Representing temporal patterns in computer-interpretable clinical Guidelines

Computer-interpretable Guidelines (CIGs) as machine-readable versions of clinical protocols have to provide appropriate constructs for the representation of different aspects of medical knowledge, namely administrative information, workflows of procedures, clinical constraints and temporal constraints. This work focuses on the latter, by aiming to develop a comprehensive representation of temporal constraints for machine readable formats of clinical protocols and provide a proper execution engine that deals with different time patterns and constraints placed on them. A model for the representation of time is presented for the CompGuide ontology in Ontology Web language (OWL) along with a comparison with the available formalisms in this field.This work is part-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 and project Scope UID/CEC/00319/2013.The work of Tiago Oliveira is supported by a FCT grant with the reference SFRH/BD/85291/2012.info:eu-repo/semantics/publishedVersio

Computerization of workflows, guidelines and care pathways: a review of implementation challenges for process-oriented health information systems

There is a need to integrate the various theoretical frameworks and formalisms for modeling clinical guidelines, workflows, and pathways, in order to move beyond providing support for individual clinical decisions and toward the provision of process-oriented, patient-centered, health information systems (HIS). In this review, we analyze the challenges in developing process-oriented HIS that formally model guidelines, workflows, and care pathways. A qualitative meta-synthesis was performed on studies published in English between 1995 and 2010 that addressed the modeling process and reported the exposition of a new methodology, model, system implementation, or system architecture. Thematic analysis, principal component analysis (PCA) and data visualisation techniques were used to identify and cluster the underlying implementation ‘challenge’ themes. One hundred and eight relevant studies were selected for review. Twenty-five underlying ‘challenge’ themes were identified. These were clustered into 10 distinct groups, from which a conceptual model of the implementation process was developed. We found that the development of systems supporting individual clinical decisions is evolving toward the implementation of adaptable care pathways on the semantic web, incorporating formal, clinical, and organizational ontologies, and the use of workflow management systems. These architectures now need to be implemented and evaluated on a wider scale within clinical settings

Optimized Time Management for Declarative Workflows

Declarative process models are increasingly used since they fit better with the nature of flexible process-aware information systems and the requirements of the stakeholders involved. When managing business processes, in addition, support for representing time and reasoning about it becomes crucial. Given a declarative process model, users may choose among different ways to execute it, i.e., there exist numerous possible enactment plans, each one presenting specific values for the given objective functions (e.g., overall completion time). This paper suggests a method for generating optimized enactment plans (e.g., plans minimizing overall completion time) from declarative process models with explicit temporal constraints. The latter covers a number of well-known workflow time patterns. The generated plans can be used for different purposes like providing personal schedules to users, facilitating early detection of critical situations, or predicting execution times for process activities. The proposed approach is applied to a range of test models of varying complexity. Although the optimization of process execution is a highly constrained problem, results indicate that our approach produces a satisfactory number of suitable solutions, i.e., solutions optimal in many cases

Deep learning cardiac motion analysis for human survival prediction

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival

The role of ontologies and decision frameworks in computer-interpretable guideline execution

Computer-Interpretable Guidelines (CIGs) are machine readable representations of Clinical Practice Guidelines (CPGs) that serve as the knowledge base in many knowledge-based systems oriented towards clinical decision support. Herein we disclose a comprehensive CIG representation model based on Web Ontology Language (OWL) along with its main components. Additionally, we present results revealing the expressiveness of the model regarding a selected set of CPGs. The CIG model then serves as the basis of an architecture for an execution system that is able to manage incomplete information regarding the state of a patient through Speculative Computation. The architecture allows for the generation of clinical scenarios when there is missing information for clinical parameters.FCT - Fundação para a Ciência e a Tecnologia (SFRH/BD/85291/ 2012)info:eu-repo/semantics/publishedVersio

