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Proposal of an integrated decision support system for Tuberculosis based on Semantic Web

Procedia computer Science 2019年 164卷 552-558页

作者： Vinícius Lima Felipe Pellison Filipe Bernardi Isabelle Carvalho Rui Rijo Domingos Alves Bioengineering Postgraduate Program University of Sao Paulo Sao Carlos Brazil Institute of Mathematical and Computer Sciences University of Sao Paulo Sao Carlos Brazil School of Technology and Management Polytechnic Institute of Leiria Leiria Portugal Centre for Research in Health Technologies and Information Systems (CINTESIS) University of Porto Porto Portugal Institute for Systems and Computers Engineering at Coimbra (INESCC) Coimbra Portugal Ribeirão Preto Medical School University of Sao Paulo Ribeirao Preto Brazil

Epidemiological surveillance of Tuberculosis (TB) requires a strong integration of different health services, programs and levels of care. The deepening and broadening of data management techniques must be constantly carried out to increase the integrality of healthcare. Otherwise, knowledge extraction and clinical and administrative decision-making processes are significantly hampered, directly affecting the management and quality of health services. Thus, this work aims to establish a computerized decision support system capable of collecting, integrating and sharing TB health data in Brazilian Unified Public Health System. Also, it will allow the monitoring of infected patients and the visualization of consolidated information of regular TB and its resistant variants for health professionals and managers. The data will be made available from heterogeneous, disconnected and unstructured sources by combining traditional web services, Semantic Web resources and security algorithms. A solid knowledge base applied to epidemiological surveillance, health information governance and clinical support will be enabled to integrate the multiple areas of TB patients care, as well as to support the creation of more accurate operational and diagnostics models.

关键词： Tuberculosis Decision Support System Health Information System Health Information Management Semantic Web

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Revised JNLPBA corpus: A revised version of biomedical NER corpus for relation extraction task

arXiv

引用

arXiv 2019年

作者： Huang, Ming-Siang Lai, Po-Ting Tsai, Richard Tzong-Han Hsu, Wen-Lian Bioinformatics Program Taiwan International Graduate Program Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang Ming University Taipei Taiwan Department of Computer Science National Tsing-Hua University Hsinchu Taiwan Intelligent Agent Systems Laboratory Institute of Information Science Academia Sinica Taipei Taiwan Intelligent Information Service Research Laboratory Department of Computer Science and Information Engineering National Central University Taoyuan Taiwan

The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to identify the mentioned NEs in plain texts for further relation extraction stage. However, the current BNER corpora, which play important roles in these tasks, paid less attention to achieve the criteria for BRE task. In this study, we present Revised JNLPBA corpus, the revision of JNLPBA corpus, to broaden the applicability of a NER corpus from BNER to BRE task. We preserve the original entity types including protein, DNA, RNA, cell line and cell type while all the abstracts in JNLPBA corpus are manually curated by domain experts again basis on the new annotation guideline focusing on the specific NEs instead of general terms. Simultaneously, several imperfection issues in JNLPBA are pointed out and made up in the new corpus. To compare the adaptability of different NER systems in Revised JNLPBA and JNLPBA corpora, the F1-measure was measured in three open sources NER systems including BANNER, Gimli and NERSuite. In the same circumstance, all the systems perform average 10% better in Revised JNLPBA than in JNLPBA. Moreover, the cross-validation test is carried out which we train the NER systems on JNLPBA/Revised JNLPBA corpora and access the performance in both protein-protein interaction extraction (PPIE) and biomedical event extraction (BEE) corpora to confirm that the newly refined Revised JNLPBA is a competent NER corpus in biomedical relation application. The revised JNLPBA corpus is freely available at ***/BNER/Content/Revised_***. Copyright © 2019, The Authors. All rights reserved.

关键词： Proteins

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Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes (vol 12, pg 631, 2020)

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GENETICS IN MEDICINE 2020年第8期22卷 1427-1427页

作者： Chang, Willie H. Mashouri, Pouria Lozano, Alexander X. Johnstone, Brittney Husic, Mia Olry, Annie Maiella, Sylvie Balci, Tugce B. Sawyer, Sarah L. Robinson, Peter N. Rath, Ana Brudno, Michael Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada Department of Computer Science Princeton University Princeton NJ USA Faculty of Medicine University of Toronto Toronto ON Canada Department of Materials Science & Engineering Stanford University Stanford CA USA Sunnybrook Health Sciences Centre Toronto ON Canada Orphanet Institut national de la santé et de la recherche médicale Paris France Medical Genetics Program of Southwestern Ontario London Health Sciences Centre London ON Canada Department of Genetics Children’s Hospital of Eastern Ontario and Children’s Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada The Jackson Laboratory for Genomic Medicine Farmington CT USA Institute for Systems Genomics University of Connecticut Farmington CT USA Department of Computer Science University of Toronto Toronto ON Canada Genetics and Genome Biology Program The Hospital for Sick Children Toronto ON Canada University Health Network Toronto ON Canada

