KETOS: Clinical decision support and machine learning as a service – A training and deployment platform based on Docker, OMOP-CDM, and FHIR Web Services

Background and objective To take full advantage of decision support, machine learning, and patient-level prediction models, it is important that models are not only created, but also deployed in a clinical setting. The KETOS platform demonstrated in this work implements a tool for researchers allowing them to perform statistical analyses and deploy resulting models in a secure environment. Methods The proposed system uses Docker virtualization to provide researchers with reproducible data analysis and development environments, accessible via Jupyter Notebook, to perform statistical analysis and develop, train and deploy models based on standardized input data. The platform is built in a modular fashion and interfaces with web services using the Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) standard to access patient data. In our prototypical implementation we use an OMOP common data model (OMOP-CDM) database. The architecture supports the entire research lifecycle from creating a data analysis environment, retrieving data, and training to final deployment in a hospital setting. Results We evaluated the platform by establishing and deploying an analysis and end user application for hemoglobin reference intervals within the University Hospital Erlangen. To demonstrate the potential of the system to deploy arbitrary models, we loaded a colorectal cancer dataset into an OMOP database and built machine learning models to predict patient outcomes and made them available via a web service. We demonstrated both the integration with FHIR as well as an example end user application. Finally, we integrated the platform with the open source DataSHIELD architecture to allow for distributed privacy preserving data analysis and training across networks of hospitals. Conclusion The KETOS platform takes a novel approach to data analysis, training and deploying decision support models in a hospital or healthcare setting. It does so in a secure and privacy-preserving manner, combining the flexibility of Docker virtualization with the advantages of standardized vocabularies, a widely applied database schema (OMOP-CDM), and a standardized way to exchange medical data (FHIR)

Automated Injection of Curated Knowledge Into Real-Time Clinical Systems: CDS Architecture for the 21st Century

abstract: Clinical Decision Support (CDS) is primarily associated with alerts, reminders, order entry, rule-based invocation, diagnostic aids, and on-demand information retrieval. While valuable, these foci have been in production use for decades, and do not provide a broader, interoperable means of plugging structured clinical knowledge into live electronic health record (EHR) ecosystems for purposes of orchestrating the user experiences of patients and clinicians. To date, the gap between knowledge representation and user-facing EHR integration has been considered an “implementation concern” requiring unscalable manual human efforts and governance coordination. Drafting a questionnaire engineered to meet the specifications of the HL7 CDS Knowledge Artifact specification, for example, carries no reasonable expectation that it may be imported and deployed into a live system without significant burdens. Dramatic reduction of the time and effort gap in the research and application cycle could be revolutionary. Doing so, however, requires both a floor-to-ceiling precoordination of functional boundaries in the knowledge management lifecycle, as well as formalization of the human processes by which this occurs. This research introduces ARTAKA: Architecture for Real-Time Application of Knowledge Artifacts, as a concrete floor-to-ceiling technological blueprint for both provider heath IT (HIT) and vendor organizations to incrementally introduce value into existing systems dynamically. This is made possible by service-ization of curated knowledge artifacts, then injected into a highly scalable backend infrastructure by automated orchestration through public marketplaces. Supplementary examples of client app integration are also provided. Compilation of knowledge into platform-specific form has been left flexible, in so far as implementations comply with ARTAKA’s Context Event Service (CES) communication and Health Services Platform (HSP) Marketplace service packaging standards. Towards the goal of interoperable human processes, ARTAKA’s treatment of knowledge artifacts as a specialized form of software allows knowledge engineers to operate as a type of software engineering practice. Thus, nearly a century of software development processes, tools, policies, and lessons offer immediate benefit: in some cases, with remarkable parity. Analyses of experimentation is provided with guidelines in how choice aspects of software development life cycles (SDLCs) apply to knowledge artifact development in an ARTAKA environment. Portions of this culminating document have been further initiated with Standards Developing Organizations (SDOs) intended to ultimately produce normative standards, as have active relationships with other bodies.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

DEPLOYR: A technical framework for deploying custom real-time machine learning models into the electronic medical record

