Predictive gene lists for breast cancer prognosis: a topographic visualisation study

Background: The controversy surrounding the non-uniqueness of predictive gene lists (PGL) of small selected subsets of genes from very large potential candidates as available in DNA microarray experiments is now widely acknowledged 1. Many of these studies have focused on constructing discriminative semi-parametric models and as such are also subject to the issue of random correlations of sparse model selection in high dimensional spaces. In this work we outline a different approach based around an unsupervised patient-specific nonlinear topographic projection in predictive gene lists. Methods: We construct nonlinear topographic projection maps based on inter-patient gene-list relative dissimilarities. The Neuroscale, the Stochastic Neighbor Embedding(SNE) and the Locally Linear Embedding(LLE) techniques have been used to construct two-dimensional projective visualisation plots of 70 dimensional PGLs per patient, classifiers are also constructed to identify the prognosis indicator of each patient using the resulting projections from those visualisation techniques and investigate whether a-posteriori two prognosis groups are separable on the evidence of the gene lists. A literature-proposed predictive gene list for breast cancer is benchmarked against a separate gene list using the above methods. Generalisation ability is investigated by using the mapping capability of Neuroscale to visualise the follow-up study, but based on the projections derived from the original dataset. Results: The results indicate that small subsets of patient-specific PGLs have insufficient prognostic dissimilarity to permit a distinction between two prognosis patients. Uncertainty and diversity across multiple gene expressions prevents unambiguous or even confident patient grouping. Comparative projections across different PGLs provide similar results. Conclusion: The random correlation effect to an arbitrary outcome induced by small subset selection from very high dimensional interrelated gene expression profiles leads to an outcome with associated uncertainty. This continuum and uncertainty precludes any attempts at constructing discriminative classifiers. However a patient's gene expression profile could possibly be used in treatment planning, based on knowledge of other patients' responses. We conclude that many of the patients involved in such medical studies are intrinsically unclassifiable on the basis of provided PGL evidence. This additional category of 'unclassifiable' should be accommodated within medical decision support systems if serious errors and unnecessary adjuvant therapy are to be avoided.

Clinical decision support system for point of care use: ontology driven design and software implementation

OBJECTIVES: The objective of this research was to design a clinical decision support system (CDSS) that supports heterogeneous clinical decision problems and runs on multiple computing platforms. Meeting this objective required a novel design to create an extendable and easy to maintain clinical CDSS for point of care support. The proposed solution was evaluated in a proof of concept implementation. METHODS: Based on our earlier research with the design of a mobile CDSS for emergency triage we used ontology-driven design to represent essential components of a CDSS. Models of clinical decision problems were derived from the ontology and they were processed into executable applications during runtime. This allowed scaling applications' functionality to the capabilities of computing platforms. A prototype of the system was implemented using the extended client-server architecture and Web services to distribute the functions of the system and to make it operational in limited connectivity conditions. RESULTS: The proposed design provided a common framework that facilitated development of diversified clinical applications running seamlessly on a variety of computing platforms. It was prototyped for two clinical decision problems and settings (triage of acute pain in the emergency department and postoperative management of radical prostatectomy on the hospital ward) and implemented on two computing platforms-desktop and handheld computers. CONCLUSIONS: The requirement of the CDSS heterogeneity was satisfied with ontology-driven design. Processing of application models described with the help of ontological models allowed having a complex system running on multiple computing platforms with different capabilities. Finally, separation of models and runtime components contributed to improved extensibility and maintainability of the system.

