Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization - Random Forests (BBO - RF) and BBO - SVM (Support Vector Machines) with gene ranking as a heuristic, for microarray gene expression analysis. This heuristic is obtained from information gain filter ranking procedure. The BBO algorithm generates a population of candidate subset of genes, as part of an ecosystem of habitats, and employs the migration and mutation processes across multiple generations of the population to improve the classification accuracy. The fitness of each gene subset is assessed by the classifiers - SVM and Random Forests. The performances of these hybrid techniques are evaluated on three cancer gene expression datasets retrieved from the Kent Ridge Biomedical datasets collection and the libSVM data repository. Our results demonstrate that genes selected by the proposed techniques yield classification accuracies comparable to previously reported algorithms.

Exponential models of distributions are widely used in machine learning for classiffication and modelling. It is well known that they can be interpreted as maximum entropy models under empirical expectation constraints. In this work, we argue that for classiffication tasks, mutual information is a more suitable information theoretic measure to be optimized. We show how the principle of minimum mutual information generalizes that of maximum entropy, and provides a comprehensive framework for building discriminative classiffiers. A game theoretic interpretation of our approach is then given, and several generalization bounds provided. We present iterative algorithms for solving the minimum information problem and its convex dual, and demonstrate their performance on various classiffication tasks. The results show that minimum information classiffiers outperform the corresponding maximum entropy models.

In this paper, a similarity-driven cluster merging method is proposed for unsuper-vised fuzzy clustering. The cluster merging method is used to resolve the problem of cluster validation. Starting with an overspecified number of clusters in the data, pairs of similar clusters are merged based on the proposed similarity-driven cluster merging criterion. The similarity between clusters is calculated by a fuzzy cluster similarity matrix, while an adaptive threshold is used for merging. In addition, a modified generalized ob- jective function is used for prototype-based fuzzy clustering. The function includes the p-norm distance measure as well as principal components of the clusters. The number of the principal components is determined automatically from the data being clustered. The properties of this unsupervised fuzzy clustering algorithm are illustrated by several experiments.

The paper describes an application of Aggregating Algorithm to the problem of regression. It generalizes earlier results concerned with plain linear regression to kernel techniques and presents an on-line algorithm which performs nearly as well as any oblivious kernel predictor. The paper contains the derivation of an estimate on the performance of this algorithm. The estimate is then used to derive an application of the Complexity Approximation Principle to kernel methods.

An autonomous variational inference algorithm for arbitrary graphical models requires the ability to optimize variational approximations over the space of model parameters as well as over the choice of tractable families used for the variational approximation. In this paper, we present a novel combination of graph partitioning algorithms with a generalized mean field (GMF) inference algorithm. This combination optimizes over disjoint clustering of variables and performs inference using those clusters. We provide a formal analysis of the relationship between the graph cut and the GMF approximation, and explore several graph partition strategies empirically. Our empirical results provide rather clear support for a weighted version of MinCut as a useful clustering algorithm for GMF inference, which is consistent with the implications from the formal analysis.

Bayesian learning in undirected graphical models|computing posterior distributions over parameters and predictive quantities is exceptionally difficult. We conjecture that for general undirected models, there are no tractable MCMC (Markov Chain Monte Carlo) schemes giving the correct equilibrium distribution over parameters. While this intractability, due to the partition function, is familiar to those performing parameter optimisation, Bayesian learning of posterior distributions over undirected model parameters has been unexplored and poses novel challenges. we propose several approximate MCMC schemes and test on fully observed binary models (Boltzmann machines) for a small coronary heart disease data set and larger artificial systems. While approximations must perform well on the model, their interaction with the sampling scheme is also important. Samplers based on variational mean- field approximations generally performed poorly, more advanced methods using loopy propagation, brief sampling and stochastic dynamics lead to acceptable parameter posteriors. Finally, we demonstrate these techniques on a Markov random field with hidden variables.

Ancestral graph models, introduced by Richardson and Spirtes (2002), generalize both Markov random fields and Bayesian networks to a class of graphs with a global Markov property that is closed under conditioning and marginalization. By design, ancestral graphs encode precisely the conditional independence structures that can arise from Bayesian networks with selection and unobserved (hidden/latent) variables. Thus, ancestral graph models provide a potentially very useful framework for exploratory model selection when unobserved variables might be involved in the data-generating process but no particular hidden structure can be specified. In this paper, we present the Iterative Conditional Fitting (ICF) algorithm for maximum likelihood estimation in Gaussian ancestral graph models. The name reflects that in each step of the procedure a conditional distribution is estimated, subject to constraints, while a marginal distribution is held fixed. This approach is in duality to the well-known Iterative Proportional Fitting algorithm, in which marginal distributions are fitted while conditional distributions are held fixed.

Methods for analysis of principal components in discrete data have existed for some time under various names such as grade of membership modelling, probabilistic latent semantic analysis, and genotype inference with admixture. In this paper we explore a number of extensions to the common theory, and present some application of these methods to some common statistical tasks. We show that these methods can be interpreted as a discrete version of ICA. We develop a hierarchical version yielding components at different levels of detail, and additional techniques for Gibbs sampling. We compare the algorithms on a text prediction task using support vector machines, and to information retrieval.

Although information extraction and coreference resolution appear together in many applications, most current systems perform them as ndependent steps. This paper describes an approach to integrated inference for extraction and coreference based on conditionally-trained undirected graphical models. We discuss the advantages of conditional probability training, and of a coreference model structure based on graph partitioning. On a data set of research paper citations, we show significant reduction in error by using extraction uncertainty to improve coreference citation matching accuracy, and using coreference to improve the accuracy of the extracted fields.

We formulate and prove an axiomatic characterization of conditional information geometry, for both the normalized and the nonnormalized cases. This characterization extends the axiomatic derivation of the Fisher geometry by Cencov and Campbell to the cone of positive conditional models, and as a special case to the manifold of conditional distributions. Due to the close connection between the conditional I-divergence and the product Fisher information metric the characterization provides a new axiomatic interpretation of the primal problems underlying logistic regression and AdaBoost.