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

Optimal Joins Using Compact Data Structures

Worst-case optimal join algorithms have gained a lot of attention in the database literature. We now count with several algorithms that are optimal in the worst case, and many of them have been implemented and validated in practice. However, the implementation of these algorithms often requires an enhanced indexing structure: to achieve optimality we either need to build completely new indexes, or we must populate the database with several instantiations of indexes such as B+-trees. Either way, this means spending an extra amount of storage space that may be non-negligible. We show that optimal algorithms can be obtained directly from a representation that regards the relations as point sets in variable-dimensional grids, without the need of extra storage. Our representation is a compact quadtree for the static indexes, and a dynamic quadtree sharing subtrees (which we dub a qdag) for intermediate results. We develop a compositional algorithm to process full join queries under this representation, and show that the running time of this algorithm is worst-case optimal in data complexity. Remarkably, we can extend our framework to evaluate more expressive queries from relational algebra by introducing a lazy version of qdags (lqdags). Once again, we can show that the running time of our algorithms is worst-case optimal

Compressed Data Structures for Dynamic Sequences

We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries: $\mathrm{access}(i,S)$ returns the $i$-th symbol in $S$, $\mathrm{rank}_a(i,S)$ counts how many times a symbol $a$ occurs among the first $i$ positions in $S$, and $\mathrm{select}_a(i,S)$ finds the position where a symbol $a$ occurs for the $i$-th time. We present the first fully-dynamic data structure for arbitrarily large alphabets that achieves optimal query times for all three operations and supports updates with worst-case time guarantees. Ours is also the first fully-dynamic data structure that needs only $nH_k+o(n\log\sigma)$ bits, where $H_k$ is the $k$-th order entropy and $n$ is the string length. Moreover our representation supports extraction of a substring $S[i..i+\ell]$ in optimal $O(\log n/\log\log n + \ell/\log_{\sigma}n)$ time

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

Concurrent Data Structures Linked in Time

Arguments about correctness of a concurrent data structure are typically carried out by using the notion of linearizability and specifying the linearization points of the data structure's procedures. Such arguments are often cumbersome as the linearization points' position in time can be dynamic (depend on the interference, run-time values and events from the past, or even future), non-local (appear in procedures other than the one considered), and whose position in the execution trace may only be determined after the considered procedure has already terminated. In this paper we propose a new method, based on a separation-style logic, for reasoning about concurrent objects with such linearization points. We embrace the dynamic nature of linearization points, and encode it as part of the data structure's auxiliary state, so that it can be dynamically modified in place by auxiliary code, as needed when some appropriate run-time event occurs. We name the idea linking-in-time, because it reduces temporal reasoning to spatial reasoning. For example, modifying a temporal position of a linearization point can be modeled similarly to a pointer update in separation logic. Furthermore, the auxiliary state provides a convenient way to concisely express the properties essential for reasoning about clients of such concurrent objects. We illustrate the method by verifying (mechanically in Coq) an intricate optimal snapshot algorithm due to Jayanti, as well as some clients

Predicate Abstraction for Linked Data Structures

We present Alias Refinement Types (ART), a new approach to the verification of correctness properties of linked data structures. While there are many techniques for checking that a heap-manipulating program adheres to its specification, they often require that the programmer annotate the behavior of each procedure, for example, in the form of loop invariants and pre- and post-conditions. Predicate abstraction would be an attractive abstract domain for performing invariant inference, existing techniques are not able to reason about the heap with enough precision to verify functional properties of data structure manipulating programs. In this paper, we propose a technique that lifts predicate abstraction to the heap by factoring the analysis of data structures into two orthogonal components: (1) Alias Types, which reason about the physical shape of heap structures, and (2) Refinement Types, which use simple predicates from an SMT decidable theory to capture the logical or semantic properties of the structures. We prove ART sound by translating types into separation logic assertions, thus translating typing derivations in ART into separation logic proofs. We evaluate ART by implementing a tool that performs type inference for an imperative language, and empirically show, using a suite of data-structure benchmarks, that ART requires only 21% of the annotations needed by other state-of-the-art verification techniques