9,642 research outputs found

    Using Neural Networks for Relation Extraction from Biomedical Literature

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    Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

    Building a semantically annotated corpus of clinical texts

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    In this paper, we describe the construction of a semantically annotated corpus of clinical texts for use in the development and evaluation of systems for automatically extracting clinically significant information from the textual component of patient records. The paper details the sampling of textual material from a collection of 20,000 cancer patient records, the development of a semantic annotation scheme, the annotation methodology, the distribution of annotations in the final corpus, and the use of the corpus for development of an adaptive information extraction system. The resulting corpus is the most richly semantically annotated resource for clinical text processing built to date, whose value has been demonstrated through its use in developing an effective information extraction system. The detailed presentation of our corpus construction and annotation methodology will be of value to others seeking to build high-quality semantically annotated corpora in biomedical domains

    Ontologies and Information Extraction

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    This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

    Enhanced services for targeted information retrieval by event extraction and data mining

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    Where Information Retrieval (IR) and Text Categorization delivers a set of (ranked) documents according to a query, users of large document collections would rather like to receive answers. Question-answering from text has already been the goal of the Message Understanding Conferences. Since then, the task of text understanding has been reduced to several more tractable tasks, most prominently Named Entity Recognition (NER) and Relation Extraction. Now, pieces can be put together to form enhanced services added on an IR system. In this paper, we present a framework which combines standard IR with machine learning and (pre-)processing for NER in order to extract events from a large document collection. Some questions can already be answered by particular events. Other questions require an analysis of a set of events. Hence, the extracted events become input to another machine learning process which delivers the final output to the user's question. Our case study is the public collection of minutes of plenary sessions of the German parliament and of petitions to the German parliament. --
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