The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

Innovative Business Model for Smart Healthcare Insurance

Information revolution and technology growth have made a considerable contribution to restraining the cost expansion and empowering the customer. They disrupted most business models in different industries. The customer-centric business model has pervaded the different sectors. Smart healthcare has made an enormous shift in patient life and raised their expectations of healthcare services quality. Healthcare insurance is an essential business in the healthcare sector; patients expect a new business model to meet their needs and enhance their wellness. This research develops a holistic smart healthcare architecture based on the recent development of information and communications technology. Then develops a disruptive healthcare insurance business model that adapts to this architecture and classifies the patient according to their technology needs. Finally, and implementing a prototype of a system that matches and suits the healthcare recipient condition to the proper healthcare insurance policy by applying Web Ontology Language (OWL) and rule-based reasoning model using SWRL using Protég

Bayesian Network Models of Causal Interventions in Healthcare Decision Making: Literature Review and Software Evaluation

This report summarises the outcomes of a systematic literature search to identify Bayesian network models used to support decision making in healthcare. After describing the search methodology, the selected research papers are briefly reviewed, with the view to identify publicly available models and datasets that are well suited to analysis using the causal interventional analysis software tool developed in Wang B, Lyle C, Kwiatkowska M (2021). Finally, an experimental evaluation of applying the software on a selection of models is carried out and preliminary results are reported.Comment: 50 pages (19 + 31 Appendix

Ontologies Applied in Clinical Decision Support System Rules:Systematic Review

BackgroundClinical decision support systems (CDSSs) are important for the quality and safety of health care delivery. Although CDSS rules guide CDSS behavior, they are not routinely shared and reused. ObjectiveOntologies have the potential to promote the reuse of CDSS rules. Therefore, we systematically screened the literature to elaborate on the current status of ontologies applied in CDSS rules, such as rule management, which uses captured CDSS rule usage data and user feedback data to tailor CDSS services to be more accurate, and maintenance, which updates CDSS rules. Through this systematic literature review, we aim to identify the frontiers of ontologies used in CDSS rules. MethodsThe literature search was focused on the intersection of ontologies; clinical decision support; and rules in PubMed, the Association for Computing Machinery (ACM) Digital Library, and the Nursing & Allied Health Database. Grounded theory and PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) 2020 guidelines were followed. One author initiated the screening and literature review, while 2 authors validated the processes and results independently. The inclusion and exclusion criteria were developed and refined iteratively. ResultsCDSSs were primarily used to manage chronic conditions, alerts for medication prescriptions, reminders for immunizations and preventive services, diagnoses, and treatment recommendations among 81 included publications. The CDSS rules were presented in Semantic Web Rule Language, Jess, or Jena formats. Despite the fact that ontologies have been used to provide medical knowledge, CDSS rules, and terminologies, they have not been used in CDSS rule management or to facilitate the reuse of CDSS rules. ConclusionsOntologies have been used to organize and represent medical knowledge, controlled vocabularies, and the content of CDSS rules. So far, there has been little reuse of CDSS rules. More work is needed to improve the reusability and interoperability of CDSS rules. This review identified and described the ontologies that, despite their limitations, enable Semantic Web technologies and their applications in CDSS rules

Desenvolvimento e análise de um sistema de recomendação para sugestão de artigos médicos no internamento do Hospital da Luz Lisboa