Knowledge engineering for mental-health risk assessment and decision support

Mental-health risk assessment practice in the UK is mainly paper-based, with little standardisation in the tools that are used across the Services. The tools that are available tend to rely on minimal sets of items and unsophisticated scoring methods to identify at-risk individuals. This means the reasoning by which an outcome has been determined remains uncertain. Consequently, there is little provision for: including the patient as an active party in the assessment process, identifying underlying causes of risk, and eecting shared decision-making. This thesis develops a tool-chain for the formulation and deployment of a computerised clinical decision support system for mental-health risk assessment. The resultant tool, GRiST, will be based on consensual domain expert knowledge that will be validated as part of the research, and will incorporate a proven psychological model of classication for risk computation. GRiST will have an ambitious remit of being a platform that can be used over the Internet, by both the clinician and the layperson, in multiple settings, and in the assessment of patients with varying demographics. Flexibility will therefore be a guiding principle in the development of the platform, to the extent that GRiST will present an assessment environment that is tailored to the circumstances in which it nds itself. XML and XSLT will be the key technologies that help deliver this exibility.

Decision support system for spare parts warehousing

Spare parts warehousing decision-making plays an important role in today's manufacturing industry as it derives an optimum inventory policy for the organizations. Previous research on spare parts warehousing decision-making did not deal with the problem holistically considering all the subjective and objective criteria of operational and strategic needs of the manufacturing companies in the process industry. This study reviews current relevant literature and develops a conceptual framework (an integrated group decision support system) for selecting the most effective warehousing option for the process industry using the analytic hierarchy process (AHP). The framework has been applied to a multinational cement manufacturing company in the UK. Three site visits, eight formal interviews, and several discussions have been undertaken with personnel of the organization, many of which have more than 20 years of experience, in order to apply the proposed decision support system (DSS). Subsequently, the DSS has been validated through a questionnaire survey in order to establish its usefulness, effectiveness for warehousing decision-making, and the possibility of adoption. The proposed DSS is an integrated framework for selecting the best warehousing option for business excellence in any manufacturing organization.

IT as enabler of sustainable farming:an empirical analysis of farmers' adoption decision of precision agriculture technology

Precision agriculture (PA) describes a suite of IT based tools which allow farmers to electronically monitor soil and crop conditions and analyze treatment options. This study tests a model explaining the difficulties of PA technology adoption. The model draws on theories of technology acceptance and diffusion of innovation and is validated using survey data from farms in Canada. Findings highlight the importance of compatibility among PA technology components and the crucial role of farmers' expertise. The model provides the theoretical and empirical basis for developing policies and initiatives to support PA technology adoption.

Decision support and the criminal justice system:an assessment of the potential for utilising technological decision support in undertaking the prosecutorial decision

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Development of a total system simulation modelling approach for management decision support

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Psychological cue use and implications for a clinical decision support system

Effective clinical decision making depends upon identifying possible outcomes for a patient, selecting relevant cues, and processing the cues to arrive at accurate judgements of each outcome's probability of occurrence. These activities can be considered as classification tasks. This paper describes a new model of psychological classification that explains how people use cues to determine class or outcome likelihoods. It proposes that clinicians respond to conditional probabilities of outcomes given cues and that these probabilities compete with each other for influence on classification. The model explains why people appear to respond to base rates inappropriately, thereby overestimating the occurrence of rare categories, and a clinical example is provided for predicting suicide risk. The model makes an effective representation for expert clinical judgements and its psychological validity enables it to generate explanations in a form that is comprehensible to clinicians. It is a strong candidate for incorporation within a decision support system for mental-health risk assessment, where it can link with statistical and pattern recognition tools applied to a database of patients. The symbiotic combination of empirical evidence and clinical expertise can provide an important web-based resource for risk assessment, including multi-disciplinary education and training. © 2002 Informa UK Ltd All rights reserved.

Decision support system for pipeline route selection

Presents information on a study which proposed a decision support system (DSS) for a petroleum pipeline route selection with the application of analytical hierarchy process. Factors governing route-selection for cross-country petroleum pipelines; Application of the DSS from an Indian perspective; Cost benefit comparison of the shortest route and the optimal route; Results and findings.

