A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called supertrees, whilst respecting the relationships in the original trees. A rooted tree exhibits an ultrametric property; that is, for any three leaves of the tree it must be that one pair has a deeper most recent common ancestor than the other pairs, or that all three have the same most recent common ancestor. This inspires a constraint programming encoding for rooted trees. We present an efficient constraint that enforces the ultrametric property over a symmetric array of constrained integer variables, with the inevitable property that the lower bounds of any three variables are mutually supportive. We show that this allows an efficient constraint-based solution to the supertree construction problem. We demonstrate that the versatility of constraint programming can be exploited to allow solutions to variants of the supertree construction problem.

We propose a novel method for approximate inference in Bayesian networks (BNs). The idea is to sample data from a BN, learn a latent tree model (LTM) from the data offline, and when online, make inference with the LTM instead of the original BN. Because LTMs are tree-structured, inference takes linear time. In the meantime, they can represent complex relationship among leaf nodes and hence the approximation accuracy is often good. Empirical evidence shows that our method can achieve good approximation accuracy at low online computational cost.

Experience in the physical sciences suggests that the only realistic means of understanding complex systems is through the use of mathematical models. Typically, this has come to mean the identification of quantitative models expressed as differential equations. Quantitative modelling works best when the structure of the model (i.e., the form of the equations) is known; and the primary concern is one of estimating the values of the parameters in the model. For complex biological systems, the model-structure is rarely known and the modeler has to deal with both model-identification and parameter-estimation. In this paper we are concerned with providing automated assistance to the first of these problems. Specifically, we examine the identification by machine of the structural relationships between experimentally observed variables. These relationship will be expressed in the form of qualitative abstractions of a quantitative model. Such qualitative models may not only provide clues to the precise quantitative model, but also assist in understanding the essence of that model. Our position in this paper is that background knowledge incorporating system modelling principles can be used to constrain effectively the set of good qualitative models. Utilising the model-identification framework provided by Inductive Logic Programming (ILP) we present empirical support for this position using a series of increasingly complex artificial datasets. The results are obtained with qualitative and quantitative data subject to varying amounts of noise and different degrees of sparsity. The results also point to the presence of a set of qualitative states, which we term kernel subsets, that may be necessary for a qualitative model-learner to learn correct models. We demonstrate scalability of the method to biological system modelling by identification of the glycolysis metabolic pathway from data.

The problem of biclustering consists of the simultaneous clustering of rows and columns of a matrix such that each of the submatrices induced by a pair of row and column clusters is as uniform as possible. In this paper we approximate the optimal biclustering by applying one-way clustering algorithms independently on the rows and on the columns of the input matrix. We show that such a solution yields a worst-case approximation ratio of 1+sqrt(2) under L1-norm for 0-1 valued matrices, and of 2 under L2-norm for real valued matrices.

This paper defines the notion of analogical dissimilarity between four objects, with a special focus on objects structured as sequences. Firstly, it studies the case where the four objects have a null analogical dissimilarity, i.e. are in analogical proportion. Secondly, when one of these objects is unknown, it gives algorithms to compute it. Thirdly, it tackles the problem of defining analogical dissimilarity, which is a measure of how far four objects are from being in analogical proportion. In particular, when objects are sequences, it gives a definition and an algorithm based on an optimal alignment of the four sequences. It gives also learning algorithms, i.e. methods to find the triple of objects in a learning sample which has the least analogical dissimilarity with a given object. Two practical experiments are described: the first is a classification problem on benchmarks of binary and nominal data, the second shows how the generation of sequences by solving analogical equations enables a handwritten character recognition system to rapidly be adapted to a new writer.

In many fields where human understanding plays a crucial role, such as bioprocesses, the capacity of extracting knowledge from data is of critical importance. Within this framework, fuzzy learning methods, if properly used, can greatly help human experts. Amongst these methods, the aim of orthogonal transformations, which have been proven to be mathematically robust, is to build rules from a set of training data and to select the most important ones by linear regression or rank revealing techniques. The OLS algorithm is a good representative of those methods. However, it was originally designed so that it only cared about numerical performance. Thus, we propose some modifications of the original method to take interpretability into account. After recalling the original algorithm, this paper presents the changes made to the original method, then discusses some results obtained from benchmark problems. Finally, the algorithm is applied to a real-world fault detection depollution problem.

In this paper we explore a class of belief update operators, in which the definition of the operator is compositional with respect to the sentence to be added. The goal is to provide an update operator that is intuitive, in that its definition is based on a recursive decomposition of the update sentence's structure, and that may be reasonably implemented. In addressing update, we first provide a definition phrased in terms of the models of a knowledge base. While this operator satisfies a core group of the benchmark Katsuno-Mendelzon update postulates, not all of the postulates are satisfied. Other Katsuno-Mendelzon postulates can be obtained by suitably restricting the syntactic form of the sentence for update, as we show. In restricting the syntactic form of the sentence for update, we also obtain a hierarchy of update operators with Winslett's standard semantics as the most basic interesting approach captured. We subsequently give an algorithm which captures this approach; in the general case the algorithm is exponential, but with some not-unreasonable assumptions we obtain an algorithm that is linear in the size of the knowledge base. Hence the resulting approach has much better complexity characteristics than other operators in some situations. We also explore other compositional belief change operators: erasure is developed as a dual operator to update; we show that a forget operator is definable in terms of update; and we give a definition of the compositional revision operator. We obtain that compositional revision, under the most natural definition, yields the Satoh revision operator.

In this paper we propose a novel algorithm, factored value iteration (FVI), for the approximate solution of factored Markov decision processes (fMDPs). The traditional approximate value iteration algorithm is modified in two ways. For one, the least-squares projection operator is modified so that it does not increase max-norm, and thus preserves convergence. The other modification is that we uniformly sample polynomially many samples from the (exponentially large) state space. This way, the complexity of our algorithm becomes polynomial in the size of the fMDP description length. We prove that the algorithm is convergent. We also derive an upper bound on the difference between our approximate solution and the optimal one, and also on the error introduced by sampling. We analyze various projection operators with respect to their computation complexity and their convergence when combined with approximate value iteration.

This report describes experimental results for a set of benchmarks on program verification. It compares the capabilities of CPBVP "Constraint Programming framework for Bounded Program Verification" [4] with the following frameworks: ESC/Java, CBMC, Blast, EUREKA and Why.

In this article we review standard null-move pruning and introduce our extended version of it, which we call verified null-move pruning. In verified null-move pruning, whenever the shallow null-move search indicates a fail-high, instead of cutting off the search from the current node, the search is continued with reduced depth. Our experiments with verified null-move pruning show that on average, it constructs a smaller search tree with greater tactical strength in comparison to standard null-move pruning. Moreover, unlike standard null-move pruning, which fails badly in zugzwang positions, verified null-move pruning manages to detect most zugzwangs and in such cases conducts a research to obtain the correct result. In addition, verified null-move pruning is very easy to implement, and any standard null-move pruning program can use verified null-move pruning by modifying only a few lines of code. 1. INTRODUCTION Until the mid-1970s most chess programs were trying to search the same way humans think, by generating "plausible" moves. By using extensive chess knowledge at each node, these programs selected a few moves which they considered plausible, and thus pruned large parts of the search tree.