In typical classification tasks, we seek a function which assigns a label to a single object. Kernel-based approaches, such as support vector machines (SVMs), which maximize the margin of confidence of the classifier, are the method of choice for many such tasks. Their popularity stems both from the ability to use high-dimensional feature spaces, and from their strong theoretical guarantees. However, many real-world tasks involve sequential, spatial, or structured data, where multiple labels must be assigned. Existing kernel-based methods ignore structure in the problem, assigning labels independently to each object, losing much useful information. Conversely, probabilistic graphical models, such as Markov networks, can represent correlations between labels, by exploiting problem structure, but cannot handle high-dimensional feature spaces, and lack strong theoretical generalization guarantees. In this paper, we present a new framework that combines the advantages of both approaches: Maximum margin Markov (M 3) networks incorporate both kernels, which efficiently deal with high-dimensional features, and the ability to capture correlations in structured data. We present an efficient algorithm for learning M 3 networks based on a compact quadratic program formulation. We provide a new theoretical bound for generalization in structured domains. Experiments on the task of handwritten character recognition and collective hypertext classification demonstrate very significant gains over previous approaches. 1

In addressing the growing problem of junk E-mail on the Internet, we examine methods for the automated construction of filters to eliminate such unwanted messages from a user's mail stream. By casting this problem in a decision theoretic framework, we are able to make use of probabilistic learning methods in conjunction with a notion of differential misclassification cost to produce filters which are especially appropriate for the nuances of this task. While this may appear, at first, to be a straight-forward text classification problem, we show that by considering domain-specific features of this problem in addition to the raw text of E-mail messages, we can produce much more accurate filters. Finally, we show the efficacy of such filters in a real world usage scenario, arguing that this technology is mature enough for deployment. Introduction As the number of users connected to the Internet continues to skyrocket, electronic mail (E-mail) is quickly becoming one of the fastest and m...

As larger and more heterogeneous text databases become available, information retrieval research will depend on the development of powerful, efficient and flexible retrieval engines. In this paper, we describe a retrieval system (INQUERY) that is based on a probabilistic retrieval model and provides support for sophisticated indexing and complex query formulation. INQUERY has been used successfully with databases containing nearly 400,000 documents. 1 Introduction The increasing interest in sophisticated information retrieval (IR) techniques has led to a number of large text databases becoming available for research. The size of these databases, both in terms of the number of documents in them, and the length of the documents that are typically full text, has presented significant challenges to IR researchers who are used to experimenting with two or three thousand document abstracts. In order to carry out research with different types of text representations, retrieval models, learni...

Belief propagation (BP) was only supposed to work for tree-like networks but works surprisingly well in many applications involving networks with loops, including turbo codes. However, there has been little understanding of the algorithm or the nature of the solutions it finds for general graphs. We show that

In this paper we present a statistical framework for modeling the appearance of objects. Our work is motivated by the pictorial structure models introduced by Fischler and Elschlager. The basic idea is to model an object by a collection of parts arranged in a deformable configuration. The appearance of each part is modeled separately, and the deformable configuration is represented by spring-like connections between pairs of parts. These models allow for qualitative descriptions of visual appearance, and are suitable for generic recognition problems. We use these models to address the problem of detecting an object in an image as well as the problem of learning an object model from training examples, and present efficient algorithms for both these problems. We demonstrate the techniques by learning models that represent faces and human bodies and using the resulting models to locate the corresponding objects in novel images.

In this paper, we examine a method for feature subset selection based on Information Theory. Initially, a framework for de ning the theoretically optimal, but computationally intractable, method for feature subset selection is presented. We show that our goal should be to eliminate a feature if it gives us little or no additional information beyond that subsumed by the remaining features. In particular, this will be the case for both irrelevant and redundant features. We then give an e cient algorithm for feature selection which computes an approximation to the optimal feature selection criterion. The conditions under which the approximate algorithm is successful are examined. Empirical results are given on a number of data sets, showing that the algorithm e ectively handles datasets with a very large number of features.

Important inference problems in statistical physics, computer vision, error-correcting coding theory, and artificial intelligence can all be reformulated as the computation of marginal probabilities on factor graphs. The belief propagation (BP) algorithm is an efficient way to solve these problems that is exact when the factor graph is a tree, but only approximate when the factor graph has cycles. We show that BP fixed points correspond to the stationary points of the Bethe approximation of the free energy for a factor graph. We explain how to obtain regionbased free energy approximations that improve the Bethe approximation, and corresponding generalized belief propagation (GBP) algorithms. We emphasize the conditions a free energy approximation must satisfy in order to be a “valid ” or “maxent-normal ” approximation. We describe the relationship between four different methods that can be used to generate valid approximations: the “Bethe method, ” the “junction graph method, ” the “cluster variation method, ” and the “region graph method.” Finally, we explain how to tell whether a region-based approximation, and its corresponding GBP algorithm, is likely to be accurate, and describe empirical results showing that GBP can significantly outperform BP.

In many supervised learning tasks, the entities to be labeled are related to each other in complex ways and their labels are not independent. For example, in hypertext classification, the labels of linked pages are highly correlated. A standard approach is to classify each entity independently, ignoring the correlations between them. Recently, Probabilistic Relational Models, a relational version of Bayesian networks, were used to define a joint probabilistic model for a collection of related entities. In this paper, we present an alternative framework that builds on (conditional) Markov networks and addresses two limitations of the previous approach. First, undirected models do not impose the acyclicity constraint that hinders representation of many important relational dependencies in directed models. Second, undirected models are well suited for discriminative training, where we optimize the conditional likelihood of the labels given the features, which generally improves classification accuracy. We show how to train these models effectively, and how to use approximate probabilistic inference over the learned model for collective classification of multiple related entities. We provide experimental results on a webpage classification task, showing that accuracy can be significantly improved by modeling relational dependencies. 1

We describe a system that supports arbitrarily complex SQL queries with ”uncertain” predicates. The query semantics is based on a probabilistic model and the results are ranked, much like in Information Retrieval. Our main focus is efficient query evaluation, a problem that has not received attention in the past. We describe an optimization algorithm that can compute efficiently most queries. We show, however, that the data complexity of some queries is #P-complete, which implies that these queries do not admit any efficient evaluation methods. For these queries we describe both an approximation algorithm and a Monte-Carlo simulation algorithm.

In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems. Key words: genetic regulatory networks, mathematical modeling, simulation, computational biology.