Finding groups in data: Cluster analysis with ants

Wepresent in this paper a modification of Lumer and Faieta’s algorithm for data clustering. This approach mimics the clustering behavior observed in real ant colonies. This algorithm discovers automatically clusters in numerical data without prior knowledge of possible number of clusters. In this paper we focus on ant-based clustering algorithms, a particular kind of a swarm intelligent system, and on the effects on the final clustering by using during the classification differentmetrics of dissimilarity: Euclidean, Cosine, and Gower measures. Clustering with swarm-based algorithms is emerging as an alternative to more conventional clustering methods, such as e.g. k-means, etc. Among the many bio-inspired techniques, ant clustering algorithms have received special attention, especially because they still require much investigation to improve performance, stability and other key features that would make such algorithms mature tools for data mining. As a case study, this paper focus on the behavior of clustering procedures in those new approaches. The proposed algorithm and its modifications are evaluated in a number of well-known benchmark datasets. Empirical results clearly show that ant-based clustering algorithms performs well when compared to another techniques

Partial mixture model for tight clustering of gene expression time-course

Background: Tight clustering arose recently from a desire to obtain tighter and potentially more informative clusters in gene expression studies. Scattered genes with relatively loose correlations should be excluded from the clusters. However, in the literature there is little work dedicated to this area of research. On the other hand, there has been extensive use of maximum likelihood techniques for model parameter estimation. By contrast, the minimum distance estimator has been largely ignored. Results: In this paper we show the inherent robustness of the minimum distance estimator that makes it a powerful tool for parameter estimation in model-based time-course clustering. To apply minimum distance estimation, a partial mixture model that can naturally incorporate replicate information and allow scattered genes is formulated. We provide experimental results of simulated data fitting, where the minimum distance estimator demonstrates superior performance to the maximum likelihood estimator. Both biological and statistical validations are conducted on a simulated dataset and two real gene expression datasets. Our proposed partial regression clustering algorithm scores top in Gene Ontology driven evaluation, in comparison with four other popular clustering algorithms. Conclusion: For the first time partial mixture model is successfully extended to time-course data analysis. The robustness of our partial regression clustering algorithm proves the suitability of the ombination of both partial mixture model and minimum distance estimator in this field. We show that tight clustering not only is capable to generate more profound understanding of the dataset under study well in accordance to established biological knowledge, but also presents interesting new hypotheses during interpretation of clustering results. In particular, we provide biological evidences that scattered genes can be relevant and are interesting subjects for study, in contrast to prevailing opinion