Clinical careflows aided by uncertainty representation models

Serie : Lecture notes in computer science, ISSN 0302-9743, vol. 8073Choosing an appropriate support for Clinical Decision Support Systems is a complicated task, and dependent on the domain in which the system will intervene. The development of wide solutions, which are transversal to different clinical specialties, is impaired by the existence of complex decision moments that reflect the uncertainty and imprecision that are often present in these processes. The need for solutions that combine the relational nature of declarative knowledge with other models, capable of handling that uncertainty, is a necessity that current systems may be faced with. Following this line of thought, this work introduces an ontology for the representation of Clinical Practice Guidelines, with a case-study regarding colorectal cancer. It also presents two models, one based on Bayesian Networks, and another one on Artificial Neural Networks, for colorectal cancer prognosis. The objective is to observe how well these two ways of obtaining and representing knowledge are complementary, and how the machine learning models perform, attending to the available information.This work is funded by National Funds through the FCT Fundacao para a Ciencia e a Tecnologia (Portuguese Foundation for Science and Technology) within project PEst-OE/EEI/UI0752/2011. The work of Tiago Oliveira is supported by a doctoral grant by FCT (SFRH/BD/85291/2012)

A caregiver support platform within the scope of an ambient assisted living ecosystem

The Ambient Assisted Living (AAL) area is in constant evolution, providing new technologies to users and enhancing the level of security and comfort that is ensured by house platforms. The Ambient Assisted Living for All (AAL4ALL) project aims to develop a new AAL concept, supported on a unified ecosystem and certification process that enables a heterogeneous environment. The concepts of Intelligent Environments, Ambient Intelligence, and the foundations of the Ambient Assisted Living are all presented in the framework of this project. In this work, we consider a specific platform developed in the scope of AAL4ALL, called UserAccess. The architecture of the platform and its role within the overall AAL4ALL concept, the implementation of the platform, and the available interfaces are presented. In addition, its feasibility is validated through a series of tests.Project “AAL4ALL”, co-financed by the European Community Fund FEDER, through COMPETE—Programa Operacional Factores de Competitividade (POFC). Foundation for Science and Technology (FCT), Lisbon, Portugal, through Project PEst-C/CTM/LA0025/2013. Project CAMCoF—Context-Aware Multimodal Communication Framework funded by ERDF—European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness) and by National Funds through the FCT—Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project FCOMP-01-0124-FEDER-028980. This work is part-funded by National Funds through the FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) within project PEst-OE/EEI/UI0752/201

SAFE-FLOW : a systematic approach for safety analysis of clinical workflows

The increasing use of technology in delivering clinical services brings substantial benefits to the healthcare industry. At the same time, it introduces potential new complications to clinical workflows that generate new risks and hazards with the potential to affect patients’ safety. These workflows are safety critical and can have a damaging impact on all the involved parties if they fail.Due to the large number of processes included in the delivery of a clinical service, it can be difficult to determine the individuals or the processes that are responsible for adverse events. Using methodological approaches and automated tools to carry out an analysis of the workflow can help in determining the origins of potential adverse events and consequently help in avoiding preventable errors. There is a scarcity of studies addressing this problem; this was a partial motivation for this thesis.The main aim of the research is to demonstrate the potential value of computer science based dependability approaches to healthcare and in particular, the appropriateness and benefits of these dependability approaches to overall clinical workflows. A particular focus is to show that model-based safety analysis techniques can be usefully applied to such areas and then to evaluate this application.This thesis develops the SAFE-FLOW approach for safety analysis of clinical workflows in order to establish the relevance of such application. SAFE-FLOW detailed steps and guidelines for its application are explained. Then, SAFE-FLOW is applied to a case study and is systematically evaluated. The proposed evaluation design provides a generic evaluation strategy that can be used to evaluate the adoption of safety analysis methods in healthcare.It is concluded that safety of clinical workflows can be significantly improved by performing safety analysis on workflow models. The evaluation results show that SAFE-FLOW is feasible and it has the potential to provide various benefits; it provides a mechanism for a systematic identification of both adverse events and safeguards, which is helpful in terms of identifying the causes of possible adverse events before they happen and can assist in the design of workflows to avoid such occurrences. The clear definition of the workflow including its processes and tasks provides a valuable opportunity for formulation of safety improvement strategies

