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Multi-field query expansion is effective for biomedical dataset retrieval

Mohamed Reda Bouadjenek, Karin Verspoor
2017 Database: The Journal of Biological Databases and Curation  
Biomedical Lexicon for Query Expansion: This method is based on a biomedical lexicon.  ...  We compare and evaluate two query expansion strategies, one based on the Rocchio method and another based on a biomedical lexicon.  ...  These marks do not imply any 'positive' or 'negative' information except for the presence or the absence of the considered concept in the query.  ... 
doi:10.1093/database/bax062 pmid:29220457 pmcid:PMC5737205 fatcat:qvnv56bcx5bunoadvulz3gnrxm

Biomedical question answering: A survey

Sofia J. Athenikos, Hyoil Han
2010 Computer Methods and Programs in Biomedicine  
for the future research development in this critical area of intersection between Artificial Intelligence, Information Retrieval, and Biomedical Informatics.  ...  Objectives: In this survey, we reviewed the current state of the art in biomedical QA (Question Answering), within a broader framework of semantic knowledge-based QA approaches, and projected directions  ...  Acknowledgement We would like to thank the anonymous reviewers for their helpful feedback. r e f e r e n c e s  ... 
doi:10.1016/j.cmpb.2009.10.003 pmid:19913938 fatcat:tv4sel4llbcnjppnn7g2tygqze

Recent Advances in Automated Question Answering In Biomedical Domain [article]

Krishanu Das Baksi
2021 arXiv   pre-print
However, it may be still tedious and time consuming to manually look for the required information or answers.  ...  The objective of automated Question Answering (QA) systems is to provide answers to user queries in a time efficient manner.  ...  Essie [85] is an information retrieval tool with term and concept query expansion, and probabilistic ranking based on CQA [50] .  ... 
arXiv:2111.05937v1 fatcat:5474jk6ozbalvmfjrgatu4tsna

Factors affecting the effectiveness of biomedical document indexing and retrieval based on terminologies

Duy Dinh, Lynda Tamine, Fatiha Boubekeur
2013 Artificial Intelligence in Medicine  
ad hoc information retrieval (IR) task.  ...  Objective: The aim of this work is to evaluate a set of indexing and retrieval strategies based on the integration of several biomedical terminologies on the available TREC Genomics collections for an  ...  research in Information Retrieval.  ... 
doi:10.1016/j.artmed.2012.08.006 pmid:23092678 fatcat:2ss3cba3njfhzpk76rbd6isuga

Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature [article]

Yu Wang, Jinchao Li, Tristan Naumann, Chenyan Xiong, Hao Cheng, Robert Tinn, Cliff Wong, Naoto Usuyama, Richard Rogahn, Zhihong Shen, Yang Qin, Eric Horvitz (+3 others)
2021 arXiv   pre-print
We propose a general approach for vertical search based on domain-specific pretraining and present a case study for the biomedical domain.  ...  for biomedical literature:  ...  , Xiaodong Liu, Adam Fourney, and Susan Dumais for contributing their expertise and shaping Microsoft Biomedical Search.  ... 
arXiv:2106.13375v1 fatcat:7q5x7agh3zcfjglpxs7bkdsrje

Methods and Trends in Information Retrieval in Big Data Genomic Research

in the biomedical and genome research.  ...  This paper described information retrieval (IR) and the common methods of finding, extracting, and mining information in genomic research through text mining, and natural language processing (NLP).  ...  IR system processes the query of users that search for any collections of data retrieved from relevant documents or provide results based on the rank.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Has Computational Linguistics Become More Applied? [chapter]

Kenneth Church
2009 Lecture Notes in Computer Science  
We evaluate our method comparing the answers given by a traditional information retrieval systemvector space model adjusted for article retrieval, instead of document retrieval-and the answers to 21 questions  ...  In this work we experiment by using natural language techniques such as lemmatizing and using manual and automatic thesauri for improving question based document retrieval.  ...  information is based on a set of templates that entail the information that we would like to extract, in Question Answering where candidate answers are snippets that entail the question we want to answer  ... 
doi:10.1007/978-3-642-00382-0_1 fatcat:oddvfzds4nfwjam2ccqeaxe2y4

A semantic graph-based approach to biomedical summarisation

Laura Plaza, Alberto Díaz, Pablo Gervás
2011 Artificial Intelligence in Medicine  
A degree-based clustering algorithm is then used to identify different themes or topics within the text.  ...  This paper presents a method for summarising biomedical scientific literature that takes into consideration the characteristics of the domain and the type of documents.  ...  Acknowledgement This research is funded by the Spanish Government through the FPU program and the projects TIN2009-14659-C03-01 and TSI 020312-2009-44.  ... 
doi:10.1016/j.artmed.2011.06.005 pmid:21752612 fatcat:bqkoamd5lzasnih7j33jvpl3dm

