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Clinical Evidence Engine: Proof-of-Concept For A Clinical-Domain-Agnostic Decision Support Infrastructure [article]

Bojian Hou and Hao Zhang and Gur Ladizhinsky and Gur Ladizhinsky and Stephen Yang and Volodymyr Kuleshov and Fei Wang and Qian Yang
2021 arXiv   pre-print
Leveraging Clinical BioBERT, the system can effectively identify clinical trial reports based on lengthy clinical questions (e.g., "risks of catheter infection among adult patients in intensive care unit  ...  This paper explores a different approach: Providing precisely relevant, scientific evidence from biomedical literature.  ...  Literature datasets created for enhancing Evidence-Based Medicine (EBM) can also catalyze novel literature mining and information retrieval capabilities.  ... 
arXiv:2111.00621v1 fatcat:gt2635v2d5g7fif6ascrz4mxai

A Review of Recent Advancement in Integrating Omics Data with Literature Mining towards Biomedical Discoveries

Kalpana Raja, Matthew Patrick, Yilin Gao, Desmond Madu, Yuyang Yang, Lam C. Tsoi
2017 International Journal of Genomics  
Text mining (also known as literature mining) is one of the commonly used approaches for automated generation of biological knowledge from the huge number of published articles.  ...  In this review paper, we discuss the recent advancement in approaches that integrate results from omics data and information generated from text mining approaches to uncover novel biomedical information  ...  The two basic strategies applied are query-based and document-based retrieval. In query-based retrieval, documents matching with the user specified query are retrieved.  ... 
doi:10.1155/2017/6213474 pmid:28331849 pmcid:PMC5346376 fatcat:7yhwtsgyqndabcrhpx7uxsx7da

CDAPubMed: a browser extension to retrieve EHR-based biomedical literature

David Perez-Rey, Ana Jimenez-Castellanos, Miguel Garcia-Remesal, Jose Crespo, Victor Maojo
2012 BMC Medical Informatics and Decision Making  
Clinical users can use CDAPubMed to: (i) load patient clinical documents, i.e., EHRs based on the Health Level 7-Clinical Document Architecture Standard (HL7-CDA), (ii) identify relevant terms for scientific  ...  Results: We have developed CDAPubMed, an open-source web browser extension to integrate EHR features in biomedical literature retrieval approaches.  ...  Regarding search engines for biomedical literature, recent efforts focused on improving citation retrieval from MEDLINE.  ... 
doi:10.1186/1472-6947-12-29 pmid:22480327 pmcid:PMC3366875 fatcat:kf55hccatzaslakmbslykyhysi

Biomedical Document Retrieval for Clinical Decision Support System

Jainisha Sankhavara
2018 Proceedings of ACL 2018, Student Research Workshop  
In this work, we are focusing on biomedical document retrieval from literature for clinical decision support systems.  ...  The availability of huge amount of biomedical literature have opened up new possibilities to apply Information Retrieval and NLP for mining documents from them.  ...  As we are focusing here on biomedical document retrieval and ranking system, biomedical literature should be in consideration.  ... 
doi:10.18653/v1/p18-3012 dblp:conf/acl/Sankhavara18 fatcat:ggpycr4cfvckrl7j4ddy733hum

Text Mining for Translational Bioinformatics

Hong-Jie Dai, Chih-Hsuan Wei, Hung-Yu Kao, Rey-Long Liu, Richard Tzong-Han Tsai, Zhiyong Lu
2015 BioMed Research International  
Rapid growth of disease related biomedical literature makes the traditional information retrieval techniques insufficient to fulfill searchers' information needs.  ...  In their work entitled "Supervised Learning Based Hypothesis Generation from Biomedical Literature," S.  ...  Rapid growth of disease related biomedical literature makes the traditional information retrieval techniques insufficient to fulfill searchers' information needs.  ... 
doi:10.1155/2015/368264 pmid:26380272 pmcid:PMC4563058 fatcat:mshc5klqsrb2vd7ik7jcauazey


Sendong Zhao, Chang Su, Andrea Sboner, Fei Wang
2019 Proceedings of the 28th ACM International Conference on Information and Knowledge Management - CIKM '19  
Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR.  ...  Learning to rank minimizes a ranking loss between biomedical articles with the query to learn the retrieval function.  ...  RELATED WORK 2.1 Biomedical Literature Retrieval There has already been a lot of research on biomedical literature retrieval [6-8, 25, 30, 39] .  ... 
doi:10.1145/3357384.3358038 dblp:conf/cikm/ZhaoSSW19 fatcat:hpll7xork5em7jkoz4kz3m3gry

Literature-Augmented Clinical Outcome Prediction [article]

Aakanksha Naik, Sravanthi Parasa, Sergey Feldman, Lucy Lu Wang, Tom Hope
2022 arXiv   pre-print
We develop methods to retrieve literature based on noisy, information-dense patient notes, and to augment existing outcome prediction models with retrieved papers in a manner that maximizes predictive  ...  We present BEEP (Biomedical Evidence-Enhanced Predictions), a novel approach for clinical outcome prediction that retrieves patient-specific medical literature and incorporates it into predictive models  ...  The authors would like to thank the members of the Semantic Scholar team, and the anonymous reviewers for their helpful feedback on this work.  ... 
arXiv:2111.08374v2 fatcat:jj5yqs24yfasrdilxmf2xuuxhm

Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics

Gregory W. Hruby, Konstantina Matsoukas, James J. Cimino, Chunhua Weng
2016 Journal of Biomedical Informatics  
We adapted a previously published conceptual framework for interactive information retrieval, which defines three entities: user, channel, and source, by elaborating on channels for query formulation in  ...  We show the current progress in biomedical informatics mainly lies in support for query execution and information modeling, primarily due to emphases on infrastructure development for data integration  ...  We surveyed both the information science literature (i.e., and biomedical informatics literature (i.e., MEDLINE).  ... 
doi:10.1016/j.jbi.2016.03.004 pmid:26972838 pmcid:PMC4837021 fatcat:m5evutghufd4xjibxisl6c4igu

Analyzing the semantics of patient data to rank records of literature retrieval

Eneida A. Mendonça, Stephen B. Johnson, Yoon-Ho Seol, James J. Cimino
2002 Proceedings of the ACL-02 workshop on Natural language processing in the biomedical domain -  
The second method identified associations between terms in the medical record, assigning them semantic types and weights based on the co-occurrence of these associations in citations of biomedical literature  ...  We believe the results encourage the use of clinical data to determine the relevance of medical literature to the care of individual patients.  ...  The association weights are based on the co-occurrence of these associations in citations of biomedical literature.  ... 
doi:10.3115/1118149.1118159 dblp:conf/acl/MendoncaJSC02 fatcat:nrjgaqq6wjaythz7e2eov2xivm

Project FAIR--The Medical Research Council's Literature Retrieval Research Project. Services

A G Pickford
1969 Proceedings of the Royal Society of Medicine  
information retrieval languages the subject field of biomedical engineering was chosen.  ...  Considerable progress has been made on the production of cheap microfiche, based on a diazo film process, and on the production of cheap packs of feature cards, based on the use of machine inversion of  ... 
pmid:5763477 pmcid:PMC2279042 fatcat:byluyghb4ff7hfufzkbfuka3gi

Thalia: semantic search engine for biomedical abstracts

Axel J Soto, Piotr Przybyła, Sophia Ananiadou, Jonathan Wren
2018 Bioinformatics  
Thalia is available via a web-based interface or a RESTful API. A key aspect of our search engine is that it is updated from PubMed on a daily basis.  ...  Although the publication rate of the biomedical literature has been growing steadily during the last decades, the accessibility of pertinent research publications for biologist and medical practitioners  ...  In this article, we present Thalia-Text mining for Highlighting, Aggregating and Linking Information in Articles-which is a semantic search tool for the biomedical literature.  ... 
doi:10.1093/bioinformatics/bty871 pmid:30329013 fatcat:aeocxyb6n5c4dib2nibt7bs3ta

Redistributed Records Collections Personality Matching using Encrypted Cryptosystem

To solve this proble m, we are proposing a private matching scheme based on identity  ...  In this paper, we focus on the issue of private matching in ide ntity-based cryptosystem over outsourced encrypted data sets that can simplify the management of certificates.  ...  Literature Survey A.  ... 
doi:10.35940/ijitee.k1332.10812s19 fatcat:w24bvwip6jgxrlnfh4q44fucfm

A New Biomedical Passage Retrieval Framework for Laboratory Medicine: Leveraging Domain-specific Ontology, Multilevel PRF, and Negation Differential Weighting

Keejun Han, Hyoeun Shim, Mun Y. Yi
2018 Journal of Healthcare Engineering  
Clinical decision support (CDS) search is performed to retrieve key medical literature that can assist the practice of medical experts by offering appropriate medical information relevant to the medical  ...  Our study results indicate that the proposed CDS search framework specifically designed for passage retrieval of biomedical literature represents a practically viable choice for clinicians as it supports  ...  (d) Final decision is made based on the retrieved passages. (e) Patient report is made based on the clinical decision for patient care.  ... 
doi:10.1155/2018/3943417 pmid:30675333 pmcid:PMC6323463 fatcat:diyx7wyfgre7feemjasxdzo57q

Mining biomedical images towards valuable information retrieval in biomedical and life sciences

Zeeshan Ahmed, Saman Zeeshan, Thomas Dandekar
2016 Database: The Journal of Biological Databases and Curation  
and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems.  ...  Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature  ...  as a stable web-based search engine for retrieving the biomedical information by extracting the text from published biomedical literature at PMC (48) .  ... 
doi:10.1093/database/baw118 pmid:27538578 pmcid:PMC4990152 fatcat:dlyhrh5nxjhutlvvw2qkgx3wei

Response to paper by R. Brian haynes, m.d., ph.d.: organizing and accessing the literature

J T Bruer
1989 Bulletin of the New York Academy of Medicine  
Haynes concentrates on the information needs of clinical end-users.  ...  The survey authors report that office-based physicians are the poorest informed members of the medical community. Office-based physicians read the fewest books.  ...  the literature retrieved.  ... 
pmid:19313067 pmcid:PMC1808818 fatcat:4glsfhdk7nglhej7c2c6ggkom4
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