A Learning Health System for Radiation Oncology

The proposed research aims to address the challenges faced by clinical data science researchers in radiation oncology accessing, integrating, and analyzing heterogeneous data from various sources. The research presents a scalable intelligent infrastructure, called the Health Information Gateway and Exchange (HINGE), which captures and structures data from multiple sources into a knowledge base with semantically interlinked entities. This infrastructure enables researchers to mine novel associations and gather relevant knowledge for personalized clinical outcomes. The dissertation discusses the design framework and implementation of HINGE, which abstracts structured data from treatment planning systems, treatment management systems, and electronic health records. It utilizes disease-specific smart templates for capturing clinical information in a discrete manner. HINGE performs data extraction, aggregation, and quality and outcome assessment functions automatically, connecting seamlessly with local IT/medical infrastructure. Furthermore, the research presents a knowledge graph-based approach to map radiotherapy data to an ontology-based data repository using FAIR (Findable, Accessible, Interoperable, Reusable) concepts. This approach ensures that the data is easily discoverable and accessible for clinical decision support systems. The dissertation explores the ETL (Extract, Transform, Load) process, data model frameworks, ontologies, and provides a real-world clinical use case for this data mapping. To improve the efficiency of retrieving information from large clinical datasets, a search engine based on ontology-based keyword searching and synonym-based term matching tool was developed. The hierarchical nature of ontologies is leveraged to retrieve patient records based on parent and children classes. Additionally, patient similarity analysis is conducted using vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) to identify similar patients based on text corpus creation methods. Results from the analysis using these models are presented. The implementation of a learning health system for predicting radiation pneumonitis following stereotactic body radiotherapy is also discussed. 3D convolutional neural networks (CNNs) are utilized with radiographic and dosimetric datasets to predict the likelihood of radiation pneumonitis. DenseNet-121 and ResNet-50 models are employed for this study, along with integrated gradient techniques to identify salient regions within the input 3D image dataset. The predictive performance of the 3D CNN models is evaluated based on clinical outcomes. Overall, the proposed Learning Health System provides a comprehensive solution for capturing, integrating, and analyzing heterogeneous data in a knowledge base. It offers researchers the ability to extract valuable insights and associations from diverse sources, ultimately leading to improved clinical outcomes. This work can serve as a model for implementing LHS in other medical specialties, advancing personalized and data-driven medicine

Research on conceptual modeling: Themes, topics, and introduction to the special issue

Conceptual modeling continues to evolve as researchers and practitioners reflect on the challenges of modeling and implementing data-intensive problems that appear in business and in science. These challenges of data modeling and representation are well-recognized in contemporary applications of big data, ontologies, and semantics, along with traditional efforts associated with methodologies, tools, and theory development. This introduction contains a review of some current research in conceptual modeling and identifies emerging themes. It also introduces the articles that comprise this special issue of papers from the 32nd International Conference on Conceptual Modeling (ER 2013).This article was supported, in part, by the J. Mack Robinson College of Business at the Georgia State University, the Marriott School of Management at Brigham Young University (EB-201313), and by the GEODAS-BI (TIN2012-37493-C03-03) project from the Spanish Ministry of Education and Competitivity

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

Grand Challenges of Traceability: The Next Ten Years

In 2007, the software and systems traceability community met at the first Natural Bridge symposium on the Grand Challenges of Traceability to establish and address research goals for achieving effective, trustworthy, and ubiquitous traceability. Ten years later, in 2017, the community came together to evaluate a decade of progress towards achieving these goals. These proceedings document some of that progress. They include a series of short position papers, representing current work in the community organized across four process axes of traceability practice. The sessions covered topics from Trace Strategizing, Trace Link Creation and Evolution, Trace Link Usage, real-world applications of Traceability, and Traceability Datasets and benchmarks. Two breakout groups focused on the importance of creating and sharing traceability datasets within the research community, and discussed challenges related to the adoption of tracing techniques in industrial practice. Members of the research community are engaged in many active, ongoing, and impactful research projects. Our hope is that ten years from now we will be able to look back at a productive decade of research and claim that we have achieved the overarching Grand Challenge of Traceability, which seeks for traceability to be always present, built into the engineering process, and for it to have "effectively disappeared without a trace". We hope that others will see the potential that traceability has for empowering software and systems engineers to develop higher-quality products at increasing levels of complexity and scale, and that they will join the active community of Software and Systems traceability researchers as we move forward into the next decade of research

User Review Analysis for Requirement Elicitation: Thesis and the framework prototype's source code

Online reviews are an important channel for requirement elicitation. However, requirement engineers face challenges when analysing online user reviews, such as data volumes, technical supports, existing techniques, and legal barriers. Juan Wang proposes a framework solving user review analysis problems for the purpose of requirement elicitation that sets up a channel from downloading user reviews to structured analysis data. The main contributions of her work are: (1) the thesis proposed a framework to solve the user review analysis problem for requirement elicitation; (2) the prototype of this framework proves its feasibility; (3) the experiments prove the effectiveness and efficiency of this framework. This resource here is the latest version of Juan Wang's PhD thesis "User Review Analysis for Requirement Elicitation" and all the source code of the prototype for the framework as the results of her thesis

Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data

Abstract Managing, processing and understanding big healthcare data is challenging, costly and demanding. Without a robust fundamental theory for representation, analysis and inference, a roadmap for uniform handling and analyzing of such complex data remains elusive. In this article, we outline various big data challenges, opportunities, modeling methods and software techniques for blending complex healthcare data, advanced analytic tools, and distributed scientific computing. Using imaging, genetic and healthcare data we provide examples of processing heterogeneous datasets using distributed cloud services, automated and semi-automated classification techniques, and open-science protocols. Despite substantial advances, new innovative technologies need to be developed that enhance, scale and optimize the management and processing of large, complex and heterogeneous data. Stakeholder investments in data acquisition, research and development, computational infrastructure and education will be critical to realize the huge potential of big data, to reap the expected information benefits and to build lasting knowledge assets. Multi-faceted proprietary, open-source, and community developments will be essential to enable broad, reliable, sustainable and efficient data-driven discovery and analytics. Big data will affect every sector of the economy and their hallmark will be ‘team science’.http://deepblue.lib.umich.edu/bitstream/2027.42/134522/1/13742_2016_Article_117.pd