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A Data-Centric Framework for Composable NLP Workflows [article]

Zhengzhong Liu, Guanxiong Ding, Avinash Bukkittu, Mansi Gupta, Pengzhi Gao, Atif Ahmed, Shikun Zhang, Xin Gao, Swapnil Singhavi, Linwei Li, Wei Wei, Zecong Hu (+6 others)
2021 arXiv   pre-print
., healthcare, finance, education) involve interoperation among multiple components, ranging from data ingestion, human annotation, to text retrieval, analysis, generation, and visualization.  ...  The whole framework is delivered through two modularized yet integratable open-source projects, namely Forte (for workflow infrastructure and NLP function processors) and Stave (for user interaction, visualization  ...  Workflow Example Infrastructure Universal Data Representation Data Representation Markup Management Data APIs Markup Type Enforcement Auto Batching IO and Serialization Training Control  ... 
arXiv:2103.01834v4 fatcat:j2lg2ianx5hjdimm4ag6bj6wma

Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies

Weihong Tay, Erwin Tantoso, Frank Eisenhaber, Wing-Cheong Wong
2019 Journal of Open Source Software  
analysis ready state and finally visualizes the clinical information and processed output in a single access-controlled and audit trailed environment.  ...  Most importantly, this data management system should provide a skeletal open-source software framework for which any appropriate OMICS pipelines and visualizers can be integrated seamlessly in a scaleable  ...  Acknowledgements We acknowledge contributions from Joanne Lee for the testing and documentation of TIMS during the genesis of this project.  ... 
doi:10.21105/joss.01533 fatcat:unjvxrhhkbgsnb4hg3xndwaxym

Towards a translational medical research ecosystem

Matthew Smith, Marian Harbach, Andrew Lewis, Susanne Mertins, Lyn Griffiths
2011 5th IEEE International Conference on Digital Ecosystems and Technologies (IEEE DEST 2011)  
to retain control over it's data and define it's own policies to ensure legal and ethical compliance; a novel interactive access control framework allows users to easily share data while adhering to their  ...  Several key contributions are made: A novel approach to managing ad-hoc research ecosystems is introduced; a new security model for translational research is developed which allows each participating cite  ...  Human Centric Information Management: A further technical aspect of translational information management is data integration.  ... 
doi:10.1109/dest.2011.5936609 fatcat:maf254giozhqnoczfvhbqkfqqu

Semantic, Cognitive, and Perceptual Computing: Paradigms That Shape Human Experience

Amit Sheth, Pramod Anantharam, Cory Henson
2016 Computer  
Unlike machine-centric computing, in which efficient data processing takes precedence over contextual tailoring, human-centric computation provides a personalized data interpretation that most users find  ...  Jones has access to a CC system similar to Watson 16 that is designed for asthma management.  ...  Computation would be carried out on a mobile device, allowing better control of data access, sharing, and privacy.  ... 
doi:10.1109/mc.2016.75 fatcat:teqeuh3yijdwxdcgsyucbieopq

Sharing mHealth Data via Named Data Networking

Haitao Zhang, Zhehao Wang, Christopher Scherb, Claudio Marxer, Jeff Burke, Lixia Zhang, Christian Tschudin
2016 Proceedings of the 2016 conference on 3rd ACM Conference on Information-Centric Networking - ACM-ICN '16  
Its design illustrates that NDN's data-centric approach to networking can be a better fit than current networking approaches for mobile health applications, especially those that foreground individuals  ...  ' control over their own data and, at the same time, target interoperability.  ...  Acknowledgements Many people contributed to NDNFit design discussions; the authors particularly thank Yingdi Yu, Van Jacobson, Alex Afanasyev, and Alex Halderman for their security-related contributions  ... 
doi:10.1145/2984356.2984379 dblp:conf/acmicn/ZhangWSMB0T16 fatcat:kr7qhzjltvbm5ey4l4xjtgroju

Isabl Platform, a digital biobank for processing multimodal patient data

Juan S. Medina-Martínez, Juan E. Arango-Ossa, Max F. Levine, Yangyu Zhou, Gunes Gundem, Andrew L. Kung, Elli Papaemmanuil
2020 BMC Bioinformatics  
Results We present Isabl, a customizable plug-and-play platform for the processing of multimodal patient-centric data.  ...  Conclusions As a digital biobank, Isabl supports continuous data utilization and automated meta analyses at scale, and serves as a catalyst for research innovation, new discoveries, and clinical translation  ...  Heme Malignancies and Department of Pediatrics for input on system design, functionality and system testing.  ... 
doi:10.1186/s12859-020-03879-7 pmid:33256603 fatcat:ehlgcmzqbvgz3cz5jhrij3dv7u

Integrated regional bioengagement framework to combat brucellosis

V Rao
2010 Prilozi  
A systems-centric framework for a national and regional strategy to combat human brucellosis is essential, and should be comprised of: a) a disease threat and surveillance framework at the national and  ...  There is clearly a need for the development of a South Eastern European regional network for sharing information aimed at disease surveillance, early reporting and efficient containment of human brucellosis  ...  Alvin Keith, Vice President, National and Defense Programs, for his commitment to technical excellence and support for this effort.  ... 
pmid:20703192 fatcat:vmyw4azuejbevir7v3dmbqkeke

Cloud Based Big Data Infrastructure: Architectural Components And Automated Provisioning

