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Mining linguistic cues for query expansion

Sheng Guo, Naren Ramakrishnan
2009 Proceeding of the 18th ACM conference on Information and knowledge management - CIKM '09  
We study this problem as one of mining linguistic cues for query expansion.  ...  In particular, we show that purely data-driven linguistic cues can be effectively mined and applied to realize a successful domain-specific query expansion framework.  ...  All these cue words are used to query-expand, to help search for new drug interactions in MEDLINE.  ... 
doi:10.1145/1645953.1645998 dblp:conf/cikm/GuoR09 fatcat:yaoxbemoqffnzdjvkzj64ftrei

Text mining tools for extracting information about microbial biodiversity in food

Estelle Chaix, Louise Deléger, Robert Bossy, Claire Nédellec
2018 Food microbiology  
We would like to thank Olivier Couvert for this advice on spore-forming microorganisms. We are grateful to the Inra MIGALE bioinformatics platform for providing computational resources.  ...  We would like to thank biologists from the French National Institute for Agricultural Research (Inra) Floril ege working group and Food Microbiome project, for their participation in the enrichment of  ...  We queried the AlvisIR Food search engine to look for microbes living in fruits in the literature 7 . A query results are shown in Fig. 7 .  ... 
doi:10.1016/j.fm.2018.04.011 fatcat:n3poizfyhbbeddt3alpthkydqm

Text Mining for Adverse Drug Events: the Promise, Challenges, and State of the Art

Rave Harpaz, Alison Callahan, Suzanne Tamang, Yen Low, David Odgers, Sam Finlayson, Kenneth Jung, Paea LePendu, Nigam H. Shah
2014 Drug Safety  
, product labeling, social media, and Web search logs-that are amenable to text-mining for pharmacovigilance.  ...  Text mining is emerging as a tool to leverage underutilized data sources that can improve pharmacovigilance, including the objective of adverse drug event detection and assessment.  ...  Acknowledgments The writing of this manuscript was supported by NIH grant U54-HG004028 for the National Center for Biomedical Ontology, and by NIGMS grant GM101430-01A1.  ... 
doi:10.1007/s40264-014-0218-z pmid:25151493 pmcid:PMC4217510 fatcat:yamkj45aovg7ba67k5gbmitka4

Event-based text mining for biology and functional genomics

S. Ananiadou, P. Thompson, R. Nawaz, J. McNaught, D. B. Kell
2014 Briefings in Functional Genomics  
Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify  ...  mining (TM) are needed to extract meaningful knowledge from it.  ...  Acknowledgements We would like to thank Dr. Makoto Miwa (NaCTeM) for his helpful comments on the manuscript.  ... 
doi:10.1093/bfgp/elu015 pmid:24907365 pmcid:PMC4499874 fatcat:qjl6uvt3wbbuplu6hrdsloyjlu

Lightly supervised acquisition of named entities and linguistic patterns for multilingual text mining

César de Pablo-Sánchez, Isabel Segura-Bedmar, Paloma Martínez, Ana Iglesias-Maqueda
2012 Knowledge and Information Systems  
intelligent applications for helping to access information.  ...  Therefore, it would be helpful for applications where annotated NERC data are not available such as those that have to deal with several western languages or information from different domains.  ...  Her main area of research interest is the application of Information Extraction Techniques to the pharmacological domain, in particular, the extraction of drug-drug interactions and the detection of drug  ... 
doi:10.1007/s10115-012-0502-0 fatcat:ukfcua2ru5cfbicckj4hwgv5my

Patient Centered Identification, Attribution, and Ranking of Adverse Drug Events

Ritwik Banerjee, I.V. Ramakrishnan, Mark Henry, Matthew Perciavalle
2015 2015 International Conference on Healthcare Informatics  
Our application utilizes heterogeneous information sources (including drug databases) to refine and transform these descriptions as well as the online database narratives using a natural language processing  ...  Information about ADEs is often available in online drug databases in the form of narrative texts, and serves as the physician's primary reference point for ADE attribution and diagnosis.  ...  Templates for mining adverse effects of drugs. Linguistic cues are in bold, while the extracted symptoms are italicized.  ... 
doi:10.1109/ichi.2015.8 dblp:conf/ichi/BanerjeeRHP15 fatcat:tmuoukngsra2pes5zfsfszb4y4

SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature

Behrouz Bokharaeian, Alberto Diaz, Nasrin Taghizadeh, Hamidreza Chitsaz, Ramyar Chavoshinejad
2017 Journal of Biomedical Semantics  
Trial Registration: Not Applicable  ...  What is more, our first experiments with the corpus show that linguistic-based confidence alongside other non-linguistic features can be utilized in order to estimate the strength of the observed SNP-phenotype  ...  MT Pilehvar (Cambridge University, UK) for her useful comments and suggestions for organizing the paper.  ... 
doi:10.1186/s13326-017-0116-2 pmid:28388928 pmcid:PMC5383945 fatcat:fekrllenifcctiuculw46hfzlq

Embedding Web-based Statistical Translation Models in Cross-Language Information Retrieval [article]

