Identifying protein complexes from protein-protein interaction (PPI) network is one of the most important tasks in proteomics. Existing computational methods try to incorporate a variety of biological evidences to enhance the quality of predicted complexes. However, it is still a challenge to integrate different types of biological information into the complexes discovery process under a unified framework. Recently, attributed network embedding methods have be proved to be remarkably effective in generating vector representations for nodes in the network. In the transformed vector space, both the topological proximity and node attributed affinity between different nodes are preserved. Therefore, such attributed network embedding methods provide us a unified framework to integrate various biological evidences into the protein complexes identification process. In this article, we propose a new method called GANE to predict protein complexes based on Gene Ontology (GO) attributed network embedding. Firstly, it learns the vector representation for each protein from a GO attributed PPI network. Based on the pair-wise vector representation similarity, a weighted adjacency matrix is constructed. Secondly, it uses the clique mining method to generate candidate cores. Consequently, seed cores are obtained by ranking candidate cores based on their densities on the weighted adjacency matrix and removing redundant cores. For each seed core, its attachments are the proteins with correlation score that is larger than a given threshold. The combination of a seed core and its attachment proteins is reported as a predicted protein complex by the GANE algorithm. For performance evaluation, we compared GANE with six protein complex identification methods on five yeast PPI networks. Experimental results showes that GANE performs better than the competing algorithms in terms of different evaluation metrics. GANE provides a framework that integrate many valuable and different biological information into the task of protein complex identification. The protein vector representation learned from our attributed PPI network can also be used in other tasks, such as PPI prediction and disease gene prediction.

The proliferation of consumer electronic products has engendered a substantial surge in data generation and information exchange, concurrently escalating the potential for security threats. Detecting anomalies effectively on attributed networks has undeniable positive significance for consumer electronic security, such as fraudulent user detection, malicious consumption actions analysis, and network threat detection. However, the lack of real tags poses great challenges for detecting anomalies. Therefore, this paper introduces an unsupervised learning framework, namely ADVANCE, to jointly optimize the graph contrastive learning module and the network reconstruction module to accurately discover the anomalies on attributed networks in unsupervised scenarios. Specifically, ADVANCE first constructs the target view and the self-enhanced view to encode view representations by maximizing the consistency between the two views with graph contrastive learning. Subsequently, a network reconstruction module is introduced to assess the anomaly status of each node based on the degree of consistency from both topological structure and node attributes perspectives. The nodes with higher reconstruction errors are considered as anomalous nodes. Finally, the two complementary modules are jointly trained to enhance the accuracy of anomaly detection. Extensive experimental results on three benchmark datasets demonstrate the remarkable effectiveness of our proposed framework in unsupervised anomaly detection.

It is crucial for doctors to fully understand the interaction between drugs in prescriptions, especially when a patient takes multiple medications at the same time during treatment. The purpose of drug drug interaction (DDI) extraction is to automatically obtain the interaction between drugs from biomedical literature. Current state-of-the-art approaches for DDI extraction task are based on artificial intelligence and natural language processing. While such existing DDI extraction methods can provide more knowledge and enhance the performance through external resources such as biomedical databases or ontologies, due to the difficulty of updating, these external resources are delayed. In fact, user generated content (UGC) is another kind of external medical resources that can be quickly updated. We are trying to use UGC resources to provide more available information for our deep learning DDI extraction method. In this paper, we present a DDI extraction approach through a new attention mechanism called full-attention which can combine the UGC information with contextual information. We conducted a series of experiments on the DDI 2013 Evaluation dataset to evaluate our method. Experiments show improved performance compared with the state of the art and UGC-DDI model achieves a competitive F-score of 0.712.

Automatically extracting entity-pair interactions from biomedical literature plays an important role in promoting the development of the biomedical field. For instance, the interactions between drugs can guide patients to take drugs correctly and avoid clinical adverse drug reactions; The interactions between proteins can help researchers design therapeutic drugs and discover disease mechanisms. However, it is found that relation instances of different classes generated from the same sentence are easily classified into the same class since their context information is almost the same. To address this issue, Triplet Loss based BERT (TL-BERT) approach is proposed in this paper, where the Triplet Loss training strategy is first introduced into the biomedical relation extraction field. Triplet Loss training strategy will increase the distances between these instances generated from the same sentence but belonging to different classes, and decrease the distances between these instances generated from different sentences but belonging to the same class. As a result, our approach can classify these instances generated from the same sentence more correctly. TL-BERT was evaluated on AIMed, BioInfer, and DDI Extraction-2013 corpus, the experimental results demonstrate that the Triplet Loss training strategy can improve the performance on both Protein-Protein interactions extraction tasks and Drug-Drug interactions detection tasks.

Entity alignment (EA), aiming to match entities with the same meaning across different knowledge graphs (KGs), is a critical step in knowledge fusion. Existing EA methods usually encode the multi-aspect features of entities as embeddings and learn to align the embeddings with supervised learning. Although these methods have achieved remarkable results, two issues have not been well addressed. Firstly, these methods require pre-aligned entity pairs to perform EA tasks, limiting their applicability in practice. Secondly, these methods overlook the unique contribution of digital attributes to EA tasks when utilising attribute information to enhance entity features. In this paper, we propose a self-supervised entity alignment framework via attribute correction. Specifically, we first design a highly effective seed pair generator based on multi-aspect features of entities to solve the labour-intensive problem of obtaining pre-aligned entity pairs. Then, a novel alignment mechanism via attribute correction is proposed to address the problem that different types of attributes have different contributions to the EA task. Extensive experiments on real-world datasets with semantic features demonstrate that our framework outperforms state-of-the-art (SOTA) EA tasks.