PurposeComputational documentation of genetic disorders is highly reliant on structured data for differential diagnosis, pathogenic variant identification, and patient matchmaking. However, most information on rare diseases (RDs) exists in freeform text, such as academic literature. To increase availability of structured RD data, we developed a crowdsourcing approach for collecting phenotype information using student *** developed Phenotate, a web application for crowdsourcing disease phenotype annotations through assignments for undergraduate genetics students. Using student-collected data, we generated composite annotations for each disease through a machine learning approach. These annotations were compared with those from clinical practitioners and gold standard curated *** Phenotate in five undergraduate genetics courses, we collected annotations for 22 diseases. Student-sourced annotations showed strong similarity to gold standards, with F-measures ranging from 0.584 to 0.868. Furthermore, clinicians used Phenotate annotations to identify diseases with comparable accuracy to other annotation sources and gold standards. For six disorders, no gold standards were available, allowing us to create some of the first structured annotations for them, while students demonstrated ability to research *** enables crowdsourcing RD phenotypic annotations through educational assignments. Presented as an intuitive web-based tool, it offers pedagogical benefits and augments the computable RD knowledgebase.

关键词： rare diseases phenotype crowdsourcing medical education machine learning

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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Odyssey process reuse: A component-based software process line approach 20

Odyssey process reuse: A component-based software process li...

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20th International Conference on Enterprise Information systems, ICEIS 2018

作者： Teixeira, Eldânae Nogueira Vasconcelos, Aline Werner, Cláudia Systems Engineering and Computer Science Program COPPE/UFRJ ZIP Code: 21945-970 P.O. Box 68511 Rio de Janeiro RJ Brazil Federal Fluminense Institute of Education Science and Technology Campos dos Goytacazes Goytacazes RJ Brazil

ISBN: (纸本)9789897582981

It is expected that managing process variations and organizing process domain knowledge in a reusable way can provide support to handle complexity in software process definition. In this context, the purpose of this paper is to describe a systematic software process reuse methodology, by combining process reuse techniques, such as Software Process Line and Component Based Process Definition, aiming to increase reuse possibilities. SPrL approach manages the variability aspect inherent to software process domain and CBPD focuses on modularizing the domain process information into process components. The proposed SPrL modelling metamodel and notation address reusable process elements, explicitly representing the variability concept in both process domain structure and behaviour. Based on the results of the evaluation studies, it was possible to get evidences of the approach feasibility, with a higher expressiveness when using the process variability notation proposed, which allow that more semantic concepts inherent to SPrL scenarios can be graphically described. Also, the set of heuristics to support mappings among artefacts in distinct abstraction levels was considered useful to keep the traceability of variability properties, relationships and restrictions. Further research is being conducted to explore ways to support project managers during the decision-making in new software process definitions. © 2018 by SCITEPRESS - Science and Technology Publications, Lda.

关键词： Decision making

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Implementation of Mobile game for Religion Learning

Implementation of Mobile game for Religion Learning

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IEEE International Conference on Teaching, Assessment and Learning for engineering (TALE)

作者： Edy Sulistiyo Vindy Nizirwan Anwar Diana Teresia Spits Warnars Setya Chendra Wibawa Goenawan Brotosaputro Dedy Prasetya Kristiadi Harco Leslie Hendric Spits Warnars Kiyota Hashimoto Electrical Engineering Department Universitas Negeri Surabaya Jawa Timur Indonesia Game Application & Technology Program School of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Computer Science Esa Unggul University Jakarta Indonesia Information Systems Department Bina Nusantara University Jakarta Indonesia Informatics Department Universitas Negeri Surabaya Jawa Timur Indonesia Information System Department Universitas Budi Luhur Jakarta Indonesia Computer Science department Raharja University Tangerang Indonesia Computer Science Department BINUS Graduate Program – Doctor of Computer Science Bina Nusantara University Jakarta Indonesia Faculty of Technology and Environment Prince Songkla University Phuket Campus Thailand

ISBN: (数字)9781728126654

ISBN: (纸本)9781728126661

Currently, the growth of information and technology is rapid. It makes a lot of things in various fields including education becoming more effective and efficient. In education, one of its implementation which is a game is proven to be a useful tool to support conventional teaching methods and bring a more natural understanding of learning materials. Moreover, as a product of the popular culture in modern society, video game mirrors the general culture practice in real life and reflects it via its own culture inside the game. This makes a video game can give a contribution to the social construction of reality as it affects the player's view towards learning in real life and vice versa. From there, we see that there is an opportunity for learning about religion to be supported by its utilization to provide an interactive and fun learning experience. In this paper, we discuss how a video game is implemented to support religious learning. The game was developed with the scrum method where we surveyed to gather the user requirements before the design step. The game design was made by using the use case diagram and storyboard, and it was built using Unity version 2017.3.0f3.

