5,806 research outputs found

    Syntax-based Transfer Learning for the Task of Biomedical Relation Extraction

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    International audienceTransfer learning (TL) proposes to enhance machine learning performance on a problem, by reusing labeled data originally designed for a related problem. In particular, domain adaptation consists, for a specific task, in reusing training data developed for the same task but a distinct domain. This is particularly relevant to the applications of deep learning in Natural Language Processing, because those usually require large annotated corpora that may not exist for the targeted domain, but exist for side domains. In this paper, we experiment with TL for the task of Relation Extraction (RE) from biomedical texts, using the TreeLSTM model. We empirically show the impact of TreeLSTM alone and with domain adaptation by obtaining better performances than the state of the art on two biomedical RE tasks and equal performances for two others, for which few annotated data are available. Furthermore, we propose an analysis of the role that syntactic features may play in TL for RE

    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

    Extracting Biomolecular Interactions Using Semantic Parsing of Biomedical Text

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    We advance the state of the art in biomolecular interaction extraction with three contributions: (i) We show that deep, Abstract Meaning Representations (AMR) significantly improve the accuracy of a biomolecular interaction extraction system when compared to a baseline that relies solely on surface- and syntax-based features; (ii) In contrast with previous approaches that infer relations on a sentence-by-sentence basis, we expand our framework to enable consistent predictions over sets of sentences (documents); (iii) We further modify and expand a graph kernel learning framework to enable concurrent exploitation of automatically induced AMR (semantic) and dependency structure (syntactic) representations. Our experiments show that our approach yields interaction extraction systems that are more robust in environments where there is a significant mismatch between training and test conditions.Comment: Appearing in Proceedings of the Thirtieth AAAI Conference on Artificial Intelligence (AAAI-16

    An Annotated Corpus for Machine Reading of Instructions in Wet Lab Protocols

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    We describe an effort to annotate a corpus of natural language instructions consisting of 622 wet lab protocols to facilitate automatic or semi-automatic conversion of protocols into a machine-readable format and benefit biological research. Experimental results demonstrate the utility of our corpus for developing machine learning approaches to shallow semantic parsing of instructional texts. We make our annotated Wet Lab Protocol Corpus available to the research community
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