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

Big data analytics for preventive medicine

© 2019, Springer-Verlag London Ltd., part of Springer Nature. Medical data is one of the most rewarding and yet most complicated data to analyze. How can healthcare providers use modern data analytics tools and technologies to analyze and create value from complex data? Data analytics, with its promise to efficiently discover valuable pattern by analyzing large amount of unstructured, heterogeneous, non-standard and incomplete healthcare data. It does not only forecast but also helps in decision making and is increasingly noticed as breakthrough in ongoing advancement with the goal is to improve the quality of patient care and reduces the healthcare cost. The aim of this study is to provide a comprehensive and structured overview of extensive research on the advancement of data analytics methods for disease prevention. This review first introduces disease prevention and its challenges followed by traditional prevention methodologies. We summarize state-of-the-art data analytics algorithms used for classification of disease, clustering (unusually high incidence of a particular disease), anomalies detection (detection of disease) and association as well as their respective advantages, drawbacks and guidelines for selection of specific model followed by discussion on recent development and successful application of disease prevention methods. The article concludes with open research challenges and recommendations

Knowledge Management approaches to model pathophysiological mechanisms and discover drug targets in Multiple Sclerosis

Multiple Sclerosis (MS) is one of the most prevalent neurodegenerative diseases for which a cure is not yet available. MS is a complex disease for numerous reasons; its etiology is unknown, the diagnosis is not exclusive, the disease course is unpredictable and therapeutic response varies from patient to patient. There are four established subtypes of MS, which are segregated based on different characteristics. Many environmental and genetic factors are considered to play a role in MS etiology, including viral infection, vitamin D deficiency, epigenetical changes and some genes. Despite the large body of diverse scientific knowledge, from laboratory findings to clinical trials, no integrated model which portrays the underlying mechanisms of the disease state of MS is available. Contemporary therapies only provide reduction in the severity of the disease, and there is an unmet need of efficient drugs. The present thesis provides a knowledge-based rationale to model MS disease mechanisms and identify potential drug candidates by using systems biology approaches. Systems biology is an emerging field which utilizes the computational methods to integrate datasets of various granularities and simulate the disease outcome. It provides a framework to model molecular dynamics with their precise interaction and contextual details. The proposed approaches were used to extract knowledge from literature by state of the art text mining technologies, integrate it with proprietary data using semantic platforms, and build different models (molecular interactions map, agent based models to simulate disease outcome, and MS disease progression model with respect to time). For better information representation, disease ontology was also developed and a methodology of automatic enrichment was derived. The models provide an insight into the disease, and several pathways were explored by combining the therapeutics and the disease-specific prescriptions. The approaches and models developed in this work resulted in the identification of novel drug candidates that are backed up by existing experimental and clinical knowledge

Identifying factors influencing practitioners’ role in access to health care for hepatitis B in Chinese populations in England

Background: Access to health care for chronic hepatitis B (CHB) is poor in migrant populations of Chinese ethnicity in England. Previous worldwide studies focusing on this problem have largely addressed population factors with few studies focusing on practitioner roles and service-related factors. The aim of this study was to identify and explore practitioner and service related barriers and facilitators to access to health care for CHB affecting Chinese populations in England. Methods: Semi-structured interviews were conducted with 21 frontline health care practitioners and two key informants to examine practitioners’ roles, attitudes and practices in relation to CHB and with Chinese populations. Thematic interpretive analysis was undertaken to identify modifiable factors in primary and secondary care and wider service factors. Relevant models guided design and analysis. Results: Factors were identified at individual practitioner level, during interaction with patients and at organizational level. Practitioners balanced complex responsibilities and CHB is low in their priorities. Professional principles, skills and knowledge are not sufficient in facilitating access in the face of clinical uncertainty, unclear policy and conflicts in funding that reflect structural barriers. Factors acting in the interaction with patients include difficulties with interpreters and understanding patient expectations from services. Facilitators were identified and included bespoke services and active interaction with Chinese community services. Organizational issues including increasing workload, lack of support and financial limitations and conflicts, were also acting as barriers to appropriate identification and referral of patients. Conclusion: Practitioners balanced numerous demands that may hamper the decision-making process, hindering the role of facilitating access to care for asymptomatic, low priority conditions. Individual patient preferences could be addressed more effectively using cross-cultural care approaches. In addition, addressing dimensions of structural racism, including the lack of effective access pathways, lack of practical support and of dissemination of clinical guidance could help address service barriers

Decision-Support for Rheumatoid Arthritis Using Bayesian Networks: Diagnosis, Management, and Personalised Care.

PhD Theses.Bayesian networks (BNs) have been widely proposed for medical decision support. One advantage of a BN is reasoning under uncertainty, which is pervasive in medicine. Another advantage is that a BN can be built from both data and knowledge and so can be applied in circumstances where a complete dataset is not available. In this thesis, we examine how BNs can be used for the decision support challenges of chronic diseases. As a case study, we study Rheumatoid Arthritis (RA), which is a chronic inflammatory disease causing swollen and painful joints. The work has been done as part of a collaborative project including clinicians from Barts and the London NHS Trust involved in the treatment of RA. The work covers three stages of decision support, with progressively less available data. The first decision support stage is diagnosis. Various criteria have been proposed by clinicians for early diagnosis but these criteria are deterministic and so do not capture diagnostic uncertainty, which is a concern for patients with mild symptoms in the early stages of the disease. We address this problem by building a BN model for diagnosing RA. The diagnostic BN model is built using both a dataset of 360 patients provided by the clinicians and their knowledge as experts in this domain. The choice of factors to include in the diagnostic model is informed by knowledge, including a model of the care pathway which shows what information is available for diagnosis. Knowledge is used to classify the factors as risk factors, relevant comorbidities, evidence of pathogenesis mechanism, signs, symptoms, and serology results, so that the structure of BN model matches the clinical understanding of RA. Since most of the factors are present in the dataset, we are able to train the parameters of the diagnostic BN from the data. This diagnostic BN model obtains promising results in differentiating RA cases from other inflammatory arthritis cases. Aware that eliciting knowledge is time-consuming and could limit the uptake of these techniques, we consider two alternative approaches. First, we compare its diagnostic performance with an alternative BN model entirely learnt from data; we argue that having a clinically meaningful structure allows us to explain clinical scenarios in a way that cannot be done with the model learnt purely from data. We also examine whether useful knowledge can be retrieved from existing vi medical ontologies, such as SNOMED CT and UMLS. Preliminary results show that it could be feasible to use such sources to partially automate knowledge collection. After patients have been diagnosed with RA, they are monitored regularly by a clinical team until the activity of their disease becomes low. The typical care arrangement has two challenges: first, regular meetings with clinicians occur infrequently at fixed intervals (e.g., every six months), during which time the activity of the disease can increase (or ‘flare’) and decrease several times. Secondly, the best medications or combinations of medications must be found for each patient, but changes can only be made when the patient visits the clinic. We therefore develop this stage of decision support in two parts: the first and simplest part looks at how the frequency of clinic appointments could be varied; the second part builds on this to support decisions to adjust medication dosage. We describe this as the ‘self-management’ decision support model. Disease activity is commonly measured with Disease Activity Score 28 (DAS28). Since the joint count parts of this can be assessed by the patient, the possibility of collecting regular (e.g., weekly) DAS28 data has been proposed. It is not yet in wide use, perhaps because of the overheads to the clinical team of reviewing data regularly. The dataset available to us for this work came from a feasibility study conducted by the clinical collaborators of one system for collecting data from patients, although the frequency is only quarterly. The aim of the ‘self-management’ decision support system is therefore to sit between patient-entered data and the clinical team, saving the work of clinically assessing all the data. Specifically, in the first part we wish to predict disease activity so that an appointment should be made sooner, distinguishing this from patients whose disease is well-managed so that the interval between appointments can be increased. To achieve this, we build a dynamic BN (DBN) model to monitor disease activity and to indicate to patients and their clinicians whether a clinical review is needed. We use the data and a set of dummy patient scenarios designed by the experts to evaluate the performance of the DBN. The second part of the ‘self-management’ decision support stage extends the DBN to give advice on adjustments to the medication dosage. This is of particular clinical interest since one class of medications used (biological disease-modifying antirheumatic drugs) are very expensive and, although effective at reducing disease activity, can have severe adverse reactions. For both these reasons, decision support that allowed a patient to ‘taper’ the dosage of medications without frequent clinic visits would be very useful. This extension does not meet all the decision support needs, which ideally would also cover decision-making about the choice of medications. However, we have found that as yet there is neither sufficient data nor knowledge for this. vii The third and final stage of decision support is targeted at patients who live with RA. RA can have profound impacts on the quality of life (QoL) of those who live with it, affecting work, financial status, friendships, and relationships. Information from patient organisations such as the leaflets prepared by the National Rheumatoid Arthritis Society (NRAS) contains advice on managing QoL, but the advice is generic, leaving it up to each patient to select the advice most relevant to their specific circumstances. Our aim is therefore to build a BN-based decision support system to personalise the recommendations for enhancing the QoL of RA patients. We have built a BN to infer three components of QoL (independence, participation, and empowerment) and shown how this can be used to target advice. Since there is no data, the BN is developed from expert knowledge and literature. To evaluate the resulting system, including the BN, we use a set of patient interviews conducted and coded by our collaborators. The recommendations of the system were compared with those of experts in a set of test scenarios created from the interviews; the comparison shows promising results

Infectious diseases management framework for Saudi Arabia (SAIF)

A Thesis Submitted to the University of Bedfordshire in partial fulfilment of the requirements for the degree of Doctor of PhilosopyInfectious disease management system area is considered as an emerging field of modern healthcare in the Gulf region. Significant technical and clinical progress and advanced technologies can be utilized to enhance the performance and ubiquity of such systems. Effective infectious disease management (IDM) can be achieved by analysing the disease management issues from the perspectives of healthcare personnel and patients. Hence, it is necessary to identify the needs and requirements of both healthcare personnel and patients for managing the infectious disease. The basic idea behind the proposed mobile IDM system in this thesis is to improve the healthcare processes in managing infectious diseases more effectively. For this purpose, internet and mobile technologies are integrated with social networking, mapping and IDM applications to improve the processes efficiency. Hence, the patients submit their health related data through their devices remotely using our application to our system database (so-called SAIF). The main objective of this PhD project was the design and development of a novel web based architecture of next-generation infectious disease management system embedding the concept of social networking tailored for Saudi patients. Following a detailed literature review which identifies the current status and potential impact of using infectious diseases management system in KSA, this thesis conducts a feasibility user perspective study for identifying the needs and the requirements of healthcare personnel and the patients for managing infectious diseases. Moreover, this thesis proposes a design and development of a novel architecture of next-generation web based infectious disease management system tailored for Saudi patients (i.e., called SAIF – infectious diseases management framework for Saudi Arabia). Further, this thesis introduces a usability study for the SAIF system to validate the acceptability of using mobile technologies amongst infected patient in KSA and Gulf region. The preliminary results of the study indicated general acceptance of the patients in using the system with higher usability rating in high affected patients. In general, the study concluded that the concept of SAIF system is considered acceptable tool in particularly with infected patients

CREATE: Concept Representation and Extraction from Heterogeneous Evidence

Traditional information retrieval methodology is guided by document retrieval paradigm, where relevant documents are returned in response to user queries. This paradigm faces serious drawback if the desired result is not explicitly present in a single document. The problem becomes more obvious when a user tries to obtain complete information about a real world entity, such as person, company, location etc. In such cases, various facts about the target entity or concept need to be gathered from multiple document sources. In this work, we present a method to extract information about a target entity based on the concept retrieval paradigm that focuses on extracting and blending information related to a concept from multiple sources if necessary. The paradigm is built around a generic notion of concept which is defined as any item that can be thought of as a topic of interest. Concepts may correspond to any real world entity such as restaurant, person, city, organization, etc, or any abstract item such as news topic, event, theory, etc. Web is a heterogeneous collection of data in different forms such as facts, news, opinions etc. We propose different models for different forms of data, all of which work towards the same goal of concept centric retrieval. We motivate our work based on studies about current trends and demands for information seeking. The framework helps in understanding the intent of content, i.e. opinion versus fact. Our work has been conducted on free text data in English. Nevertheless, our framework can be easily transferred to other languages

New Methodology for Measuring Semantic Functional Similarity Based on Bidirectional Integration

1.2 billion users in facebook, 17 million articles in Wikipedia, and 190 million tweets per day have demanded significant increase of information processing through Internet in recent years. Similarly life sciences and bioinformatics also have faced issues of processing Big data due to the explosion of publicly available genomic information resulted from the Human Genome Project (HGP) and the increasing usage of high throughput technology. HGP was completed in 2003 and resulted in identifying 20,000-25,000 genes in human DNA and determining the sequences of three billion human base pairs. The information requires huge amount of data storage and becomes difficult to process using on-hand database management tools or traditional data processing applications. This thesis introduces new method, Biological and Statistical Mean (BSM) score to calculate functional similarity between gene products (GPs) that can help to extract biologically relevant and statistically robust information from large-scale biomedical, genomic and proteomic data sources. BSM score is defined by 16 different scoring matrices derived from principles of multi-view learning in machine learning algorithm and five different databases including Gene Ontology, UniProt, SCOP, CATH, and KUPS. The proposed method also shows how diverse databases and principles in machine learning theory can be integrated into a simple scoring function, and how the simple concept can give significant impact on the studies in biomedical and human life sciences. The comprehensive evaluations and performance comparisons with other conventional methods show that BSM score clearly outperforms other methods in terms of sensitivity of clustering similarity functional groups and coverage of identifying related genes. As a part of potential applications handling large amount of diverse data sources in medical domain, this thesis introduces similarity-based drug target identification and disease networks using BSM scores. Application of BSM score is freely available through http://www.ittc.ku.edu/chenlab/goal