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.

Integrated project evaluation and selection using multiple-attribute decision-making technique

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again till the statutory regulatory authority approves the project. Moreover, project analysis through above process often results sub-optimal project as financial analysis may eliminate better options, as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system, which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple-attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2005 Elsevier B.V. All rights reserved.

Multiple attribute decision making approach to petroleum pipeline route selection

Petroleum pipelines are the nervous system of the oil industry, as this transports crude oil from sources to refineries and petroleum products from refineries to demand points. Therefore, the efficient operation of these pipelines determines the effectiveness of the entire business. Pipeline route selection plays a major role when designing an effective pipeline system, as the health of the pipeline depends on its terrain. The present practice of route selection for petroleum pipelines is governed by factors such as the shortest distance, constructability, minimal effects on the environment, and approachability. Although this reduces capital expenditure, it often proves to be uneconomical when life cycle costing is considered. This study presents a route selection model with the application of an Analytic Hierarchy Process (AHP), a multiple attribute decision making technique. AHP considers all the above factors along with the operability and maintainability factors interactively. This system has been demonstrated here through a case study of pipeline route selection, from an Indian perspective. A cost-benefit comparison of the shortest route (conventionally selected) and optimal route establishes the effectiveness of the model.

The dynamics of a genetic algorithm under stabilizing selection

A formalism recently introduced by Prugel-Bennett and Shapiro uses the methods of statistical mechanics to model the dynamics of genetic algorithms. To be of more general interest than the test cases they consider. In this paper, the technique is applied to the subset sum problem, which is a combinatorial optimization problem with a strongly non-linear energy (fitness) function and many local minima under single spin flip dynamics. It is a problem which exhibits an interesting dynamics, reminiscent of stabilizing selection in population biology. The dynamics are solved under certain simplifying assumptions and are reduced to a set of difference equations for a small number of relevant quantities. The quantities used are the population's cumulants, which describe its shape, and the mean correlation within the population, which measures the microscopic similarity of population members. Including the mean correlation allows a better description of the population than the cumulants alone would provide and represents a new and important extension of the technique. The formalism includes finite population effects and describes problems of realistic size. The theory is shown to agree closely to simulations of a real genetic algorithm and the mean best energy is accurately predicted.

Decision support system for project selection

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical, and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again until the statutory regulatory authority approves the project. Moreover, project analysis through the above process often results in suboptimal projects as financial analysis may eliminate better options as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select an optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2008, IGI Global.

Selection of power market structure using the analytic hierarchy process

Selection of a power market structure from the available alternatives is an important activity within an overall power sector reform programme. The evaluation criteria for selection are both subjective as well as objective in nature and the selection of alternatives is characterised by their conflicting nature. This study demonstrates a methodology for power market structure selection using the analytic hierarchy process (AHP), a multiple attribute decision-making technique, to model the selection methodology with the active participation of relevant stakeholders in a workshop environment. The methodology is applied to a hypothetical case of a State Electricity Board reform in India.

Risk-based model aids selection of pipeline inspection, maintenance strategies

The existing method of pipeline monitoring, which requires an entire pipeline to be inspected periodically, wastes time and is expensive. A risk-based model that reduces the amount of time spent on inspection has been developed. This model not only reduces the cost of maintaining petroleum pipelines, but also suggests an efficient design and operation philosophy, construction method and logical insurance plans.The risk-based model uses analytic hierarchy process, a multiple attribute decision-making technique, to identify factors that influence failure on specific segments and analyze their effects by determining the probabilities of risk factors. The severity of failure is determined through consequence analysis, which establishes the effect of a failure in terms of cost caused by each risk factor and determines the cumulative effect of failure through probability analysis.