New Resources and Perspectives for Biomedical Event Extraction

Event extraction is a major focus of recent work in biomedical information extraction. Despite substantial advances, many challenges still remain for reliable automatic extraction of events from text. We introduce a new biomedical event extraction resource consisting of analyses automatically created by systems participating in the recent BioNLP Shared Task (ST) 2011. In providing for the first time the outputs of a broad set of state-ofthe-art event extraction systems, this resource opens many new opportunities for studying aspects of event extraction, from the identification of common errors to the study of effective approaches to combining the strengths of systems. We demonstrate these opportunities through a multi-system analysis on three BioNLP ST 2011 main tasks, focusing on events that none of the systems can successfully extract. We further argue for new perspectives to the performance evaluation of domain event extraction systems, considering a document-level, “off-the-page ” representation and evaluation to complement the mentionlevel evaluations pursued in most recent work.

Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011

We present the preparation, resources, results and analysis of three tasks of the BioNLP Shared Task 2011: the main tasks on Infectious Diseases (ID) and Epigenetics and Post-translational Modifications (EPI), and the supporting task on Entity Relations (REL). The two main tasks represent extensions of the event extraction model introduced in the BioNLP Shared Task 2009 (ST'09) to two new areas of biomedical scientific literature, each motivated by the needs of specific biocuration tasks. The ID task concerns the molecular mechanisms of infection, virulence and resistance, focusing in particular on the functions of a class of signaling systems that are ubiquitous in bacteria. The EPI task is dedicated to the extraction of statements regarding chemical modifications of DNA and proteins, with particular emphasis on changes relating to the epigenetic control of gene expression. By contrast to these two application-oriented main tasks, the REL task seeks to support extraction in general by separating challenges relating to part-of relations into a subproblem that can be addressed by independent systems. Seven groups participated in each of the two main tasks and four groups in the supporting task. The participating systems indicated advances in the capability of event extraction methods and demonstrated generalization in many aspects: from abstracts to full texts, from previously considered subdomains to new ones, and from the ST'09 extraction targets to other entities and events. The highest performance achieved in the supporting task REL, 58% F-score, is broadly comparable with levels reported for other relation extraction tasks. For the ID task, the highest-performing system achieved 56% F-score, comparable to the state-of-the-art performance at the established ST'09 task. In the EPI task, the best result was 53% F-score for the full set of extraction targets and 69% F-score for a reduced set of core extraction targets, approaching a level of performance sufficient for user-facing applications. In this study, we extend on previously reported results and perform further analyses of the outputs of the participating systems. We place specific emphasis on aspects of system performance relating to real-world applicability, considering alternate evaluation metrics and performing additional manual analysis of system outputs. We further demonstrate that the strengths of extraction systems can be combined to improve on the performance achieved by any system in isolation. The manually annotated corpora, supporting resources, and evaluation tools for all tasks are available from http://www.bionlp-st.org and the tasks continue as open challenges for all interested parties

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Computer-aided biomimetics : semi-open relation extraction from scientific biological texts

Engineering inspired by biology – recently termed biom* – has led to various ground-breaking technological developments. Example areas of application include aerospace engineering and robotics. However, biom* is not always successful and only sporadically applied in industry. The reason is that a systematic approach to biom* remains at large, despite the existence of a plethora of methods and design tools. In recent years computational tools have been proposed as well, which can potentially support a systematic integration of relevant biological knowledge during biom*. However, these so-called Computer-Aided Biom* (CAB) tools have not been able to fill all the gaps in the biom* process. This thesis investigates why existing CAB tools fail, proposes a novel approach – based on Information Extraction – and develops a proof-of-concept for a CAB tool that does enable a systematic approach to biom*. Key contributions include: 1) a disquisition of existing tools guides the selection of a strategy for systematic CAB, 2) a dataset of 1,500 manually-annotated sentences, 3) a novel Information Extraction approach that combines the outputs from a supervised Relation Extraction system and an existing Open Information Extraction system. The implemented exploratory approach indicates that it is possible to extract a focused selection of relations from scientific texts with reasonable accuracy, without imposing limitations on the types of information extracted. Furthermore, the tool developed in this thesis is shown to i) speed up a trade-off analysis by domain-experts, and ii) also improve the access to biology information for non-exper

Computer-Aided Biomimetics : Semi-Open Relation Extraction from scientific biological texts

Engineering inspired by biology – recently termed biom* – has led to various groundbreaking technological developments. Example areas of application include aerospace engineering and robotics. However, biom* is not always successful and only sporadically applied in industry. The reason is that a systematic approach to biom* remains at large, despite the existence of a plethora of methods and design tools. In recent years computational tools have been proposed as well, which can potentially support a systematic integration of relevant biological knowledge during biom*. However, these so-called Computer-Aided Biom* (CAB) tools have not been able to fill all the gaps in the biom* process. This thesis investigates why existing CAB tools fail, proposes a novel approach – based on Information Extraction – and develops a proof-of-concept for a CAB tool that does enable a systematic approach to biom*. Key contributions include: 1) a disquisition of existing tools guides the selection of a strategy for systematic CAB, 2) a dataset of 1,500 manually-annotated sentences, 3) a novel Information Extraction approach that combines the outputs from a supervised Relation Extraction system and an existing Open Information Extraction system. The implemented exploratory approach indicates that it is possible to extract a focused selection of relations from scientific texts with reasonable accuracy, without imposing limitations on the types of information extracted. Furthermore, the tool developed in this thesis is shown to i) speed up a trade-off analysis by domain-experts, and ii) also improve the access to biology information for nonexperts

A unified framework to identify and extract uncertainty cues, holders, and scopes in one fell-swoop

Uncertainty refers to the language aspects that express hypotheses and speculations where propositions are held as (un)certain, (im)probable, or (im)possible. Automatic uncertainty analysis is crucial for several Natural Language Processing (NLP) applications that need to distinguish between factual (i.e. certain) and nonfactual (i.e. negated or uncertain) information. Typically, a comprehensive automatic uncertainty analyzer has three machine learning models for uncertainty detection, attribution, and scope extraction. To-date, and to the best of my knowledge, current research on uncertainty automatic analysis has only focused on uncertainty attribution and scope extraction, and has typically tackled each task with a different machine learning approach. Furthermore, current research on uncertainty automatic analysis has been restricted to specific languages, particularly English, and to specific linguistic genres, including biomedical and newswire texts, Wikipedia articles, and product reviews. In this research project, I attempt to address the aforementioned limitations of current research on automatic uncertainty analysis. First, I develop a machine learning model for uncertainty attribution, the task typically neglected in automatic uncertainty analysis. Second, I propose a unified framework to identify and extract uncertainty cues, holders, and scopes in one-fell swoop by casting each task as a supervised token sequence labeling problem. Third, I choose to work on the Arabic language, in contrast to English, the most commonly studied language in the literature of automatic uncertainty analysis. Finally, I work on the understudied linguistic genre of tweets. This research project results in a novel NLP tool, i.e., a comprehensive automatic uncertainty analyzer for Arabic tweets, with a practical impact on NLP applications that rely on uncertainty automatic analysis. The tool yields an F1 score of 0.759, averaged across its three machine learning models. Furthermore, through this research, the research community and I gain insights into (1) the challenges presented by Arabic as an agglutinative morphologically-rich language with a flexible word order, in contrast to English; (2) the challenges of the linguistic genre of tweets for uncertainty automatic analysis; and (3) the type of challenges that my proposed unified framework successfully addresses and boosts performance for