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Evaluation of Clinical Text Segmentation to Facilitate Cohort Retrieval

Tracy Edinger, Dina Demner-Fushman, Aaron M Cohen, Steven Bedrick, William Hersh
2018 AMIA Annual Symposium Proceedings  
Clinical text poses difficulties to searching, although chart notes incorporate structure that may facilitate accurate retrieval.  ...  We manually evaluated a subset of retrieved documents to compare query performance.  ...  Although the effectiveness of each segmentation strategy has been evaluated, no studies could be located that demonstrate whether segmenting improves the performance of searching clinical text.  ... 
pmid:29854131 pmcid:PMC5977655 fatcat:stlwlkjrzffwtmwq4ej7zlftui

Evaluation of Doc'EDS: a French semantic search tool to query health documents from a clinical data warehouse

Thibaut Pressat-Laffouilhère, Pierre Balayé, Badisse Dahamna, Romain Lelong, Kévin Billey, Stéfan J. Darmoni, Julien Grosjean
2022 BMC Medical Informatics and Decision Making  
Conclusion In this formal evaluation, we have shown that Doc'EDS is able to deal with language subtleties to enhance an advanced full text search in French health documents.  ...  The Doc'EDS system provides a graphic user interface to search documents in French. The aim of this study was to present the Doc'EDS tool and to provide a formal evaluation of its semantic features.  ...  Acknowledgements The authors are grateful to Nikki Sabourin-Gibbs (Rouen University Hospital) for her help with editing the manuscript.  ... 
doi:10.1186/s12911-022-01762-4 pmid:35135538 pmcid:PMC8822768 fatcat:o355dsgmgrbrnfq4w7wddpwkga

Problem-oriented Prefetching for an Integrated Clinical Imaging Workstation

A. A. T. Bui, M. F. McNitt-Gray, J. G. Goldin, A. F. Cardenas, D. R. Aberle
2001 JAMIA Journal of the American Medical Informatics Association  
To accurately evaluate the temporal evolution of a medical condition, access to historical data is required to facilitate comparison of a patient's current status with findings from past examinations.  ...  Preliminary evaluation of the prefetching algorithm using classic information retrieval measures showed that the system had high recall (100 percent), correctly identifying and retrieving data for all  ...  The use of natural language processing on free-text reports to handle the context of findings may increase the level of precision in document searching and facilitate searching of related terms for diagnoses  ... 
doi:10.1136/jamia.2001.0080242 pmid:11320069 pmcid:PMC131032 fatcat:urtj3dchiferzbpbucpy55pmym

Criteria2Query: a natural language interface to clinical databases for cohort definition

Chi Yuan, Patrick B Ryan, Casey Ta, Yixuan Guo, Ziran Li, Jill Hardin, Rupa Makadia, Peng Jin, Ning Shang, Tian Kang, Chunhua Weng
2019 JAMIA Journal of the American Medical Informatics Association  
Data-driven cohort definition is appealing but requires substantial knowledge of terminologies and clinical data models.  ...  Criteria2Query is a natural language interface that facilitates human-computer collaboration for cohort definition and execution using clinical databases.  ...  CT, NS, ZL, JH, RM, and JP contributed to the design and evaluation of the system. YG and TK contributed to individual modules or prior versions of the system.  ... 
doi:10.1093/jamia/ocy178 pmid:30753493 pmcid:PMC6402359 fatcat:5xg4qbkqsbc3vjnr4rvg2dahw4

A Knowledge-Based Approach to Medical Records Retrieval

Dina Demner-Fushman, Swapna Abhyankar, Antonio Jimeno-Yepes, Russell F. Loane, Bastien Rance, François-Michel Lang, Nicholas C. Ide, Emilia Apostolova, Alan R. Aronson
2011 Text Retrieval Conference  
Based on the clinical documentation standards and knowledge of the clinical documentation structure, we split each report type into sections corresponding to different categories of clinical content, with  ...  The NLM LHC team approached the cohort selection task of the 2011 Medical Records Track as a question answering problem.  ...  We then automatically segmented all of the documents based on these rules and manually evaluated the segmentation.  ... 
dblp:conf/trec/Demner-FushmanAJLRLIAA11 fatcat:jssejefuqjdwhepv2rub2ovifa

Exploration of Artificial Intelligence Use with ARIES in Multiple Myeloma Research

Loda, Krebs, Danhof, Schreder, Solimando, Strifler, Rasche, Kortüm, Kerscher, Knop, Puppe, Einsele (+1 others)
2019 Journal of Clinical Medicine  
We therefore created a MM-specific ontology to accelerate the information extraction (IE) out of unstructured text.  ...  Our tool easily accelerates the integration of research evidence into everyday clinical practice.  ...  Acknowledgments: The text was edited during revision by A.J. Davis, English Experience Language Services, Göttingen, Germany. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/jcm8070999 pmid:31324026 pmcid:PMC6678083 fatcat:min5tvpfonapvhkq55dj26laxu

Automated mapping of pharmacy orders from two electronic health record systems to RxNorm within the STRIDE clinical data warehouse

Penni Hernandez, Tanya Podchiyska, Susan Weber, Todd Ferris, Henry Lowe
2009 AMIA Annual Symposium Proceedings  
A formal evaluation of this algorithm on 1.5 million pharmacy orders showed that the system could accurately assign pharmacy orders in over 96% of cases.  ...  This paper describes the algorithm and discusses some of the causes of failures in mapping to RxNorm.  ...  Accurate, standards-based, representation of medications assures a common understanding of the data, which facilitates retrieval, analysis, and sharing of pharmacy data for CTR.  ... 
pmid:20351858 pmcid:PMC2815471 fatcat:ilgnejl37fhqpm3uvhnuiv63dq

CERC: an interactive content extraction, recognition, and construction tool for clinical and biomedical text

Eva K Lee, Karan Uppal
2020 BMC Medical Informatics and Decision Making  
The performance of the MINTS algorithm is evaluated on a test set consisting of the remaining 32 full-text CRAFT articles and 30 clinical case reports using the ROUGE toolkit.  ...  Automated summarization of scientific literature and patient records is essential for enhancing clinical decision-making and facilitating precision medicine.  ...  and Thomas Adams, Chenman Cheng, Scott Eckhaus, Qixuan Hou, Ayush Kayastha, Chris Kwan, Eunho Kwon, Di Liu, Joe Malecki, Autumn Phillips, and Peijue Zhang, who helped with the initial usage and testing of  ... 
doi:10.1186/s12911-020-01330-8 pmid:33323109 fatcat:neac7vl5fncibnx3kxcktyqmba

Multi-modal Patient Cohort Identification from EEG Report and Signal Data

Travis R Goodwin, Sanda M Harabagiu
2017 AMIA Annual Symposium Proceedings  
This problem can be addressed by providing clinical experts with the ability to automatically retrieve similar EEG signals and EEG reports through a patient cohort retrieval system operating on a vast  ...  Evaluations of the MERCuRY system measured the relevance of the patient cohorts, obtaining MAP scores of 69.87% and a NDCG of 83.21%.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
pmid:28269938 pmcid:PMC5333290 fatcat:6xaqgqwzt5hbhflbbpeswkp2li

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

Chung-Chi Huang, Zhiyong Lu
2015 Briefings in Bioinformatics  
Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community  ...  One effective way to improve the state of the art is through competitions.  ...  Acknowledgement The authors would like to thank Dr. 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

Movement disorders ontology for clinically oriented and clinicians-driven data mining of multi-center cohorts in Parkinson's disease [article]

