This paper proposes a history-based structured learning approach that jointly extracts entities and relations in a sentence. We introduce a novel simple and flexible table representation of entities and relations. We investigate several feature settings, search orders, and learning methods with inexact search on the table. The experimental results demonstrate that a joint learning approach significantly outperforms a pipeline approach by incorporating global features and by selecting appropriate learning methods and search orders.

This paper proposes a novel approach to train word embeddings to capture antonyms. Word embeddings have shown to capture synonyms and analogies. Such word embeddings, however, cannot capture antonyms since they depend on the distributional hypothesis. Our approach utilizes supervised synonym and antonym information from thesauri, as well as distributional information from large-scale unlabelled text data. The evaluation results on the GRE antonym question task show that our model outperforms the state-of-the-art systems and it can answer the antonym questions in the F-score of 89%.

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BackgroundDue to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events.ResultsThis article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical Markup Framework, an ISO standard.ConclusionsThe BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring.