Automated Measurement of Adherence to Traumatic Brain Injury (TBI) Guidelines using Neurological ICU Data

Using a combination of physiological and treatment information from neurological ICU data-sets, adherence to traumatic brain injury (TBI) guidelines on hypotension, intracranial pressure (ICP) and cerebral perfusion pressure (CPP) is calculated automatically. The ICU output is evaluated to capture pressure events and actions taken by clinical staff for patient management, and are then re-expressed as simplified process models. The official TBI guidelines from the Brain Trauma Foundation are similarly evaluated, so the two structures can be compared and a quantifiable distance between the two calculated (the measure of adherence). The methods used include: the compilation of physiological and treatment information into event logs and subsequently process models; the expression of the BTF guidelines in process models within the real-time context of the ICU; a calculation of distance between the two processes using two algorithms (“Direct” and “Weighted”) building on work conducted in th e business process domain. Results are presented across two categories each with clinical utility (minute-by-minute and single patient stays) using a real ICU data-set. Results of two sample patients using a weighted algorithm show a non-adherence level of 6.25% for 42 mins and 56.25% for 708 mins and non-adherence of 18.75% for 17 minutes and 56.25% for 483 minutes. Expressed as two combinatorial metrics (duration/non-adherence (A) and duration * non-adherence (B)), which together indicate the clinical importance of the non-adherence, one has a mean of A=4.63 and B=10014.16 and the other a mean of A=0.43 and B=500.0

Medical Big Data Analysis in Hospital Information System

The rapidly increasing medical data generated from hospital information system (HIS) signifies the era of Big Data in the healthcare domain. These data hold great value to the workflow management, patient care and treatment, scientific research, and education in the healthcare industry. However, the complex, distributed, and highly interdisciplinary nature of medical data has underscored the limitations of traditional data analysis capabilities of data accessing, storage, processing, analyzing, distributing, and sharing. New and efficient technologies are becoming necessary to obtain the wealth of information and knowledge underlying medical Big Data. This chapter discusses medical Big Data analysis in HIS, including an introduction to the fundamental concepts, related platforms and technologies of medical Big Data processing, and advanced Big Data processing technologies

Construction of Empirical Care Pathways Process Models from Multiple Real-World Datasets

Care pathways (CPWs) are "multidisciplinary care plans that detail essential care steps for patients with specific clinical problems." While CPWs impact on health or cost outcomes is vastly studied, an in-depth analysis of the real-world implementation of the CPWs is an area that still remains underexplored. The present work describes how to apply an existing process mining methodology to construct the empirical CPW process models. These process models are a unique piece of information for health services research: for example to evaluate their conformance against the theoretical CPW described on clinical guidelines or to evaluate the impact of the process in health outcomes. To this purpose, this work relies on the design and implementation of a solution that a) synthesizes the expert knowledge on how health care is delivered within and across providers as an activity log, and b) constructs the CPW process model from that activity log using process mining techniques. Unlike previous research based on ad hoc data captures, current approach is built on the linkage of various heterogeneous real-world data (RWD) sets that share a minimum semantic linkage. RWD, defined as secondary use of routinely collected data as opposite to ad hoc data extractions, is a unique source of information for the CPW analysis due to its coverage of the caregiving activities and its wide availability. The viability of the solution is demonstrated by constructing the CPW process model of Code Stroke (Acute Stroke CPW) in the Aragon region (Spain)

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

A Process Modelling Framework Based on Point Interval Temporal Logic with an Application to Modelling Patient Flows

This thesis considers an application of a temporal theory to describe and model the patient journey in the hospital accident and emergency (A&E) department. The aim is to introduce a generic but dynamic method applied to any setting, including healthcare. Constructing a consistent process model can be instrumental in streamlining healthcare issues. Current process modelling techniques used in healthcare such as flowcharts, unified modelling language activity diagram (UML AD), and business process modelling notation (BPMN) are intuitive and imprecise. They cannot fully capture the complexities of the types of activities and the full extent of temporal constraints to an extent where one could reason about the flows. Formal approaches such as Petri have also been reviewed to investigate their applicability to the healthcare domain to model processes. Additionally, to schedule patient flows, current modelling standards do not offer any formal mechanism, so healthcare relies on critical path method (CPM) and program evaluation review technique (PERT), that also have limitations, i.e. finish-start barrier. It is imperative to specify the temporal constraints between the start and/or end of a process, e.g., the beginning of a process A precedes the start (or end) of a process B. However, these approaches failed to provide us with a mechanism for handling these temporal situations. If provided, a formal representation can assist in effective knowledge representation and quality enhancement concerning a process. Also, it would help in uncovering complexities of a system and assist in modelling it in a consistent way which is not possible with the existing modelling techniques. The above issues are addressed in this thesis by proposing a framework that would provide a knowledge base to model patient flows for accurate representation based on point interval temporal logic (PITL) that treats point and interval as primitives. These objects would constitute the knowledge base for the formal description of a system. With the aid of the inference mechanism of the temporal theory presented here, exhaustive temporal constraints derived from the proposed axiomatic system’ components serves as a knowledge base. The proposed methodological framework would adopt a model-theoretic approach in which a theory is developed and considered as a model while the corresponding instance is considered as its application. Using this approach would assist in identifying core components of the system and their precise operation representing a real-life domain deemed suitable to the process modelling issues specified in this thesis. Thus, I have evaluated the modelling standards for their most-used terminologies and constructs to identify their key components. It will also assist in the generalisation of the critical terms (of process modelling standards) based on their ontology. A set of generalised terms proposed would serve as an enumeration of the theory and subsume the core modelling elements of the process modelling standards. The catalogue presents a knowledge base for the business and healthcare domains, and its components are formally defined (semantics). Furthermore, a resolution theorem-proof is used to show the structural features of the theory (model) to establish it is sound and complete. After establishing that the theory is sound and complete, the next step is to provide the instantiation of the theory. This is achieved by mapping the core components of the theory to their corresponding instances. Additionally, a formal graphical tool termed as point graph (PG) is used to visualise the cases of the proposed axiomatic system. PG facilitates in modelling, and scheduling patient flows and enables analysing existing models for possible inaccuracies and inconsistencies supported by a reasoning mechanism based on PITL. Following that, a transformation is developed to map the core modelling components of the standards into the extended PG (PG*) based on the semantics presented by the axiomatic system. A real-life case (from the King’s College hospital accident and emergency (A&E) department’s trauma patient pathway) is considered to validate the framework. It is divided into three patient flows to depict the journey of a patient with significant trauma, arriving at A&E, undergoing a procedure and subsequently discharged. Their staff relied upon the UML-AD and BPMN to model the patient flows. An evaluation of their representation is presented to show the shortfalls of the modelling standards to model patient flows. The last step is to model these patient flows using the developed approach, which is supported by enhanced reasoning and scheduling

Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table