Temporal convolution attention model for sepsis clinical assistant diagnosis prediction

Sepsis is an organ failure disease caused by an infection acquired in an intensive care unit (ICU), which leads to a high mortality rate. Developing intelligent monitoring and early warning systems for sepsis is a key research area in the field of smart healthcare. Early and accurate identification of patients at high risk of sepsis can help doctors make the best clinical decisions and reduce the mortality rate of patients with sepsis. However, the scientific understanding of sepsis remains inadequate, leading to slow progress in sepsis research. With the accumulation of electronic medical records (EMRs) in hospitals, data mining technologies that can identify patient risk patterns from the vast amount of sepsis-related EMRs and the development of smart surveillance and early warning models show promise in reducing mortality. Based on the Medical Information Mart for Intensive Care Ⅲ, a massive dataset of ICU EMRs published by MIT and Beth Israel Deaconess Medical Center, we propose a Temporal Convolution Attention Model for Sepsis Clinical Assistant Diagnosis Prediction (TCASP) to predict the incidence of sepsis infection in ICU patients. First, sepsis patient data is extracted from the EMRs. Then, the incidence of sepsis is predicted based on various physiological features of sepsis patients in the ICU. Finally, the TCASP model is utilized to predict the time of the first sepsis infection in ICU patients. The experiments show that the proposed model achieves an area under the receiver operating characteristic curve (AUROC) score of 86.9% (an improvement of 6.4% ) and an area under the precision-recall curve (AUPRC) score of 63.9% (an improvement of 3.9% ) compared to five state-of-the-art models

Use of deep learning to develop continuous-risk models for adverse event prediction from electronic health records

Early prediction of patient outcomes is important for targeting preventive care. This protocol describes a practical workflow for developing deep-learning risk models that can predict various clinical and operational outcomes from structured electronic health record (EHR) data. The protocol comprises five main stages: formal problem definition, data pre-processing, architecture selection, calibration and uncertainty, and generalizability evaluation. We have applied the workflow to four endpoints (acute kidney injury, mortality, length of stay and 30-day hospital readmission). The workflow can enable continuous (e.g., triggered every 6 h) and static (e.g., triggered at 24 h after admission) predictions. We also provide an open-source codebase that illustrates some key principles in EHR modeling. This protocol can be used by interdisciplinary teams with programming and clinical expertise to build deep-learning prediction models with alternate data sources and prediction tasks

Rethinking Human-AI Collaboration in Complex Medical Decision Making: A Case Study in Sepsis Diagnosis

Today's AI systems for medical decision support often succeed on benchmark datasets in research papers but fail in real-world deployment. This work focuses on the decision making of sepsis, an acute life-threatening systematic infection that requires an early diagnosis with high uncertainty from the clinician. Our aim is to explore the design requirements for AI systems that can support clinical experts in making better decisions for the early diagnosis of sepsis. The study begins with a formative study investigating why clinical experts abandon an existing AI-powered Sepsis predictive module in their electrical health record (EHR) system. We argue that a human-centered AI system needs to support human experts in the intermediate stages of a medical decision-making process (e.g., generating hypotheses or gathering data), instead of focusing only on the final decision. Therefore, we build SepsisLab based on a state-of-the-art AI algorithm and extend it to predict the future projection of sepsis development, visualize the prediction uncertainty, and propose actionable suggestions (i.e., which additional laboratory tests can be collected) to reduce such uncertainty. Through heuristic evaluation with six clinicians using our prototype system, we demonstrate that SepsisLab enables a promising human-AI collaboration paradigm for the future of AI-assisted sepsis diagnosis and other high-stakes medical decision making.Comment: Under submission to CHI202

