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OBJECTIVES: In this paper, we study the development and domain-adaptation of statistical syntactic parsers for three different clinical domains in Finnish. METHODS AND MATERIALS: The materials include text from daily nursing notes written by nurses in an intensive care unit, physicians' notes from cardiology patients' health records, and daily nursing notes from cardiology patients' health records. The parsing is performed with the statistical parser of Bohnet (http://code.google.com/p/mate-tools/, accessed: 22 November 2013). RESULTS: A parser trained only on general language performs poorly in all clinical subdomains, the labelled attachment score (LAS) ranging from 59.4% to 71.4%, whereas domain data combined with general language gives better results, the LAS varying between 67.2% and 81.7%. However, even a small amount of clinical domain data quickly outperforms this and also clinical data from other domains is more beneficial (LAS 71.3-80.0%) than general language only. The best results (LAS 77.4-84.6%) are achieved by using as training data the combination of all the clinical treebanks. CONCLUSIONS: In order to develop a good syntactic parser for clinical language variants, a general language resource is not mandatory, while data from clinical fields is. However, in addition to the exact same clinical domain, also data from other clinical domains is useful. [ABSTRACT FROM AUTHOR]

Summary: Objective: The amount of new discoveries (as published in the scientific literature) in the biomedical area is growing at an exponential rate. This growth makes it very difficult to filter the most relevant results, and thus the extraction of the core information becomes very expensive. Therefore, there is a growing interest in text processing approaches that can deliver selected information from scientific publications, which can limit the amount of human intervention normally needed to gather those results. Materials and methods: This paper presents and evaluates an approach aimed at automating the process of extracting functional relations (e.g. interactions between genes and proteins) from scientific literature in the biomedical domain. The approach, using a novel dependency-based parser, is based on a complete syntactic analysis of the corpus. Results: We have implemented a state-of-the-art text mining system for biomedical literature, based on a deep-linguistic, full-parsing approach. The results are validated on two different corpora: the manually annotated genomics information access (GENIA) corpus and the automatically annotated arabidopsis thaliana circadian rhythms (ATCR) corpus. Conclusion: We show how a deep-linguistic approach (contrary to common belief) can be used in a real world text mining application, offering high-precision relation extraction, while at the same time retaining a sufficient recall. [Copyright &y& Elsevier]

Aspect-based sentiment analysis is a natural language processing task whose aim is to automatically classify the sentiment associated with a specific aspect of a written text. In this study, we propose a novel model for aspect-based sentiment analysis, which exploits the dependency parse tree of a sentence using graph convolution to classify the sentiment of a given aspect. To evaluate this model in the domain of health and well-being, where this task is biased toward negative sentiment, we used a corpus of drug reviews. Specific aspects were grounded in the Unified Medical Language System, a large repository of inter-related biomedical concepts and the corresponding terminology. Our experiments demonstrated that graph convolution approach outperforms standard deep learning architectures on the task of aspect-based sentiment analysis. Moreover, graph convolution over dependency parse trees (F-score of 0.8179) outperforms the same approach over a flat sequence representation of sentences (F-score of 0.7332). These results bring the performance of sentiment analysis in health and well-being in line with the state of the art in other domains. [ABSTRACT FROM AUTHOR]