A Linear-Time Algorithm for Optimal Tree Sibling Partitioning and its Application to XML Data Stores

Document insertion into a native XML Data Store (XDS) requires to partition the document tree into a number of storage units with limited capacity, such as records on disk pages. As intra partition navigation is much faster than navigation between partitions, minimizing the number of partitions has a beneficial effect on query performance. We present a linear time algorithm to optimally partition an ordered, labeled, weighted tree such that each partition does not exceed a fixed weight limit. Whereas traditionally tree partitioning algorithms only allow child nodes to share a partition with their parent node (i.e. a partition corresponds to a subtree), our algorithm also considers partitions containing several subtrees as long as their roots are adjacent siblings. We call this sibling partitioning. Based on our study of the optimal algorithm, we further introduce two novel, near-optimal heuristics. They are easier to implement, do not need to hold the whole document instance in memory, and require much less runtime than the optimal algorithm. Finally, we provide an experimental study comparing our novel and existing algorithms. One important finding is that compared to partitioning that exclusively considers parent-child partitions, including sibling partitioning as well can decrease the total number of partitions by more than 90%, and improve query performance by more than a factor of two

Algorithms for learning parsimonious context trees

Parsimonious context trees, PCTs, provide a sparse parameterization of conditional probability distributions. They are particularly powerful for modeling context-specific independencies in sequential discrete data. Learning PCTs from data is computationally hard due to the combinatorial explosion of the space of model structures as the number of predictor variables grows. Under the score-and-search paradigm, the fastest algorithm for finding an optimal PCT, prior to the present work, is based on dynamic programming. While the algorithm can handle small instances fast, it becomes infeasible already when there are half a dozen four-state predictor variables. Here, we show that common scoring functions enable the use of new algorithmic ideas, which can significantly expedite the dynamic programming algorithm on typical data. Specifically, we introduce a memoization technique, which exploits regularities within the predictor variables by equating different contexts associated with the same data subset, and a bound-and-prune technique, which exploits regularities within the response variable by pruning parts of the search space based on score upper bounds. On real-world data from recent applications of PCTs within computational biology the ideas are shown to reduce the traversed search space and the computation time by several orders of magnitude in typical cases.Peer reviewe

Synthesizing species trees from gene trees using the parameterized and graph-theoretic approaches

Gene trees describe how parts of the species have evolved over time, and it is assumed that gene trees have evolved along the branches of the species tree. However, some of gene trees are often discordant with the corresponding species tree due to the complicated evolution history of genes. To overcome this obstacle, median problems have emerged as a major tool for synthesizing species trees by reconciling discordance in a given collection of gene trees. Given a collection of gene trees and a cost function, the median problem seeks a tree, called median tree, that minimizes the overall cost to the gene trees. Median tree problems are typically NP-hard, and there is an increased interest in making such median tree problems available for large-scale species tree construction. In this thesis work, we first show that the gene duplication median tree problem satisfied the weaker version of the Pareto property and propose a parameterized algorithm to solve the gene duplication median tree problem. Second, we design two efficient methods to handle the issues of applying the parameterized algorithm to unrooted gene trees which are sampled from the different species. Third, we introduce the graph-theoretic formulation of the Robinson-Foulds median tree problem and a new tree edit operation. Fourth, we propose a new metric between two phylogenetic trees and examine the statistical properties of the metric. Finally, we propose a new clustering criteria in a bipartite network and propose a new NP-hard problem and its ILP formulation

Fast Construction of Nets in Low Dimensional Metrics, and Their Applications

We present a near linear time algorithm for constructing hierarchical nets in finite metric spaces with constant doubling dimension. This data-structure is then applied to obtain improved algorithms for the following problems: Approximate nearest neighbor search, well-separated pair decomposition, compact representation scheme, doubling measure, and computation of the (approximate) Lipschitz constant of a function. In all cases, the running (preprocessing) time is near-linear and the space being used is linear.Comment: 41 pages. Extensive clean-up of minor English error