A modular, open-source information extraction framework for identifying clinical concepts and processes of care in clinical narratives

In this thesis, a synthesis is presented of the knowledge models required by clinical informa- tion systems that provide decision support for longitudinal processes of care. Qualitative research techniques and thematic analysis are novelly applied to a systematic review of the literature on the challenges in implementing such systems, leading to the development of an original conceptual framework. The thesis demonstrates how these process-oriented systems make use of a knowledge base derived from workflow models and clinical guidelines, and argues that one of the major barriers to implementation is the need to extract explicit and implicit information from diverse resources in order to construct the knowledge base. Moreover, concepts in both the knowledge base and in the electronic health record (EHR) must be mapped to a common ontological model. However, the majority of clinical guideline information remains in text form, and much of the useful clinical information residing in the EHR resides in the free text fields of progress notes and laboratory reports. In this thesis, it is shown how natural language processing and information extraction techniques provide a means to identify and formalise the knowledge components required by the knowledge base. Original contributions are made in the development of lexico-syntactic patterns and the use of external domain knowledge resources to tackle a variety of information extraction tasks in the clinical domain, such as recognition of clinical concepts, events, temporal relations, term disambiguation and abbreviation expansion. Methods are developed for adapting existing tools and resources in the biomedical domain to the processing of clinical texts, and approaches to improving the scalability of these tools are proposed and evalu- ated. These tools and techniques are then combined in the creation of a novel approach to identifying processes of care in the clinical narrative. It is demonstrated that resolution of coreferential and anaphoric relations as narratively and temporally ordered chains provides a means to extract linked narrative events and processes of care from clinical notes. Coreference performance in discharge summaries and progress notes is largely dependent on correct identification of protagonist chains (patient, clinician, family relation), pronominal resolution, and string matching that takes account of experiencer, temporal, spatial, and anatomical context; whereas for laboratory reports additional, external domain knowledge is required. The types of external knowledge and their effects on system performance are identified and evaluated. Results are compared against existing systems for solving these tasks and are found to improve on them, or to approach the performance of recently reported, state-of-the- art systems. Software artefacts developed in this research have been made available as open-source components within the General Architecture for Text Engineering framework

