Galois lattice theory for probabilistic visual landmarks

This paper presents an original application of the Galois lattice theory, the visual landmark selection for topological localization of an autonomous mobile robot, equipped with a color camera. First, visual landmarks have to be selected in order to characterize a structural environment. Second, such landmarks have to be detected and updated for localization. These landmarks are combinations of attributes, and the selection process is done through a Galois lattice. This paper exposes the landmark selection process and focuses on probabilistic landmarks, which give the robot thorough information on how to locate itself. As a result, landmarks are no longer binary, but probabilistic. The full process of using such landmarks is described in this paper and validated through a robotics experiment

Search based algorithms for test sequence generation in functional testing

Information and Software Technology (DOI: 10.1016/j.infsof.2014.07.014)The generation of dynamic test sequences from a formal specification, complementing traditional testing methods in order to find errors in the source code. Objective In this paper we extend one specific combinatorial test approach, the Classification Tree Method (CTM), with transition information to generate test sequences. Although we use CTM, this extension is also possible for any combinatorial testing method. Method The generation of minimal test sequences that fulfill the demanded coverage criteria is an NP-hard problem. Therefore, search-based approaches are required to find such (near) optimal test sequences. Results The experimental analysis compares the search-based technique with a greedy algorithm on a set of 12 hierarchical concurrent models of programs extracted from the literature. Our proposed search-based approaches (GTSG and ACOts) are able to generate test sequences by finding the shortest valid path to achieve full class (state) and transition coverage. Conclusion The extended classification tree is useful for generating of test sequences. Moreover, the experimental analysis reveals that our search-based approaches are better than the greedy deterministic approach, especially in the most complex instances. All presented algorithms are actually integrated into a professional tool for functional testing.Spanish Ministry of Economy and Competitiveness and FEDER under contract TIN2011-28194 and fellowship BES-2012-055967. Project 8.06/5.47.4142 in collaboration with the VSB-Tech. Univ. of Ostrava, Universidad de Málaga, Andalucía Tech. and EU Grant ICT-257574 (FITTEST project)

The mean, variance and limiting distribution of two statistics sensitive to phylogenetic tree balance

For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool of analysis is a coupling argument with another well-known index called the Sackin statistic. Asymptotics for the mean, variance and covariance of these two statistics are obtained, as well as their limiting joint distribution for large phylogenies. Under the Yule model, the limiting distribution arises as a solution of a functional fixed point equation. Under the uniform model, the limiting distribution is the Airy distribution. The cornerstone of this study is the fact that the probabilistic models for phylogenetic trees are strongly related to the random permutation and the Catalan models for binary search trees.Comment: Published at http://dx.doi.org/10.1214/105051606000000547 in the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

On Polynomial Time Constructions of Minimum Height Decision Tree

A decision tree T in B_m:={0,1}^m is a binary tree where each of its internal nodes is labeled with an integer in [m]={1,2,...,m}, each leaf is labeled with an assignment a in B_m and each internal node has two outgoing edges that are labeled with 0 and 1, respectively. Let A subset {0,1}^m. We say that T is a decision tree for A if (1) For every a in A there is one leaf of T that is labeled with a. (2) For every path from the root to a leaf with internal nodes labeled with i_1,i_2,...,i_k in[m], a leaf labeled with a in A and edges labeled with xi_{i_1},...,xi_{i_k}in {0,1}, a is the only element in A that satisfies a_{i_j}=xi_{i_j} for all j=1,...,k. Our goal is to write a polynomial time (in n:=|A| and m) algorithm that for an input A subseteq B_m outputs a decision tree for A of minimum depth. This problem has many applications that include, to name a few, computer vision, group testing, exact learning from membership queries and game theory. Arkin et al. and Moshkov [Esther M. Arkin et al., 1998; Mikhail Ju. Moshkov, 2004] gave a polynomial time (ln |A|)- approximation algorithm (for the depth). The result of Dinur and Steurer [Irit Dinur and David Steurer, 2014] for set cover implies that this problem cannot be approximated with ratio (1-o(1))* ln |A|, unless P=NP. Moshkov studied in [Mikhail Ju. Moshkov, 2004; Mikhail Ju. Moshkov, 1982; Mikhail Ju. Moshkov, 1982] the combinatorial measure of extended teaching dimension of A, ETD(A). He showed that ETD(A) is a lower bound for the depth of the decision tree for A and then gave an exponential time ETD(A)/log(ETD(A))-approximation algorithm and a polynomial time 2(ln 2)ETD(A)-approximation algorithm. In this paper we further study the ETD(A) measure and a new combinatorial measure, DEN(A), that we call the density of the set A. We show that DEN(A) <=ETD(A)+1. We then give two results. The first result is that the lower bound ETD(A) of Moshkov for the depth of the decision tree for A is greater than the bounds that are obtained by the classical technique used in the literature. The second result is a polynomial time (ln 2)DEN(A)-approximation (and therefore (ln 2)ETD(A)-approximation) algorithm for the depth of the decision tree of A. We then apply the above results to learning the class of disjunctions of predicates from membership queries [Nader H. Bshouty et al., 2017]. We show that the ETD of this class is bounded from above by the degree d of its Hasse diagram. We then show that Moshkov algorithm can be run in polynomial time and is (d/log d)-approximation algorithm. This gives optimal algorithms when the degree is constant. For example, learning axis parallel rays over constant dimension space

