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

Updated version of final design and of the architecture of SEAMLESS-IF

Agricultural and Food Policy, Environmental Economics and Policy, Farm Management, Land Economics/Use, Livestock Production/Industries,

Improving National and Homeland Security through a proposed Laboratory for Information Globalization and Harmonization Technologies (LIGHT)

A recent National Research Council study found that: "Although there are many private and public databases that contain information potentially relevant to counter terrorism programs, they lack the necessary context definitions (i.e., metadata) and access tools to enable interoperation with other databases and the extraction of meaningful and timely information" [NRC02, p.304, emphasis added] That sentence succinctly describes the objectives of this project. Improved access and use of information are essential to better identify and anticipate threats, protect against and respond to threats, and enhance national and homeland security (NHS), as well as other national priority areas, such as Economic Prosperity and a Vibrant Civil Society (ECS) and Advances in Science and Engineering (ASE). This project focuses on the creation and contributions of a Laboratory for Information Globalization and Harmonization Technologies (LIGHT) with two interrelated goals: (1) Theory and Technologies: To research, design, develop, test, and implement theory and technologies for improving the reliability, quality, and responsiveness of automated mechanisms for reasoning and resolving semantic differences that hinder the rapid and effective integration (int) of systems and data (dmc) across multiple autonomous sources, and the use of that information by public and private agencies involved in national and homeland security and the other national priority areas involving complex and interdependent social systems (soc). This work builds on our research on the COntext INterchange (COIN) project, which focused on the integration of diverse distributed heterogeneous information sources using ontologies, databases, context mediation algorithms, and wrapper technologies to overcome information representational conflicts. The COIN approach makes it substantially easier and more transparent for individual receivers (e.g., applications, users) to access and exploit distributed sources. Receivers specify their desired context to reduce ambiguities in the interpretation of information coming from heterogeneous sources. This approach significantly reduces the overhead involved in the integration of multiple sources, improves data quality, increases the speed of integration, and simplifies maintenance in an environment of changing source and receiver context - which will lead to an effective and novel distributed information grid infrastructure. This research also builds on our Global System for Sustainable Development (GSSD), an Internet platform for information generation, provision, and integration of multiple domains, regions, languages, and epistemologies relevant to international relations and national security. (2) National Priority Studies: To experiment with and test the developed theory and technologies on practical problems of data integration in national priority areas. Particular focus will be on national and homeland security, including data sources about conflict and war, modes of instability and threat, international and regional demographic, economic, and military statistics, money flows, and contextualizing terrorism defense and response. Although LIGHT will leverage the results of our successful prior research projects, this will be the first research effort to simultaneously and effectively address ontological and temporal information conflicts as well as dramatically enhance information quality. Addressing problems of national priorities in such rapidly changing complex environments requires extraction of observations from disparate sources, using different interpretations, at different points in times, for different purposes, with different biases, and for a wide range of different uses and users. This research will focus on integrating information both over individual domains and across multiple domains. Another innovation is the concept and implementation of Collaborative Domain Spaces (CDS), within which applications in a common domain can share, analyze, modify, and develop information. Applications also can span multiple domains via Linked CDSs. The PIs have considerable experience with these research areas and the organization and management of such large scale international and diverse research projects. The PIs come from three different Schools at MIT: Management, Engineering, and Humanities, Arts & Social Sciences. The faculty and graduate students come from about a dozen nationalities and diverse ethnic, racial, and religious backgrounds. The currently identified external collaborators come from over 20 different organizations and many different countries, industrial as well as developing. Specific efforts are proposed to engage even more women, underrepresented minorities, and persons with disabilities. The anticipated results apply to any complex domain that relies on heterogeneous distributed data to address and resolve compelling problems. This initiative is supported by international collaborators from (a) scientific and research institutions, (b) business and industry, and (c) national and international agencies. Research products include: a System for Harmonized Information Processing (SHIP), a software platform, and diverse applications in research and education which are anticipated to significantly impact the way complex organizations, and society in general, understand and manage critical challenges in NHS, ECS, and ASE

Improving National and Homeland Security through a proposed Laboratory for nformation Globalization and Harmonization Technologies (LIGHT)

