Microbial community pattern detection in human body habitats via ensemble clustering framework

The human habitat is a host where microbial species evolve, function, and continue to evolve. Elucidating how microbial communities respond to human habitats is a fundamental and critical task, as establishing baselines of human microbiome is essential in understanding its role in human disease and health. However, current studies usually overlook a complex and interconnected landscape of human microbiome and limit the ability in particular body habitats with learning models of specific criterion. Therefore, these methods could not capture the real-world underlying microbial patterns effectively. To obtain a comprehensive view, we propose a novel ensemble clustering framework to mine the structure of microbial community pattern on large-scale metagenomic data. Particularly, we first build a microbial similarity network via integrating 1920 metagenomic samples from three body habitats of healthy adults. Then a novel symmetric Nonnegative Matrix Factorization (NMF) based ensemble model is proposed and applied onto the network to detect clustering pattern. Extensive experiments are conducted to evaluate the effectiveness of our model on deriving microbial community with respect to body habitat and host gender. From clustering results, we observed that body habitat exhibits a strong bound but non-unique microbial structural patterns. Meanwhile, human microbiome reveals different degree of structural variations over body habitat and host gender. In summary, our ensemble clustering framework could efficiently explore integrated clustering results to accurately identify microbial communities, and provide a comprehensive view for a set of microbial communities. Such trends depict an integrated biography of microbial communities, which offer a new insight towards uncovering pathogenic model of human microbiome.Comment: BMC Systems Biology 201

A Method to Improve the Analysis of Cluster Ensembles

Clustering is fundamental to understand the structure of data. In the past decade the cluster ensembleproblem has been introduced, which combines a set of partitions (an ensemble) of the data to obtain a singleconsensus solution that outperforms all the ensemble members. However, there is disagreement about which arethe best ensemble characteristics to obtain a good performance: some authors have suggested that highly differentpartitions within the ensemble are beneï¬ cial for the ï¬ nal performance, whereas others have stated that mediumdiversity among them is better. While there are several measures to quantify the diversity, a better method toanalyze the best ensemble characteristics is necessary. This paper introduces a new ensemble generation strategyand a method to make slight changes in its structure. Experimental results on six datasets suggest that this isan important step towards a more systematic approach to analyze the impact of the ensemble characteristics onthe overall consensus performance.Fil: Pividori, Milton Damián. Universidad Tecnologica Nacional. Facultad Regional Santa Fe. Centro de Investigacion y Desarrollo de Ingenieria en Sistemas de Informacion; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; ArgentinaFil: Stegmayer, Georgina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; Argentina. Universidad Tecnologica Nacional. Facultad Regional Santa Fe. Centro de Investigacion y Desarrollo de Ingenieria en Sistemas de Informacion; ArgentinaFil: Milone, Diego Humberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingeniería y Ciencias Hídricas. Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional; Argentin

EC3: Combining Clustering and Classification for Ensemble Learning

Classification and clustering algorithms have been proved to be successful individually in different contexts. Both of them have their own advantages and limitations. For instance, although classification algorithms are more powerful than clustering methods in predicting class labels of objects, they do not perform well when there is a lack of sufficient manually labeled reliable data. On the other hand, although clustering algorithms do not produce label information for objects, they provide supplementary constraints (e.g., if two objects are clustered together, it is more likely that the same label is assigned to both of them) that one can leverage for label prediction of a set of unknown objects. Therefore, systematic utilization of both these types of algorithms together can lead to better prediction performance. In this paper, We propose a novel algorithm, called EC3 that merges classification and clustering together in order to support both binary and multi-class classification. EC3 is based on a principled combination of multiple classification and multiple clustering methods using an optimization function. We theoretically show the convexity and optimality of the problem and solve it by block coordinate descent method. We additionally propose iEC3, a variant of EC3 that handles imbalanced training data. We perform an extensive experimental analysis by comparing EC3 and iEC3 with 14 baseline methods (7 well-known standalone classifiers, 5 ensemble classifiers, and 2 existing methods that merge classification and clustering) on 13 standard benchmark datasets. We show that our methods outperform other baselines for every single dataset, achieving at most 10% higher AUC. Moreover our methods are faster (1.21 times faster than the best baseline), more resilient to noise and class imbalance than the best baseline method.Comment: 14 pages, 7 figures, 11 table