Machine learning (ML) applications in healthcare are extensively researched, but successful translations to the bedside are scant. Healthcare institutions are establishing frameworks to govern and promote the implementation of accurate, actionable and reliable models that integrate with clinical workflow. Such governance frameworks require an accompanying technical framework to deploy models in a resource efficient manner. Here we present DEPLOYR, a technical framework for enabling real-time deployment and monitoring of researcher created clinical ML models into a widely used electronic medical record (EMR) system. We discuss core functionality and design decisions, including mechanisms to trigger inference based on actions within EMR software, modules that collect real-time data to make inferences, mechanisms that close-the-loop by displaying inferences back to end-users within their workflow, monitoring modules that track performance of deployed models over time, silent deployment capabilities, and mechanisms to prospectively evaluate a deployed model's impact. We demonstrate the use of DEPLOYR by silently deploying and prospectively evaluating twelve ML models triggered by clinician button-clicks in Stanford Health Care's production instance of Epic. Our study highlights the need and feasibility for such silent deployment, because prospectively measured performance varies from retrospective estimates. By describing DEPLOYR, we aim to inform ML deployment best practices and help bridge the model implementation gap

A collaborative platform for management of chronic diseases via guideline-driven individualized care plans

Older age is associated with an increased accumulation of multiple chronic conditions. The clinical management of patients suffering from multiple chronic conditions is very complex, disconnected and time-consuming with the traditional care settings. Integrated care is a means to address the growing demand for improved patient experience and health outcomes of multimorbid and long-term care patients. Care planning is a prevalent approach of integrated care, where the aim is to deliver more personalized and targeted care creating shared care plans by clearly articulating the role of each provider and patient in the care process. In this paper, we present a method and corresponding implementation of a semi-automatic care plan management tool, integrated with clinical decision support services which can seamlessly access and assess the electronic health records (EHRs) of the patient in comparison with evidence based clinical guidelines to suggest personalized recommendations for goals and interventions to be added to the individualized care plans. We also report the results of usability studies carried out in four pilot sites by patients and clinicians

Peer-to-Peer Personal Health Record

Indiana University-Purdue University Indianapolis (IUPUI)Patients and providers need to exchange medical records. Electronic Health Records and Health Information Exchanges leave a patient’s health record fragmented and controlled by the provider. This thesis proposes a Peer-to-Peer Personal Health Record network that can be extended with third-party services. This design enables patient control of health records and the tracing of exchanges. Additionally, as a demonstration of the functionality of a potential third-party, a Hypertension Predictor is developed using MEPS data and deployed as a service in the proposed framework

Cardea: An Open Automated Machine Learning Framework for Electronic Health Records

An estimated 180 papers focusing on deep learning and EHR were published between 2010 and 2018. Despite the common workflow structure appearing in these publications, no trusted and verified software framework exists, forcing researchers to arduously repeat previous work. In this paper, we propose Cardea, an extensible open-source automated machine learning framework encapsulating common prediction problems in the health domain and allows users to build predictive models with their own data. This system relies on two components: Fast Healthcare Interoperability Resources (FHIR) -- a standardized data structure for electronic health systems -- and several AUTOML frameworks for automated feature engineering, model selection, and tuning. We augment these components with an adaptive data assembler and comprehensive data- and model- auditing capabilities. We demonstrate our framework via 5 prediction tasks on MIMIC-III and Kaggle datasets, which highlight Cardea's human competitiveness, flexibility in problem definition, extensive feature generation capability, adaptable automatic data assembler, and its usability

A Unified Health Information System Framework for Connecting Data, People, Devices, and Systems

The COVID-19 pandemic has heightened the necessity for pervasive data and system interoperability to manage healthcare information and knowledge. There is an urgent need to better understand the role of interoperability in improving the societal responses to the pandemic. This paper explores data and system interoperability, a very specific area that could contribute to fighting COVID-19. Specifically, the authors propose a unified health information system framework to connect data, systems, and devices to increase interoperability and manage healthcare information and knowledge. A blockchain-based solution is also provided as a recommendation for improving the data and system interoperability in healthcare

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