Software Architectures and Efficient Data Sharing for Promoting Continuous Drug Re-purposing

The proposed layered and component based architectural style enables data sharing and accessibility of computational software components across problem domains in Biomedical Science. However, it also opens door to translational informatics, which bridges the gap between knowledge generated in biomedical science and clinical practices. Software applications generated from such an architectural style, are able to support continues drug repurposing. They exploit the semantic which exists, and is available across biomedical problem domains, between drug chemical compounds, their biological targets, particularly unintentional targets and drug therapeutic effects. The excerpt from the proposed software architectures has already been deployed in computationally light-weight software applications which based drug repurposing on reasoning upon collected available semantic. However a full scale implementation of the ideas of data sharing across the spectrum of biomedical research and disciplines, would require some changes in the way therapeutic drugs are discovered, tested and approved

Diagnosis and Risk Prediction of Dilated Cardiomyopathy in the Era of Big Data and Genomics

Dilated cardiomyopathy (DCM) is a leading cause of heart failure and life-threatening ventricular arrhythmias (LTVA). Work-up and risk stratification of DCM is clinically challenging, as there is great heterogeneity in phenotype and genotype. Throughout the last decade, improved genetic testing of patients has identified genotype–phenotype associations and enhanced evaluation of at-risk relatives leading to better patient prognosis. The field is now ripe to explore opportunities to improve personalised risk assessments. Multivariable risk models presented as “risk calculators” can incorporate a multitude of clinical variables and predict outcome (such as heart failure hospitalisations or LTVA). In addition, genetic risk scores derived from genome/exome-wide association studies can estimate an individual’s lifetime genetic risk of developing DCM. The use of clinically granular investigations, such as late gadolinium enhancement on cardiac magnetic resonance imaging, is warranted in order to increase predictive performance. To this end, constructing big data infrastructures improves accessibility of data by using electronic health records, existing research databases, and disease registries. By applying methods such as machine and deep learning, we can model complex interactions, identify new phenotype clusters, and perform prognostic modelling. This review aims to provide an overview of the evolution of DCM definitions as well as its clinical work-up and considerations in the era of genomics. In addition, we present exciting examples in the field of big data infrastructures, personalised prognostic assessment, and artificial intelligence

Diagnosis and Prognosis of Occupational disorders based on Machine Learn- ing Techniques applied to Occupational Profiles

