TransFOL: A Logical Query Model for Complex Relational Reasoning in Drug-Drug Interaction.

Predicting drug-drug interaction (DDI) plays a crucial role in drug recommendation and discovery. However, wet lab methods are prohibitively expensive and time-consuming due to drug interactions. In recent years, deep learning methods have gained widespread use in drug reasoning. Although these methods have demonstrated effectiveness, they can only predict the interaction between a drug pair and do not contain any other information. However, DDI is greatly affected by various other biomedical factors (such as the dose of the drug). As a result, it is challenging to apply them to more complex and meaningful reasoning tasks. Therefore, this study regards DDI as a link prediction problem on knowledge graphs and proposes a DDI prediction model based on Cross-Transformer and Graph Convolutional Networks (GCN) in first-order logical query form, TransFOL. In the model, a biomedical query graph is first built to learn the embedding representation. Subsequently, an enhancement module is designed to aggregate the semantics of entities and relations. Cross-Transformer is used for encoding to obtain semantic information between nodes, and GCN is used to gather neighbour information further and predict inference results. To evaluate the performance of TransFOL on common DDI tasks, we conduct experiments on two benchmark datasets. The experimental results indicate that our model outperforms state-of-the-art methods on traditional DDI tasks. Additionally, we introduce different biomedical information in the other two experiments to make the settings more realistic. Experimental results verify the strong drug reasoning ability and generalization of TransFOL in complex settings. Data and code are available at https://github.com/Cheng0829/TransFOL.

Risk adjustment for regional healthcare funding allocations with ensemble methods: an empirical study and interpretation.

We experiment with recent ensemble machine learning methods in estimating healthcare costs, utilizing Finnish data containing rich individual-level information on healthcare costs, socioeconomic status and diagnostic data from multiple registries. Our data are a random 10% sample (553,675 observations) from the Finnish population in 2017. Using annual healthcare cost in 2017 as a response variable, we compare the performance of Random forest, Gradient Boosting Machine (GBM) and eXtreme Gradient Boosting (XGBoost) to linear regression. As machine learning methods are often seen as unsuitable in risk adjustment applications because of their relative opaqueness, we also introduce visualizations from the machine learning literature to help interpret the contribution of individual variables to the prediction. Our results show that ensemble machine learning methods can improve predictive performance, with all of them significantly outperforming linear regression, and that a certain level of interpretation can be provided for them. We also find individual-level socioeconomic variables to improve prediction accuracy and that their effect is larger for machine learning methods. However, we find that the predictions used for funding allocations are sensitive to model selection, highlighting the need for comprehensive robustness testing when estimating risk adjustment models used in applications.

Automated clinical coding: what, why, and where we are?

Clinical coding is the task of transforming medical information in a patient's health records into structured codes so that they can be used for statistical analysis. This is a cognitive and time-consuming task that follows a standard process in order to achieve a high level of consistency. Clinical coding could potentially be supported by an automated system to improve the efficiency and accuracy of the process. We introduce the idea of automated clinical coding and summarise its challenges from the perspective of Artificial Intelligence (AI) and Natural Language Processing (NLP), based on the literature, our project experience over the past two and half years (late 2019-early 2022), and discussions with clinical coding experts in Scotland and the UK. Our research reveals the gaps between the current deep learning-based approach applied to clinical coding and the need for explainability and consistency in real-world practice. Knowledge-based methods that represent and reason the standard, explainable process of a task may need to be incorporated into deep learning-based methods for clinical coding. Automated clinical coding is a promising task for AI, despite the technical and organisational challenges. Coders are needed to be involved in the development process. There is much to achieve to develop and deploy an AI-based automated system to support coding in the next five years and beyond.

Natural language processing applied to mental illness detection: a narrative review.

Mental illness is highly prevalent nowadays, constituting a major cause of distress in people's life with impact on society's health and well-being. Mental illness is a complex multi-factorial disease associated with individual risk factors and a variety of socioeconomic, clinical associations. In order to capture these complex associations expressed in a wide variety of textual data, including social media posts, interviews, and clinical notes, natural language processing (NLP) methods demonstrate promising improvements to empower proactive mental healthcare and assist early diagnosis. We provide a narrative review of mental illness detection using NLP in the past decade, to understand methods, trends, challenges and future directions. A total of 399 studies from 10,467 records were included. The review reveals that there is an upward trend in mental illness detection NLP research. Deep learning methods receive more attention and perform better than traditional machine learning methods. We also provide some recommendations for future studies, including the development of novel detection methods, deep learning paradigms and interpretable models.

A Survey on Knowledge Graphs: Representation, Acquisition, and Applications.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction toward cognition and human-level intelligence. In this survey, we provide a comprehensive review of the knowledge graph covering overall research topics about: 1) knowledge graph representation learning; 2) knowledge acquisition and completion; 3) temporal knowledge graph; and 4) knowledge-aware applications and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning are reviewed. We further explore several emerging topics, including metarelational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of data sets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Does the magic of BERT apply to medical code assignment? A quantitative study.

Unsupervised pretraining is an integral part of many natural language processing systems, and transfer learning with language models has achieved remarkable results in downstream tasks. In the clinical application of medical code assignment, diagnosis and procedure codes are inferred from lengthy clinical notes such as hospital discharge summaries. However, it is not clear if pretrained models are useful for medical code prediction without further architecture engineering. This paper conducts a comprehensive quantitative analysis of various contextualized language models' performances, pretrained in different domains, for medical code assignment from clinical notes. We propose a hierarchical fine-tuning architecture to capture interactions between distant words and adopt label-wise attention to exploit label information. Contrary to current trends, we demonstrate that a carefully trained classical CNN outperforms attention-based models on a MIMIC-III subset with frequent codes. Our empirical findings suggest directions for building robust medical code assignment models.