In this work we addressed the problem of capturing sequential information contained in longitudinal electronic health records (EHRs). Clinical notes, which is a particular type of EHR data, are a rich source of information and practitioners often develop clever solutions how to maximise the sequential information contained in free-texts. We proposed a systematic methodology for learning from chronological events available in clinical notes. The proposed methodological path signature framework creates a non-parametric hierarchical representation of sequential events of any type and can be used as features for downstream statistical learning tasks. The methodology was developed and externally validated using the largest in the UK secondary care mental health EHR data on a specific task of predicting survival risk of patients diagnosed with Alzheimer’s disease. The signature-based model was compared to a common survival random forest model. Our results showed a 15.4% increase of risk prediction AUC at the time point of 20 months after the first admission to a specialist memory clinic and the signature method outperformed the baseline mixed-effects model by 13.2 %.

Machine Reading Comprehension (MRC) is the task of answering a question over a paragraph of text. While neural MRC systems gain popularity and achieve noticeable performance, issues are being raised with the methodology used to establish their performance, particularly concerning the data design of gold standards that are used to evaluate them. There is but a limited understanding of the challenges present in this data, which makes it hard to draw comparisons and formulate reliable hypotheses. As a first step towards alleviating the problem, this paper proposes a unifying framework to systematically investigate the present linguistic features, required reasoning and background knowledge and factual correctness on one hand, and the presence of lexical cues as a lower bound for the requirement of understanding on the other hand. We propose a qualitative annotation schema for the first and a set of approximative metrics for the latter. In a first application of the framework, we analyse modern MRC gold standards and present our findings: the absence of features that contribute towards lexical ambiguity, the varying factual correctness of the expected answers and the presence of lexical cues, all of which potentially lower the reading comprehension complexity and quality of the evaluation data.

The medical concept normalisation task aims to map textual descriptions to standard terminologies such as SNOMED-CT or MedDRA. Existing publicly available datasets annotated using different terminologies cannot be simply merged and utilised, and therefore become less valuable when developing machine learning-based concept normalisation systems. To address that, we designed a data harmonisation pipeline and engineered a corpus of 27,979 textual descriptions simultaneously mapped to both MedDRA and SNOMED-CT, sourced from five publicly available datasets across biomedical and social media domains. The pipeline can be used in the future to integrate new datasets into the corpus and also could be applied in relevant data curation tasks. We also described a method to merge different terminologies into a single concept graph preserving their relations and demonstrated that representation learning approach based on random walks on a graph can efficiently encode both hierarchical and equivalent relations and capture semantic similarities not only between concepts inside a given terminology but also between concepts from different terminologies. We believe that making a corpus and embeddings for cross-terminology medical concept normalisation available to the research community would contribute to a better understanding of the task.

One of the main challenges in biomedical text mining is the identification of terminology, which is a key factor for accessing and integrating the information stored in literature. Manual creation of biomedical terminologies cannot keep pace with the data that becomes available. Still, many of them have been used in attempts to recognise terms in literature, but their suitability for text mining has been questioned as substantial re-engineering is needed to tailor the resources for automatic processing. Several approaches have been suggested to automatically integrate and map between resources, but the problems of extensive variability of lexical representations and ambiguity have been revealed. In this paper we present a methodology to automatically maintain a biomedical terminological database, which contains automatically extracted terms, their mutual relationships, features and possible annotations that can be useful in text processing. In addition to TermDB, a database used for terminology management and storage, we present the following modules that are used to populate the database: TerMine (recognition, extraction and normalisation of terms from literature), AcroTerMine (extraction and clustering of acronyms and their long forms), AnnoTerm (annotation and classification of terms), and ClusTerm (extraction of term associations and clustering of terms).