A recent National Research Council study found that: "Although there are many private and public databases that contain information potentially relevant to counter terrorism programs, they lack the necessary context definitions (i.e., metadata) and access tools to enable interoperation with other databases and the extraction of meaningful and timely information" [NRC02, p.304, emphasis added] That sentence succinctly describes the objectives of this project. Improved access and use of information are essential to better identify and anticipate threats, protect against and respond to threats, and enhance national and homeland security (NHS), as well as other national priority areas, such as Economic Prosperity and a Vibrant Civil Society (ECS) and Advances in Science and Engineering (ASE). This project focuses on the creation and contributions of a Laboratory for Information Globalization and Harmonization Technologies (LIGHT) with two interrelated goals: (1) Theory and Technologies: To research, design, develop, test, and implement theory and technologies for improving the reliability, quality, and responsiveness of automated mechanisms for reasoning and resolving semantic differences that hinder the rapid and effective integration (int) of systems and data (dmc) across multiple autonomous sources, and the use of that information by public and private agencies involved in national and homeland security and the other national priority areas involving complex and interdependent social systems (soc). This work builds on our research on the COntext INterchange (COIN) project, which focused on the integration of diverse distributed heterogeneous information sources using ontologies, databases, context mediation algorithms, and wrapper technologies to overcome information representational conflicts. The COIN approach makes it substantially easier and more transparent for individual receivers (e.g., applications, users) to access and exploit distributed sources. Receivers specify their desired context to reduce ambiguities in the interpretation of information coming from heterogeneous sources. This approach significantly reduces the overhead involved in the integration of multiple sources, improves data quality, increases the speed of integration, and simplifies maintenance in an environment of changing source and receiver context - which will lead to an effective and novel distributed information grid infrastructure. This research also builds on our Global System for Sustainable Development (GSSD), an Internet platform for information generation, provision, and integration of multiple domains, regions, languages, and epistemologies relevant to international relations and national security. (2) National Priority Studies: To experiment with and test the developed theory and technologies on practical problems of data integration in national priority areas. Particular focus will be on national and homeland security, including data sources about conflict and war, modes of instability and threat, international and regional demographic, economic, and military statistics, money flows, and contextualizing terrorism defense and response. Although LIGHT will leverage the results of our successful prior research projects, this will be the first research effort to simultaneously and effectively address ontological and temporal information conflicts as well as dramatically enhance information quality. Addressing problems of national priorities in such rapidly changing complex environments requires extraction of observations from disparate sources, using different interpretations, at different points in times, for different purposes, with different biases, and for a wide range of different uses and users. This research will focus on integrating information both over individual domains and across multiple domains. Another innovation is the concept and implementation of Collaborative Domain Spaces (CDS), within which applications in a common domain can share, analyze, modify, and develop information. Applications also can span multiple domains via Linked CDSs. The PIs have considerable experience with these research areas and the organization and management of such large scale international and diverse research projects. The PIs come from three different Schools at MIT: Management, Engineering, and Humanities, Arts & Social Sciences. The faculty and graduate students come from about a dozen nationalities and diverse ethnic, racial, and religious backgrounds. The currently identified external collaborators come from over 20 different organizations and many different countries, industrial as well as developing. Specific efforts are proposed to engage even more women, underrepresented minorities, and persons with disabilities. The anticipated results apply to any complex domain that relies on heterogeneous distributed data to address and resolve compelling problems. This initiative is supported by international collaborators from (a) scientific and research institutions, (b) business and industry, and (c) national and international agencies. Research products include: a System for Harmonized Information Processing (SHIP), a software platform, and diverse applications in research and education which are anticipated to significantly impact the way complex organizations, and society in general, understand and manage critical challenges in NHS, ECS, and ASE

Big Data Coordination Platform: Full Proposal 2017-2022

This proposal for a Big Data and ICT Platform therefore focuses on enhancing CGIAR and partner capacity to deliver big data management, analytics and ICT-focused solutions to CGIAR target geographies and communities. The ultimate goal of the platform is to harness the capabilities of Big Data to accelerate and enhance the impact of international agricultural research. It will support CGIAR’s mission by creating an enabling environment where data are expertly managed and used effectively to strengthen delivery on CGIAR SRF’s System Level Outcome (SLO) targets. Critical gaps were identified during the extensive scoping consultations with CGIAR researchers and partners (provided in Annex 8). The Platform will achieve this through ambitious partnerships with initiatives and organizations outside CGIAR, both upstream and downstream, public and private. It will focus on promoting CGIAR-wide collaboration across CRPs and Centers, in addition to developing new partnership models with big data leaders at the global level. As a result, CGIAR and partner capacity will be enhanced, external partnerships will be leveraged, and an institutional culture of collaborative data management and analytics will be established. Important international public goods such as new global and regional datasets will be developed, alongside new methods that support CGIAR to use the data revolution as an additional means of delivering on SLOs

A decision support system for corporations cyber security risk management

This thesis presents a decision aiding system named C3-SEC (Contex-aware Corporative Cyber Security), developed in the context of a master program at Polytechnic Institute of Leiria, Portugal. The research dimension and the corresponding software development process that followed are presented and validated with an application scenario and case study performed at Universidad de las Fuerzas Armadas ESPE – Ecuador. C3-SEC is a decision aiding software intended to support cyber risks and cyber threats analysis of a corporative information and communications technological infrastructure. The resulting software product will help corporations Chief Information Security Officers (CISO) on cyber security risk analysis, decision-making and prevention measures for the infrastructure and information assets protection. The work is initially focused on the evaluation of the most popular and relevant tools available for risk assessment and decision making in the cyber security domain. Their properties, metrics and strategies are studied and their support for cyber security risk analysis, decision-making and prevention is assessed for the protection of organization's information assets. A contribution for cyber security experts decision support is then proposed by the means of reuse and integration of existing tools and C3-SEC software. C3-SEC extends existing tools features from the data collection and data analysis (perception) level to a full context-ware reference model. The software developed makes use of semantic level, ontology-based knowledge representation and inference supported by widely adopted standards, as well as cyber security standards (CVE, CPE, CVSS, etc.) and cyber security information data sources made available by international authorities, to share and exchange information in this domain. C3-SEC development follows a context-aware systems reference model addressing the perception, comprehension, projection and decision/action layers to create corporative scale cyber security situation awareness

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges