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Distributed Contextualization of Biomedical Data: A Case Study in Precision Medicine

Sirine Sayadi, Estelle Geffard, Mario Sudholt, Nicolas Vince, Pierre-Antoine Gourraud
2020 2020 IEEE/ACS 17th International Conference on Computer Systems and Applications (AICCSA)  
An important aspect of precision medicine consists in patient-centered contextualization analyses that are used as part of biomedical interactive tools.  ...  However, performance and the security and privacy concerns of sharing sensitive biomedical data can become a major issue.  ...  The experiments presented in this paper were carried out using the Grid5000 experimental testbed, see www.grid5000.fr.  ... 
doi:10.1109/aiccsa50499.2020.9316502 fatcat:oowgdwu3rrdfxngax6rfyklhsq

Secure Distribution of Factor Analysis of Mixed Data (FAMD) and Its Application to Personalized Medicine of Transplanted Patients

Sirine Sayadi, Estelle Geffard, Mario Südholt, Nicolas Vince, Pierre-Antoine Gourraud
2021 International Conference on Advanced Information Networking and Applications  
In this paper we motivate the use of distributed implementations for FAMD analyses in the context of the development of a personalised medicine application called KITAPP.  ...  We present a new distribution method for FAMD and evaluate its implementation in a multi-site setting based on real data.  ...  -We present a novel distributed FAMD algorithm for dimension reduction in the presence of sensitive data in precision medicine and apply it to a contextualization problem.  ... 
doi:10.1007/978-3-030-75100-5_44 dblp:conf/aina/SayadiGSVG21 fatcat:ccci3n5xpva73cdmg55kwgcwya

Including Vulnerable Populations in the Assessment of Data From Vulnerable Populations

Latifa Jackson, Caitlin Kuhlman, Fatimah Jackson, P. Keolu Fox
2019 Frontiers in Big Data  
Here we present three case studies: (1) Describing a novel genomic dataset being developed with clinical and ethnographic insights in African Americans, (2) Demonstrating how a tutorial that enables data  ...  Data science has made great strides in harnessing the power of big data to improve human life across a broad spectrum of disciplines.  ...  and as a platform for broadly beneficial precision medicine.  ... 
doi:10.3389/fdata.2019.00019 pmid:33693342 pmcid:PMC7931941 fatcat:oljphmaqerd5xkb2vns5vc2qpa

Precision Medicine and Big Data

G. Owen Schaefer, E Shyong Tai, Shirley Sun
2019 Asian Bioethics Review  
the Ethical Framework for Big Data in Health and Research (Xafis et al. 2019) to a case study on clinical genomic data sharing.  ...  Our discussion is meant to be of use to those involved in the practice as well as governance and oversight of precision medicine to address ethical concerns that arise in a coherent and systematic manner  ...  For discussion of broader implications of depositing biomedical data in repositories, see the case study at the end of ; for discussion of issues in sharing real-world data with for-profit entities, see  ... 
doi:10.1007/s41649-019-00094-2 pmid:33717316 pmcid:PMC7747352 fatcat:rgp4zwamg5ha3dfywoqsoljqme

HARNESSING BIG DATA FOR PRECISION MEDICINE: INFRASTRUCTURES AND APPLICATIONS

KUN-HSING YU, STEVEN N. HART, RACHEL GOLDFEDER, QIANGFENG CLIFF ZHANG, STEPHEN C. J. PARKER, MICHAEL SNYDER
2016 Biocomputing 2017  
Acknowledgments Her primary areas of research include infrastructure and standards to enable research collaboration and integrative data analysis; informatics to enable precision medicine; and ethical,  ...  Tenenbaum worked as a program manager at Microsoft Corporation in Redmond, WA for six years before pursuing a PhD in biomedical informatics at Stanford University.  ...  With the growing number and size of biomedical datasets worldwide, we envision that approaches discussed in this workshop will facilitate the development of precision medicine.  ... 
doi:10.1142/9789813207813_0058 pmid:27897013 fatcat:y3dbcwj5ire6dhblwd5oaniozy

Privacy, Data Mining, and Digital Profiling in Online Patient Narratives

Kirsten Ostherr
2018 Catalyst Feminism Theory Technoscience  
Yet, precisely because of their public nature, these patient stories are unprotected sources of data that are barred from integration into health care data ecologies where clinical action takes place.  ...  This article compares patient-driven illness narratives and clinic-driven illness narratives to uncover a set of unrecognized assumptions about trust and privacy in health discourses.  ...  Without the contextual richness found in these stories, the explanatory power of biomedical data is greatly diminished.  ... 
doi:10.28968/cftt.v4i1.29628 fatcat:ul2vlfu6prgkbhgw3itwlma7jm

Will Big Data and personalized medicine do the gender dimension justice?

