A common problem encountered in such disciplines as statistics, data analysis, signal processing, and neural network research, is nding a suitable representation of multivariate data. For computational and conceptual simplicity, such a representation is often sought as a linear transformation of the original data. Well-known linear transformation methods include, for example, principal component analysis, factor analysis, and projection pursuit. A recently developed linear transformation method is independent component analysis (ICA), in which the desired representation is the one that minimizes the statistical dependence of the components of the representation. Such a representation seems to capture the essential structure of the data in many applications. In this paper, we survey the existing theory and methods for ICA. 1

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The simple Bayesian classifier is known to be optimal when attributes are independent given the class, but the question of whether other sufficient conditions for its optimality exist has so far not been explored. Empirical results showing that it performs surprisingly well in many domains containing clear attribute dependences suggest that the answer to this question may be positive. This article shows that, although the Bayesian classifier's probability estimates are only optimal under quadratic loss if the independence assumption holds, the classifier itself can be optimal under zero-one loss (misclassification rate) even when this assumption is violated by a wide margin. The region of quadratic-loss optimality of the Bayesian classifier is in fact a second-order infinitesimal fraction of the region of zero-one optimality. This implies that the Bayesian classifier has a much greater range of applicability than previously thought. For example, in this article it is shown to be opti...

Abstract. We propose a simple approach to combining first-order logic and probabilistic graphical models in a single representation. A Markov logic network (MLN) is a first-order knowledge base with a weight attached to each formula (or clause). Together with a set of constants representing objects in the domain, it specifies a ground Markov network containing one feature for each possible grounding of a first-order formula in the KB, with the corresponding weight. Inference in MLNs is performed by MCMC over the minimal subset of the ground network required for answering the query. Weights are efficiently learned from relational databases by iteratively optimizing a pseudo-likelihood measure. Optionally, additional clauses are learned using inductive logic programming techniques. Experiments with a real-world database and knowledge base in a university domain illustrate the promise of this approach.

We explore the use of end-to-end multicast traffic as measurement probes to infer network-internal characteristics. We have developed in an earlier paper [2] a Maximum Likelihood Estimator for packet loss rates on individual links based on losses observed by multicast receivers. This technique exploits the inherent correlation between such observations to infer the performance of paths between branch points in the multicast tree spanning the probe source and its receivers. We evaluate through analysis and simulation the accuracy of our estimator under a variety of network conditions. In particular, we report on the error between inferred loss rates and actual loss rates as we vary the network topology, propagation delay, packet drop policy, background traffic mix, and probe traffic type. In all but one case, estimated losses and probe losses agree to within 2 percent on average. We feel this accuracy is enough to reliably identify congested links in a wide-area internetwork. Keywords---Internet performance, end-to-end measurements, Maximum Likelihood Estimator, tomography I.

In gene expression data, a bicluster is a subset of the genes exhibiting consistent patterns over a subset of the conditions. We propose a new method to detect significant biclusters in large expression datasets. Our approach is graph theoretic coupled with statistical modelling of the data. Under plausible assumptions, our algorithm is polynomial and is guaranteed to find the most significant biclusters. We tested our method on a collection of yeast expression profiles and on a human cancer dataset. Cross validation results show high specificity in assigning function to genes based on their biclusters, and we are able to annotate in this way 196 uncharacterized yeast genes. We also demonstrate how the biclusters lead to detecting new concrete biological associations. In cancer data we are able to detect and relate finer tissue types than was previously possible. We also show that the method outperforms the biclustering algorithm of Cheng and Church (2000).

Genome-wide expression profiles of genetic mutants provide a wide variety of measurements of cellular responses to perturbations. Typical analysis of such data identifies genes affected by perturbation and uses clustering to group genes of similar function. In this paper we discover a finer structure of interactions between genes, such as causality, mediation, activation, and inhibition by using a Bayesian network framework. We extend this framework to correctly handle perturbations, and to identify significant subnetworks of interacting genes. We apply this method to expression data of S. cerevisiae mutants and uncover a variety of structured metabolic, signaling and regulatory pathways. Contact: danab@cs.huji.ac.il

. Learning multiple descriptions for each class in the data has been shown to reduce generalization error but the amount of error reduction varies greatly from domain to domain. This paper presents a novel empirical analysis that helps to understand this variation. Our hypothesis is that the amount of error reduction is linked to the "degree to which the descriptions for a class make errors in a correlated manner." We present a precise and novel definition for this notion and use twenty-nine data sets to show that the amount of observed error reduction is negatively correlated with the degree to which the descriptions make errors in a correlated manner. We empirically show that it is possible to learn descriptions that make less correlated errors in domains in which many ties in the search evaluation measure (e.g. information gain) are experienced during learning. The paper also presents results that help to understand when and why multiple descriptions are a help (irrelevant attribute...

We develop a model for examining data that consists of pairwise measurements, for example, presence or absence of links between pairs of objects. Examples include protein interactions and gene regulatory networks, collections of author-recipient email, and social networks. Analyzing such data with probabilistic models requires special assumptions, since the usual independence or exchangeability assumptions no longer hold. We introduce a class of latent variable models for pairwise measurements: mixed membership stochastic blockmodels. Models in this class combine a global model of dense patches of connectivity (blockmodel) and a local model to instantiate nodespecific variability in the connections (mixed membership). We develop a general variational inference algorithm for fast approximate posterior inference. We demonstrate the advantages of mixed membership stochastic blockmodels with applications to social networks and protein interaction networks.

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