Paul Thompson


pdf bib
Semantic Annotation for Improved Safety in Construction Work
Paul Thompson | Tim Yates | Emrah Inan | Sophia Ananiadou
Proceedings of the Twelfth Language Resources and Evaluation Conference

Risk management is a vital activity to ensure employee safety in construction projects. Various documents provide important supporting evidence, including details of previous incidents, consequences and mitigation strategies. Potential hazards may depend on a complex set of project-specific attributes, including activities undertaken, location, equipment used, etc. However, finding evidence about previous projects with similar attributes can be problematic, since information about risks and mitigations is usually hidden within and may be dispersed across a range of different free text documents. Automatic named entity recognition (NER), which identifies mentions of concepts in free text documents, is the first stage in structuring knowledge contained within them. While developing NER methods generally relies on annotated corpora, we are not aware of any such corpus targeted at concepts relevant to construction safety. In response, we have designed a novel named entity annotation scheme and associated guidelines for this domain, which covers hazards, consequences, mitigation strategies and project attributes. Four health and safety experts used the guidelines to annotate a total of 600 sentences from accident reports; an average inter-annotator agreement rate of 0.79 F-Score shows that our work constitutes an important first step towards developing tools for detailed semantic analysis of construction safety documents.


pdf bib
Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016)
Sophia Ananiadou | Riza Batista-Navarro | Kevin Bretonnel Cohen | Dina Demner-Fushman | Paul Thompson
Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM2016)

pdf bib
Identifying Content Types of Messages Related to Open Source Software Projects
Yannis Korkontzelos | Paul Thompson | Sophia Ananiadou
Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC'16)

Assessing the suitability of an Open Source Software project for adoption requires not only an analysis of aspects related to the code, such as code quality, frequency of updates and new version releases, but also an evaluation of the quality of support offered in related online forums and issue trackers. Understanding the content types of forum messages and issue trackers can provide information about the extent to which requests are being addressed and issues are being resolved, the percentage of issues that are not being fixed, the cases where the user acknowledged that the issue was successfully resolved, etc. These indicators can provide potential adopters of the OSS with estimates about the level of available support. We present a detailed hierarchy of content types of online forum messages and issue tracker comments and a corpus of messages annotated accordingly. We discuss our experiments to classify forum messages and issue tracker comments into content-related classes, i.e.~to assign them to nodes of the hierarchy. The results are very encouraging.


pdf bib
Comparable Study of Event Extraction in Newswire and Biomedical Domains
Makoto Miwa | Paul Thompson | Ioannis Korkontzelos | Sophia Ananiadou
Proceedings of COLING 2014, the 25th International Conference on Computational Linguistics: Technical Papers

pdf bib
The Strategic Impact of META-NET on the Regional, National and International Level
Georg Rehm | Hans Uszkoreit | Sophia Ananiadou | Núria Bel | Audronė Bielevičienė | Lars Borin | António Branco | Gerhard Budin | Nicoletta Calzolari | Walter Daelemans | Radovan Garabík | Marko Grobelnik | Carmen García-Mateo | Josef van Genabith | Jan Hajič | Inma Hernáez | John Judge | Svetla Koeva | Simon Krek | Cvetana Krstev | Krister Lindén | Bernardo Magnini | Joseph Mariani | John McNaught | Maite Melero | Monica Monachini | Asunción Moreno | Jan Odijk | Maciej Ogrodniczuk | Piotr Pęzik | Stelios Piperidis | Adam Przepiórkowski | Eiríkur Rögnvaldsson | Michael Rosner | Bolette Pedersen | Inguna Skadiņa | Koenraad De Smedt | Marko Tadić | Paul Thompson | Dan Tufiş | Tamás Váradi | Andrejs Vasiļjevs | Kadri Vider | Jolanta Zabarskaite
Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14)

This article provides an overview of the dissemination work carried out in META-NET from 2010 until early 2014; we describe its impact on the regional, national and international level, mainly with regard to politics and the situation of funding for LT topics. This paper documents the initiative’s work throughout Europe in order to boost progress and innovation in our field.