Conflict resolution in clinical treatments

Dissertação de mestrado integrado em Engenharia InformáticaCurrently, in the health area, there is a need for systems that provide support for the decision of health professionals through specific recommendations for each patient based on Clinical Practice Guidelines (CPGs) for automatic interpretation. CPGs are documents that have enormous importance in the daily life of health professionals, playing a key role in reducing variations in medical practice, improving the quality of health care, and reducing health care costs. These documents reflect knowledge about how best to diagnose and treat diseases in the form of a list of clinical recommendations. However, there may be conflicts and interactions in the application of these clinical recommendations, that which in their maximum exponent may impair the patient’s clinical condition. These conflicts are transported to decision support systems, creating the need to develop computational methods to solve these same conflicts. In the case of multimorbid patients, this resolution of conflicts can be very problematic because these patients suffer from several pathologies at the same time, and that the use of a drug for one particular pathology may have a detrimental effect on the application of another drug in another pathology. Therefore, the objective of this dissertation topic is the determination of conflicts and interactions between drugs and the determination of these same alternatives.Atualmente na área da saúde, existe uma necessidade de existirem sistemas que forneçam apoio à decisão dos profissionais de saúde através de recomendações específicas para cada paciente com base em protocolos clínicos para interpretação automática. Os protocolos clínicos são documentos que têm enorme importância no dia-a-dia dos profissionais de saúde, desempenhando um papel fundamental na redução das variações na prática médica, na melhoria da qualidade dos cuidados de saúde e na redução dos custos de saúde. Estes documentos reflectem o conhecimento sobre a melhor forma de diagnosticar e tratar doenças na forma de uma lista de recomendações clínicas. Contudo, podem existir conflitos e interações na aplicação destas recomendações clínicas, que no seu expoente máximo poderão levar a um agravamento do estado clínico do paciente, nomeadamente no caso da aplicação de diferentes fármacos. Estes conflitos são transportados para os sistemas de apoio à decisão, criando a necessidade de desenvolver métodos computacionais de resolução destes mesmos conflitos. No caso dos pacientes multimórbidos esta resolução de conflitos pode ser bastante problemática devido ao facto destes pacientes sofrerem de várias patologias ao mesmo tempo, e que a utilização de um fármaco para uma determinada patologia possa vir a ter um efeito nocivo na aplicação de outro fármaco noutra patologia. Sendo assim, o objetivo deste tema de dissertação é a determinação dos conflitos e interações entre fármacos e a determinação dessas mesmas alternativas

Big data analytics:Computational intelligence techniques and application areas

Big Data has significant impact in developing functional smart cities and supporting modern societies. In this paper, we investigate the importance of Big Data in modern life and economy, and discuss challenges arising from Big Data utilization. Different computational intelligence techniques have been considered as tools for Big Data analytics. We also explore the powerful combination of Big Data and Computational Intelligence (CI) and identify a number of areas, where novel applications in real world smart city problems can be developed by utilizing these powerful tools and techniques. We present a case study for intelligent transportation in the context of a smart city, and a novel data modelling methodology based on a biologically inspired universal generative modelling approach called Hierarchical Spatial-Temporal State Machine (HSTSM). We further discuss various implications of policy, protection, valuation and commercialization related to Big Data, its applications and deployment

A comprehensive clinical guideline model and a reasoning mechanism for AAL systems

The progressive ageing of population combined with the need for comfort in situations of disease and disability are pushing healthcare organizations and governments to find new solutions to enable people to live longer in their preferred environment, while having access to quality healthcare services. iGenda is an Ambient Assisted Living platform that provides constant monitoring to people with this type of needs. The use of a Computer-Interpretable Guideline model for decision making is one of the features of this platform. The model used to represent Clinical Practice Guidelines gathers a set of features that make guidelines more dynamic and easily implementable. The model is defined using Ontology Web Language, profiting from the existing constructors provided by this language. It is based on a set of primitive tasks, namely Plans, Actions, Questions and Decisions. Focusing on decision support, a method for dealing with incomplete information about the clinical parameters of a health record is presented. The objective is to keep a continuous flow of information through the decision process and assuring that an outcome is always achieved. The usefulness of the integration of guideline recommendations with a reason mechanism capable of handling incomplete information is demonstrated through a case study about the diagnosis of metabolic syndrome.(undefined