Development of Artificial Intelligence Algorithms for Early Diagnosis of Sepsis

Sepsis is a prevalent syndrome that manifests itself through an uncontrolled response from the body to an infection, that may lead to organ dysfunction. Its diagnosis is urgent since early treatment can reduce the patients’ chances of having long-term consequences. Yet, there are many obstacles to achieving this early detection. Some stem from the syndrome’s pathogenesis, which lacks a characteristic biomarker. The available clinical detection tools are either too complex or lack sensitivity, in both cases delaying the diagnosis. Another obstacle relates to modern technology, that when paired with the many clinical parameters that are monitored to detect sepsis, result in extremely heterogenous and complex medical records, which constitute a big obstacle for the responsible clinicians, that are forced to analyse them to diagnose the syndrome. To help achieve this early diagnosis, as well as understand which parameters are most relevant to obtain it, an approach based on the use of Artificial Intelligence algorithms is proposed in this work, with the model being implemented in the alert system of a sepsis monitoring platform. This platform uses a Random Forest algorithm, based on supervised machine learning classification, that is capable of detecting the syndrome in two different scenarios. The earliest detection can happen if there are only five vital sign parameters available for measurement, namely heart rate, systolic and diastolic blood pressures, blood oxygen saturation level, and body temperature, in which case, the model has a score of 83% precision and 62% sensitivity. If besides the mentioned variables, laboratory analysis measurements of bilirubin, creatinine, hemoglobin, leukocytes, platelet count, and Creactive protein levels are available, the platform’s sensitivity increases to 77%. With this, it has also been found that the blood oxygen saturation level is one of the most important variables to take into account for the task, in both cases. Once the platform is tested in real clinical situations, together with an increase in the available clinical data, it is believed that the platform’s performance will be even better.A sépsis é uma síndrome com elevada incidência a nível global, que se manifesta através de uma resposta desregulada por parte do organismo a uma infeção, podendo resultar em disfunções orgânicas generalizadas. O diagnóstico da mesma é urgente, uma vez que um tratamento precoce pode reduzir as hipóteses de consequências a longo prazo para os doentes. Apesar desta necessidade, existem vários obstáculos. Alguns deles advêm da patogenia da síndrome, que carece de um biomarcador específico. As ferramentas de deteção clínica são demasiado complexas, ou pouco sensíveis, em ambos os casos atrasando o diagnóstico. Outro obstáculo relaciona-se com os avanços da tecnologia, que, com os vários parâmetros clínicos que são monitorizados, resulta em registos médicos heterogéneos e complexos, o que constitui um grande obstáculo para os profissionais de saúde, que se vêm forçados a analisá-los para diagnosticar a síndrome. Para atingir este diagnóstico precoce, bem como compreender quais os parâmetros mais relevantes para o alcançar, é proposta neste trabalho uma abordagem baseada num algoritmo de Inteligência Artificial, sendo o modelo implementado no sistema de alerta de uma plataforma de monitorização de sépsis. Esta plataforma utiliza um classificador Random Forest baseado em aprendizagem automática supervisionada, capaz de diagnosticar a síndrome de duas formas. Uma deteção mais precoce pode ocorrer através de cinco parâmetros vitais, nomeadamente frequência cardíaca, pressão arterial sistólica e diastólica, nível de saturação de oxigénio no sangue e temperatura corporal, caso em que o modelo atinge valores de 83% de precisão e 62% de sensibilidade. Se, para além das variáveis mencionadas, estiverem disponíveis análises laboratoriais de bilirrubina, creatinina, hemoglobina, leucócitos, contagem de plaquetas e níveis de proteína C-reativa, a sensibilidade da plataforma sobre para 77%. Concluiu-se que o nível de saturação de oxigénio no sangue é uma das variáveis mais importantes a ter em conta para o diagnóstico, em ambos os casos. A partir do momento que a plataforma venha a ser utilizada em situações clínicas reais, com o consequente aumento dos dados disponíveis, crê-se que o desempenho venha a ser ainda melhor

LSTM Models to Support the Selective Antibiotic Treatment Strategy of Dairy Cows in the Dry Period

Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced Analytics, specialization in Data ScienceUdder inflammation, known as mastitis, is the most significant disease of dairy cows worldwide, invoking substantial economic losses. The current common strategy to reduce this problem is the prophylactic administration of antibiotics treatment of cows during their dry period. Paradoxically, the indiscriminate use of antibiotics in animals and humans has been the leading cause of antimicrobial resistance, a concern in several public health organizations. In light of these assumptions, at the beginning of 2022, the European Union made it illegal to routinely administer antibiotics on farms, with Regulation 2019/6 of 11 December 2018. Considering this new scenario, the objective of this study was to produce a model that supports the decisions of veterinarians when administering antibiotics in the dry period of dairy cows. Deep learning models were used, namely LSTM layers that operate with dynamic features from milk recordings and a dense layer that uses static features. Two approaches were chosen to deal with this problem. The first is based on a binary classification model that considers the occurrence of mastitis within 60 days after calving. The second approach was a multiclass classification model based on veterinary expert judgment. In each approach, three models were implemented, a Vanilla LSTM, a Stacked LSTM, and a Stacked LSTM with a dense layer working in parallel. The best performances from binary and multiclass approaches were 65% and 84% accuracy, respectively. It was possible to conclude that the models of the multiclass classification approach had better performance than the other classification. The capture of long- and short-term dependencies in the LSTM models, especially with the combination of static features, obtained promising results, which will undoubtedly contribute to producing a machine learning system with a prompt and affordable response, allowing for a reduction in the administration of antibiotics in dairy cows to the strictly necessary

Advancing the Understanding of Clinical Sepsis Using Gene Expression-Driven Machine Learning to Improve Patient Outcomes

Sepsis remains a major challenge that necessitates improved approaches to enhance patient outcomes. This study explored the potential of Machine Learning (ML) techniques to bridge the gap between clinical data and gene expression information to better predict and understand sepsis. We discuss the application of ML algorithms, including neural networks, deep learning, and ensemble methods, to address key evidence gaps and overcome the challenges in sepsis research. The lack of a clear definition of sepsis is highlighted as a major hurdle, but ML models offer a workaround by focusing on endpoint prediction. We emphasize the significance of gene transcript information and its use in ML models to provide insights into sepsis pathophysiology and biomarker identification. Temporal analysis and integration of gene expression data further enhance the accuracy and predictive capabilities of ML models for sepsis. Although challenges such as interpretability and bias exist, ML research offers exciting prospects for addressing critical clinical problems, improving sepsis management, and advancing precision medicine approaches. Collaborative efforts between clinicians and data scientists are essential for the successful implementation and translation of ML models into clinical practice. ML has the potential to revolutionize our understanding of sepsis and significantly improve patient outcomes. Further research and collaboration between clinicians and data scientists are needed to fully understand the potential of ML in sepsis management