A Decision Support System for Liver Diseases Prediction: Integrating Batch Processing, Rule-Based Event Detection and SPARQL Query

Liver diseases pose a significant global health burden, impacting a substantial number of individuals and exerting substantial economic and social consequences. Rising liver problems are considered a fatal disease in many countries, such as Egypt, Molda, etc. The objective of this study is to construct a predictive model for liver illness using Basic Formal Ontology (BFO) and detection rules derived from a decision tree algorithm. Based on these rules, events are detected through batch processing using the Apache Jena framework. Based on the event detected, queries can be directly processed using SPARQL. To make the ontology operational, these Decision Tree (DT) rules are converted into Semantic Web Rule Language (SWRL). Using this SWRL in the ontology for predicting different types of liver disease with the help of the Pellet and Drool inference engines in Protege Tools, a total of 615 records are taken from different liver diseases. After inferring the rules, the result can be generated for the patient according to the DT rules, and other patient-related details along with different precautionary suggestions can be obtained based on these results. Combining query results of batch processing and ontology-generated results can give more accurate suggestions for disease prevention and detection. This work aims to provide a comprehensive approach that is applicable for liver disease prediction, rich knowledge graph representation, and smart querying capabilities. The results show that combining RDF data, SWRL rules, and SPARQL queries for analysing and predicting liver disease can help medical professionals to learn more about liver diseases and make a Decision Support System (DSS) for health care

Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review

Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset

Clinical text data in machine learning: Systematic review

Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation