Techniques for clustering gene expression data

Many clustering techniques have been proposed for the analysis of gene expression data obtained from microarray experiments. However, choice of suitable method(s) for a given experimental dataset is not straightforward. Common approaches do not translate well and fail to take account of the data profile. This review paper surveys state of the art applications which recognises these limitations and implements procedures to overcome them. It provides a framework for the evaluation of clustering in gene expression analyses. The nature of microarray data is discussed briefly. Selected examples are presented for the clustering methods considered

A fuzzy c-means bi-sonar-based Metaheuristic Optimization Algorithm

Fuzzy clustering is an important problem which is the subject of active research in several real world applications. Fuzzy c-means (FCM) algorithm is one of the most popular fuzzy clustering techniques because it is efficient, straightforward, and easy to implement. Fuzzy clustering methods allow the objects to belong to several clusters simultaneously, with different degrees of membership. Objects on the boundaries between several classes are not forced to fully belong to one of the classes, but rather are assigned membership degrees between 0 and 1 indicating their partial membership. However FCM is sensitive to initialization and is easily trapped in local optima. Bi-sonar optimization (BSO) is a stochastic global Metaheuristic optimization tool and is a relatively new algorithm. In this paper a hybrid fuzzy clustering method FCB based on FCM and BSO is proposed which makes use of the merits of both algorithms. Experimental results show that this proposed method is efficient and reveals encouraging results

Big data-driven fuzzy cognitive map for prioritising IT service procurement in the public sector

YesThe prevalence of big data is starting to spread across the public and private sectors however, an impediment to its widespread adoption orientates around a lack of appropriate big data analytics (BDA) and resulting skills to exploit the full potential of big data availability. In this paper, we propose a novel BDA to contribute towards this void, using a fuzzy cognitive map (FCM) approach that will enhance decision-making thus prioritising IT service procurement in the public sector. This is achieved through the development of decision models that capture the strengths of both data analytics and the established intuitive qualitative approach. By taking advantages of both data analytics and FCM, the proposed approach captures the strength of data-driven decision-making and intuitive model-driven decision modelling. This approach is then validated through a decision-making case regarding IT service procurement in public sector, which is the fundamental step of IT infrastructure supply for publics in a regional government in the Russia federation. The analysis result for the given decision-making problem is then evaluated by decision makers and e-government expertise to confirm the applicability of the proposed BDA. In doing so, demonstrating the value of this approach in contributing towards robust public decision-making regarding IT service procurement.EU FP7 project Policy Compass (Project No. 612133

Classification of Event-Related Potentials Associated with Response Errors in Actors and Observers Based on Autoregressive Modeling

Event-Related Potentials (ERPs) provide non-invasive measurements of the electrical activity on the scalp related to the processing of stimuli and preparation of responses by the brain. In this paper an ERP-signal classification method is proposed for discriminating between ERPs of correct and incorrect responses of actors and of observers seeing an actor making such responses. The classification method targeted signals containing error-related negativity (ERN) and error positivity (Pe) components, which are typically associated with error processing in the human brain. Feature extraction consisted of Multivariate Autoregressive modeling combined with the Simulated Annealing technique. The resulting information was subsequently classified by means of an Artificial Neural Network (ANN) using back-propagation algorithm under the “leave-one-out cross-validation” scenario and the Fuzzy C-Means (FCM) algorithm. The ANN consisted of a multi-layer perceptron (MLP). The approach yielded classification rates of up to 85%, both for the actors’ correct and incorrect responses and the corresponding ERPs of the observers. The electrodes needed for such classifications were situated mainly at central and frontal areas. Results provide indications that the classification of the ERN is achievable. Furthermore, the availability of the Pe signals, in addition to the ERN, improves the classification, and this is more pronounced for observers’ signals. The proposed ERP-signal classification method provides a promising tool to study error detection and observational-learning mechanisms in performance monitoring and joint-action research, in both healthy and patient populations

Ensemble clustering via heuristic optimisation

This thesis was submitted for the degree of Doctor of Philosophy and was awarded by Brunel UniversityTraditional clustering algorithms have different criteria and biases, and there is no single algorithm that can be the best solution for a wide range of data sets. This problem often presents a significant obstacle to analysts in revealing meaningful information buried among the huge amount of data. Ensemble Clustering has been proposed as a way to avoid the biases and improve the accuracy of clustering. The difficulty in developing Ensemble Clustering methods is to combine external information (provided by input clusterings) with internal information (i.e. characteristics of given data) effectively to improve the accuracy of clustering. The work presented in this thesis focuses on enhancing the clustering accuracy of Ensemble Clustering by employing heuristic optimisation techniques to achieve a robust combination of relevant information during the consensus clustering stage. Two novel heuristic optimisation-based Ensemble Clustering methods, Multi-Optimisation Consensus Clustering (MOCC) and K-Ants Consensus Clustering (KACC), are developed and introduced in this thesis. These methods utilise two heuristic optimisation algorithms (Simulated Annealing and Ant Colony Optimisation) for their Ensemble Clustering frameworks, and have been proved to outperform other methods in the area. The extensive experimental results, together with a detailed analysis, will be presented in this thesis