Dublin City University at QA@CLEF 2008

We describe our participation in Multilingual Question Answering at CLEF 2008 using German and English as our source and target languages respectively. The system was built using UIMA (Unstructured Information Management Architecture) as underlying framework

Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

NLSC: Unrestricted Natural Language-based Service Composition through Sentence Embeddings

Current approaches for service composition (assemblies of atomic services) require developers to use: (a) domain-specific semantics to formalize services that restrict the vocabulary for their descriptions, and (b) translation mechanisms for service retrieval to convert unstructured user requests to strongly-typed semantic representations. In our work, we argue that effort to developing service descriptions, request translations, and matching mechanisms could be reduced using unrestricted natural language; allowing both: (1) end-users to intuitively express their needs using natural language, and (2) service developers to develop services without relying on syntactic/semantic description languages. Although there are some natural language-based service composition approaches, they restrict service retrieval to syntactic/semantic matching. With recent developments in Machine learning and Natural Language Processing, we motivate the use of Sentence Embeddings by leveraging richer semantic representations of sentences for service description, matching and retrieval. Experimental results show that service composition development effort may be reduced by more than 44\% while keeping a high precision/recall when matching high-level user requests with low-level service method invocations.Comment: This paper will appear on SCC'19 (IEEE International Conference on Services Computing) on July 1

Methodological considerations concerning manual annotation of musical audio in function of algorithm development

In research on musical audio-mining, annotated music databases are needed which allow the development of computational tools that extract from the musical audiostream the kind of high-level content that users can deal with in Music Information Retrieval (MIR) contexts. The notion of musical content, and therefore the notion of annotation, is ill-defined, however, both in the syntactic and semantic sense. As a consequence, annotation has been approached from a variety of perspectives (but mainly linguistic-symbolic oriented), and a general methodology is lacking. This paper is a step towards the definition of a general framework for manual annotation of musical audio in function of a computational approach to musical audio-mining that is based on algorithms that learn from annotated data. 1

Using distributional similarity to organise biomedical terminology

We investigate an application of distributional similarity techniques to the problem of structural organisation of biomedical terminology. Our application domain is the relatively small GENIA corpus. Using terms that have been accurately marked-up by hand within the corpus, we consider the problem of automatically determining semantic proximity. Terminological units are dened for our purposes as normalised classes of individual terms. Syntactic analysis of the corpus data is carried out using the Pro3Gres parser and provides the data required to calculate distributional similarity using a variety of dierent measures. Evaluation is performed against a hand-crafted gold standard for this domain in the form of the GENIA ontology. We show that distributional similarity can be used to predict semantic type with a good degree of accuracy

A classification-based approach to economic event detection in Dutch news text

Breaking news on economic events such as stock splits or mergers and acquisitions has been shown to have a substantial impact on the financial markets. As it is important to be able to automatically identify events in news items accurately and in a timely manner, we present in this paper proof-of-concept experiments for a supervised machine learning approach to economic event detection in newswire text. For this purpose, we created a corpus of Dutch financial news articles in which 10 types of company-specific economic events were annotated. We trained classifiers using various lexical, syntactic and semantic features. We obtain good results based on a basic set of shallow features, thus showing that this method is a viable approach for economic event detection in news text