Clinical decision support: Knowledge representation and uncertainty management

Programa Doutoral em Engenharia BiomédicaDecision-making in clinical practice is faced with many challenges due to the inherent risks of being a health care professional. From medical error to undesired variations in clinical practice, the mitigation of these issues seems to be tightly connected to the adherence to Clinical Practice Guidelines as evidence-based recommendations The deployment of Clinical Practice Guidelines in computational systems for clinical decision support has the potential to positively impact health care. However, current approaches to Computer-Interpretable Guidelines evidence a set of issues that leave them wanting. These issues are related with the lack of expressiveness of their underlying models, the complexity of knowledge acquisition with their tools, the absence of support to the clinical decision making process, and the style of communication of Clinical Decision Support Systems implementing Computer-Interpretable Guidelines. Such issues pose as obstacles that prevent these systems from showing properties like modularity, flexibility, adaptability, and interactivity. All these properties reflect the concept of living guidelines. The purpose of this doctoral thesis is, thus, to provide a framework that enables the expression of these properties. The modularity property is conferred by the ontological definition of Computer-Interpretable Guidelines and the assistance in guideline acquisition provided by an editing tool, allowing for the management of multiple knowledge patterns that can be reused. Flexibility is provided by the representation primitives defined in the ontology, meaning that the model is adjustable to guidelines from different categories and specialities. On to adaptability, this property is conferred by mechanisms of Speculative Computation, which allow the Decision Support System to not only reason with incomplete information but to adapt to changes of state, such as suddenly knowing the missing information. The solution proposed for interactivity consists in embedding Computer-Interpretable Guideline advice directly into the daily life of health care professionals and provide a set of reminders and notifications that help them to keep track of their tasks and responsibilities. All these solutions make the CompGuide framework for the expression of Clinical Decision Support Systems based on Computer-Interpretable Guidelines.A tomada de decisão na prática clínica enfrenta inúmeros desafios devido aos riscos inerentes a ser um profissional de saúde. Desde o erro medico até às variações indesejadas da prática clínica, a atenuação destes problemas parece estar intimamente ligada à adesão a Protocolos Clínicos, uma vez que estes são recomendações baseadas na evidencia. A operacionalização de Protocolos Clínicos em sistemas computacionais para apoio à decisão clínica apresenta o potencial de ter um impacto positivo nos cuidados de saúde. Contudo, as abordagens atuais a Protocolos Clínicos Interpretáveis por Maquinas evidenciam um conjunto de problemas que as deixa a desejar. Estes problemas estão relacionados com a falta de expressividade dos modelos que lhes estão subjacentes, a complexidade da aquisição de conhecimento utilizando as suas ferramentas, a ausência de suporte ao processo de decisão clínica e o estilo de comunicação dos Sistemas de Apoio à Decisão Clínica que implementam Protocolos Clínicos Interpretáveis por Maquinas. Tais problemas constituem obstáculos que impedem estes sistemas de apresentarem propriedades como modularidade, flexibilidade, adaptabilidade e interatividade. Todas estas propriedades refletem o conceito de living guidelines. O propósito desta tese de doutoramento é, portanto, o de fornecer uma estrutura que possibilite a expressão destas propriedades. A modularidade é conferida pela definição ontológica dos Protocolos Clínicos Interpretáveis por Maquinas e pela assistência na aquisição de protocolos fornecida por uma ferramenta de edição, permitindo assim a gestão de múltiplos padrões de conhecimento que podem ser reutilizados. A flexibilidade é atribuída pelas primitivas de representação definidas na ontologia, o que significa que o modelo é ajustável a protocolos de diferentes categorias e especialidades. Quanto à adaptabilidade, esta é conferida por mecanismos de Computação Especulativa que permitem ao Sistema de Apoio à Decisão não só raciocinar com informação incompleta, mas também adaptar-se a mudanças de estado, como subitamente tomar conhecimento da informação em falta. A solução proposta para a interatividade consiste em incorporar as recomendações dos Protocolos Clínicos Interpretáveis por Maquinas diretamente no dia a dia dos profissionais de saúde e fornecer um conjunto de lembretes e notificações que os auxiliam a rastrear as suas tarefas e responsabilidades. Todas estas soluções constituem a estrutura CompGuide para a expressão de Sistemas de Apoio à Decisão Clínica baseados em Protocolos Clínicos Interpretáveis por Máquinas.The work of the PhD candidate Tiago José Martins Oliveira is supported by a grant from FCT - Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) with the reference SFRH/BD/85291/ 2012

