Search for the end of a path in the d-dimensional grid and in other graphs

We consider the worst-case query complexity of some variants of certain \cl{PPAD}-complete search problems. Suppose we are given a graph $G$ and a vertex $s \in V(G)$. We denote the directed graph obtained from $G$ by directing all edges in both directions by $G'$. $D$ is a directed subgraph of $G'$ which is unknown to us, except that it consists of vertex-disjoint directed paths and cycles and one of the paths originates in $s$. Our goal is to find an endvertex of a path by using as few queries as possible. A query specifies a vertex $v\in V(G)$, and the answer is the set of the edges of $D$ incident to $v$, together with their directions. We also show lower bounds for the special case when $D$ consists of a single path. Our proofs use the theory of graph separators. Finally, we consider the case when the graph $G$ is a grid graph. In this case, using the connection with separators, we give asymptotically tight bounds as a function of the size of the grid, if the dimension of the grid is considered as fixed. In order to do this, we prove a separator theorem about grid graphs, which is interesting on its own right

A Fast Quartet Tree Heuristic for Hierarchical Clustering

The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the $3{n \choose 4}$ weighted quartet topologies on $n$ objects, where optimality means that the summed weight of the embedded quartet topologies is optimal (so it can be the case that the optimal tree embeds all quartets as nonoptimal topologies). We present a Monte Carlo heuristic, based on randomized hill climbing, for approximating the optimal weight tree, given the quartet topology weights. The method repeatedly transforms a dendrogram, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. The problem and the solution heuristic has been extensively used for general hierarchical clustering of nontree-like (non-phylogeny) data in various domains and across domains with heterogeneous data. We also present a greatly improved heuristic, reducing the running time by a factor of order a thousand to ten thousand. All this is implemented and available, as part of the CompLearn package. We compare performance and running time of the original and improved versions with those of UPGMA, BioNJ, and NJ, as implemented in the SplitsTree package on genomic data for which the latter are optimized. Keywords: Data and knowledge visualization, Pattern matching--Clustering--Algorithms/Similarity measures, Hierarchical clustering, Global optimization, Quartet tree, Randomized hill-climbing,Comment: LaTeX, 40 pages, 11 figures; this paper has substantial overlap with arXiv:cs/0606048 in cs.D

Agglomerative Clustering of Growing Squares

We study an agglomerative clustering problem motivated by interactive glyphs in geo-visualization. Consider a set of disjoint square glyphs on an interactive map. When the user zooms out, the glyphs grow in size relative to the map, possibly with different speeds. When two glyphs intersect, we wish to replace them by a new glyph that captures the information of the intersecting glyphs. We present a fully dynamic kinetic data structure that maintains a set of $n$ disjoint growing squares. Our data structure uses $O(n (\log n \log\log n)^2)$ space, supports queries in worst case $O(\log^3 n)$ time, and updates in $O(\log^7 n)$ amortized time. This leads to an $O(n\alpha(n)\log^7 n)$ time algorithm to solve the agglomerative clustering problem. This is a significant improvement over the current best $O(n^2)$ time algorithms.Comment: 14 pages, 7 figure

High-rate self-synchronizing codes

Self-synchronization under the presence of additive noise can be achieved by allocating a certain number of bits of each codeword as markers for synchronization. Difference systems of sets are combinatorial designs which specify the positions of synchronization markers in codewords in such a way that the resulting error-tolerant self-synchronizing codes may be realized as cosets of linear codes. Ideally, difference systems of sets should sacrifice as few bits as possible for a given code length, alphabet size, and error-tolerance capability. However, it seems difficult to attain optimality with respect to known bounds when the noise level is relatively low. In fact, the majority of known optimal difference systems of sets are for exceptionally noisy channels, requiring a substantial amount of bits for synchronization. To address this problem, we present constructions for difference systems of sets that allow for higher information rates while sacrificing optimality to only a small extent. Our constructions utilize optimal difference systems of sets as ingredients and, when applied carefully, generate asymptotically optimal ones with higher information rates. We also give direct constructions for optimal difference systems of sets with high information rates and error-tolerance that generate binary and ternary self-synchronizing codes.Comment: 9 pages, no figure, 2 tables. Final accepted version for publication in the IEEE Transactions on Information Theory. Material presented in part at the International Symposium on Information Theory and its Applications, Honolulu, HI USA, October 201

A New Quartet Tree Heuristic for Hierarchical Clustering

We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the case that the optimal tree embeds all quartets as non-optimal topologies). We present a heuristic for reconstructing the optimal-weight tree, and a canonical manner to derive the quartet-topology weights from a given distance matrix. The method repeatedly transforms a bifurcating tree, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. This contrasts to other heuristic search methods from biological phylogeny, like DNAML or quartet puzzling, which, repeatedly, incrementally construct a solution from a random order of objects, and subsequently add agreement values.Comment: 22 pages, 14 figure