Language Modeling Approaches to Information Retrieval

Protima Banerjee, Hyo-Il Han
2009 Journal of Computing Science and Engineering  
of language modeling for XML retrieval and future trends.  ...  In this article, we discuss current research in the application of language modeling to information retrieval, the role of semantics in the language modeling framework, cluster-based language models, use  ...  retrieval and question answering.  ... 
doi:10.5626/jcse.2009.3.3.143 fatcat:ixxzdlrevfd35jemld6vfdrndi

Survey on challenges of Question Answering in the Semantic Web

Konrad Höffner, Sebastian Walter, Edgard Marx, Ricardo Usbeck, Jens Lehmann, Axel-Cyrille Ngonga Ngomo, Marta Sabou
2017 Semantic Web Journal  
Semantic Question Answering (SQA) removes two major access requirements to the Semantic Web: the mastery of a formal query language like SPARQL and knowledge of a specific vocabulary.  ...  We identify common challenges, structure solutions, and provide recommendations for future systems.  ...  Acknowledgements This work has been supported by the FP7 project GeoKnow (GA No. 318159), the BMWI Project SAKE (Project No. 01MD15006E) and by the Eurostars projects DIESEL (E!9367) and QAMEL (E!  ... 
doi:10.3233/sw-160247 fatcat:lzlupslbqbcbnlayqi7uy4ok2e

Recent progress in automatically extracting information from the pharmacogenomic literature

Yael Garten, Adrien Coulet, Russ B Altman
2010 Pharmacogenomics (London)  
Acknowledgements The authors would like to thank Connie M Oshiro for comments on the manuscript and Nicholas P Tatonetti for useful discussions and assistance creating the figures.  ...  We also thank the three anonymous reviewers for their excellent comments.  ...  Main approaches for biomedical NER The approaches for biomedical NER fall into three main categories: lexicon-based, rule-based, and statistical or machine-learning based.  ... 
doi:10.2217/pgs.10.136 pmid:21047206 pmcid:PMC3035632 fatcat:7g3jwc4hjfetbb5phmzstzhjeu

Exploiting Social Annotations for Personalizing Retrieval

Eman Sayed, Abeer Korany, Akram Salah, Hesham Hefny
2017 International Journal of Intelligent Engineering and Systems  
This may be due to the huge number of web resources, and unidentified user's interests and domain. This paper proposes exploiting social annotations for improving retrieval based on personalization.  ...  Then, the additional knowledge leads to improve the retrieved results to be close to user's interests. So, it retrieved different results for the same query based on the user's interests.  ...  This comparison aims to answer two essential questions; the first is "Are Tags considered as a Good Reflection of Resources Content?"  ... 
doi:10.22266/ijies2017.1231.21 fatcat:25wha56rlnaujippisqsen6cvi

A Review of Towered Big-Data Service Model for Biomedical Text-Mining Databases

Alshreef Abed, Jingling Yuan, Lin Li
2017 International Journal of Advanced Computer Science and Applications  
The fast development of these accumulations makes it progressively troublesome for people to get to the required information in an advantageous and viable way.  ...  Text mining can help us mine information and knowledge from a mountain of text, and is now widely applied in biomedical research.  ...  and question answering and the seven interdisciplinary fields based on computational linguistics: artificial intelligence, data mining, natural language processing and information retrieval [29] .  ... 
doi:10.14569/ijacsa.2017.080804 fatcat:juylimcz4jdbhmifhrz6so7ciq

Excavating the mother lode of human-generated text: A systematic review of research that uses the wikipedia corpus

Mohamad Mehdi, Chitu Okoli, Mostafa Mesgari, Finn Årup Nielsen, Arto Lanamäki
2017 Information Processing & Management  
Moreover, a Wikipedia link-based query expansion method for feed retrieval proved to outperform other methods with no query expansion. Theobald et al.  ...  retrieval 3 Cross-language information retrieval 6 Data mining 5 Query processing 8 Ranking and clustering systems 15 Text classification 10 Other information retrieval topics 8 Natural  ... 
doi:10.1016/j.ipm.2016.07.003 fatcat:qgjeatizfzbyjkbo4rsuxea76y

Federated Search [chapter]

Susan Dumais, Magdalena Balazinska, Jeong-Hyon Hwang, Mehul A. Shah, Raimondo Schettini, Gianluigi Ciocca, Isabella Gagliardi, Manoranjan Dash, Poon Wei Koot, Benjamin Bustos, Tobias Schreck, Vassilis Plachouras (+37 others)
2009 Encyclopedia of Database Systems  
Federated search (federated information retrieval or distributed information retrieval) is a technique for searching multiple text collections simultaneously.  ...  Less than a year after, Diaz [2009] proposed a click-based classifier for integration of news answers into web search results-as the first large-scale published study on aggregated search that won the  ...  Acknowledgements The authors are grateful to Jamie Callan and reviewers for their insightful comments.  ... 
doi:10.1007/978-0-387-39940-9_2631 fatcat:qanovfuxgndphhxidpxfzqloi4
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