1,347 research outputs found

    Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search™

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    Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition’s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through phrase parsing and word sense disambiguation.
Result: Here we have carried out several projects to "teach" the CSIR lexicon medical, biochemical and molecular biological language and acronyms from curated web-based free sources. Vocabulary from the Alliance for Cell Signaling (AfCS), the Human Genome Nomenclature Consortium (HGNC), the United Medical Language System (UMLS) Meta-thesaurus, and The International Union of Pure and Applied Chemistry (IUPAC) was introduced into the CSIR dictionary and curated. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym information has been encoded. The present implementation can be found at http://MEDLINE.cognition.com. 
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    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

    Decorrelation and shallow semantic patterns for distributional clustering of nouns and verbs

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    Distributional approximations to lexical semantics are very useful not only in helping the creation of lexical semantic resources (Kilgariff et al., 2004; Snow et al., 2006), but also when directly applied in tasks that can benefit from large-coverage semantic knowledge such as coreference resolution (Poesio et al., 1998; Gasperin and Vieira, 2004; Versley, 2007), word sense disambiguation (Mc- Carthy et al., 2004) or semantical role labeling (Gordon and Swanson, 2007). We present a model that is built from Webbased corpora using both shallow patterns for grammatical and semantic relations and a window-based approach, using singular value decomposition to decorrelate the feature space which is otherwise too heavily influenced by the skewed topic distribution of Web corpora

    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

    A Semantic Question Answering Framework for Large Data Sets

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    Traditionally, the task of answering natural language questions has involved a keyword-based document retrieval step, followed by in-depth processing of candidate answer documents and paragraphs. This post-processing uses semantics to various degrees. In this article, we describe a purely semantic question answering (QA) framework for large document collections. Our high-precision approach transforms the semantic knowledge extracted from natural language texts into a language-agnostic RDF representation and indexes it into a scalable triplestore. In order to facilitate easy access to the information stored in the RDF semantic index, a user's natural language questions are translated into SPARQL queries that return precise answers back to the user. The robustness of this framework is ensured by the natural language reasoning performed on the RDF store, by the query relaxation procedures, and the answer ranking techniques. The improvements in performance over a regular free text search index-based question answering engine prove that QA systems can benefit greatly from the addition and consumption of deep semantic information
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