pdf bib
Building a semantically annotated corpus for congestive heart and renal failure from clinical records and the literature
Noha Alnazzawi | Paul Thompson | Sophia Ananiadou
Proceedings of the 5th International Workshop on Health Text Mining and Information Analysis (Louhi)

pdf bib
Predicting military and veteran suicide risk: Cultural aspects
Paul Thompson | Craig Bryan | Chris Poulin
Proceedings of the Workshop on Computational Linguistics and Clinical Psychology: From Linguistic Signal to Clinical Reality


pdf bib
Extending an interoperable platform to facilitate the creation of multilingual and multimodal NLP applications
Georgios Kontonatsios | Paul Thompson | Riza Theresa Batista-Navarro | Claudiu Mihăilă | Ioannis Korkontzelos | Sophia Ananiadou
Proceedings of the 51st Annual Meeting of the Association for Computational Linguistics: System Demonstrations

pdf bib
Towards a Better Understanding of Discourse: Integrating Multiple Discourse Annotation Perspectives Using UIMA
Claudiu Mihăilă | Georgios Kontonatsios | Riza Theresa Batista-Navarro | Paul Thompson | Ioannis Korkontzelos | Sophia Ananiadou
Proceedings of the 7th Linguistic Annotation Workshop and Interoperability with Discourse


pdf bib
A three-way perspective on scientific discourse annotation for knowledge extraction
Maria Liakata | Paul Thompson | Anita de Waard | Raheel Nawaz | Henk Pander Maat | Sophia Ananiadou
Proceedings of the Workshop on Detecting Structure in Scholarly Discourse

pdf bib
Biomedical Chinese-English CLIR Using an Extended CMeSH Resource to Expand Queries
Xinkai Wang | Paul Thompson | Jun’ichi Tsujii | Sophia Ananiadou
Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC'12)

Cross-lingual information retrieval (CLIR) involving the Chinese language has been thoroughly studied in the general language domain, but rarely in the biomedical domain, due to the lack of suitable linguistic resources and parsing tools. In this paper, we describe a Chinese-English CLIR system for biomedical literature, which exploits a bilingual ontology, the ``eCMeSH Tree"""". This is an extension of the Chinese Medical Subject Headings (CMeSH) Tree, based on Medical Subject Headings (MeSH). Using the 2006 and 2007 TREC Genomics track data, we have evaluated the performance of the eCMeSH Tree in expanding queries. We have compared our results to those obtained using two other approaches, i.e. pseudo-relevance feedback (PRF) and document translation (DT). Subsequently, we evaluate the performance of different combinations of these three retrieval methods. Our results show that our method of expanding queries using the eCMeSH Tree can outperform the PRF method. Furthermore, combining this method with PRF and DT helps to smooth the differences in query expansion, and consequently results in the best performance amongst all experiments reported. All experiments compare the use of two different retrieval models, i.e. Okapi BM25 and a query likelihood language model. In general, the former performs slightly better.

pdf bib
Identification of Manner in Bio-Events
Raheel Nawaz | Paul Thompson | Sophia Ananiadou
Proceedings of the Eighth International Conference on Language Resources and Evaluation (LREC'12)

Due to the rapid growth in the volume of biomedical literature, there is an increasing requirement for high-performance semantic search systems, which allow biologists to perform precise searches for events of interest. Such systems are usually trained on corpora of documents that contain manually annotated events. Until recently, these corpora, and hence the event extraction systems trained on them, focussed almost exclusively on the identification and classification of event arguments, without taking into account how the textual context of the events could affect their interpretation. Previously, we designed an annotation scheme to enrich events with several aspects (or dimensions) of interpretation, which we term meta-knowledge, and applied this scheme to the entire GENIA corpus. In this paper, we report on our experiments to automate the assignment of one of these meta-knowledge dimensions, i.e. Manner, to recognised events. Manner is concerned with the rate, strength intensity or level of the event. We distinguish three different values of manner, i.e., High, Low and Neutral. To our knowledge, our work represents the first attempt to classify the manner of events. Using a combination of lexical, syntactic and semantic features, our system achieves an overall accuracy of 99.4%.


