In this paper we consider sparse and identifiable linear latent variable (factor) and linear Bayesian network models for parsimonious analysis of multivariate data. We propose a computationally efficient method for joint parameter and model inference, and model comparison. It consists of a fully Bayesian hierarchy for sparse models using slab and spike priors (two-component delta-function and continuous mixtures), non-Gaussian latent factors and a stochastic search over the ordering of the variables. The framework, which we call SLIM (Sparse Linear Identifiable Multivariate modeling), is validated and bench-marked on artificial and real biological data sets. SLIM is closest in spirit to LiNGAM (Shimizu et al., 2006), but differs substantially in inference, Bayesian network structure learning and model comparison. Experimentally, SLIM performs equally well or better than LiNGAM with comparable computational complexity. We attribute this mainly to the stochastic search strategy used, and to parsimony (sparsity and identifiability), which is an explicit part of the model. We propose two extensions to the basic i.i.d. linear framework: non-linear dependence on observed variables, called SNIM (Sparse Non-linear Identifiable Multivariate modeling) and allowing for correlations between latent variables, called CSLIM (Correlated SLIM), for the temporal and/or spatial data. The source code and scripts are available from http://cogsys.imm.dtu.dk/slim/.

Motivation: Biomarker discovery from high-dimensional data is a crucial problem with enormous applications in biology and medicine. It is also extremely challenging from a statistical viewpoint, but surprisingly few studies have investigated the relative strengths and weaknesses of the plethora of existing feature selection methods. Methods: We compare 32 feature selection methods on 4 public gene expression datasets for breast cancer prognosis, in terms of predictive performance, stability and functional interpretability of the signatures they produce. Results: We observe that the feature selection method has a significant influence on the accuracy, stability and interpretability of signatures. Simple filter methods generally outperform more complex embedded or wrapper methods, and ensemble feature selection has generally no positive effect. Overall a simple Student's t-test seems to provide the best results. Availability: Code and data are publicly available at http://cbio.ensmp.fr/~ahaury/.

The proliferation of online information sources has led to an increased use of wrappers for extracting data from Web sources. While most of the previous research has focused on quick and efficient generation of wrappers, the development of tools for wrapper maintenance has received less attention. This is an important research problem because Web sources often change in ways that prevent the wrappers from extracting data correctly. We present an efficient algorithm that learns structural information about data from positive examples alone. We describe how this information can be used for two wrapper maintenance applications: wrapper verification and reinduction. The wrapper verification system detects when a wrapper is not extracting correct data, usually because the Web source has changed its format. The reinduction algorithm automatically recovers from changes in the Web source by identifying data on Web pages so that a new wrapper may be generated for this source. To validate our approach, we monitored 27 wrappers over a period of a year. The verification algorithm correctly discovered 35 of the 37 wrapper changes, and made 16 mistakes, resulting in precision of 0.73 and recall of 0.95. We validated the reinduction algorithm on ten Web sources. We were able to successfully reinduce the wrappers, obtaining precision and recall values of 0.90 and 0.80 on the data extraction task.

Hierarchical task decomposition is a method used in many agent systems to organize agent knowledge. This work shows how the combination of a hierarchy and persistent assertions of knowledge can lead to difficulty in maintaining logical consistency in asserted knowledge. We explore the problematic consequences of persistent assumptions in the reasoning process and introduce novel potential solutions. Having implemented one of the possible solutions, Dynamic Hierarchical Justification, its effectiveness is demonstrated with an empirical analysis.

The SHOP2 planning system received one of the awards for distinguished performance in the 2002 International Planning Competition. This paper describes the features of SHOP2 which enabled it to excel in the competition, especially those aspects of SHOP2 that deal with temporal and metric planning domains.