Process mining : conformance and extension

Today’s business processes are realized by a complex sequence of tasks that are performed throughout an organization, often involving people from different departments and multiple IT systems. For example, an insurance company has a process to handle insurance claims for their clients, and a hospital has processes to diagnose and treat patients. Because there are many activities performed by different people throughout the organization, there is a lack of transparency about how exactly these processes are executed. However, understanding the process reality (the "as is" process) is the first necessary step to save cost, increase quality, or ensure compliance. The field of process mining aims to assist in creating process transparency by automatically analyzing processes based on existing IT data. Most processes are supported by IT systems nowadays. For example, Enterprise Resource Planning (ERP) systems such as SAP log all transaction information, and Customer Relationship Management (CRM) systems are used to keep track of all interactions with customers. Process mining techniques use these low-level log data (so-called event logs) to automatically generate process maps that visualize the process reality from different perspectives. For example, it is possible to automatically create process models that describe the causal dependencies between activities in the process. So far, process mining research has mostly focused on the discovery aspect (i.e., the extraction of models from event logs). This dissertation broadens the field of process mining to include the aspect of conformance and extension. Conformance aims at the detection of deviations from documented procedures by comparing the real process (as recorded in the event log) with an existing model that describes the assumed or intended process. Conformance is relevant for two reasons: 1. Most organizations document their processes in some form. For example, process models are created manually to understand and improve the process, comply with regulations, or for certification purposes. In the presence of existing models, it is often more important to point out the deviations from these existing models than to discover completely new models. Discrepancies emerge because business processes change, or because the models did not accurately reflect the real process in the first place (due to the manual and subjective creation of these models). If the existing models do not correspond to the actual processes, then they have little value. 2. Automatically discovered process models typically do not completely "fit" the event logs from which they were created. These discrepancies are due to noise and/or limitations of the used discovery techniques. Furthermore, in the context of complex and diverse process environments the discovered models often need to be simplified to obtain useful insights. Therefore, it is crucial to be able to check how much a discovered process model actually represents the real process. Conformance techniques can be used to quantify the representativeness of a mined model before drawing further conclusions. They thus constitute an important quality measurement to effectively use process discovery techniques in a practical setting. Once one is confident in the quality of an existing or discovered model, extension aims at the enrichment of these models by the integration of additional characteristics such as time, cost, or resource utilization. By extracting aditional information from an event log and projecting it onto an existing model, bottlenecks can be highlighted and correlations with other process perspectives can be identified. Such an integrated view on the process is needed to understand root causes for potential problems and actually make process improvements. Furthermore, extension techniques can be used to create integrated simulation models from event logs that resemble the real process more closely than manually created simulation models. In Part II of this thesis, we provide a comprehensive framework for the conformance checking of process models. First, we identify the evaluation dimensions fitness, decision/generalization, and structure as the relevant conformance dimensions.We develop several Petri-net based approaches to measure conformance in these dimensions and describe five case studies in which we successfully applied these conformance checking techniques to real and artificial examples. Furthermore, we provide a detailed literature review of related conformance measurement approaches (Chapter 4). Then, we study existing model evaluation approaches from the field of data mining. We develop three data mining-inspired evaluation approaches for discovered process models, one based on Cross Validation (CV), one based on the Minimal Description Length (MDL) principle, and one using methods based on Hidden Markov Models (HMMs). We conclude that process model evaluation faces similar yet different challenges compared to traditional data mining. Additional challenges emerge from the sequential nature of the data and the higher-level process models, which include concurrent dynamic behavior (Chapter 5). Finally, we point out current shortcomings and identify general challenges for conformance checking techniques. These challenges relate to the applicability of the conformance metric, the metric quality, and the bridging of different process modeling languages. We develop a flexible, language-independent conformance checking approach that provides a starting point to effectively address these challenges (Chapter 6). In Part III, we develop a concrete extension approach, provide a general model for process extensions, and apply our approach for the creation of simulation models. First, we develop a Petri-net based decision mining approach that aims at the discovery of decision rules at process choice points based on data attributes in the event log. While we leverage classification techniques from the data mining domain to actually infer the rules, we identify the challenges that relate to the initial formulation of the learning problem from a process perspective. We develop a simple approach to partially overcome these challenges, and we apply it in a case study (Chapter 7). Then, we develop a general model for process extensions to create integrated models including process, data, time, and resource perspective.We develop a concrete representation based on Coloured Petri-nets (CPNs) to implement and deploy this model for simulation purposes (Chapter 8). Finally, we evaluate the quality of automatically discovered simulation models in two case studies and extend our approach to allow for operational decision making by incorporating the current process state as a non-empty starting point in the simulation (Chapter 9). Chapter 10 concludes this thesis with a detailed summary of the contributions and a list of limitations and future challenges. The work presented in this dissertation is supported and accompanied by concrete implementations, which have been integrated in the ProM and ProMimport frameworks. Appendix A provides a comprehensive overview about the functionality of the developed software. The results presented in this dissertation have been presented in more than twenty peer-reviewed scientific publications, including several high-quality journals

The strategic value of targeted knowledge management - case study of an Australian refrigeration company

