Error-Correcting Data Structures

We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been corrupted by a constant fraction of errors. This new model is the common generalization of (static) data structures and locally decodable error-correcting codes. The main issue is the tradeoff between the space used by the data structure and the time (number of probes) needed to answer a query about the encoded object. We prove a number of upper and lower bounds on various natural error-correcting data structure problems. In particular, we show that the optimal length of error-correcting data structures for the Membership problem (where we want to store subsets of size s from a universe of size n) is closely related to the optimal length of locally decodable codes for s-bit strings.Comment: 15 pages LaTeX; an abridged version will appear in the Proceedings of the STACS 2009 conferenc

Nifty Data Structures Projects

For computer science, and many technical fields, it is recognized that projects with real-world applicability play a significant roll in what students get out of the course. Creating applicable projects for upper division such as our data structures classes is very difficult and time consuming. We have utilized the Nifty assignments concept and applied it locally to an upper division data structures course. Our primary goal is to provide a forum for the sharing of data structure project ideas and materials (as applicable).https://digitalscholarship.unlv.edu/btp_expo/1062/thumbnail.jp

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

Dynamic Range Majority Data Structures

Given a set $P$ of coloured points on the real line, we study the problem of answering range $\alpha$-majority (or "heavy hitter") queries on $P$. More specifically, for a query range $Q$, we want to return each colour that is assigned to more than an $\alpha$-fraction of the points contained in $Q$. We present a new data structure for answering range $\alpha$-majority queries on a dynamic set of points, where $\alpha \in (0,1)$. Our data structure uses O(n) space, supports queries in $O((\lg n) / \alpha)$ time, and updates in $O((\lg n) / \alpha)$ amortized time. If the coordinates of the points are integers, then the query time can be improved to $O(\lg n / (\alpha \lg \lg n) + (\lg(1/\alpha))/\alpha))$. For constant values of $\alpha$, this improved query time matches an existing lower bound, for any data structure with polylogarithmic update time. We also generalize our data structure to handle sets of points in d-dimensions, for $d \ge 2$, as well as dynamic arrays, in which each entry is a colour.Comment: 16 pages, Preliminary version appeared in ISAAC 201

Active data structures on GPGPUs

Active data structures support operations that may affect a large number of elements of an aggregate data structure. They are well suited for extremely fine grain parallel systems, including circuit parallelism. General purpose GPUs were designed to support regular graphics algorithms, but their intermediate level of granularity makes them potentially viable also for active data structures. We consider the characteristics of active data structures and discuss the feasibility of implementing them on GPGPUs. We describe the GPU implementations of two such data structures (ESF arrays and index intervals), assess their performance, and discuss the potential of active data structures as an unconventional programming model that can exploit the capabilities of emerging fine grain architectures such as GPUs

Lock-free Concurrent Data Structures

Concurrent data structures are the data sharing side of parallel programming. Data structures give the means to the program to store data, but also provide operations to the program to access and manipulate these data. These operations are implemented through algorithms that have to be efficient. In the sequential setting, data structures are crucially important for the performance of the respective computation. In the parallel programming setting, their importance becomes more crucial because of the increased use of data and resource sharing for utilizing parallelism. The first and main goal of this chapter is to provide a sufficient background and intuition to help the interested reader to navigate in the complex research area of lock-free data structures. The second goal is to offer the programmer familiarity to the subject that will allow her to use truly concurrent methods.Comment: To appear in "Programming Multi-core and Many-core Computing Systems", eds. S. Pllana and F. Xhafa, Wiley Series on Parallel and Distributed Computin