Work-related disorders have a global influence on people’s well-being and quality of life and are a financial burden for organizations because they reduce productivity, increase absenteeism, and promote early retirement. Work-related musculoskeletal disorders, in particular, represent a significant fraction of the total in all occupational contexts. In automotive and industrial settings where workers are exposed to work-related muscu- loskeletal disorders risk factors, occupational physicians are responsible for monitoring workers’ health protection profiles. Occupational technicians report in the Occupational Health Protection Profiles database to understand which exposure to occupational work- related musculoskeletal disorder risk factors should be ensured for a given worker. Occu- pational Health Protection Profiles databases describe the occupational physician states, and which exposure the physicians considers necessary to ensure the worker’s health protection in terms of their functional work ability. The application of Human-Centered explainable artificial intelligence can support the decision making to go from worker’s Functional Work Ability to explanations by integrating explainability into medical (re- striction) and supporting in two decision contexts: prognosis and diagnosis of individual, work related and organizational risk condition. Although previous machine learning ap- proaches provided good predictions, their application in an actual occupational setting is limited because their predictions are difficult to interpret and hence, not actionable. In this thesis, injured body parts in which the ability changed in a worker’s functional work ability status are targeted. On the one hand, artificial intelligence algorithms can help technical teams, occupational physicians, and ergonomists determine a worker’s workplace risk via the diagnosis and prognosis of body part(s) injuries; on the other hand, these approaches can help prevent work-related musculoskeletal disorders by identifying which processes are lacking in working condition improvement and which workplaces have a better match between the remaining functional work abilities. A sample of 2025 for the prognosis part (from the years of 2019 to 2020) and 7857 for the prognosis part of Occupational Health Protection Profiles based on Functional Work Ability textual re- ports in the Portuguese language in automotive industry factory. Machine learning-based Natural Language Processing methods were implemented to extract standardized infor- mation. The prognosis and diagnosis of Occupational Health Protection Profiles factors were developed in reliable Human-Centered explainable artificial intelligence system to promote a trustworthy Human-Centered explainable artificial intelligence system (enti- tled Industrial microErgo application). The most suitable regression models to predict the next medical appointment for the injured body regions were the models based on CatBoost regression, with R square and an RMSLE of 0.84 and 1.23 weeks, respectively. In parallel, CatBoost’s best regression model for most body parts is the prediction of the next injured body parts based on these two errors. This information can help tech- nical industrial teams understand potential risk factors for Occupational Health Protec- tion Profiles and identify warning signs of the early stages of musculoskeletal disorders.Os transtornos relacionados ao trabalho têm influência global no bem-estar e na quali- dade de vida das pessoas e são um ônus financeiro para as organizações, pois reduzem a produtividade, aumentam o absenteísmo e promovem a aposentadoria precoce. Os distúr- bios osteomusculares relacionados ao trabalho, em particular, representam uma fração significativa do total em todos os contextos ocupacionais. Em ambientes automotivos e industriais onde os trabalhadores estão expostos a fatores de risco de distúrbios osteomus- culares relacionados ao trabalho, os médicos do trabalho são responsáveis por monitorar os perfis de proteção à saúde dos trabalhadores. Os técnicos do trabalho reportam-se à base de dados dos Perfis de Proteção da Saúde Ocupacional para compreender quais os fatores de risco de exposição a perturbações músculo-esqueléticas relacionadas com o tra- balho que devem ser assegurados para um determinado trabalhador. As bases de dados de Perfis de Proteção à Saúde Ocupacional descrevem os estados do médico do trabalho e quais exposições os médicos consideram necessária para garantir a proteção da saúde do trabalhador em termos de sua capacidade funcional para o trabalho. A aplicação da inteligência artificial explicável centrada no ser humano pode apoiar a tomada de decisão para ir da capacidade funcional de trabalho do trabalhador às explicações, integrando a explicabilidade à médica (restrição) e apoiando em dois contextos de decisão: prognóstico e diagnóstico da condição de risco individual, relacionado ao trabalho e organizacional . Embora as abordagens anteriores de aprendizado de máquina tenham fornecido boas pre- visões, sua aplicação em um ambiente ocupacional real é limitada porque suas previsões são difíceis de interpretar e portanto, não acionável. Nesta tese, as partes do corpo lesiona- das nas quais a habilidade mudou no estado de capacidade funcional para o trabalho do trabalhador são visadas. Por um lado, os algoritmos de inteligência artificial podem aju- dar as equipes técnicas, médicos do trabalho e ergonomistas a determinar o risco no local de trabalho de um trabalhador por meio do diagnóstico e prognóstico de lesões em partes do corpo; por outro lado, essas abordagens podem ajudar a prevenir distúrbios muscu- loesqueléticos relacionados ao trabalho, identificando quais processos estão faltando na melhoria das condições de trabalho e quais locais de trabalho têm uma melhor correspon- dência entre as habilidades funcionais restantes do trabalho. Para esta tese, foi utilizada uma base de dados com Perfis de Proteção à Saúde Ocupacional, que se baseiam em relató- rios textuais de Aptidão para o Trabalho em língua portuguesa, de uma fábrica da indús- tria automóvel (Auto Europa). Uma amostra de 2025 ficheiros foi utilizada para a parte de prognóstico (de 2019 a 2020) e uma amostra de 7857 ficheiros foi utilizada para a parte de diagnóstico. . Aprendizado de máquina- métodos baseados em Processamento de Lingua- gem Natural foram implementados para extrair informações padronizadas. O prognóstico e diagnóstico dos fatores de Perfis de Proteção à Saúde Ocupacional foram desenvolvidos em um sistema confiável de inteligência artificial explicável centrado no ser humano (inti- tulado Industrial microErgo application). Os modelos de regressão mais adequados para prever a próxima consulta médica para as regiões do corpo lesionadas foram os modelos baseados na regressão CatBoost, com R quadrado e RMSLE de 0,84 e 1,23 semanas, res- pectivamente. Em paralelo, a previsão das próximas partes do corpo lesionadas com base nesses dois erros relatados pelo CatBoost como o melhor modelo de regressão para a mai- oria das partes do corpo. Essas informações podem ajudar as equipes técnicas industriais a entender os possíveis fatores de risco para os Perfis de Proteção à Saúde Ocupacio- nal e identificar sinais de alerta dos estágios iniciais de distúrbios musculoesqueléticos