Yuri Demchenko, Fatih Turkmen, Christophe Blanchet, Charles Loomis, Caees de Laat
2016 Zenodo  
the following components of the Big Data technologies: Big Data definition, Data Management including data lifecycle and data structures, Big Data Infrastructure (generically cloud based), Data Analytics  ...  The paper discusses importance of automation of all stages of the Big Data applications developments, deployment and management and refers to existing cloud automation tools and new developments in the  ...  different stages of their transformation  Data location, search, accessData integrity and identifiability, referral integrity  Data security and data centric access controlData ownership, personally  ... 
doi:10.5281/zenodo.59159 fatcat:yxvau4m65vgkffgwwmy7nwrdmy

Cyberthreats to Hospitals: Panacea, a Toolkit for People-Centric Cybersecurity

2021 Journal of Strategic Innovation and Sustainability  
Healthcare is a rich source of valuable data and its defences are weak.  ...  The purpose of this work is to present a cybersecurity toolkit for connected devices and people.  ...  the visual effectiveness of the different views and for dominating the inherent complexity of the managed data, explicitly supporting the situational awareness phases of perception and comprehension.  ... 
doi:10.33423/jsis.v16i3.4449 fatcat:33dhm7ghprc7jkjxmua3y6trle

The Cancer Biomedical Informatics Grid (caBIGTM): Creating a Platform for Personalized, Molecular Medicine

K. H Buetow
2008 AACR Education book  
Th e caBIG TM infrastructure is a model for the personalized medicine IT infrastructure required throughout biomedicine.  ...  Users can access grid services and data programmatically using locally managed access control policies and using strongly typed data objects in XML format. caGrid infrastructure also provides strong semantic  ...  integrates with radiology PACS systems and visualization tools, 3) caArray, a microarray experiment annotation and data management system, 4) geWorkbench, a desktop application for microarray data analysis  ... 
doi:10.1158/aacr.edb-08-8150 fatcat:5ecxwd4jubh3pafqa4bimdhuwi

Boosting Economic Growth Through Advanced Machine Vision [chapter]

Soha Maad, Samir Garbaya, Nizar Ayadi, Saida Bouakaz
2012 Human-Centric Machine Vision  
PageId=688&LanguageId=0 www.intechopen.com Human-Centric Machine Vision www.intechopen.comHuman-Centric Machine Vision http://www.dceb.ie/networking/sprint-start www.intechopen.com Human-Centric  ...  SCADA stands for Supervisory Control and Data Acquisition. It generally refers to the control system of the industry which is a computer system that controls and monitors a process.  ...  Recently, the algorithms for the processing of the visual information have greatly evolved, providing efficient and effective solutions to cope with the variability and the complexity of real-world environments  ... 
doi:10.5772/34639 fatcat:wdcezcvhkvgonnx5uqfx7645wa

An Approach for Managing Clinical Trial Applications Using Semantic Information Models [chapter]

Hans-Georg Fill, Ilona Reischl
2010 Lecture Notes in Business Information Processing  
In particular, the approach can be used for the generation of user-centric visualizations, performance and compliance analyses and the distribution of the contained knowledge within an organization and  ...  The management of clinical trial applications by public authorities is a complex process involving several regulations, actors, and IT systems.  ...  In this context, a combination of meta modeling and semantic modeling techniques were used for three purposes: a. to create user-centric visualizations for managing the complexity of the processes, b.  ... 
doi:10.1007/978-3-642-12186-9_56 fatcat:sg7skqm35bhczi5ugeb564tq3e

Health Care Virtual Environment System Reinforced by Hadoop and Cloud

Vidyashree S K
2016 International Journal Of Engineering And Computer Science  
This system consists of a data collection layer with a unified standard, a data management layer for distributed storage and parallel computing, and a data-oriented service layer.  ...  To provide a more convenient service and environment of healthcare, this paper proposes a cyber-physical system for patient-centric healthcare applications and services, called Health-CPS, built on cloud  ...  management, deployment management, optimization management, monitoring management, visualization management, and privilege management. 3) Development platform provides a uniform API, data access, and  ... 
doi:10.18535/ijecs/v5i5.06 fatcat:lllvgcegpzgrfjtmskh75kijti

Electronic Health Record Standards - A Brief Overview

M. Eichelberg, T. Aden, J. Riesmeier, A. Dogac, G. B. Laleci
2006 2006 ITI 4th International Conference on Information & Communications Technology  
To address the resulting interoperability problems, several electronic health record (EHR) standards that enable structured clinical content for the purpose of exchange are currently under development.  ...  Most medical information systems store clinical information about patients in proprietary format.  ...  The visualization of reports for a human reader is regarded to be out of scope.  ... 
doi:10.1109/itict.2006.358222 fatcat:bfo6wxvc4rb6pnmkcw7iqsrw2q

PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data

Steven N. Hart, Raymond M. Moore, Michael T. Zimmermann, Gavin R. Oliver, Jan B. Egan, Alan H. Bryce, Jean-Pierre A. Kocher
2015 PeerJ  
PANDA represents 34 data/annotations as icons in the graph while maintaining the other data elements (i.e. other columns for 35 the table of annotations).  ...  Annotation) Explorer, a 31 visualization tool that integrates gene-level annotation in the context of biological pathways to help 32 interpret complex data from disparate sources.  ...  PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data Steven N Hart, Raymond M Moore, Michael T Zimmermann, Gavin R Oliver, Jan B Egan, Alan H Bryce, Jean-Pierre A  ... 
doi:10.7717/peerj.970 pmid:26038725 pmcid:PMC4451017 fatcat:zexukr4wlzejlav3b3edcsjx5i
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