31,156 research outputs found

    Knowledge-based gene expression classification via matrix factorization

    Get PDF
    Motivation: Modern machine learning methods based on matrix decomposition techniques, like independent component analysis (ICA) or non-negative matrix factorization (NMF), provide new and efficient analysis tools which are currently explored to analyze gene expression profiles. These exploratory feature extraction techniques yield expression modes (ICA) or metagenes (NMF). These extracted features are considered indicative of underlying regulatory processes. They can as well be applied to the classification of gene expression datasets by grouping samples into different categories for diagnostic purposes or group genes into functional categories for further investigation of related metabolic pathways and regulatory networks. Results: In this study we focus on unsupervised matrix factorization techniques and apply ICA and sparse NMF to microarray datasets. The latter monitor the gene expression levels of human peripheral blood cells during differentiation from monocytes to macrophages. We show that these tools are able to identify relevant signatures in the deduced component matrices and extract informative sets of marker genes from these gene expression profiles. The methods rely on the joint discriminative power of a set of marker genes rather than on single marker genes. With these sets of marker genes, corroborated by leave-one-out or random forest cross-validation, the datasets could easily be classified into related diagnostic categories. The latter correspond to either monocytes versus macrophages or healthy vs Niemann Pick C disease patients.Siemens AG, MunichDFG (Graduate College 638)DAAD (PPP Luso - Alem˜a and PPP Hispano - Alemanas

    Accuracy, Scalability, and Efficiency of Mixed-Element USM3D for Benchmark Three-Dimensional Flows

    Get PDF
    The unstructured, mixed-element, cell-centered, finite-volume flow solver USM3D is enhanced with new capabilities including parallelization, line generation for general unstructured grids, improved discretization scheme, and optimized iterative solver. The paper reports on the new developments to the flow solver and assesses the accuracy, scalability, and efficiency. The USM3D assessments are conducted using a baseline method and the recent hierarchical adaptive nonlinear iteration method framework. Two benchmark turbulent flows, namely, a subsonic separated flow around a three-dimensional hemisphere-cylinder configuration and a transonic flow around the ONERA M6 wing are considered

    A Spatial Agent-Based Model of N-Person Prisoner's Dilemma Cooperation in a Socio-Geographic Community

    Get PDF
    The purpose of this paper is to present a spatial agent-based model of N-person prisoner's dilemma that is designed to simulate the collective communication and cooperation within a socio-geographic community. Based on a tight coupling of REPAST and a vector Geographic Information System, the model simulates the emergence of cooperation from the mobility behaviors and interaction strategies of citizen agents. To approximate human behavior, the agents are set as stochastic learning automata with Pavlovian personalities and attitudes. A review of the theory of the standard prisoner's dilemma, the iterated prisoner's dilemma, and the N-person prisoner's dilemma is given as well as an overview of the generic architecture of the agent-based model. The capabilities of the spatial N-person prisoner's dilemma component are demonstrated with several scenario simulation runs for varied initial cooperation percentages and mobility dynamics. Experimental results revealed that agent mobility and context preservation bring qualitatively different effects to the evolution of cooperative behavior in an analyzed spatial environment.Agent Based Modeling, Cooperation, Prisoners Dilemma, Spatial Interaction Model, Spatially Structured Social Dilemma, Geographic Information Systems

    Outcome prediction based on microarray analysis: a critical perspective on methods

    Get PDF
    <p>Abstract</p> <p>Background</p> <p>Information extraction from microarrays has not yet been widely used in diagnostic or prognostic decision-support systems, due to the diversity of results produced by the available techniques, their instability on different data sets and the inability to relate statistical significance with biological relevance. Thus, there is an urgent need to address the statistical framework of microarray analysis and identify its drawbacks and limitations, which will enable us to thoroughly compare methodologies under the same experimental set-up and associate results with confidence intervals meaningful to clinicians. In this study we consider gene-selection algorithms with the aim to reveal inefficiencies in performance evaluation and address aspects that can reduce uncertainty in algorithmic validation.</p> <p>Results</p> <p>A computational study is performed related to the performance of several gene selection methodologies on publicly available microarray data. Three basic types of experimental scenarios are evaluated, i.e. the independent test-set and the 10-fold cross-validation (CV) using maximum and average performance measures. Feature selection methods behave differently under different validation strategies. The performance results from CV do not mach well those from the independent test-set, except for the support vector machines (SVM) and the least squares SVM methods. However, these wrapper methods achieve variable (often low) performance, whereas the hybrid methods attain consistently higher accuracies. The use of an independent test-set within CV is important for the evaluation of the predictive power of algorithms. The optimal size of the selected gene-set also appears to be dependent on the evaluation scheme. The consistency of selected genes over variation of the training-set is another aspect important in reducing uncertainty in the evaluation of the derived gene signature. In all cases the presence of outlier samples can seriously affect algorithmic performance.</p> <p>Conclusion</p> <p>Multiple parameters can influence the selection of a gene-signature and its predictive power, thus possible biases in validation methods must always be accounted for. This paper illustrates that independent test-set evaluation reduces the bias of CV, and case-specific measures reveal stability characteristics of the gene-signature over changes of the training set. Moreover, frequency measures on gene selection address the algorithmic consistency in selecting the same gene signature under different training conditions. These issues contribute to the development of an objective evaluation framework and aid the derivation of statistically consistent gene signatures that could eventually be correlated with biological relevance. The benefits of the proposed framework are supported by the evaluation results and methodological comparisons performed for several gene-selection algorithms on three publicly available datasets.</p