Antonio Carnevale, Emanuela A. Tangari, Andrea Iannone, Elena Sartini
2021 AI & Society: The Journal of Human-Centred Systems and Machine Intelligence  
The first two sections of the paper provide a definition of "Big Data" and illustrate the uses of Big Data in medicine.  ...  in personalized medicine.  ...  Therefore, if on the one hand case-by-case is good for clinically contextualizing precision medicine, on the other hand, the universality of the fight against certain forms of injustice should never cease  ... 
doi:10.1007/s00146-021-01234-9 pmid:34092931 pmcid:PMC8169394 fatcat:tcnraffzlbflneo6belbvb5ofm

Data Science in Biomedicine [article]

Yovaninna Alarcón-Soto, Jenifer Espasandín-Domínguez, Ipek Guler, Mercedes Conde-Amboage, Francisco Gude-Sampedro, Klaus Langohr, Carmen Cadarso-Suárez, Guadalupe Gómez-Melis
2019 arXiv   pre-print
Biomedical Data Science (BDS) presents the challenge of dealing with data coming from a range of biological and medical research, focusing on methodologies to advance the biomedical science discoveries  ...  We highlight the role of Data Science in Biomedicine.  ...  Work of M. Conde-Amboage has been supported by post-doctoral grant from Ministry of Culture, Education and University Planning and Ministry of Economy, Employment and Industry of Galician Government.  ... 
arXiv:1909.04486v1 fatcat:kv7iisak6zdt5krczjbsnzx3ai

My Data, My Choice? - German Patient Organizations' Attitudes towards Big Data-Driven Approaches in Personalized Medicine. An Empirical-Ethical Study

Carolin Martina Rauter, Sabine Wöhlke, Silke Schicktanz
2021 Journal of medical systems  
in terms of data accuracy ('veracity') to facilitate the generation and analyzation of messy data sets within a short and highly efficient time period ('velocity') to provide insights into previously  ...  Personalized medicine (PM) operates with biological data to optimize therapy or prevention and to achieve cost reduction.  ...  The funding body had no influence on the design of the study, the collection, analysis, and interpretation of data, and on writing the manuscript. We would like to thank Dr.  ... 
doi:10.1007/s10916-020-01702-7 pmid:33616768 fatcat:2cos3icf6bcrbe34lvgxfojoky

Enhancing Clinical Data and Clinical Research Data with Biomedical Ontologies - Insights from the Knowledge Representation Perspective

Jonathan P. Bona, Fred W. Prior, Meredith N. Zozus, Mathias Brochhausen
2019 IMIA Yearbook of Medical Informatics  
Our aim is to clarify the representational differences between traditional data management and semantic-web-based data management by providing use cases of clinical data and clinical research data re-representation  ...  Objectives: There exists a communication gap between the biomedical informatics community on one side and the computer science/artificial intelligence community on the other side regarding the meaning  ...  Nolan assisted with data retrieval and data interpretation in the PRISM research presented in this paper. The authors thank the editors and external reviewers for their valuable input.  ... 
doi:10.1055/s-0039-1677912 pmid:31419826 pmcid:PMC6697506 fatcat:o5pk74rqebhsfhhmt5aems2z2q

Mixed Methods for the Interpretation of Longitudinal Gerontologic Data

Peter H. Van Ness, Terri R. Fried, Thomas M. Gill
2011 Journal of Mixed Methods Research  
study of changes in functional disability over time embedded in the Precipitating Events Project-a major longitudinal, quantitative study of functional disability among older persons.  ...  The importance of interpretation becomes especially evident when qualitative and quantitative methods are combined in a single clinical research project and when the data being analyzed are longitudinal  ...  Gill is the recipient of a Midcareer Investigator Award in Patient-Oriented Research (K24AG021507) from the National Institute on Aging. Dr.  ... 
doi:10.1177/1558689811412973 pmid:22582035 pmcid:PMC3347468 fatcat:hsnf556o25gw7agzwtjfvdkdo4

Long-term preservation of biomedical research data

Vivek Navale, Matthew McAuliffe
2018 F1000Research  
We believe that involvement of data stewards early in the digital data life-cycle management process can significantly contribute towards long term preservation of biomedical data.  ...  In this opinion article, we discuss specific actions that researchers and institutions can take to make research data a continued resource even after research projects have reached the end of their lifecycle  ...  This is a timely scientific undertaking and stands as an important, original contribution to the body of research on data preservation in the context of big data, biomedical research, and data management  ... 
doi:10.12688/f1000research.16015.1 fatcat:masj3htmw5ginkkbsa53sps7pm

Easing the Questioning of Semantic Biomedical Data

Arnaldo Pereira, Rui Pedro Lopes, Jose Luis Oliveira
2021 2021 IEEE 34th International Symposium on Computer-Based Medical Systems (CBMS)  
In particular, the questioning of biomedical data presents specific challenges for which there are still no mature proposals for production environments.  ...  Semantic technologies offer the ability to describe data and to map and linking distributed repositories, creating a network where the searching interface is a single entry point.  ...  In the case of biomedical sciences, we find that the wide variety of repositories responds to concrete needs.  ... 
doi:10.1109/cbms52027.2021.00044 fatcat:xmj7lugmwrc5hjdvkbsmebrqlu

An Effective Approach to Biomedical Information Extraction with Limited Training Data [article]

Siddhartha Jonnalagadda
2011 arXiv   pre-print
Overall, the two main contributions of this work include the application of sentence simplification to association extraction as described above, and the use of distributional semantics for concept extraction  ...  This approach renders all the advantages offered in other semi-supervised machine learning systems, and, unlike other proposed semi-supervised approaches, it can be used on top of different basic frameworks  ...  and precision in all cases.  ... 
arXiv:1107.5752v2 fatcat:n7rtfgpvarh7do2xar6opjec5q

Differentiating Sense through Semantic Interaction Data

T Elizabeth Workman, Charlene Weir, Thomas C Rindflesch
2017 AMIA Annual Symposium Proceedings  
We explore the use of interaction frequency data between semantic elements as a means to differentiate concept pairs, using semantic predications extracted from the biomedical literature.  ...  We conclude with a discussion on how these findings may be applied to natural language processing of clinical text.  ...  National Library of Medicine, National Institutes of Health.  ... 
pmid:28269921 pmcid:PMC5333208 fatcat:rqvxa5hemzfhvi5woxuemt7q7a
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