Inferring actual treatment pathways from patient records.

OBJECTIVE: Treatment pathways are step-by-step plans outlining the recommended medical care for specific diseases; they get revised when different treatments are found to improve patient outcomes. Examining health records is an important part of this revision process, but inferring patients' actual treatments from health data is challenging due to complex event-coding schemes and the absence of pathway-related annotations. The objective of this study is to develop a method for inferring actual treatment steps for a particular patient group from administrative health records - a common form of tabular healthcare data - and address several technique- and methodology-based gaps in treatment pathway-inference research. METHODS: We introduce Defrag, a method for examining health records to infer the real-world treatment steps for a particular patient group. Defrag learns the semantic and temporal meaning of healthcare event sequences, allowing it to reliably infer treatment steps from complex healthcare data. To our knowledge, Defrag is the first pathway-inference method to utilise a neural network (NN), an approach made possible by a novel, self-supervised learning objective. We also developed a testing and validation framework for pathway inference, which we use to characterise and evaluate Defrag's pathway inference ability, establish benchmarks, and compare against baselines. RESULTS: We demonstrate Defrag's effectiveness by identifying best-practice pathway fragments for breast cancer, lung cancer, and melanoma in public healthcare records. Additionally, we use synthetic data experiments to demonstrate the characteristics of the Defrag inference method, and to compare Defrag to several baselines, where it significantly outperforms non-NN-based methods. CONCLUSIONS: Defrag offers an innovative and effective approach for inferring treatment pathways from complex health data. Defrag significantly outperforms several existing pathway-inference methods, but computationally-derived treatment pathways are still difficult to compare against clinical guidelines. Furthermore, the open-source code for Defrag and the testing framework are provided to encourage further research in this area.

Machine learning for administrative health records: A systematic review of techniques and applications.

Machine learning provides many powerful and effective techniques for analysing heterogeneous electronic health records (EHR). Administrative Health Records (AHR) are a subset of EHR collected for administrative purposes, and the use of machine learning on AHRs is a growing subfield of EHR analytics. Existing reviews of EHR analytics emphasise that the data-modality of the EHR limits the breadth of suitable machine learning techniques, and pursuable healthcare applications. Despite emphasising the importance of data modality, the literature fails to analyse which techniques and applications are relevant to AHRs. AHRs contain uniquely well-structured, categorically encoded records which are distinct from other data-modalities captured by EHRs, and they can provide valuable information pertaining to how patients interact with the healthcare system. This paper systematically reviews AHR-based research, analysing 70 relevant studies and spanning multiple databases. We identify and analyse which machine learning techniques are applied to AHRs and which health informatics applications are pursued in AHR-based research. We also analyse how these techniques are applied in pursuit of each application, and identify the limitations of these approaches. We find that while AHR-based studies are disconnected from each other, the use of AHRs in health informatics research is substantial and accelerating. Our synthesis of these studies highlights the utility of AHRs for pursuing increasingly complex and diverse research objectives despite a number of pervading data- and technique-based limitations. Finally, through our findings, we propose a set of future research directions that can enhance the utility of AHR data and machine learning techniques for health informatics research.