Investigating mental health risk assessment in primary care and the potential role of a structured decision support tool, GRiST

Aim: To explore current risk assessment processes in general practice and Improving Access to Psychological Therapies (IAPT) services, and to consider whether the Galatean Risk and Safety Tool (GRiST) can help support improved patient care. Background: Much has been written about risk assessment practice in secondary mental health care, but little is known about how it is undertaken at the beginning of patients' care pathways, within general practice and IAPT services. Methods: Interviews with eight general practice and eight IAPT clinicians from two primary care trusts in the West Midlands, UK, and eight service users from the same region. Interviews explored current practice and participants' views and experiences of mental health risk assessment. Two focus groups were also carried out, one with general practice and one with IAPT clinicians, to review interview findings and to elicit views about GRiST from a demonstration of its functionality. Data were analysed using thematic analysis. Findings Variable approaches to mental health risk assessment were observed. Clinicians were anxious that important risk information was being missed, and risk communication was undermined. Patients felt uninvolved in the process, and both clinicians and patients expressed anxiety about risk assessment skills. Clinicians were positive about the potential for GRiST to provide solutions to these problems. Conclusions: A more structured and systematic approach to risk assessment in general practice and IAPT services is needed, to ensure important risk information is captured and communicated across the care pathway. GRiST has the functionality to support this aspect of practice.

Case-based Reasoning Method for Real-time Expert Diagnostics Systems

The method of case-based reasoning for a solution of problems of real-time diagnostics and forecasting in intelligent decision support systems (IDSS) is considered. Special attention is drawn to case library structure for real-time IDSS (RT IDSS) and algorithm of k-nearest neighbors type. This work was supported by RFBR.

Support tools for paediatric inpatient prescribers:a review

Prescribing support for paediatrics is diverse and includes both standard texts and electronic tools. Evidence concerning who should be supported and by what method is limited. This review aims to collate the current information available on prescribing support in paediatrics. Many tools designed to support prescribers are technology based. For example, electronic prescribing and smart phone applications. There is a focus on prescriber education both at undergraduate and postgraduate level. In the UK, the majority of inpatient prescribing is done by junior medical staff. It is important to ensure they are competent on qualification and supported in this role. A UK national prescribing assessment is being trialled to test for competence on graduation and there are also tools available to test paediatric prescribing after qualification. No information is available on the tools and resources UK prescribers currently use to support their decision making. One US study reported a decrease in the availability of paediatric prescribing information in a popular reference text. There is limited evidence to show that decisionsupport tools improve patient outcomes, however, there is growing confirmation that electronic prescribing reduces medication errors. There have been reports of new error types, such as selection errors, occurring with the use of electronic prescribing. Another concern with computerised decision-support systems is deciding what alerts should be presented to the prescriber and when/how often in order to avoid alert fatigue. There is little published concerning paediatric alerts perhaps as a consequence of commercial systems often not including paediatric specific support.

A decision support system for supplier selection and order allocation in stochastic, multi-stakeholder and multi-criteria environments

Integrated supplier selection and order allocation is an important decision for both designing and operating supply chains. This decision is often influenced by the concerned stakeholders, suppliers, plant operators and customers in different tiers. As firms continue to seek competitive advantage through supply chain design and operations they aim to create optimized supply chains. This calls for on one hand consideration of multiple conflicting criteria and on the other hand consideration of uncertainties of demand and supply. Although there are studies on supplier selection using advanced mathematical models to cover a stochastic approach, multiple criteria decision making techniques and multiple stakeholder requirements separately, according to authors' knowledge there is no work that integrates these three aspects in a common framework. This paper proposes an integrated method for dealing with such problems using a combined Analytic Hierarchy Process-Quality Function Deployment (AHP-QFD) and chance constrained optimization algorithm approach that selects appropriate suppliers and allocates orders optimally between them. The effectiveness of the proposed decision support system has been demonstrated through application and validation in the bioenergy industry.

A Real-time Decision Support System Prototype for Management of a Power Block

This paper describes the basic tools for a real-time decision support system of a semiotic type on the example of the prototype for management and monitoring of a nuclear power block implemented on the basis of the tool complex G2+GDA using cognitive graphics and parallel processing. This work was supported by RFBR (project 02-07-90042).