VHPOP is a partial order causal link (POCL) planner loosely based on UCPOP. It draws from the experience gained in the early to mid 1990's on flaw selection strategies for POCL planning, and combines this with more recent developments in the field of domain independent planning such as distance based heuristics and reachability analysis. We present an adaptation of the additive heuristic for plan space planning, and modify it to account for possible reuse of existing actions in a plan. We also propose a large set of novel flaw selection strategies, and show how these can help us solve more problems than previously possible by POCL planners. VHPOP also supports planning with durative actions by incorporating standard techniques for temporal constraint reasoning. We demonstrate that the same heuristic techniques used to boost the performance of classical POCL planning can be effective in domains with durative actions as well. The result is a versatile heuristic POCL planner competitive with established CSP-based and heuristic state space planners.

We describe a system for specifying the effects of actions. Unlike those commonly used in AI planning, our system uses an action description language that allows one to specify the effects of actions using domain rules, which are state constraints that can entail new action effects from old ones. Declaratively, an action domain in our language corresponds to a nonmonotonic causal theory in the situation calculus. Procedurally, such an action domain is compiled into a set of logical theories, one for each action in the domain, from which fully instantiated successor state-like axioms and STRIPS-like systems are then generated. We expect the system to be a useful tool for knowledge engineers writing action specifications for classical AI planning systems, GOLOG systems, and other systems where formal specifications of actions are needed.

Policies of Markov Decision Processes (MDPs) determine the next action to execute from the current state and, possibly, the history (the past states). When the number of states is large, succinct representations are often used to compactly represent both the MDPs and the policies in a reduced amount of space. In this paper, some problems related to the size of succinctly represented policies are analyzed. Namely, it is shown that some MDPs have policies that can only be represented in space super-polynomial in the size of the MDP, unless the polynomial hierarchy collapses. This fact motivates the study of the problem of deciding whether a given MDP has a policy of a given size and reward. Since some algorithms for MDPs work by finding a succinct representation of the value function, the problem of deciding the existence of a succinct representation of a value function of a given size and reward is also considered.

F or sev eral small lusters of no des upp er and lo w er b ounds on the marginal v alues are omputed indep enden tly of the rest of the net w ork. The range of allo w ed proba-bilit y distributions o v er the surrounding no des is restri ted using earlier omputed b ounds. As w e will sho w, this an b e onsidered as a set of onstrain ts in a linear programming problem of whi h the ob je tiv e fun tion is the marginal probabilit y of the en ter no des. In this w a y kno wledge ab out the maginals of neigh b ouring lusters is passed to other lusters thereb y tigh tening the b ounds on their marginals. W e sho w that sharp b ounds an b e obtained for undire ted and dire ted graphs that are used for pra ti al appli ations, but for whi h exa t omputations are infeasible. F or small net w orks an exa t omputation of the marginal probabilities for ertain no des is feasible (see, for example Zhang & P o ole, 1994). Unfortunately, due to an exp onen tial s aling of the omputational omplexit y, these exa t algorithms so on fail for somewhat more omplex and more realisti net w orks. T o deal with this omputational problem t w o main streams an b e distinguished. Firstly, there is the approa h of appro ximating the exa t solution.

Bayesian belief networks have grown to prominence because they provide compact representations for many problems for which probabilistic inference is appropriate, and there are algorithms to exploit this compactness. The next step is to allow compact representations of the conditional probabilities of a variable given its parents. In this paper we present such a representation that exploits contextual independence in terms of parent contexts; which variables act as parents may depend on the value of other variables. The internal representation is in terms of contextual factors (confactors) that is simply a pair of a context and a table. The algorithm, contextual variable elimination, is based on the standard variable elimination algorithm that eliminates the non-query variables in turn, but when eliminating a variable, the tables that need to be multiplied can depend on the context. This algorithm reduces to standard variable elimination when there is no contextual independence structure to exploit. We show how this can be much more efficient than variable elimination when there is structure to exploit. We explain why this new method can exploit more structure than previous methods for structured belief network inference and an analogous algorithm that uses trees.