the optimal GNN architecture by exploring the performance of all GNN architectures in the search space. Through comprehensive experiments on two benchmark datasets, we demonstrate that the GNN architecture generated by AutoCDRP surpasses state-of-the-art designs. Notably, the optimal GNN architecture identified by AutoCDRP consistently outperforms the best baseline architecture from the first epoch, providing further evidence of its effectiveness. Availability and implementation: https://github.com/BeObm/AutoCDRP.

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. However, they failed to capture higher-order feature information of all objects based on the X-ray images because the topology of the X-ray images’ dimensions does not always come with some spatially regular locality properties, which makes defining a spatial kernel filter in X-ray images non-trivial. This paper proposes a principal neighborhood aggregation-based graph convolutional network (PNA-GCN) for pneumonia detection. In PNA-GCN, we propose a new graph-based feature construction utilizing the transfer learning technique to extract features and then construct the graph from images. Then, we propose a graph convolutional network with principal neighborhood aggregation. We integrate multiple aggregation functions in a single layer with degree-scalers to capture more effective information in a single layer to exploit the underlying properties of the graph structure. The experimental results show that PNA-GCN can perform best in the pneumonia detection task on a real-world dataset against the state-of-the-art baseline methods.

It is significant to comprehend the relationship between metabolic pathway and molecular pathway for synthesizing new molecules, for instance optimizing drug metabolization. In bioinformatics fields, multi-label prediction of metabolic pathways is a typical manner to understand this relationship. Graph neural networks (GNNs) have become an effective method to extract molecular structure's features for multi-label prediction of metabolic pathways. Though GNNs can effectively capture structural features from molecular structure graphs, building a well-performed GNN model for a given molecular structure data set requires the manual design of the GNN architecture and fine-tuning of the hyperparameters, which are time-consuming and rely on expert experience. To address the above challenge, we design an end-to-end automatic molecular structure representation learning framework named AutoMSR that can design the optimal GNN model based on a given molecular structure data set without manual intervention. We propose a multi-seed age evolution (MSAE) search algorithm to identify the optimal GNN architecture from the GNN architecture subspace. For a given molecular structure data set, AutoMSR first uses MSAE to search the GNN architecture, and then it adopts a tree-structured parzen estimator to obtain the best hyperparameters in the hyperparameters subspace. Finally, AutoMSR automatically constructs the optimal GNN model based on the best GNN architecture and hyperparameters to extract the molecular structure features for multi-label metabolic pathway prediction. We test the performance of AutoMSR on the real data set KEGG. The experiment results show that AutoMSR outperforms baseline methods on different multi-label classification evaluation metrics.