The communities that we live in affect our health in ways that are complex and hard to define. Moreover, our understanding of the place-based processes affecting health and inequalities is limited. This undermines the development of robust policy interventions to improve local health and well-being. News media provides social and community information that may be useful in health studies. Here we propose a methodology for characterising neighbourhoods by using local news articles. More specifically, we show how we can use Natural Language Processing (NLP) to unlock further information about neighbourhoods by analysing, geoparsing and clustering news articles. Our work is novel because we combine street-level geoparsing tailored to the locality with clustering of full news articles, enabling a more detailed examination of neighbourhood characteristics. We evaluate our outputs and show via a confluence of evidence, both from a qualitative and a quantitative perspective, that the themes we extract from news articles are sensible and reflect many characteristics of the real world. This is significant because it allows us to better understand the effects of neighbourhoods on health. Our findings on neighbourhood characterisation using news data will support a new generation of place-based research which examines a wider set of spatial processes and how they affect health, enabling new epidemiological research. • Novel methodology for characterising neighbourhoods based on local news. • Natural Language Processing can create meaningful neighbourhood characterisations from local news articles. • Extensive quantitative and qualitative evaluation show analysis is sound.

This paper presents the new facilities provided in defoe, a parallel toolbox for querying a wealth of digitised newspapers and books at scale. defoe has been extended to work with further Natural Language Processing () tools such as the Edinburgh Geoparser, to store the preprocessed text in several storage facilities and to support different types of queries and analyses. We have also extended the collection of XML schemas supported by defoe, increasing the versatility of the tool for the analysis of digital historical textual data at scale. Finally, we have conducted several studies in which we worked with humanities and social science researchers who posed complex and interested questions to large-scale digital collections. Results shows that defoe allows researchers to conduct their studies and obtain results faster, while all the large-scale text mining complexity is automatically handled by defoe.

Abstract Using natural language processing, it is possible to extract structured information from raw text in the electronic health record (EHR) at reasonably high accuracy. However, the accurate distinction between negated and non-negated mentions of clinical terms remains a challenge. EHR text includes cases where diseases are stated not to be present or only hypothesised, meaning a disease can be mentioned in a report when it is not being reported as present. This makes tasks such as document classification and summarisation more difficult. We have developed the rule-based EdIE-R-Neg, part of an existing text mining pipeline called EdIE-R (Edinburgh Information Extraction for Radiology reports), developed to process brain imaging reports, ( https://www.ltg.ed.ac.uk/software/edie-r/ ) and two machine learning approaches; one using a bidirectional long short-term memory network and another using a feedforward neural network. These were developed on data from the Edinburgh Stroke Study (ESS) and tested on data from routine reports from NHS Tayside (Tayside). Both datasets consist of written reports from medical scans. These models are compared with two existing rule-based models: pyConText (Harkema et al. 2009. Journal of Biomedical Informatics42(5), 839–851), a python implementation of a generalisation of NegEx, and NegBio (Peng et al. 2017. NegBio: A high-performance tool for negation and uncertainty detection in radiology reports. arXiv e-prints, p. arXiv:1712.05898 ), which identifies negation scopes through patterns applied to a syntactic representation of the sentence. On both the test set of the dataset from which our models were developed, as well as the largely similar Tayside test set, the neural network models and our custom-built rule-based system outperformed the existing methods. EdIE-R-Neg scored highest on F1 score, particularly on the test set of the Tayside dataset, from which no development data were used in these experiments, showing the power of custom-built rule-based systems for negation detection on datasets of this size. The performance gap of the machine learning models to EdIE-R-Neg on the Tayside test set was reduced through adding development Tayside data into the ESS training set, demonstrating the adaptability of the neural network models.

Abstract A vast amount of usable electronic data is in the form of unstructured text. The relation extraction task aims to identify useful information in text (e.g. PersonW works for OrganisationX, GeneY encodes ProteinZ) and recode it in a format such as a relational database or RDF triplestore that can be more effectively used for querying and automated reasoning. A number of resources have been developed for training and evaluating automatic systems for relation extraction in different domains. However, comparative evaluation is impeded by the fact that these corpora use different markup formats and notions of what constitutes a relation. We describe the preparation of corpora for comparative evaluation of relation extraction across domains based on the publicly available ACE 2004, ACE 2005 and BioInfer data sets. We present a common document type using token standoff and including detailed linguistic markup, while maintaining all information in the original annotation. The subsequent reannotation process normalises the two data sets so that they comply with a notion of relation that is intuitive, simple and informed by the semantic web. For the ACE data, we describe an automatic process that automatically converts many relations involving nested, nominal entity mentions to relations involving non-nested, named or pronominal entity mentions. For example, the first entity is mapped from ‘one’ to ‘Amidu Berry’ in the membership relation described in ‘Amidu Berry, one half of PBS’. Moreover, we describe a comparably reannotated version of the BioInfer corpus that flattens nested relations, maps part-whole to part-part relations and maps n-ary to binary relations. Finally, we summarise experiments that compare approaches to generic relation extraction, a knowledge discovery task that uses minimally supervised techniques to achieve maximally portable extractors. These experiments illustrate the utility of the corpora.1

We describe a set of experiments using machine learning techniques for the task of extractive summarisation. The research is part of a summarisation project for which we use a corpus of judgments of the UK House of Lords. We present classification results for naïve Bayes and maximum entropy and we explore methods for scoring the summary-worthiness of a sentence. We present sample output from the system, illustrating the utility of rhetorical status information, which provides a means for structuring summaries and tailoring them to different types of users.

BACKGROUND: Good automatic information extraction tools offer hope for automatic processing of the exploding biomedical literature, and successful named entity recognition is a key component for such tools. METHODS: We present a maximum-entropy based system incorporating a diverse set of features for identifying gene and protein names in biomedical abstracts. RESULTS: This system was entered in the BioCreative comparative evaluation and achieved a precision of 0.83 and recall of 0.84 in the "open" evaluation and a precision of 0.78 and recall of 0.85 in the "closed" evaluation. CONCLUSION: Central contributions are rich use of features derived from the training data at multiple levels of granularity, a focus on correctly identifying entity boundaries, and the innovative use of several external knowledge sources including full MEDLINE abstracts and web searches.

This paper reports on a number of experiments which are designed to investigate the extent to which current NLP resources are able to syntactically and semantically analyse biomedical text. We address two tasks: (a) parsing a real corpus with a hand-built wide-coverage grammar, producing both syntactic analyses and logical forms and (b) automatically computing the interpretation of compound nouns where the head is a nominalisation (e.g. hospital arrival means an arrival at hospital, while patient arrival means an arrival of a patient). For the former task we demonstrate that flexible and yet constrained pre-processing techniques are crucial to success: these enable us to use part-of-speech tags to overcome inadequate lexical coverage, and to package up complex technical expressions prior to parsing so that they are blocked from creating misleading amounts of syntactic complexity. We argue that the XML-processing paradigm is ideally suited for automatically preparing the corpus for parsing. For the latter task, we compute interpretations of the compounds by exploiting surface cues and meaning paraphrases, which in turn are extracted from the parsed corpus. This provides an empirical setting in which we can compare the utility of a comparatively deep parser vs. a shallow one, exploring the trade-off between resolving attachment ambiguities on the one hand and generating errors in the parses on the other. We demonstrate that a model of the meaning of compound nominalisations is achievable with the aid of current broad-coverage parsers.

We report on the SUM project which applies automatic summarisation techniques to the legal domain. We describe our methodology whereby sentences from the text are classified according to their rhetorical role in order that particular types of sentence can be extracted to form a summary. We describe some experiments with judgments of the House of Lords: we have performed automatic linguistic annotation of a small sample set and then hand-annotated the sentences in the set in order to explore the relationship between linguistic features and argumentative roles. We use state-of-the-art NLP techniques to perform the linguistic annotation using XML-based tools and a combination of rule-based and statistical methods. We focus here on the predictive capacity of tense and aspect features for a classifier.

We describe the use of XML tokenisation, tagging and mark-up tools to prepare a corpus for parsing. Our techniques are generally applicable but here we focus on parsing Medline abstracts with the ANLT wide-coverage grammar. Hand-crafted grammars inevitably lack coverage but many coverage failures are due to inadequacies of their lexicons. We describe a method of gaining a degree of robustness by interfacing POS tag information with the existing lexicon. We also show that XML tools provide a sophisticated approach to pre-processing, helping to ameliorate the 'messiness' in real language data and improve parse performance.

We describe an implementation in Carpenter's typed feature formalism, ALE, of a discourse grammar of the kind proposed by Scha, Polanyi, et al.We examine their method for resolving

We describe a methodology and associated software system for the construction of a large lexicon from an existing machine-readable (published) dictionary. The lexicon serves as a component of an English morphological and syntactic analyser and contains entries with grammatical definitions compatible with the word and sentence grammar employed by the analyser. We describe a software system with two integrated components. One of these is capable of extracting syntactically rich, theory-neutral lexical templates from a suitable machine-readable source. The second supports interactive and semi-automatic generation and testing of target lexical entries in order to derive a sizeable, accurate and consistent lexicon from the source dictionary which contains partial (and occasionally in-accurate) information. Finally, we evaluate the utility of the Longman Dictionary of Contemporary English as a suitable source dictionary for the target lexicon.