Deep learning aided clinical decision support

Abstract

Medical professionals create vast amounts of clinical texts during patient care. Often, these documents describe medical cases from anamnesis to the final clinical outcome. Automated understanding and selection of relevant medical records pose an opportunity to assist medical doctors in their day-to-day work on a large scale. However, clinical text understanding is challenging, especially when dealing with clinical narratives such as nursing notes or diagnostic reports. These clinical documents differ extensively in length, structure, vocabulary, and lexical and grammatical correctness. In addition, they are highly context-dependent. For all these reasons, approaches based on syntactic rules and discrete text representation often fail to address the variety of clinical narratives propagating unrecoverable errors to downstream applications. Therefore, this thesis focuses on evaluating and designing methods and models that are generalizable and adaptable enough to deal with these challenges. Our goal is to enable text-based clinical decision support systems to utilize the knowledge from clinical archives and medical publications. We aim to design methods that can scale up to the growing amount of clinical documents in hospital archives. A fundamental problem in achieving deep-learning-enabled clinical decision support systems is designing a patient representation that captures all relevant information for automated processing. We engage these challenges by designing a framework for deep-learning-enabled differential diagnosis support. Guided by the needs emerging from this framework, we design and evaluate methods based on three information representation paradigms: (1) Discrete relation extraction using the open information extraction paradigm. (2) Neural text representations based on language and topic modeling. (3) Combining complementary neural text representations. Our framework translates clinical diagnostic steps and pathways to statistical and deep-learning-based models. Accordingly, we can show that deep-learning-enabled differential diagnosis benefits from contextualized information representations. Further, we identify shortcomings of the open information extraction paradigm in a comprehensive benchmark. We design a distributed text representation model based on topical information. Our extensive large-scale experiment results show that topical distributed text representations capture information complementary to language modeling-based approaches across domains, thus enabling a holistic text representation for medical texts. Our experiments with medical doctors using our prototypical implementation of the deep-learning-enabled differential diagnosis process validate this framework. Moreover, we identify seven crucial design challenges for text-based clinical decision support systems based on our qualitative and quantitative findings.