Biomedical evidence engineering for data-driven discovery.

MOTIVATION: With the rapid development of precision medicine, a large amount of health data (such as electronic health records, gene sequencing, medical images, etc.) has been produced. It encourages more and more interest in data-driven insight discovery from these data. A reasonable way to verify the derived insights is by checking evidence from biomedical literature. However, manual verification is inefficient and not scalable. Therefore, an intelligent technique is necessary to solve this problem. RESULTS: This article introduces a framework for biomedical evidence engineering, addressing this problem more effectively. The framework consists of a biomedical literature retrieval module and an evidence extraction module. The retrieval module ensembles several methods and achieves state-of-the-art performance in biomedical literature retrieval. A BERT-based evidence extraction model is proposed to extract evidence from literature in response to queries. Moreover, we create a dataset with 1 million examples of biomedical evidence, 10 000 of which are manually annotated. AVAILABILITY AND IMPLEMENTATION: Datasets are available at https://github.com/SendongZhao.

Understanding Patient Query With Weak Supervision From Doctor Response.

Currently, the need for high-quality dialogue systems that assist users to conduct self-diagnosis is rapidly increasing. Slot filling for automatic diagnosis, which converts medical queries into structured representations, plays an important role in diagnostic dialogue systems. However, the lack of high-quality datasets limits the performance of slot filling. While medical communities like AskAPatient usually have multiple rounds of diagnostic dialogue containing colloquial input and professional responses from doctors. Therefore, the data of diagnostic dialogue in medical communities can be utilized to solve the main challenges in slot filling. This paper proposes a two-step training framework to make full use of these unlabeled dialogue data in medical communities. To promote further researches, we provide a Chinese dataset with 2,652 annotated samples and a large amount of unlabeled samples. Experimental results on the dataset demonstrate the effectiveness of the proposed method with an increase of 6.32% in Micro F1 and 8.20% in Macro F1 on average over strong baselines.

Recent advances in biomedical literature mining.

The recent years have witnessed a rapid increase in the number of scientific articles in biomedical domain. These literature are mostly available and readily accessible in electronic format. The domain knowledge hidden in them is critical for biomedical research and applications, which makes biomedical literature mining (BLM) techniques highly demanding. Numerous efforts have been made on this topic from both biomedical informatics (BMI) and computer science (CS) communities. The BMI community focuses more on the concrete application problems and thus prefer more interpretable and descriptive methods, while the CS community chases more on superior performance and generalization ability, thus more sophisticated and universal models are developed. The goal of this paper is to provide a review of the recent advances in BLM from both communities and inspire new research directions.

Graph convolutional networks for computational drug development and discovery.

Despite the fact that deep learning has achieved remarkable success in various domains over the past decade, its application in molecular informatics and drug discovery is still limited. Recent advances in adapting deep architectures to structured data have opened a new paradigm for pharmaceutical research. In this survey, we provide a systematic review on the emerging field of graph convolutional networks and their applications in drug discovery and molecular informatics. Typically we are interested in why and how graph convolution networks can help in drug-related tasks. We elaborate the existing applications through four perspectives: molecular property and activity prediction, interaction prediction, synthesis prediction and de novo drug design. We briefly introduce the theoretical foundations behind graph convolutional networks and illustrate various architectures based on different formulations. Then we summarize the representative applications in drug-related problems. We also discuss the current challenges and future possibilities of applying graph convolutional networks to drug discovery.