263 research outputs found
Statistical structures for internet-scale data management
Efficient query processing in traditional database management systems relies on statistics on base data. For centralized systems, there is a rich body of research results on such statistics, from simple aggregates to more elaborate synopses such as sketches and histograms. For Internet-scale distributed systems, on the other hand, statistics management still poses major challenges. With the work in this paper we aim to endow peer-to-peer data management over structured overlays with the power associated with such statistical information, with emphasis on meeting the scalability challenge. To this end, we first contribute efficient, accurate, and decentralized algorithms that can compute key aggregates such as Count, CountDistinct, Sum, and Average. We show how to construct several types of histograms, such as simple Equi-Width, Average-Shifted Equi-Width, and Equi-Depth histograms. We present a full-fledged open-source implementation of these tools for distributed statistical synopses, and report on a comprehensive experimental performance evaluation, evaluating our contributions in terms of efficiency, accuracy, and scalability
Efficient Dynamic Approximate Distance Oracles for Vertex-Labeled Planar Graphs
Let be a graph where each vertex is associated with a label. A
Vertex-Labeled Approximate Distance Oracle is a data structure that, given a
vertex and a label , returns a -approximation of
the distance from to the closest vertex with label in . Such
an oracle is dynamic if it also supports label changes. In this paper we
present three different dynamic approximate vertex-labeled distance oracles for
planar graphs, all with polylogarithmic query and update times, and nearly
linear space requirements
Composite repetition-aware data structures
In highly repetitive strings, like collections of genomes from the same
species, distinct measures of repetition all grow sublinearly in the length of
the text, and indexes targeted to such strings typically depend only on one of
these measures. We describe two data structures whose size depends on multiple
measures of repetition at once, and that provide competitive tradeoffs between
the time for counting and reporting all the exact occurrences of a pattern, and
the space taken by the structure. The key component of our constructions is the
run-length encoded BWT (RLBWT), which takes space proportional to the number of
BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it
with data structures from LZ77 indexes, which take space proportional to the
number of LZ77 factors, and with the compact directed acyclic word graph
(CDAWG), which takes space proportional to the number of extensions of maximal
repeats. The combination of CDAWG and RLBWT enables also a new representation
of the suffix tree, whose size depends again on the number of extensions of
maximal repeats, and that is powerful enough to support matching statistics and
constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from
previous version
Longest Common Prefixes with -Errors and Applications
Although real-world text datasets, such as DNA sequences, are far from being
uniformly random, average-case string searching algorithms perform
significantly better than worst-case ones in most applications of interest. In
this paper, we study the problem of computing the longest prefix of each suffix
of a given string of length over a constant-sized alphabet that occurs
elsewhere in the string with -errors. This problem has already been studied
under the Hamming distance model. Our first result is an improvement upon the
state-of-the-art average-case time complexity for non-constant and using
only linear space under the Hamming distance model. Notably, we show that our
technique can be extended to the edit distance model with the same time and
space complexities. Specifically, our algorithms run in time on average using space. We show that our
technique is applicable to several algorithmic problems in computational
biology and elsewhere
The Heaviest Induced Ancestors Problem Revisited
We revisit the heaviest induced ancestors problem, which has several interesting applications in string matching. Let T_1 and T_2 be two weighted trees, where the weight W(u) of a node u in either of the two trees is more than the weight of u\u27s parent. Additionally, the leaves in both trees are labeled and the labeling of the leaves in T_2 is a permutation of those in T_1. A node x in T_1 and a node y in T_2 are induced, iff their subtree have at least one common leaf label. A heaviest induced ancestor query HIA(u_1,u_2) is: given a node u_1 in T_1 and a node u_2 in T_2, output the pair (u_1^*,u_2^*) of induced nodes with the highest combined weight W(u^*_1) + W(u^*_2), such that u_1^* is an ancestor of u_1 and u^*_2 is an ancestor of u_2. Let n be the number of nodes in both trees combined and epsilon >0 be an arbitrarily small constant. Gagie et al. [CCCG\u27 13] introduced this problem and proposed three solutions with the following space-time trade-offs:
- an O(n log^2n)-word data structure with O(log n log log n) query time
- an O(n log n)-word data structure with O(log^2 n) query time
- an O(n)-word data structure with O(log^{3+epsilon}n) query time.
In this paper, we revisit this problem and present new data structures, with improved bounds. Our results are as follows.
- an O(n log n)-word data structure with O(log n log log n) query time
- an O(n)-word data structure with O(log^2 n/log log n) query time.
As a corollary, we also improve the LZ compressed index of Gagie et al. [CCCG\u27 13] for answering longest common substring (LCS) queries. Additionally, we show that the LCS after one edit problem of size n [Amir et al., SPIRE\u27 17] can also be reduced to the heaviest induced ancestors problem over two trees of n nodes in total. This yields a straightforward improvement over its current solution of O(n log^3 n) space and O(log^3 n) query time
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