 This thesis is a study of design and implementation of an engineering knowledge management system to facilitate knowledge capture, sharing and reuse to both ensure business continuity and resolve a make-span problem in an Australian refrigeration company. The company had encountered problems with a number of engineering staff in the small product development team leaving the company and taking their expertise with them. This situation has impacted the business continuity of the company, because the knowledge and expertise used in the refrigerated display cabinet development process is a combination of explicit and tacit knowledge as the engineers conduct the product development process intuitively. Records of previous design and testing processes were either non-existent or stored in ways that were not accessible. The other business problem in the company resulted from product development taking too long, in effect from 6 weeks up to the worst case of one year. The company needed research solutions to both of these problems to strategically maintain the competitiveness of the company business. This research applied a single case study research method with a problem-solving paradigm, Design Science methodology, to develop and then test solutions. Design Science as a research methodology has two components, first design development and second, design evaluation. The researcher developed an engineering knowledge based system as an artefact to solve the problem of enabling company business continuity. Using ontology as a structural base, the KBS contains both knowledge elements captured from the engineers during the data collection process and existing knowledge artefacts in the company. The research used a set of multilayered research techniques, including semi-formal and formal interviews, serendipitous interviews, group meetings, observation and shadowing, to capture and then structure both the tacit and explicit knowledge. The resultant ontology was used to build the KBS to store both tacit and explicit knowledge and answer the engineers’ questions about their existing and previous product development processes. The KBS developed in this research is a knowledge repository to maintain records of the products design and testing processes in a searchable form. Use and then an evaluation of the system by the engineers and the executive staff of the company confirmed that the intention of the system to address the business continuity problem by knowledge capture, classification and storage was achieved and met the company’s business needs. This research also applied Heuristic Process Mining to the knowledge stored in the KBS to address the second problem identified initially by the company, that of lengthy make span in new product design and development. HPM is a technique using mathematical models to find relationships between tasks in the process. HMP measures dependency and frequency values between tasks and tasks with low D/F value can be eliminated from the process. This then can lead to the shorter product testing process. The research showed that the application of HPM to the stored process knowledge in the KMS was able to significantly reduce the product design and testing process in the company

Aide à la conception de workflows personnalisés : application à la prise en charge à domicile

Aujourd'hui, les TIC sont reconnues comme un élément inéluctable pour améliorer les pratiques et les usages du secteur de la santé et particulièrement celui de la PAD. Cependant, malgré tout l'engouement et les avancés accomplies dans ce domaine, un problème de coordination et de continuité des soins personnalisés aux patients subsiste toujours. Un système de gestion de workflow semble approprié pour assurer cette coordination de la PAD. Toutefois, les caractéristiques des processus de la PAD, que nous avons identifié, compliquent la conception de ce workflow. En effet, le processus de la PAD a la particularité d'être un processus, personnalisé pour chaque patient, collaboratif évoluant dans un environnement très dynamique et incertain avec une forte contrainte temporelle. Dans le but d'améliorer la coordination en tenant compte des caractéristiques des processus de la PAD, nous avons proposé une approche de conception d'un workflow personnalisé basé sur les modèles de connaissances et guidée par une approche dirigée par les modèles. Cette approche préconise l'utilisation d'ontologies du domaine de la PAD et du BPMN dans un processus de transformations qui aboutit à la conception d'un workflow personnalisé pour un patient donnée selon son profil. Les travaux développés dans ce mémoire présentent une partie de cette approche qui consiste à construire un processus BPMN personnalisé. Les contributions, que nous y exposons sont : premièrement, la conception d'une ontologie du domaine de la PAD. Cette ontologie inclut : le profil patient (pathologie, entourage, environnement,...), l'aspect organisationnel de la PAD (le rôle de chaque intervenant) et le traitement ou les interventions nécessaires pour chaque pathologie. Deuxièmement une proposition de règles de correspondances entre les termes du domaine de la PAD et du BPMN. Finalement des requêtes permettant la conception d'un processus BPMN personnalisé. Cette approche a été testée sur un cas d'étude de la PAD qui montre son bon fonctionnement.Today, ICT is recognized as a requirement to improve the practices of the health sector and particularly the home care area. However, despite all the advances accomplished in this field, a problem of coordination and continuity of personalized care remains. A workflow management system seems appropriate to ensure the coordination of home care. However, the characteristics of the home care processes complicate the design of the workflow. Indeed, the processes of home care need to be customized for each patient, collaborative, evolving in a very dynamic and uncertain environment with a strong time constraint. In order to improve the coordination taking into account the characteristics of the home care process, we propose an approach to design a custom workflow models based on knowledge and guided by a model driven approach. This approach advocates the use of ontologies in the field of home care and BPMN into a process of transformation that leads to the design of a custom workflow for a given patient according to his profile. The work developed in this thesis are part of this approach is to build a customized BPMN process. Contributions are: first, the design of an ontology for home care. This ontology includes: patient profile (pathology, environment, ...), the organizational aspect of the home care (the role of each actor) and the treatment or interventions necessary for each pathology. Secondly, a proposal of correspondence rules between the terms in the field of home care and BPMN. Finally queries are performed to design a customized BPMN process. This approach has been tested on a significative case study