Biomedical subjects

Volker Roth

Publications and source records attributed to Volker Roth.

3 recordsLinked to original sources

PubMed2004

Bayesian class discovery in microarray datasets.

A novel approach to class discovery in gene expression datasets is presented. In the context of clinical diagnosis, the central goal of class discovery algorithms is to simultaneously find putative (sub-)types of diseases and to identify informative subsets of genes with disease-type specific expression profile. Contrary to many other approaches in the literature, the method presented implements a wrapper strategy for feature selection, in the sense that the features are directly selected by optimizing the discriminative power of the used partitioning algorithm. The usual combinatorial problems associated with wrapper approaches are overcome by a Bayesian inference mechanism. On the technical side, we present an efficient optimization algorithm with guaranteed local convergence property. The only free parameter of the optimization method is selected by a resampling-based stability analysis. Experiments with Leukemia and Lymphoma datasets demonstrate that our method is able to correctly infer partitions and corresponding subsets of genes which both are relevant in a biological sense. Moreover, the frequently observed problem of ambiguities caused by different but equally high-scoring partitions is successfully overcome by the model selection method proposed.

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PubMed2004

The generalized LASSO.

In the last few years, the support vector machine (SVM) method has motivated new interest in kernel regression techniques. Although the SVM has been shown to exhibit excellent generalization properties in many experiments, it suffers from several drawbacks, both of a theoretical and a technical nature: the absence of probabilistic outputs, the restriction to Mercer kernels, and the steep growth of the number of support vectors with increasing size of the training set. In this paper, we present a different class of kernel regressors that effectively overcome the above problems. We call this approach generalized LASSO regression. It has a clear probabilistic interpretation, can handle learning sets that are corrupted by outliers, produces extremely sparse solutions, and is capable of dealing with large-scale problems. For regression functionals which can be modeled as iteratively reweighted least-squares (IRLS) problems, we present a highly efficient algorithm with guaranteed global convergence. This defies a unique framework for sparse regression models in the very rich class of IRLS models, including various types of robust regression models and logistic regression. Performance studies for many standard benchmark datasets effectively demonstrate the advantages of this model over related approaches.

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PubMed2004

Stability-based validation of clustering solutions.

Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract "natural" group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a particularly important model selection question. We introduce a measure of cluster stability to assess the validity of a cluster model. This stability measure quantifies the reproducibility of clustering solutions on a second sample, and it can be interpreted as a classification risk with regard to class labels produced by a clustering algorithm. The preferred number of clusters is determined by minimizing this classification risk as a function of the number of clusters. Convincing results are achieved on simulated as well as gene expression data sets. Comparisons to other methods demonstrate the competitive performance of our method and its suitability as a general validation tool for clustering solutions in real-world problems.

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