Knowledge graphs (KGs) have been widely used in the field of artificial intelligence, such as in information retrieval, natural language processing, recommendation systems, etc. However, the open nature of KGs often implies that they are incomplete, having self-defects. This creates the need to build a more complete knowledge graph for enhancing the practical utilization of KGs. Link prediction is a fundamental task in knowledge graph completion that utilizes existing relations to infer new relations so as to build a more complete knowledge graph. Numerous methods have been proposed to perform the link-prediction task based on various representation techniques. Among them, KG-embedding models have significantly advanced the state of the art in the past few years. In this paper, we provide a comprehensive survey on KG-embedding models for link prediction in knowledge graphs. We first provide a theoretical analysis and comparison of existing methods proposed to date for generating KG embedding. Then, we investigate several representative models that are classified into five categories. Finally, we conducted experiments on two benchmark datasets to report comprehensive findings and provide some new insights into the strengths and weaknesses of existing models.

Motivation: Polypharmacy is the combined use of drugs for the treatment of diseases. However, it often shows a high risk of side effects. Due to unnecessary interactions of combined drugs, the side effects of polypharmacy increase the risk of disease and even lead to death. Thus, obtaining abundant and comprehensive information on the side effects of polypharmacy is a vital task in the healthcare industry. Early traditional methods used machine learning techniques to predict side effects. However, they often make costly efforts to extract features of drugs for prediction. Later, several methods based on knowledge graphs are proposed. They are reported to outperform traditional methods. However, they still show limited performance by failing to model complex relations of side effects among drugs. Results: To resolve the above problems, we propose a novel model by further incorporating complex relations of side effects into knowledge graph embeddings. Our model can translate and transmit multidirectional semantics with fewer parameters, leading to better scalability in large-scale knowledge graphs. Experimental evaluation shows that our model outperforms state-of-the-art models in terms of the average area under the ROC and precision–recall curves. Availability and implementation: Code and data are available at: https://github.com/galaxysunwen/MSTE-master.

The clinical data are often multimodal and consist of both structured data and unstructured data. The modeling of clinical data has become a very important and challenging problem in healthcare big data analytics. Most existing systems focus on only one type of data. In this paper, we propose a knowledge graph-based method to build the linkage between various types of multimodal data. First, we build a semantic-rich knowledge base using both medical dictionaries and practical clinical data collected from hospitals. Second, we propose a graph modeling method to bridge the gap between different types of data, and the multimodal clinical data of each patient are fused and modeled as one unified profile graph. To capture the temporal evolution of the patient’s clinical case, the profile graph is represented as a sequence of evolving graphs. Third, we develop a lazy learning algorithm for automatic diagnosis based on graph similarity search. To evaluate our method, we conduct experimental studies on ICU patient diagnosis and Orthopaedics patient classification. The results show that our method could outperform the baseline algorithms. We also implement a real automatic diagnosis system for clinical use. The results obtained from the hospital demonstrate high precision.

With its increasing incidence, cancer has become one of the main causes of worldwide mortality. In this work, we mainly propose a novel attention-based neural network model named Gated Graph ATtention network (GGAT) for cancer prediction, where a gating mechanism (GM) is introduced to work with the attention mechanism (AM), to break through the previous work’s limitation of 1-hop neighbourhood reasoning. In this way, our GGAT is capable of fully mining the potential correlation between related samples, helping for improving the cancer prediction accuracy. Additionally, to simplify the datasets, we propose a hybrid feature selection algorithm to strictly select gene features, which significantly reduces training time without affecting prediction accuracy. To the best of our knowledge, our proposed GGAT achieves the state-of-the-art results in cancer prediction task on LIHC, LUAD, KIRC compared to other traditional machine learning methods and neural network models, and improves the accuracy by 1% to 2% on Cora dataset, compared to the state-of-the-art graph neural network methods.

Healthcare question answering (HQA) is a challenging task as questions are generally non-factoid. Recent neural systems are reported to have performance gains. However, little attention has been given to HQA as datasets are generally too small to train a neural model from scratch. Recently, several systems have been proposed to learn context representations for HQA. Despite moderate progress, these systems have not been thoroughly compared with state-of-the-art neural models, and the mentioned models are tested only on self-created datasets. To address the challenges, we develop a new joint model to incorporate both context and knowledge embeddings into neural ranking architectures. First, we adapt context embedding pre-trained from large open-domain corpus to small healthcare datasets. Second, we learn knowledge embedding from knowledge graphs to provide external information for understanding non-factoid questions. To evaluate our framework, we adapt many state-of-the-art methods for general QA to HQA, by injecting the context or knowledge information only, or both of them. Extensive experiments are conducted to compare our approach with those adapted methods and current HQA systems. The results show that our approach achieves the state-of-the-art performance on both HealthQA and NFCorpus datasets. The source codes are available at https://github.com/emmali808/HQADeepHelper.