pdf bib
Promoting Interoperability of Resources in META-SHARE
Paul Thompson | Yoshinobu Kano | John McNaught | Steve Pettifer | Teresa Attwood | John Keane | Sophia Ananiadou
Proceedings of the Workshop on Language Resources, Technology and Services in the Sharing Paradigm


pdf bib
Evaluating a meta-knowledge annotation scheme for bio-events
Raheel Nawaz | Paul Thompson | Sophia Ananiadou
Proceedings of the Workshop on Negation and Speculation in Natural Language Processing

pdf bib
Meta-Knowledge Annotation of Bio-Events
Raheel Nawaz | Paul Thompson | John McNaught | Sophia Ananiadou
Proceedings of the Seventh International Conference on Language Resources and Evaluation (LREC'10)

Biomedical corpora annotated with event-level information provide an important resource for the training of domain-specific information extraction (IE) systems. These corpora concentrate primarily on creating classified, structured representations of important facts and findings contained within the text. However, bio-event annotations often do not take into account additional information (meta-knowledge) that is expressed within the textual context of the bio-event, e.g., the pragmatic/rhetorical intent and the level of certainty ascribed to a particular bio-event by the authors. Such additional information is indispensible for correct interpretation of bio-events. Therefore, an IE system that simply presents a list of “bare” bio-events, without information concerning their interpretation, is of little practical use. We have addressed this sparseness of meta-knowledge available in existing bio-event corpora by developing a multi-dimensional annotation scheme tailored to bio-events. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed about different bio-events. To our knowledge, our scheme is unique within the field with regards to the diversity of meta-knowledge aspects annotated for each event.


pdf bib
Three BioNLP Tools Powered by a Biological Lexicon
Yutaka Sasaki | Paul Thompson | John McNaught | Sophia Ananiadou
Proceedings of the Demonstrations Session at EACL 2009


pdf bib
Building a Bio-Event Annotated Corpus for the Acquisition of Semantic Frames from Biomedical Corpora
Paul Thompson | Philip Cotter | John McNaught | Sophia Ananiadou | Simonetta Montemagni | Andrea Trabucco | Giulia Venturi
Proceedings of the Sixth International Conference on Language Resources and Evaluation (LREC'08)

This paper reports on the design and construction of a bio-event annotated corpus which was developed with a specific view to the acquisition of semantic frames from biomedical corpora. We describe the adopted annotation scheme and the annotation process, which is supported by a dedicated annotation tool. The annotated corpus contains 677 abstracts of biomedical research articles.

pdf bib
Event Frame Extraction Based on a Gene Regulation Corpus
Yutaka Sasaki | Paul Thompson | Philip Cotter | John McNaught | Sophia Ananiadou
Proceedings of the 22nd International Conference on Computational Linguistics (Coling 2008)


pdf bib
Advances in Open Domain Question Answering, edited by Tomek Strzalkowski and Sanda Harabagiu
Paul Thompson
Computational Linguistics, Volume 33, Number 4, December 2007


pdf bib
Learning to Classify Utterances in a Task-Oriented Dialogue
William Black | Paul Thompson | Adam Funk | Andrew Conroy
Proceedings of the 2003 EACL Workshop on Dialogue Systems: interaction, adaptation and styes of management

pdf bib
Dynamic Integration of Distributed Semantic Services: Infrastructure for Process Queries and Question Answering
Paul Thompson
Companion Volume of the Proceedings of HLT-NAACL 2003 - Demonstrations


pdf bib
Name Searching and Information Retrieval
Paul Thompson | Christopher C. Dozier
Second Conference on Empirical Methods in Natural Language Processing