关键词： Games Land mobile radio Education computer science Operating systems Information systems Media

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A single-phase distributed generation system with load power compensation capability using linear quadratic regulator 13

A single-phase distributed generation system with load power...

引用

13th IEEE International Conference on Industry Applications, INDUSCON 2018

作者： Fogli, Gabriel A. De Fernandes, Marcelo C. De Faria, Jose A. T. Barbosa, Pedro G. De Almeida, Pedro M. Department of Electrical Engineering Federal University of Ouro Preto João Monlevade MG Brazil Power Electronics and Automation Group Electrical Engineering Program Federal University of Juiz de Fora MG Brazil Department of Electrical Computer and Systems Engineering Rensselaer Polytechnic Institute TroyNY United States Flextronics Institute of Technology Sorocaba SP Brazil

ISBN: (纸本)9781538679951

This paper presents design steps of a distributed generation system with load power compensation. A single-phase full-bridge converter is used to connect the alternative source to the mains. Besides injecting active power, the distributed generation also provides load power compensation capability. In this context, a current reference strategy based on single-phase circuit theory is proposed for grid-connected multi-task converters. The main idea is to synthesize the signal reference for control loop generating orthogonal signals from grid voltage and current load. A Third Order Sinusoidal Integrator is used to extract fundamental component and generate the orthogonal waveforms of grid voltage and load current. Current controller loop for interface converter is developed based on Linear Quadratic Regulator theory. Simulation results are presented to verify the system behavior. © 2018 IEEE.

关键词： Distributed power generation

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Building a quantum engineering undergraduate program

arXiv

引用

arXiv 2021年

作者： Asfaw, Abraham Blais, Alexandre Brown, Kenneth R. Candelaria, Jonathan Cantwell, Christopher Carr, Lincoln D. Combes, Joshua Debroy, Dripto M. Donohue, John M. Economou, Sophia E. Edwards, Emily Fox, Michael F.J. Girvin, Steven M. Ho, Alan Hurst, Hilary M. Jacob, Zubin Johnson, Blake R. Johnston-Halperin, Ezekiel Joynt, Robert Kapit, Eliot Klein-Seetharaman, Judith Laforest, Martin Lewandowski, H.J. Lynn, Theresa W. McRae, Corey Rae H. Merzbacher, Celia Michalakis, Spyridon Narang, Prineha Oliver, William D. Palsberg, Jens Pappas, David P. Raymer, Michael G. Reilly, David J. Saffman, Mark Searles, Thomas A. Shapiro, Jeffrey H. Singh, Chandralekha IBM Quantum IBM T. J. Watson Research Center Yorktown HeightsNY United States Institut Quantique Département de Physique Université de Sherbrooke SherbrookeQCJ1K 2R1 Canada Canadian Institute for Advanced Research TorontoONM5G 1M1 Canada The Duke Quantum Center Department of Physics Department of Electrical and Computer Engineering Department of Chemistry Duke University DurhamNC27708 United States SystemX Program Department of Electrical Engineering Stanford University StanfordCA94305 United States Department of Physics and Astronomy University of Southern California Los AngelesCA90089 United States The Quantum Engineering Program Department of Physics Colorado School of Mines GoldenCO80401 United States The Department of Electrical Computer and Energy Engineering University of Colorado Boulder BoulderCO80309 United States The Institute for Quantum Computing University of Waterloo WaterlooONN2L 3G1 Canada The Department of Physics Virginia Tech BlacksburgVA24061 United States The IQUIST University of Illinois Urbana-Champaign UrbanaIL61801 United States JILA National Institute of Standards and Technology The University of Colorado BoulderCO80309 United States Department of Physics University of Colorado Boulder BoulderCO80309 United States The Department of Physics Imperial College London Prince Consort Road LondonSW7 2AZ United Kingdom The Yale Quantum Institute Department of Physics Yale University New HavenCT06520 United States Google Research VeniceCA90291 United States The Department of Physics & Astronomy San José State University San JoséCA95192 United States The School of Electrical and Computer Engineering Purdue University Indiana West Lafayatte47907 United States The Department of Physics The Ohio State University ColumbusOH43210 United States The Department of Physics University of Wisconsin-Madison 1150 University Avenue MadisonWI53706 United States The Quantitative Biosciences and Engineering

