The stable roommates problem with globally-ranked pairs

We introduce a restriction of the stable roommates problem in which roommate pairs are ranked globally. In contrast to the unrestricted problem, weakly stable matchings are guaranteed to exist, and additionally, they can be found in polynomial time. However, it is still the case that strongly stable matchings may not exist, and so we consider the complexity of finding weakly stable matchings with various desirable properties. In particular, we present a polynomial-time algorithm to find a rank-maximal (weakly stable) matching. This is the first generalization of an algorithm due to [Irving et al. 06] to a nonbipartite setting. Also, we describe several hardness results in an even more restricted setting for each of the problems of finding weakly stable matchings that are of maximum size, are egalitarian, have minimum regret, and admit the minimum number of weakly blocking pairs

Small Superpatterns for Dominance Drawing

We exploit the connection between dominance drawings of directed acyclic graphs and permutations, in both directions, to provide improved bounds on the size of universal point sets for certain types of dominance drawing and on superpatterns for certain natural classes of permutations. In particular we show that there exist universal point sets for dominance drawings of the Hasse diagrams of width-two partial orders of size O(n^{3/2}), universal point sets for dominance drawings of st-outerplanar graphs of size O(n\log n), and universal point sets for dominance drawings of directed trees of size O(n^2). We show that 321-avoiding permutations have superpatterns of size O(n^{3/2}), riffle permutations (321-, 2143-, and 2413-avoiding permutations) have superpatterns of size O(n), and the concatenations of sequences of riffles and their inverses have superpatterns of size O(n\log n). Our analysis includes a calculation of the leading constants in these bounds.Comment: ANALCO 2014, This version fixes an error in the leading constant of the 321-superpattern siz

A hybrid algorithm for Bayesian network structure learning with application to multi-label learning

We present a novel hybrid algorithm for Bayesian network structure learning, called H2PC. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. The algorithm is based on divide-and-conquer constraint-based subroutines to learn the local structure around a target variable. We conduct two series of experimental comparisons of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning. First, we use eight well-known Bayesian network benchmarks with various data sizes to assess the quality of the learned structure returned by the algorithms. Our extensive experiments show that H2PC outperforms MMHC in terms of goodness of fit to new data and quality of the network structure with respect to the true dependence structure of the data. Second, we investigate H2PC's ability to solve the multi-label learning problem. We provide theoretical results to characterize and identify graphically the so-called minimal label powersets that appear as irreducible factors in the joint distribution under the faithfulness condition. The multi-label learning problem is then decomposed into a series of multi-class classification problems, where each multi-class variable encodes a label powerset. H2PC is shown to compare favorably to MMHC in terms of global classification accuracy over ten multi-label data sets covering different application domains. Overall, our experiments support the conclusions that local structural learning with H2PC in the form of local neighborhood induction is a theoretically well-motivated and empirically effective learning framework that is well suited to multi-label learning. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available.Comment: arXiv admin note: text overlap with arXiv:1101.5184 by other author

Detection of recombination in DNA multiple alignments with hidden markov models

CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected