Bidirectional LSTM for Named Entity Recognition in Twitter Messages

In this paper, we present our approach for named entity recognition in Twitter messages that we used in our participation in the Named Entity Recognition in Twitter shared task at the COLING 2016 Workshop on Noisy User-generated text (WNUT). The main challenge that we aim to tackle in our participation is the short, noisy and colloquial nature of tweets, which makes named entity recognition in Twitter messages a challenging task. In particular, we investigate an approach for dealing with this problem by enabling bidirectional long short-term memory (LSTM) to automatically learn orthographic features without requiring feature engineering. In comparison with other systems participating in the shared task, our system achieved the most effective performance on both the ‘segmentation and categorisation’ and the ‘segmentation only’ sub-tasks

Adapting phrase-based machine translation to normalise medical terms in social media messages

Previous studies have shown that health reports in social media, such as DailyStrength and Twitter, have potential for monitoring health conditions (e.g. adverse drug reactions, infectious diseases) in particular communities. However, in order for a machine to understand and make inferences on these health conditions, the ability to recognise when laymen’s terms refer to a particular medical concept (i.e. text normalisation) is required. To achieve this, we propose to adapt an existing phrase-based machine translation (MT) technique and a vector representation of words to map between a social media phrase and a medical concept. We evaluate our proposed approach using a collection of phrases from tweets related to adverse drug reactions. Our experimental results show that the combination of a phrase-based MT technique and the similarity between word vector representations outperforms the baselines that apply only either of them by up to 55%.This work was supported by the EPSRC [grant number EP/M005089/1].This is the author accepted manuscript. The final version is available from the Association for Computational Linguistics via https://aclweb.org/anthology/D/D15/D15-1194.pd

Modelling the combination of generic and target domain embeddings in a convolutional neural network for sentence classification

Word embeddings have been successfully exploited in systems for NLP tasks, such as parsing and text classification. It is intuitive that word embeddings created from a larger corpus would provide a better coverage of vocabulary. Meanwhile, word embeddings trained on a corpus related to the given task or target domain would more effectively represent the semantics of terms. However, in some emerging domains (e.g. bio-surveillance using social media data), it may be difficult to find a domain corpus that is large enough for creating effective word embeddings. To deal with this problem, we propose novel approaches that use both word embeddings created from generic and target domain corpora. Our experimental results on sentence classifi- cation tasks show that our approaches significantly improve the performance of an existing convolutional neural network that achieved state-of-the-art performances on several text classification tasks.Engineering and Physical Sciences Research Council (Grant ID: EP/M005089/1)This is the final version of the article. It first appeared from the Association for Computational Linguistics via http://www.aclweb.org/anthology/W/W16

Modelling the usefulness of document collections for query expansion in patient search

Dealing with the medical terminology is a challenge when searching for patients based on the relevance of their medical records towards a given query. Existing work used query expansion (QE) to extract expansion terms from different document collections to improve query representation. However, the usefulness of particular document collections for QE was not measured and taken into account during retrieval. In this work, we investigate two automatic approaches that measure and leverage the usefulness of document collections when exploiting multiple document collections to improve query representation. These two approaches are based on resource selection and learning to rank techniques, respectively. We evaluate our approaches using the TREC Medical Records track’s test collection. Our results show the potential of the proposed approaches, since they can effectively exploit 14 different document collections, including both domain-specific (e.g. MEDLINE abstracts) and generic (e.g. blogs and webpages) collections, and significantly outperform existing effective baselines, including the best systems participating at the TREC Medical Records track. Our analysis shows that the different collections are not equally useful for QE, while our two approaches can automatically weight the usefulness of expansion terms extracted from different document collections effectively.This is the author accepted manuscript. The final version is available from ACM via http://dx.doi.org/10.1145/2806416.280661

Vancouver Welcomes You! Minimalist Location Metonymy Resolution

Named entities are frequently used in a metonymic manner. They serve as references to related entities such as people and organisations. Accurate identification and interpretation of metonymy can be directly beneficial to various NLP applications, such as Named Entity Recognition and Geographical Parsing. Until now, metonymy resolution (MR) methods mainly relied on parsers, taggers, dictionaries, external word lists and other handcrafted lexical resources. We show how a minimalist neural approach combined with a novel predicate window method can achieve state-of-the-art results on the SemEval 2007 task on Metonymy Resolution. Additionally, we contribute with a new Wikipedia-based MR dataset called RelocaR, which is tailored towards locations as well as improving previous deficiencies in annotation guidelines

