DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biological features of cellular systems. In this paper, we propose a new framework for discovering interactions between genes based on multiple expression measurements. This framework builds on the use of Bayesian networks for representing statistical dependencies. A Bayesian network is a graph-based model of joint multivariate probability distributions that captures properties of conditional independence between variables. Such models are attractive for their ability to describe complex stochastic processes and because they provide a clear methodology for learning from (noisy) observations. We start by showing how Bayesian networks can describe interactions between genes. We then describe a method for recovering gene interactions from microarray data using tools for learning Bayesian networks. Finally, we demonstrate this method on the S. cerevisiae cell-cycle measurements of Spellman et al. (1998). Key words: gene expression, microarrays, Bayesian methods. 1.

building block for automated diagnosis and control

. Probabilistic networks (also known as Bayesian belief networks) allow a compact description of complex stochastic relationships among several random variables. They are rapidly becoming the tool of choice for uncertain reasoning in artificial intelligence. In this paper, we investigate the problem of learning probabilistic networks with known structure and hidden variables. This is an important problem, because structure is much easier to elicit from experts than numbers, and the world is rarely fully observable. We present a gradient-based algorithmand show that the gradient can be computed locally, using information that is available as a byproduct of standard probabilistic network inference algorithms. Our experimental results demonstrate that using prior knowledge about the structure, even with hidden variables, can significantly improve the learning rate of probabilistic networks. We extend the method to networks in which the conditional probability tables are described using a ...

This paper describes the mixtures-of-trees model, a probabilistic model for discrete multidimensional domains. Mixtures-of-trees generalize the probabilistic trees of Chow and Liu [6] in a different and complementary direction to that of Bayesian networks. We present efficient algorithms for learning mixtures-of-trees models in maximum likelihood and Bayesian frameworks. We also discuss additional efficiencies that can be obtained when data are “sparse, ” and we present data structures and algorithms that exploit such sparseness. Experimental results demonstrate the performance of the model for both density estimation and classification. We also discuss the sense in which tree-based classifiers perform an implicit form of feature selection, and demonstrate a resulting insensitivity to irrelevant attributes.

In this paper we show that efficient object recognition can be obtained by combining informative features with linear classification. The results demonstrate the superiority of informative class-specific features, as compared with generic type features such as wavelets, for the task of object recognition. We show that information rich features can reach optimal performance with simple linear separation rules, while generic feature based classifiers require more complex classification schemes. This is significant because efficient and optimal methods have been developed for spaces that allow linear separation. To compare different strategies for feature extraction, we trained and compared classifiers working in feature spaces of the same low dimensionality, using two feature types (image fragments vs. wavelets) and two classification rules (linear hyperplane and a Bayesian Network). The results show that by maximizing the individual information of the features, it is possible to obtain efficient classification by a simple linear separating rule, as well as more efficient learning. 1.

The growing problem of unsolicited bulk e-mail, also known as "spare", has generated a need for reliable anti-spam e-mail filters. Filters of this type have so far been based mostly on manually constructed keyword patterns. An alternative approach has recently been proposed, whereby a Naive Bayesian classifier is trained automatically to detect spam messages. We test this approach on a large collection of personal e-mail messages, which we make publicly available in "encrypted " form contributing towards standard benchmarks. We introduce appropriate cost-sensitive measures, investigating at the same time the effect of attribute-set size, training-corpus size, lemmatization, and stop lists, issues that have not been explored in previous experiments. Finally, the Naive Bayesian filter is compared, in terms of performance, to a filter that uses keyword patterns, and which is part of a widely used e-mail reader. Keywords filtering/routing; text categorization; machine learning and IR; evaluation (general); test collections I.

. In this paper we present a simple linear-time centroid-based document classification algorithm, that despite its simplicity and robust performance, has not been extensively studied and analyzed. Our experiments show that this centroid-based classifier consistently and substantially outperforms other algorithms such as Naive Bayesian, k-nearest-neighbors, and C4.5, on a wide range of datasets. Our analysis shows that the similarity measure used by the centroidbased scheme allows it to classify a new document based on how closely its behavior matches the behavior of the documents belonging to different classes. This matching allows it to dynamically adjust for classes with different densities and accounts for dependencies between the terms in the different classes. 1 Introduction We have seen a tremendous growth in the volume of online text documents available on the Internet, digital libraries, news sources, and company-wide intranets. It has been forecasted that these docu...

3 and Jinyan Li 2 1

automated diagnosis, selfhealing and selfmonitoring systems, statistical induction and

In this paper, we empirically evaluate algorithms for learning four types of Bayesian network (BN) classifiers -- Naïve-Bayes, tree augmented Naïve-Bayes, BN augmented Naïve-Bayes and general BNs, where the latter two are learned using two variants of a conditional-independence (CI) based BNlearning algorithm. Experimental results show the obtained classifiers, learned using the CI based algorithms, are competitive with (or superior to) the best known classifiers, based on both Bayesian networks and other formalisms; and that the computational time for learning and using these classifiers is relatively small. Moreover, these results also suggest a way to learn yet more effective classifiers; we demonstrate empirically that this new algorithm does work as expected. Collectively, these results argue that BN classifiers deserve more attention in machine learning and data mining communities. 1 INTRODUCTION Many tasks -- including fault diagnosis, pattern recognition and forecasting -- c...