Wessel Kraaij, Jian-Yun Nie, Michel Simard
2003 arXiv   pre-print
These results open the perspective of constructing a fully automatic query translation device for CLIR at a very low cost.  ...  The Web provides a vast resource for the automatic construction of parallel corpora which can be used to train statistical translation models automatically.  ...  We would like to thank Xerox Research Center Europe (XRCE) for making their Xelda toolkit available to us.  ... 
arXiv:cs/0312008v1 fatcat:hztoxce3frcgpbsmegftpg4rdu

Embedding Web-Based Statistical Translation Models in Cross-Language Information Retrieval

Wessel Kraaij, Jian-Yun Nie, Michel Simard
2003 Computational Linguistics  
These results open the perspective of constructing a fully automatic query translation device for CLIR at a very low cost.  ...  The Web provides a vast resource for the automatic construction of parallel corpora that can be used to train statistical translation models automatically.  ...  We would like to thank Xerox Research Center Europe (XRCE) for making its Xelda toolkit available to us.  ... 
doi:10.1162/089120103322711587 fatcat:dkxidh7b3vdszodokvwhjd4nre

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain.  ...  KBC was supported by NIH grants 'Construction of a Full Text Corpus for Biomedical Text Mining' (#1G08LM009639-01) and 'Technology Development for a Molecular Biology Knowledge-base' (#5R01 LM008111-03  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy

Clinical Natural Language Processing in languages other than English: opportunities and challenges

Aurélie Névéol, Hercules Dalianis, Sumithra Velupillai, Guergana Savova, Pierre Zweigenbaum
2018 Journal of Biomedical Semantics  
to another language, and (iii) studies focusing on a particular clinical application.  ...  Conclusion: We show the advantages and drawbacks of each method, and highlight the appropriate application context.  ...  Recently, researchers produced annotated corpora for tasks such as machine translation [54, 55] , de-identification in French [56] and Swedish [57] , drug-drug interaction in Spanish [58] , named  ... 
doi:10.1186/s13326-018-0179-8 pmid:29602312 pmcid:PMC5877394 fatcat:xas3ynaltjeuhgdymutha7akvi

Deriving marketing intelligence from online discussion

Natalie Glance, Matthew Hurst, Kamal Nigam, Matthew Siegler, Robert Stockton, Takashi Tomokiyo
2005 Proceeding of the eleventh ACM SIGKDD international conference on Knowledge discovery in data mining - KDD '05  
This paper argues that applications for mining large volumes of textual data for marketing intelligence should provide two key elements: a suite of powerful mining and visualization technologies and an  ...  interactive analysis environment which allows for rapid generation and testing of hypotheses.  ...  Our system allows for six different categories of terms to be specified which are combined to construct the complex boolean query for the search. These include: • Product terms, and Competitor terms.  ... 
doi:10.1145/1081870.1081919 dblp:conf/kdd/GlanceHNSST05 fatcat:3l3obqej4remtoxmbicba5txfa

Basic Building Blocks for Clinical Text Processing [chapter]

Hercules Dalianis
2018 Clinical Text Mining  
For more details on the concepts in this section, see the following comprehensible textbooks in computational linguistics: Mitkov (2005) , Jurafsky and Martin (2014) and Clark et al. (2013).  ...  Word processing such as morphological processing, lemmatisation, stemming, compound splitting, abbreviation detection and expansion.  ...  In clinical text mining one task is to detect an adverse drug event, by detecting the relation between a drug and a finding or symptom.  ... 
doi:10.1007/978-3-319-78503-5_7 fatcat:pqwyc2vm2zh2vlky7bzo5da3pa

Evidence-based Recommender System for a COVID-19 Publication Analytics Service

Roland Oruche, Vidya Gundlapalli, Aditya P. Biswal, Prasad Calyam, Mauro Lemus Alarcon, Yuanxun Zhang, Naga Ramya Bhamidipati, Abhiram Malladi, Hariharan Regunath
2021 IEEE Access  
However, these applications lack the ability to filter articles in accordance with the Levels of Evidence Pyramid [3] shown in Fig. 1 .  ...  that integrates a queried user interface to retrieve latest peer-reviewed articles.  ...  One notable service that attempts to help data consumers to mine literature on current pandemic-related problems is the IBM Deep Search [5] .  ... 
doi:10.1109/access.2021.3083583 fatcat:bgtl36ev7bedphpqs2omjjctky

Developing a hybrid dictionary-based bio-entity recognition technique

Min Song, Hwanjo Yu, Wook-Shin Han
2015 BMC Medical Informatics and Decision Making  
In addition, the proposed technique adopts text mining techniques in the merging stage of similar entities such as Part of Speech (POS) expansion, stemming, and the exploitation of the contextual cues  ...  to further improve the performance.  ...  Drug-drug interaction is another application area of NER.  ... 
doi:10.1186/1472-6947-15-s1-s9 pmid:26043907 pmcid:PMC4460617 fatcat:23l3qeel65fc7ldqsyh2fkatca
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