Ariel E. Bayá

How Many Clusters: A Validation Index for Arbitrary-Shaped Clusters

Clustering validation indexes are intended to assess the goodness of clustering results. Many methods used to estimate the number of clusters rely on a validation index as a key element to find the correct answer. This paper presents a new validation index based on graph concepts, which has been designed to find arbitrary shaped clusters by exploiting the spatial layout of the patterns and their clustering label. This new clustering index is combined with a solid statistical detection framework, the gap statistic. The resulting method is able to find the right number of arbitrary-shaped clusters in diverse situations, as we show with examples where this information is available. A comparison with several relevant validation methods is carried out using artificial and gene expression data sets. The results are very encouraging, showing that the underlying structure in the data can be more accurately detected with the new clustering index. Our gene expression data results also indicate that this new index is stable under perturbation of the input data.

Multiscale recognition of legume varieties based on leaf venation images

Abstract In this work we propose an automatic low cost procedure aimed at classifying legume species and varieties based exclusively on the characterization and analysis of the leaf venation network. The identification of leaf venation patterns which are characteristic for each species or variety is not an easy task since in some situations (specially for cultivars from the same species) the vein differences are visually indistinguishable for humans. The proposed procedure takes as input leaf images acquired using a standard scanner, processes the images in order to segment the veins at different scales, and measures different traits on them. We use these features in combination with modern automatic classifiers and feature selection techniques in order to perform recognition. The process was initially applied to recognize three different legumes in order to evaluate the improvements over previous works in the literature, and then it was employed to distinguish three diverse soybean cultivars. The results show the improvements achieved by the usage of the multiscale features. The cultivar recognition is a more challenging problem, since the experts cannot distinguish evident differences in plain sight. However, we achieve acceptable classification results. We also analyze the feature relevance and identify, for each classifier, a small set of distinctive traits to differentiate the species and varieties.

Gene set enrichment analysis using non-parametric scores

Gene Set Enrichment Analysis (GSEA) is a well-known technique used for studying groups of functionally related genes and their correlation with phenotype. This method creates a ranked list of genes, which is used to calculate an enrichment score. In this work, we introduce two different metrics for gene ranking in GSEA, namely the Wilcoxon and the Baumgartner-Weis-Schindler tests. The advantage of these metrics is that they do not assume any particular distribution on the data. We compared them with the signal-to-noise ratio metric originally proposed by the developers of GSEA on a type 2 diabetes mellitus (DM2) database. Statistical significance is evaluated by means of false discovery rate and p-value calculations. Results show that the Baumgartner-WeisSchindler test detects more pathways with statistical significance. One of them could be related to DM2, according to the literature, but further research is needed.

Clustering stability for automated color image segmentation

Abstract Clustering is a well-established technique for segmentation. However, clustering validation is rarely used for this purpose. In this work we adapt a clustering validation method, Clustering Stability (CS), to automatically segment images. CS is not limited by image dimensionality nor by the clustering algorithm. We show clustering and validation acting together as a data-driven process able to find the optimum number of partitions according to our proposed color-texture feature representation. We also describe how to adapt CS to detect the best settings required for feature extraction. The segmentation solutions found by our method are supported by a stability score named STI, which provides an objective quantifiable metric to obtain the final segmentation results. Furthermore, the STI allows to compare multiple alternative solutions and select the most appropriate according to the index meaning. We successfully test our procedure on texture and natural images, and 3D MRI data.

Inferring Unknown Biological Function by Integration of GO Annotations and Gene Expression Data

Characterizing genes with semantic information is an important process regarding the description of gene products. In spite that complete genomes of many organisms have been already sequenced, the biological functions of all of their genes are still unknown. Since experimentally studying the functions of those genes, one by one, would be unfeasible, new computational methods for gene functions inference are needed. We present here a novel computational approach for inferring biological function for a set of genes with previously unknown function, given a set of genes with well-known information. This approach is based on the premise that genes with similar behaviour should be grouped together. This is known as the guilt-by-association principle. Thus, it is possible to take advantage of clustering techniques to obtain groups of unknown genes that are co-clustered with genes that have well-known semantic information (GO annotations). Meaningful knowledge to infer unknown semantic information can therefore be provided by these well-known genes. We provide a method to explore the potential function of new genes according to those currently annotated. The results obtained indicate that the proposed approach could be a useful and effective tool when used by biologists to guide the inference of biological functions for recently discovered genes. Our work sets an important landmark in the field of identifying unknown gene functions through clustering, using an external source of biological input. A simple web interface to this proposal can be found at http://fich.unl.edu.ar/sinc/webdemo/gamma-am/.

Improved graph-based metrics for clustering high-dimensional datasets

Clustering is one of the most used tools for data analysis. Unfortunately, most methods suffer from a lack of performance when dealing with high dimensional spaces. Recently, some works showed evidence that the use of graph-based metrics can moderate this problem. In particular, the Penalized K-Nearest Neighbour Graph metric (PKNNG) showed good results in several situations. In this work we propose two improvements to this metric that makes it suitable for application to very different domains. First, we introduce an appropriate way to manage outliers, a typical problem in graph-based metrics. Then, we propose a simple method to select an optimal value of K, the number of neighbours considered in the k-nn graph. We analyze the proposed modifications using both artificial and real data, finding strong evidence that supports our improvements. Then we compare our new method to other graph based metrics, showing that it achieves a good performance on high dimensional datasets coming from very different domains, including DNA microarrays and face and digits image recognition problems.

Improved gene expression clustering with the parameter-free PKNNG metric

In this work we introduce a modification to an automatic non-supervised rule to select the parameters of a previously presented graph-based metric. This rule maximizes a clustering quality index providing the best possible solution from a clustering quality point of view. We apply our parameter-free PKNNG metric on gene expression data to show that the best quality solutions are also the ones that are more related to the biological classes. Finally, we compare our parameter-free metric with a group of state-of-the-art clustering algorithms. Our results indicate that our parameter-free metric performs as well as the state-of-the-art clustering methods.