Modelling Relevance towards Multiple Inclusion Criteria when Ranking Patients

In the medical domain, information retrieval systems can be used for identifying cohorts (i.e. patients) required for clinical studies. However, a challenge faced by such search systems is to retrieve the cohorts whose medical histories cover the inclusion criteria specified in a query, which are often complex and include multiple medical conditions. For example, a query may aim to find patients with both 'lupus nephritis' and 'thrombotic thrombocytopenic purpura'. In a typical best-match retrieval setting, any patient exhibiting all of the inclusion criteria should naturally be ranked higher than a patient that only exhibits a subset, or none, of the criteria. In this work, we extend the two main existing models for ranking patients to take into account the coverage of the inclusion criteria by adapting techniques from recent research into coverage-based diversification. We propose a novel approach for modelling the coverage of the query inclusion criteria within the records of a particular patient, and thereby rank highly those patients whose medical records are likely to cover all of the specified criteria. In particular, our proposed approach estimates the relevance of a patient, based on the mixture of the probability that the patient is retrieved by a patient ranking model for a given query, and the likelihood that the patient's records cover the query criteria. The latter is measured using the relevance towards each of the criteria stated in the query, represented in the form of sub-queries. We thoroughly evaluate our proposed approach using the test collection provided by the TREC 2011 and 2012 Medical Records track. Our results show significant improvements over existing strong baselines

What’s missing in geographical parsing?

Geographical data can be obtained by converting place names from free-format text into geographical coordinates. The ability to geo-locate events in textual reports represents a valuable source of information in many real-world applications such as emergency responses, real-time social media geographical event analysis, understanding location instructions in auto-response systems and more. However, geoparsing is still widely regarded as a challenge because of domain language diversity, place name ambiguity, metonymic language and limited leveraging of context as we show in our analysis. Results to date, whilst promising, are on laboratory data and unlike in wider NLP are often not cross-compared. In this study, we evaluate and analyse the performance of a number of leading geoparsers on a number of corpora and highlight the challenges in detail. We also publish an automatically geotagged Wikipedia corpus to alleviate the dearth of (open source) corpora in this domain.We gratefully acknowledge the funding support of the Natural Environment Research Council (NERC) Ph.D. Studentship NE/M009009/1 (MG) and EPSRC (NC and NL: Grant No. EP/M005089/1

Towards the semantic interpretation of personal health messages from social media

Recent attempts have been made to utilise social media platforms, such as Twitter, to provide early warning and monitoring of health threats in populations (i.e. Internet biosurveillance). It has been shown in the literature that a system based on keyword matching that exploits social media messages could report flu surveillance well ahead of the Centers of Disease Control and Prevention (CDC). However, we argue that a simple keyword matching may not capture semantic interpretation of social media messages that would enable healthcare experts or machines to extract and leverage medical knowledge from social media messages. In this paper, we motivate and describe a new task that aims to tackle this technology gap by extracting semantic interpretation of medical terms mentioned in social media messages, which are typically written in layman’s language. Achieving such a task would enable an automatic integration between the data about direct patient experiences extracted from social media and existing knowledge from clinical databases, which leads to advances in the use of community health experiences in healthcare services.The authors gratefully acknowledge funding from the EPSRC (grant number EP/M005089/1)This is the author accepted manuscript. The final version is available from ACM via http://dx.doi.org/10.1145/2811271.281127

Processing Spatial Keyword Query as a Top-k Aggregation Query

We examine the spatial keyword search problem to retrieve objects of interest that are ranked based on both their spatial proximity to the query location as well as the textual relevance of the object’s keywords. Existing solutions for the problem are based on either using a combination of textual and spatial indexes or using specialized hybrid indexes that integrate the indexing of both textual and spatial attribute values. In this paper, we propose a new approach that is based on modeling the problem as a top-k aggregation problem which enables the design of a scalable and efficient solution that is based on the ubiquitous inverted list index. Our performance study demonstrates that our approach outperforms the state-of-theart hybrid methods by a wide margin

Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016) at the 26th International Conference on Computational Linguistics (COLING 2016)

End-to-end neural network models for named entity recognition (NER) have shown to achieve effective performances on general domain datasets (e.g. newswire), without requiring additional hand-crafted features. However, in biomedical domain, recent studies have shown that hand-engineered features (e.g. orthographic features) should be used to attain effective performance, due to the complexity of biomedical terminology (e.g. the use of acronyms and complex gene names). In this work, we propose a novel approach that allows a neural network model based on a long short-term memory (LSTM) to automatically learn orthographic features and incorporate them into a model for biomedical NER. Importantly, our bi-directional LSTM model learns and leverages orthographic features on an end-to-end basis. We evaluate our approach by comparing against existing neural network models for NER using three well-established biomedical datasets. Our experimental results show that the proposed approach consistently outperforms these strong baselines across all of the three datasets