12 research outputs found

    A System for Identifying Named Entities in Biomedical Text: how Results From two Evaluations Reflect on Both the System and the Evaluations

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    We present a maximum entropy-based system for identifying named entities (NEs) in biomedical abstracts and present its performance in the only two biomedical named entity recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match F-score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evaluation. We discuss our system in detail, including its rich use of local features, attention to correct boundary identification, innovative use of external knowledge resources, including parsing and web searches, and rapid adaptation to new NE sets. We also discuss in depth problems with data annotation in the evaluations which caused the final performance to be lower than optimal

    Boosting Drug Named Entity Recognition using an Aggregate Classifier

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    AbstractObjectiveDrug named entity recognition (NER) is a critical step for complex biomedical NLP tasks such as the extraction of pharmacogenomic, pharmacodynamic and pharmacokinetic parameters. Large quantities of high quality training data are almost always a prerequisite for employing supervised machine-learning techniques to achieve high classification performance. However, the human labour needed to produce and maintain such resources is a significant limitation. In this study, we improve the performance of drug NER without relying exclusively on manual annotations.MethodsWe perform drug NER using either a small gold-standard corpus (120 abstracts) or no corpus at all. In our approach, we develop a voting system to combine a number of heterogeneous models, based on dictionary knowledge, gold-standard corpora and silver annotations, to enhance performance. To improve recall, we employed genetic programming to evolve 11 regular-expression patterns that capture common drug suffixes and used them as an extra means for recognition.MaterialsOur approach uses a dictionary of drug names, i.e. DrugBank, a small manually annotated corpus, i.e. the pharmacokinetic corpus, and a part of the UKPMC database, as raw biomedical text. Gold-standard and silver annotated data are used to train maximum entropy and multinomial logistic regression classifiers.ResultsAggregating drug NER methods, based on gold-standard annotations, dictionary knowledge and patterns, improved the performance on models trained on gold-standard annotations, only, achieving a maximum F-score of 95%. In addition, combining models trained on silver annotations, dictionary knowledge and patterns are shown to achieve comparable performance to models trained exclusively on gold-standard data. The main reason appears to be the morphological similarities shared among drug names.ConclusionWe conclude that gold-standard data are not a hard requirement for drug NER. Combining heterogeneous models build on dictionary knowledge can achieve similar or comparable classification performance with that of the best performing model trained on gold-standard annotations

    SinNer@Clef-Hipe2020 : Sinful adaptation of SotA models for Named Entity Recognition in French and German

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    International audienceIn this article we present the approaches developed by the Sorbonne-INRIA for NER (SinNer) team for the CLEF-HIPE 2020 challenge on Named Entity Processing on old newspapers. The challenge proposed various tasks for three languages, among them we focused on Named Entity Recognition in French and German texts. The best system we proposed ranked third for these two languages, it uses FastText em-beddings and Elmo language models (FrELMo and German ELMo). We show that combining several word representations enhances the quality of the results for all NE types and that the segmentation in sentences has an important impact on the results

    Information retrieval and text mining technologies for chemistry

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    Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio

    Entities with quantities : extraction, search, and ranking

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    Quantities are more than numeric values. They denote measures of the world’s entities such as heights of buildings, running times of athletes, energy efficiency of car models or energy production of power plants, all expressed in numbers with associated units. Entity-centric search and question answering (QA) are well supported by modern search engines. However, they do not work well when the queries involve quantity filters, such as searching for athletes who ran 200m under 20 seconds or companies with quarterly revenue above $2 Billion. State-of-the-art systems fail to understand the quantities, including the condition (less than, above, etc.), the unit of interest (seconds, dollar, etc.), and the context of the quantity (200m race, quarterly revenue, etc.). QA systems based on structured knowledge bases (KBs) also fail as quantities are poorly covered by state-of-the-art KBs. In this dissertation, we developed new methods to advance the state-of-the-art on quantity knowledge extraction and search.Zahlen sind mehr als nur numerische Werte. Sie beschreiben Maße von EntitĂ€ten wie die Höhe von GebĂ€uden, die Laufzeit von Sportlern, die Energieeffizienz von Automodellen oder die Energieerzeugung von Kraftwerken - jeweils ausgedrĂŒckt durch Zahlen mit zugehörigen Einheiten. EntitĂ€tszentriete Anfragen und direktes Question-Answering werden von Suchmaschinen hĂ€ufig gut unterstĂŒtzt. Sie funktionieren jedoch nicht gut, wenn die Fragen Zahlenfilter beinhalten, wie z. B. die Suche nach Sportlern, die 200m unter 20 Sekunden gelaufen sind, oder nach Unternehmen mit einem Quartalsumsatz von ĂŒber 2 Milliarden US-Dollar. Selbst moderne Systeme schaffen es nicht, QuantitĂ€ten, einschließlich der genannten Bedingungen (weniger als, ĂŒber, etc.), der Maßeinheiten (Sekunden, Dollar, etc.) und des Kontexts (200-Meter-Rennen, Quartalsumsatz usw.), zu verstehen. Auch QA-Systeme, die auf strukturierten Wissensbanken (“Knowledge Bases”, KBs) aufgebaut sind, versagen, da quantitative Eigenschaften von modernen KBs kaum erfasst werden. In dieser Dissertation werden neue Methoden entwickelt, um den Stand der Technik zur Wissensextraktion und -suche von QuantitĂ€ten voranzutreiben. Unsere HauptbeitrĂ€ge sind die folgenden: ‱ ZunĂ€chst prĂ€sentieren wir Qsearch [Ho et al., 2019, Ho et al., 2020] – ein System, das mit erweiterten Fragen mit QuantitĂ€tsfiltern umgehen kann, indem es Hinweise verwendet, die sowohl in der Frage als auch in den Textquellen vorhanden sind. Qsearch umfasst zwei HauptbeitrĂ€ge. Der erste Beitrag ist ein tiefes neuronales Netzwerkmodell, das fĂŒr die Extraktion quantitĂ€tszentrierter Tupel aus Textquellen entwickelt wurde. Der zweite Beitrag ist ein neuartiges Query-Matching-Modell zum Finden und zur Reihung passender Tupel. ‱ Zweitens, um beim Vorgang heterogene Tabellen einzubinden, stellen wir QuTE [Ho et al., 2021a, Ho et al., 2021b] vor – ein System zum Extrahieren von QuantitĂ€tsinformationen aus Webquellen, insbesondere Ad-hoc Webtabellen in HTML-Seiten. Der Beitrag von QuTE umfasst eine Methode zur VerknĂŒpfung von QuantitĂ€ts- und EntitĂ€tsspalten, fĂŒr die externe Textquellen genutzt werden. Zur Beantwortung von Fragen kontextualisieren wir die extrahierten EntitĂ€ts-QuantitĂ€ts-Paare mit informativen Hinweisen aus der Tabelle und stellen eine neue Methode zur Konsolidierung und verbesserteer Reihung von Antwortkandidaten durch Inter-Fakten-Konsistenz vor. ‱ Drittens stellen wir QL [Ho et al., 2022] vor – eine Recall-orientierte Methode zur Anreicherung von Knowledge Bases (KBs) mit quantitativen Fakten. Moderne KBs wie Wikidata oder YAGO decken viele EntitĂ€ten und ihre relevanten Informationen ab, ĂŒbersehen aber oft wichtige quantitative Eigenschaften. QL ist frage-gesteuert und basiert auf iterativem Lernen mit zwei HauptbeitrĂ€gen, um die KB-Abdeckung zu verbessern. Der erste Beitrag ist eine Methode zur Expansion von Fragen, um einen grĂ¶ĂŸeren Pool an Faktenkandidaten zu erfassen. Der zweite Beitrag ist eine Technik zur Selbstkonsistenz durch BerĂŒcksichtigung der Werteverteilungen von QuantitĂ€ten

    An exploratory study using the predicate-argument structure to develop methodology for measuring semantic similarity of radiology sentences

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    Indiana University-Purdue University Indianapolis (IUPUI)The amount of information produced in the form of electronic free text in healthcare is increasing to levels incapable of being processed by humans for advancement of his/her professional practice. Information extraction (IE) is a sub-field of natural language processing with the goal of data reduction of unstructured free text. Pertinent to IE is an annotated corpus that frames how IE methods should create a logical expression necessary for processing meaning of text. Most annotation approaches seek to maximize meaning and knowledge by chunking sentences into phrases and mapping these phrases to a knowledge source to create a logical expression. However, these studies consistently have problems addressing semantics and none have addressed the issue of semantic similarity (or synonymy) to achieve data reduction. To achieve data reduction, a successful methodology for data reduction is dependent on a framework that can represent currently popular phrasal methods of IE but also fully represent the sentence. This study explores and reports on the benefits, problems, and requirements to using the predicate-argument statement (PAS) as the framework. A convenient sample from a prior study with ten synsets of 100 unique sentences from radiology reports deemed by domain experts to mean the same thing will be the text from which PAS structures are formed

    Natural Language Processing Resources for Finnish. Corpus Development in the General and Clinical Domains

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