    Application of expert systems in project management decision aiding

    Get PDF
    The feasibility of developing an expert systems-based project management decision aid to enhance the performance of NASA project managers was assessed. The research effort included extensive literature reviews in the areas of project management, project management decision aiding, expert systems technology, and human-computer interface engineering. Literature reviews were augmented by focused interviews with NASA managers. Time estimation for project scheduling was identified as the target activity for decision augmentation, and a design was developed for an Integrated NASA System for Intelligent Time Estimation (INSITE). The proposed INSITE design was judged feasible with a low level of risk. A partial proof-of-concept experiment was performed and was successful. Specific conclusions drawn from the research and analyses are included. The INSITE concept is potentially applicable in any management sphere, commercial or government, where time estimation is required for project scheduling. As project scheduling is a nearly universal management activity, the range of possibilities is considerable. The INSITE concept also holds potential for enhancing other management tasks, especially in areas such as cost estimation, where estimation-by-analogy is already a proven method

    CHORUS Deliverable 2.1: State of the Art on Multimedia Search Engines

    Get PDF
    Based on the information provided by European projects and national initiatives related to multimedia search as well as domains experts that participated in the CHORUS Think-thanks and workshops, this document reports on the state of the art related to multimedia content search from, a technical, and socio-economic perspective. The technical perspective includes an up to date view on content based indexing and retrieval technologies, multimedia search in the context of mobile devices and peer-to-peer networks, and an overview of current evaluation and benchmark inititiatives to measure the performance of multimedia search engines. From a socio-economic perspective we inventorize the impact and legal consequences of these technical advances and point out future directions of research

    Nonlinear Transformations and Radar Detector Design

    Get PDF
    A nonlinear transformation is introduced, which can be used to compress a series of random variables. For a certain class of random variables, the compression results in the removal of unknown distributional parameters from the resultant series. Hence, the application of this transformation is investigated from a radar target detection perspective. It will be shown that it is possible to achieve the constant false alarm rate property through a simple manipulation of this transformation. Due to the effect the transformation has on the cell under test, it is necessary to couple the approach with binary integration to achieve reasonable results. This is demonstrated in an X-band maritime surveillance radar detection context

    International White Book on DER Protection : Review and Testing Procedures

    Get PDF
    This white book provides an insight into the issues surrounding the impact of increasing levels of DER on the generator and network protection and the resulting necessary improvements in protection testing practices. Particular focus is placed on ever increasing inverter-interfaced DER installations and the challenges of utility network integration. This white book should also serve as a starting point for specifying DER protection testing requirements and procedures. A comprehensive review of international DER protection practices, standards and recommendations is presented. This is accompanied by the identifi cation of the main performance challenges related to these protection schemes under varied network operational conditions and the nature of DER generator and interface technologies. Emphasis is placed on the importance of dynamic testing that can only be delivered through laboratory-based platforms such as real-time simulators, integrated substation automation infrastructure and fl exible, inverter-equipped testing microgrids. To this end, the combination of fl exible network operation and new DER technologies underlines the importance of utilising the laboratory testing facilities available within the DERlab Network of Excellence. This not only informs the shaping of new protection testing and network integration practices by end users but also enables the process of de-risking new DER protection technologies. In order to support the issues discussed in the white paper, a comparative case study between UK and German DER protection and scheme testing practices is presented. This also highlights the level of complexity associated with standardisation and approval mechanisms adopted by different countries
    corecore