A minimal descriptor of an ancestral recombinations graph

<p>Abstract</p> <p>Background</p> <p>Ancestral Recombinations Graph (ARG) is a phylogenetic structure that encodes both duplication events, such as mutations, as well as genetic exchange events, such as recombinations: this captures the (genetic) dynamics of a population evolving over generations.</p> <p>Results</p> <p>In this paper, we identify structure-preserving and samples-preserving core of an ARG <it>G</it> and call it the minimal descriptor ARG of <it>G</it>. Its structure-preserving characteristic ensures that all the branch lengths of the marginal trees of the minimal descriptor ARG are identical to that of <it>G</it> and the samples-preserving property asserts that the patterns of genetic variation in the samples of the minimal descriptor ARG are exactly the same as that of <it>G</it>. We also prove that even an unbounded <it>G</it> has a finite minimal descriptor, that continues to preserve certain (graph-theoretic) properties of <it>G</it> and for an appropriate class of ARGs, our estimate (Eqn 8) as well as empirical observation is that the expected reduction in the number of vertices is exponential.</p> <p>Conclusions</p> <p>Based on the definition of this lossless and bounded structure, we derive local properties of the vertices of a minimal descriptor ARG, which lend itself very naturally to the design of efficient sampling algorithms. We further show that a class of minimal descriptors, that of binary ARGs, models the standard coalescent exactly (Thm 6).</p

Sampling ARG of multiple populations under complex configurations of subdivision and admixture.

Abstract Motivation: Simulating complex evolution scenarios of multiple populations is an important task for answering many basic questions relating to population genomics. Apart from the population samples, the underlying Ancestral Recombinations Graph (ARG) is an additional important means in hypothesis checking and reconstruction studies. Furthermore, complex simulations require a plethora of interdependent parameters making even the scenario-specification highly non-trivial. Results: We present an algorithm SimRA that simulates generic multiple population evolution model with admixture. It is based on random graphs that improve dramatically in time and space requirements of the classical algorithm of single populations. Using the underlying random graphs model, we also derive closed forms of expected values of the ARG characteristics i.e., height of the graph, number of recombinations, number of mutations and population diversity in terms of its defining parameters. This is crucial in aiding the user to specify meaningful parameters for the complex scenario simulations, not through trial-and-error based on raw compute power but intelligent parameter estimation. To the best of our knowledge this is the first time closed form expressions have been computed for the ARG properties. We show that the expected values closely match the empirical values through simulations. Finally, we demonstrate that SimRA produces the ARG in compact forms without compromising any accuracy. We demonstrate the compactness and accuracy through extensive experiments. Availability and implementation: SimRA (Simulation based on Random graph Algorithms) source, executable, user manual and sample input-output sets are available for downloading at: https://github.com/ComputationalGenomics/SimRA Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

The Weight Function in the Subtree Kernel is Decisive

Tree data are ubiquitous because they model a large variety of situations, e.g., the architecture of plants, the secondary structure of RNA, or the hierarchy of XML files. Nevertheless, the analysis of these non-Euclidean data is difficult per se. In this paper, we focus on the subtree kernel that is a convolution kernel for tree data introduced by Vishwanathan and Smola in the early 2000's. More precisely, we investigate the influence of the weight function from a theoretical perspective and in real data applications. We establish on a 2-classes stochastic model that the performance of the subtree kernel is improved when the weight of leaves vanishes, which motivates the definition of a new weight function, learned from the data and not fixed by the user as usually done. To this end, we define a unified framework for computing the subtree kernel from ordered or unordered trees, that is particularly suitable for tuning parameters. We show through eight real data classification problems the great efficiency of our approach, in particular for small datasets, which also states the high importance of the weight function. Finally, a visualization tool of the significant features is derived.Comment: 36 page