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Biomedical Document Retrieval for Clinical Decision Support System

Jainisha Sankhavara
2018 Proceedings of ACL 2018, Student Research Workshop  
We compare statistical and NLP based approaches of query reformulation for biomedical document retrieval. Also, we have modeled the biomedical document retrieval as a learning to rank problem.  ...  The availability of huge amount of biomedical literature have opened up new possibilities to apply Information Retrieval and NLP for mining documents from them.  ...  In this article, we have presented a preliminary study of statistical and NLP based biomedical document retrieval techniques for clinical decision support systems.  ... 
doi:10.18653/v1/p18-3012 dblp:conf/acl/Sankhavara18 fatcat:ggpycr4cfvckrl7j4ddy733hum

Evaluation of biomedical text-mining systems: Lessons learned from information retrieval

W. Hersh
2005 Briefings in Bioinformatics  
Biomedical text-mining systems have great promise for improving the efficiency and productivity of biomedical researchers. However, such systems are still not in routine use.  ...  One impediment to their development is the lack of systematic and rigorous evaluation, comparable to the approaches developed for information retrieval systems.  ...  Acknowledgments This work was supported by grant ITR-0325160 from the National Science Foundation and earlier grants from the National Library of Medicine.  ... 
doi:10.1093/bib/6.4.344 pmid:16420733 fatcat:n7p6o2yhnnbezgf5lrgloljsim

Performance Comparison of Ad-Hoc Retrieval Models over Full-Text vs. Titles of Documents [chapter]

Ahmed Saleh, Tilman Beck, Lukas Galke, Ansgar Scherp
2018 Lecture Notes in Computer Science  
While there are many studies on information retrieval models using full-text, there are presently no comparison studies of full-text retrieval vs. retrieval only over the titles of documents.  ...  In this paper, we compare different retrieval models regarding their search performance on the full-text vs. only titles of documents.  ...  However, to the best of our knowledge, there are no recent studies that use state-of-the-art retrieval techniques to compare ad-hoc retrieval over titles with ad-hoc retrieval over full-text.  ... 
doi:10.1007/978-3-030-04257-8_30 fatcat:wwxzjk57urcgrakcnwn4iecu7u

A Comparative Analysis of Active Learning for Biomedical Text Mining

Usman Naseem, Matloob Khushi, Shah Khalid Khan, Kamran Shaukat, Mohammad Ali Moni
2021 Applied System Innovation  
We performed a comparative investigation of various AL techniques using ML and deep learning (DL) based strategies on three unique biomedical datasets.  ...  AL has been successfully applied to labelling speech recognition and text classification, however, there is a lack of literature investigating its use for clinical purposes.  ...  Acknowledgments: Authors acknowledge and thank Junchi Li and Hengze Liu for their contribution to the project. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/asi4010023 fatcat:e37me7znw5fp5enlh6v4ak55zy

Evaluating performance of biomedical image retrieval systems—An overview of the medical image retrieval task at ImageCLEF 2004–2013

Jayashree Kalpathy-Cramer, Alba García Seco de Herrera, Dina Demner-Fushman, Sameer Antani, Steven Bedrick, Henning Müller
2015 Computerized Medical Imaging and Graphics  
Medical(image(retrieval(and(classification(have(been(extremely(active(research(topics(over( the( past( 15( years.( With( the( ImageCLEF( benchmark( in( medical( image( retrieval( and( classification( a  ...  of( image( retrieval( approaches( and( systems( began( as( a( research( field( over( two( decades( ago( [5,34, 38] , ( progress( has( been( slow( for( a( variety( of( reasons.( One( problem( is( the( inability  ...  (consists(of(images( and(annotations(for(modality(classification;(images(and(associated(text(for(ad-hoc(retrieval;( and(case(descriptions(with(images(for(case-based(retrieval.  ... 
doi:10.1016/j.compmedimag.2014.03.004 pmid:24746250 pmcid:PMC4177510 fatcat:xuck5guwojexviqczz4keargjm

Improving imbalanced scientific text classification using sampling strategies and dictionaries

L Borrajo, R Romero, E L Iglesias, C M Redondo Marey
2011 Journal of Integrative Bioinformatics  
One of the systems affected are those related to the recovery and classification of scientific documentation.  ...  Another purpose of this paper is to study the use of dictionaries in the classification of biomedical texts.  ...  Acknowledgements This work has been partially funded by the Spanish Ministry of Science and Innovation, the Plan E from the Spanish Government and the European Union from the ERDF (TIN2009-14057-C03-02  ... 
doi:10.2390/biecoll-jib-2011-176 pmid:21926439 fatcat:r7oujlh3sbaxzdkcnxhauobsjm

Improving imbalanced scientific text classification using sampling strategies and dictionaries

L. Borrajo, R. Romero, E. L. Iglesias, C. M. Redondo Marey
2011 Journal of Integrative Bioinformatics  
the use of dictionaries in the classification of biomedical texts.  ...  Experiments are conducted with three different dictionaries (BioCreative, NLPBA, and an ad-hoc subset of the UniProt database named Protein) using the mentioned classifiers and sampling strategies.Best  ...  Acknowledgements This work has been partially funded by the Spanish Ministry of Science and Innovation, the Plan E from the Spanish Government and the European Union from the ERDF (TIN2009-14057-C03-02  ... 
doi:10.1515/jib-2011-176 fatcat:2wtq6qpnvfcibcutkyv6vge4xy

Automatically extracting information needs from complex clinical questions

Yong-gang Cao, James J. Cimino, John Ely, Hong Yu
2010 Journal of Biomedical Informatics  
We achieved an F1 score of 76.0% for the task of general topic classification and 58.0% for keyword extraction. Our systems have been implemented into the larger question answering system AskHERMES.  ...  We report here on two natural language processing models, namely, automatic topic assignment and keyword identification, that together automatically and effectively extract information needs from ad hoc  ...  Acknowledgments The authors acknowledge support from the National Library of Medicine, Grant No. 1R01LM009836, and from the University of Wisconsin-Milwaukee, a MiTAG grant.  ... 
doi:10.1016/j.jbi.2010.07.007 pmid:20670693 pmcid:PMC2991382 fatcat:rm3hug5kkzfkhf3t55ssgtf6tq

Topic Modeling Technique for Text Mining Over Biomedical Text Corpora through Hybrid Inverse Documents Frequency and Fuzzy K-Means Clustering

Junaid Rashid, Syed Muhammad Adnan Shah, Aun Irtaza, Toqeer Mahmood, Muhammad Wasif Nisar, Muhammad Shafiq, Akber Gardezi
2019 IEEE Access  
Topic modeling is one of the popular techniques for information retrieval based on themes from the biomedical documents.  ...  Afterward, the classification and clustering for text mining are performed with a probability of topics in the documents.  ...  Proposed topic modeling technique improves the classification accuracy for biomedical datasets and provides a new technique for text mining over biomedical datasets.  ... 
doi:10.1109/access.2019.2944973 fatcat:yqwkq6crgfc2jmvwip7fzxdoja

Using argumentation to retrieve articles with similar citations: An inquiry into improving related articles search in the MEDLINE digital library

I TBAHRITI, C CHICHESTER, F LISACEK, P RUCH
2006 International Journal of Medical Informatics  
A linear weighting combination of the moves is proposed, which significantly improves retrieval of related articles.  ...  We extracted citation lists from a set of 3200 full-text papers originating from a narrow domain. In parallel, we recovered the corresponding MEDLINE records for analysis of the argumentative moves.  ...  Acknowledgements We would like to thank Patrick Brechbiehl for his assistance in organizing the computing environment and Ron Appel for his support.  ... 
doi:10.1016/j.ijmedinf.2005.06.007 pmid:16165395 fatcat:rxdsamwfprhshfccpxghwd4w7a

Community challenges in biomedical text mining over 10 years: success, failure and the future

Chung-Chi Huang, Zhiyong Lu
2015 Briefings in Bioinformatics  
Next, we describe the general workflow of organizing a Biomedical NLP (BioNLP) challenge and involved stakeholders (task organizers, task data producers, task participants and end users).  ...  Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties.  ...  Robert Leaman for his help of proofreading this article and the anonymous reviewers for their helpful comments and suggestions.  ... 
doi:10.1093/bib/bbv024 pmid:25935162 pmcid:PMC4719069 fatcat:z7wlyvovnnbrrkufmqaxycqdyi

Keyphrase extraction-based query expansion in digital libraries

Min Song, Il Yeol Song, Robert B. Allen, Zoran Obradovic
2006 Proceedings of the 6th ACM/IEEE-CS joint conference on Digital libraries - JCDL '06  
The keyphrases are extracted from the retrieved documents and weighted with an algorithm based on information gain and co-occurrence of phrases.  ...  We test our techniques on TREC 5, 6, and 7 as well as a MEDLINE collection. The experimental results show that the use of keyphrases with POS phrase categorization produces the best average precision.  ...  Table 2 : 2 Documents and queries used in TREC ad hoc tasks.  ... 
doi:10.1145/1141753.1141800 dblp:conf/jcdl/SongSAO06 fatcat:es4eb65w2vg6pjhoaqr2fltpvq

A Feedback-Based Approach to Utilizing Embeddings for Clinical Decision Support

Chenhao Yang, Ben He, Canjia Li, Jungang Xu
2017 Data Science and Engineering  
This paper proposes a novel feedback-based approach which considers the semantic association between a retrieved biomedical article and a pseudo feedback set.  ...  Most of the existing CDS methods do not sufficiently consider the semantic relation between texts, hence the potential in improving the performance in biomedical articles retrieval.  ...  , and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s41019-017-0052-2 fatcat:ok6lg3granep3bzgtdsorkvctq

TAKES: Two-step Approach for Knowledge Extraction in Biomedical Digital Libraries

Min Song
2014 Journal of Information Science Theory and Practice  
These TREC ad hoc test sets have been used in many different tracks of TREC including the TREC-5 routing track, the TREC-7 ad hoc track, and the TREC-8 ad hoc track.  ...  The ad hoc task investigates the performance of systems that search a static document collection using new query statements.  ... 
doi:10.1633/jistap.2014.2.1.1 fatcat:zouat6iefzecldddnylkojzmiu

Automatically extracting information needs from Ad Hoc clinical questions

Hong Yu, Yong-Gang Cao
2008 AMIA Annual Symposium Proceedings  
Our best systems or methods showed F-score of 76% for the task of question-topic classification and an average F-score of 56% for extracting keywords from ad hoc clinical questions.  ...  We then evaluated different methods for automatically extracting keywords from an ad hoc clinical question.  ...  Cimino and associates [10] proposed a framework for automatically analyzing ad hoc medical questions. In this framework, an ad hoc question (e.g., "How do I treat Hansen's disease?")  ... 
pmid:18999100 pmcid:PMC2655957 fatcat:3vwprkq6brdttaxpffbwxmoi4y
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