The rapidly growing quantum information science and engineering (QISE) industry will require both quantum-aware and quantum-proficient engineers at the bachelor's level. We provide a roadmap for building a quantum engineering education program to satisfy this need. For quantum-aware engineers, we describe how to design a first quantum engineering course accessible to all STEM students. For the education and training of quantum-proficient engineers, we detail both a quantum engineering minor accessible to all STEM majors, and a quantum track directly integrated into individual engineering majors. We propose that such programs typically require only three or four newly developed courses that complement existing engineering and science classes available on most larger campuses. We describe a conceptual quantum information science course for implementation at any post-secondary institution, including community colleges and military schools. QISE presents extraordinary opportunities to work towards rectifying issues of inclusivity and equity that continue to be pervasive within engineering. We present a plan to do so and describe how quantum engineering education presents an excellent set of education research opportunities. Finally, we outline a hands-on training plan on quantum hardware, a key component of any quantum engineering program, with a variety of technologies including optics, atoms and ions, cryogenic and solid-state technologies, nanofabrication, and control and readout electronics. Our recommendations provide a flexible framework that can be tailored for academic institutions ranging from teaching and undergraduate-focused two- and four-year colleges to research-intensive universities. © 2021, CC BY.

关键词： engineering education

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Unifying femtosecond and picosecond single-pulse magnetic switching in GdFeCo

arXiv

引用

arXiv 2020年

作者： Jakobs, F. Ostler, T.A. Lambert, C.-H. Yang, Y. Salahuddin, S. Wilson, R.B. Gorchon, J. Bokor, J. Atxitia, U. Dahlem Center for Complex Quantum Systems and Fachbereich Physik Freie Universität Berlin Berlin14195 Germany LiégeB-4000 Belgium College of Business Technology and Engineering Sheffield Hallam University Howard Street SheffieldS1 1WB United Kingdom Department of Electrical Engineering and Computer Sciences University of California BerkeleyCA94720 United States Department of Materials Science and Engineering University of California BerkeleyCA94720 United States Lawrence Berkeley National Laboratory 1 Cyclotron Road BerkeleyCA94720 United States Department of Mechanical Engineering and Materials Science and Engineering Program University of California RiversideCA92521 United States ETH Zurich Hönggerbergring 64 Zürich8093 Switzerland Portland Technology Development Department Intel Corp. HillsboroOR97006 United States Universite de Lorraine CNRS IJL NancyF-54000 France

Many questions are still open regarding the physical mechanisms behind the magnetic switching in GdFeCo alloys by single optical pulses. Phenomenological models suggest a femtosecond scale exchange relaxation between sublattice magnetization as the driving mechanism for switching. The recent observation of thermally induced switching in GdFeCo by using both several picosecond optical laser pulse as well as electric current pulses has questioned this previous understanding. This has raised the question of whether or not the same switching mechanics are acting at the femoand picosecond scales. In this work, we aim at filling this gap in the understanding of the switching mechanisms behind thermal single-pulse switching. To that end, we have studied experimentally thermal single-pulse switching in GdFeCo alloys, for a wide range of system parameters, such as composition, laser power and pulse duration. We provide a quantitative description of the switching dynamics using atomistic spin dynamics methods with excellent agreement between the model and our experiments across a wide range of parameters and timescales, ranging from femtoseconds to picoseconds. Furthermore, we find distinct element-specific damping parameters as a key ingredient for switching with long picosecond pulses and argue, that switching with pulse durations as long as 15 picoseconds is possible due to a low damping constant of Gd. Our findings can be easily extended to speed up dynamics in other contexts where ferrimagnetic GdFeCo alloys have been already demonstrated to show fast and energy-efficient processes, e.g. domain-wall motion in a track and spin-orbit torque switching in spintronics devices. Copyright © 2020, The Authors. All rights reserved.

关键词： Ternary alloys

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On Stability of Event-Triggered systems With Sliding Mode Control

On Stability of Event-Triggered Systems With Sliding Mode Co...

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International Workshop on Variable Structure systems, VSS

作者： Abhisek K. Behera Bijnan Bandyopadhyay Department of Electrical and Computer Engineering Seoul National University Seoul South Korea Interdisciplinary Program in Systems and Control Engineering Indian Institute of Technology Bombay Mumbai India

In this paper, we investigate the stability of a controlled system in the event-triggering framework. By designing the triggering scheme, the control signals are updated when it is demanded subject to some satisfactory system performance. However, the stability of the system is not yet fully investigated with respect to the triggering conditions. So, the main purpose of the paper is to analyse the stability of the system with respect to the proposed triggering scheme. In this paper, sliding mode control (SMC) is used to design the event-triggered control. Our analysis proposes a new notion called bounded event property for the event which guarantees the triggering instants are generated in finite-time for all possible values of the triggering parameter. It is shown that the event-triggered SMC ensures possess the bounded event property and moreover the proposed triggering mechanism also guarantees the stability of the closed loop system stability.

关键词： Stability analysis Trajectory Closed loop systems Manifolds Steady-state Sliding mode control System performance

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