The internet advances have led to an increase of data and information availability. This overload of information tends to compromise the capacity to manage and filter the available data. In the health domain, the increasing digitalization in healthcare led to a substantial rise of the recorded data. Various recommendation systems (RS) have been developed to help healthcare professionals integrate all information and make efficient and effective decisions. Here, a preliminary RS based on collaborative filtering is proposed to reduce the time that healthcare professionals spend in registering medical items consumed during patients’ hospitalization. For that purpose, the RS was built to perform suggestions of the medical items and respective quantities needed in the first day of hospitalization of a patient. Data regarding the diagnostics, surgical procedures and medical item records associated to surgeries of inpatients during a period of one year in Hospital da Luz Lisboa was filtered, restructured, and analysed (N = 5088 surgeries) for the construction of the RS. A 75-25% split of the data was considered with a 4-fold cross-validation procedure applied on the train set to tune the hyperparameters settings for the algorithm. The RS was then tested and evaluated regarding its overall performance in terms of accuracy, classification performance, and coverage. The same measures were applied to assess the quality of the recommendations for each medical specialty of the hospital. Furthermore, the trust of healthcare professionals in the RS was also assessed. A moderate overall performance was achieved (precision = 0.608, recall = 0.729, F1-Measure = 0.663, RMSE = 6.901) and the quality of the algorithm’s recommendations varied between medical specialties. Additionally, the algorithm presented higher values of precision, recall and F1-Measure in the predictions of the most frequently registered medical items in the test set, which corresponded to approximately 85% of the consumptions in the first day of hospitalization. Regarding the coverage of the RS, approximately 80% of the medical items used in the test set were never recommended by the algorithm, corresponding to only 5.57% of the consumptions. Lastly, although in the point of view of hospital’s nurses there is some trust in the RS results, several suggestions were given for further improvements of the algorithm. Despite the limitations of the RS, the observed results represent a starting point for the development of a tool that can support healthcare professionals of Hospital da Luz Lisboa in registering medical items needed during inpatients’ hospitalization.Os avanços da internet têm aumentado a quantidade de informação disponível, pelo que o seu excesso tende a dificultar a capacidade de gestão e filtragem da mesma. Este fenómeno pode ser observado no domínio da saúde onde a digitalização dos serviços médicos levou a um aumento substancial dos dados registados nos hospitais. Com o intuito de ajudar os profissionais de saúde a integrar toda a informação e, assim, realizarem decisões eficientes e efetivas, vários sistemas de recomendação (SR) foram desenvolvidos. Neste projeto, propõe-se um SR preliminar baseado em filtragem colaborativa para reduzir o tempo despendido pelos profissionais de saúde do Hospital da Luz Lisboa no registo de artigos médicos consumidos durante o período de internamento de doentes. Para isso, o SR foi desenvolvido de modo a formular recomendações relativamente aos artigos médicos e respetivas quantidades necessárias para o primeiro dia de internamento de um doente. A construção do SR teve por base os diagnósticos, procedimentos cirúrgicos e registos de consumos de artigos médicos associados a propostas cirúrgicas de doentes que foram internados no período de um ano no Hospital da Luz Lisboa. O conjunto de dados foi filtrado, reestruturado e analisado (N = 5088 propostas cirúrgicas), para posteriormente ser dividido em conjuntos de treino e de teste (75-25%). Foi aplicada uma 4-fold cross-validation sobre o conjunto de treino para a afinação dos hiperparâmetros do algoritmo, sendo o SR foi testado e avaliado relativamente às suas recomendações a nível global e em cada especialidade médica do hospital em termos de accuracy, classification performance e coverage. Foi igualmente avaliado o grau de confiança no SR por parte dos profissionais de saúde do hospital. O SR apresentou uma performance global razoável (precisão = 0.608, sensibilidade = 0.729, F1 = 0.663, RMSE = 6.901) e demonstrou diferentes níveis de qualidade de recomendações dependendo da especialidade médica. Os melhores valores de precisão, sensibilidade e F1 foram observados nas previsões dos artigos médicos mais frequentemente registados, que correspondem a cerca de 85% dos consumos feitos no primeiro dia de internamento dos doentes do conjunto de teste. O algoritmo nunca sugeriu aproximadamente 80% dos artigos médicos utilizados no conjunto de teste, no entanto, estes apenas correspondiam 5.57% dos consumos totais. Por fim, e embora do ponto de vista dos enfermeiros do hospital haja alguma confiança nos resultados do SR, foram dadas sugestões para futuros ajustes do algoritmo. Não obstante as limitações do SR, os resultados obtidos representam um ponto de partida para o desenvolvimento de uma ferramenta de apoio aos profissionais de saúde do Hospital da Luz nos registos dos artigos médicos necessários durante o internamento de doentes.Mestrado em Estatística Médic

Developing artificial intelligence and machine learning to support primary care research and practice

This thesis was motivated by the potential to use everyday data , especially that collected in electronic health records (EHRs) as part of healthcare delivery, to improve primary care for clients facing complex clinical and/or social situations. Artificial intelligence (AI) techniques can identify patterns or make predictions with these data, producing information to learn about and inform care delivery. Our first objective was to understand and critique the body of literature on AI and primary care. This was achieved through a scoping review wherein we found the field was at an early stage of maturity, primarily focused on clinical decision support for chronic conditions in high-income countries, with low levels of primary care involvement and model evaluation in real-world settings. Our second objective was to demonstrate how AI methods can be applied to problems in descriptive epidemiology. To achieve this, we collaborated with the Alliance for Healthier Communities, which provides team-based primary health care through Community Health Centres (CHCs) across Ontario to clients who experience barriers to regular care. We described sociodemographic, clinical, and healthcare use characteristics of their adult primary care population using EHR data from 2009-2019. We used both simple statistical and unsupervised learning techniques, applied with an epidemiological lens. In addition to substantive findings, we identified potential avenues for future learning initiatives, including the development of decision support tools, and methodological considerations therein. Our third objective was to advance interpretable AI methodology that is well-suited for heterogeneous data, and is applicable in clinical epidemiology as well as other settings. To achieve this, we developed a new hybrid feature- and similarity-based model for supervised learning. There are two versions, fit by convex optimization with a sparsity-inducing penalty on the kernel (similarity) portion of the model. We compared our hybrid models with solely feature- and similarity-based approaches using synthetic data and using CHC data to predict future loneliness or social isolation. We also proposed a new strategy for kernel construction with indicator-coded data. Altogether, this thesis progressed AI for primary care in general and for a particular health care organization, while making research contributions to epidemiology and to computer science

A Hierarchical Decision Model to Evaluate Healthcare Organization\u27s Readiness to Implement Clinical Decision Support Systems

Clinical Decision Support Systems (CDSS) are essential tools for healthcare organizations as well as for healthcare providers to improve clinical care. However, successful implementation of CDSS can be challenging. Therefore, before implementing CDSS, it is crucial to assess the readiness of healthcare organizations to implement these tools. Through a literature review, the first step of this research explores the concept of clinical decision support and CDSS, discussing their features, characteristics, and organizational hurdles to implementation. It also provides perspectives on CDSS adoption in the context of Information Systems and Health Technology. The review helped identify research gaps, objectives, and questions. To address these gaps and attempt to answer the research questions, a Hierarchical Decision Model (HDM) is proposed. The model allows us to assess the readiness of healthcare organizations for CDSS implementation. It presents four perspectives and sixteen criteria for a multi-dimensional assessment. The methodology involves expert panels for the HDM model\u27s refinement, validation, and quantification. Two case studies are then presented to demonstrate the HDM model\u27s application in identifying real-world CDSS implementation challenges and providing insights and recommendations. The research contributions are evaluated against the identified gaps in the literature review, with limitations and future research presented. In conclusion, this research provides valuable insights into CDSS implementation readiness assessment and highlights the need for careful consideration and planning. The proposed HDM model offers a valuable framework for healthcare organizations to evaluate their readiness for CDSS implementation