Deepak K Gupta, Massimo Marano, Raj Aurora, James Boyd, Satya Sahoo
2020 medRxiv   pre-print
The current version of MDO is focused on parkinsonian disorders with 203 concepts modeled in three broad categories of: (1) neurological findings, (2) treatment plans, and (3) instruments used to evaluate  ...  This leads to high level of uncertainty in the prediction of diagnosis and progression for an individual patient on clinical grounds.  ...  Acknowledgement This project was supported in part by the Clinical and Translational Science Collaborative (CTSC) of Cleveland which is funded by the National Institutes of Health (NIH), National Center  ... 
doi:10.1101/2020.11.09.20228577 fatcat:yqnltnwnizfplhhyvhait7lkaq

Is there a need for biomedical CBIR systems in clinical practice? Outcomes from a usability study

Sameer Antani, Zhiyun Xue, L. Rodney Long, Deborah Bennett, Sarah Ward, George R. Thoma, William W. Boonn, Brent J. Liu
2011 Medical Imaging 2011: Advanced PACS-based Imaging Informatics and Therapeutic Applications  
We used the study to not only evaluate the system for software errors and ease of use, but also to explore its "user readiness", and to identify obstacles that hamper practical use of such systems, in  ...  Articles in the literature routinely describe advances in Content Based Image Retrieval (CBIR) and its potential for improving clinical practice, biomedical research and education.  ...  They also illustrate our vision in attempting to unify three crucial topics in medical image segmentation: ground truth collection, automatic image segmentation, and segmentation evaluation.  ... 
doi:10.1117/12.878268 fatcat:bxx3vftkabdbdhbwlafatee2h4

A systematic review of the clinical application of data-driven population segmentation analysis

Shi Yan, Yu Heng Kwan, Chuen Seng Tan, Julian Thumboo, Lian Leng Low
2018 BMC Medical Research Methodology  
The evaluations of segmentation outcome require the interplay of data analytics and subject matter expertise. The optimal framework for segmentation requires further research.  ...  Although widely applied, there is no systematic review on the clinical application of data-driven population segmentation analysis.  ...  Acknowledgements We would like to thank Librarian Dr. Amy Chou at National University of Singapore Medical Library for her advice on the search strategies.  ... 
doi:10.1186/s12874-018-0584-9 fatcat:xno3dsueanamhe6mvogpaw3ueu

Fast and robust extraction of hippocampus from MR images for diagnostics of Alzheimer's disease

Jyrki Lötjönen, Robin Wolz, Juha Koikkalainen, Valtteri Julkunen, Lennart Thurfjell, Roger Lundqvist, Gunhild Waldemar, Hilkka Soininen, Daniel Rueckert
2011 NeuroImage  
The method was evaluated in three cohorts consisting altogether about 1000 cases, the main emphasis being in the analysis of the ADNI cohort.  ...  As hippocampus is known to be among the first areas affected by the disease, fast and robust definition of hippocampus volume would be of great importance in the clinical decision making.  ...  Private sector contributions to ADNI are facilitated by the Foundation for the National Institutes of Health (  ... 
doi:10.1016/j.neuroimage.2011.01.062 pmid:21281717 pmcid:PMC3554788 fatcat:awvkrrpslfdebagqaa5xz7vimm

First-Line A Direct Aspiration First-Pass Technique vs. First-Line Stent Retriever for Acute Ischemic Stroke Therapy: A Meta-Analysis

Kevin Li-Chun Hsieh, Kai-I Chuang, Hsu-Huei Weng, Sho-Jen Cheng, Yu Chiang, Cheng-Yu Chen
2018 Frontiers in Neurology  
A total of 1623 papers were found, and 4 articles were included in our meta-analysis. The Critical Appraisal Skills Programme tools were applied to evaluate the quality of studies.  ...  A direct aspiration first-pass technique (ADAPT) is proposed to be a faster thrombectomy technique than the stent retriever technique.  ...  internal carotid artery to the M2 segment of MCA (17) .  ... 
doi:10.3389/fneur.2018.00801 pmid:30319531 pmcid:PMC6167481 fatcat:hbrplt4ejjar3gn5yqxvutf2ri
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