Succinct Data Structures for Retrieval and Approximate Membership

The retrieval problem is the problem of associating data with keys in a set. Formally, the data structure must store a function f: U ->{0,1}^r that has specified values on the elements of a given set S, a subset of U, |S|=n, but may have any value on elements outside S. Minimal perfect hashing makes it possible to avoid storing the set S, but this induces a space overhead of Theta(n) bits in addition to the nr bits needed for function values. In this paper we show how to eliminate this overhead. Moreover, we show that for any k query time O(k) can be achieved using space that is within a factor 1+e^{-k} of optimal, asymptotically for large n. If we allow logarithmic evaluation time, the additive overhead can be reduced to O(log log n) bits whp. The time to construct the data structure is O(n), expected. A main technical ingredient is to utilize existing tight bounds on the probability of almost square random matrices with rows of low weight to have full row rank. In addition to direct constructions, we point out a close connection between retrieval structures and hash tables where keys are stored in an array and some kind of probing scheme is used. Further, we propose a general reduction that transfers the results on retrieval into analogous results on approximate membership, a problem traditionally addressed using Bloom filters. Again, we show how to eliminate the space overhead present in previously known methods, and get arbitrarily close to the lower bound. The evaluation procedures of our data structures are extremely simple (similar to a Bloom filter). For the results stated above we assume free access to fully random hash functions. However, we show how to justify this assumption using extra space o(n) to simulate full randomness on a RAM

Fast Succinct Retrieval and Approximate Membership Using Ribbon

A retrieval data structure for a static function f: S → {0,1}^r supports queries that return f(x) for any x ∈ S. Retrieval data structures can be used to implement a static approximate membership query data structure (AMQ), i.e., a Bloom filter alternative, with false positive rate 2^{-r}. The information-theoretic lower bound for both tasks is r|S| bits. While succinct theoretical constructions using (1+o(1))r|S| bits were known, these could not achieve very small overheads in practice because they have an unfavorable space-time tradeoff hidden in the asymptotic costs or because small overheads would only be reached for physically impossible input sizes. With bumped ribbon retrieval (BuRR), we present the first practical succinct retrieval data structure. In an extensive experimental evaluation BuRR achieves space overheads well below 1% while being faster than most previously used retrieval data structures (typically with space overheads at least an order of magnitude larger) and faster than classical Bloom filters (with space overhead ≥ 44%). This efficiency, including favorable constants, stems from a combination of simplicity, word parallelism, and high locality. We additionally describe homogeneous ribbon filter AMQs, which are even simpler and faster at the price of slightly larger space overhead

Fast Scalable Construction of (Minimal Perfect Hash) Functions

Recent advances in random linear systems on finite fields have paved the way for the construction of constant-time data structures representing static functions and minimal perfect hash functions using less space with respect to existing techniques. The main obstruction for any practical application of these results is the cubic-time Gaussian elimination required to solve these linear systems: despite they can be made very small, the computation is still too slow to be feasible. In this paper we describe in detail a number of heuristics and programming techniques to speed up the resolution of these systems by several orders of magnitude, making the overall construction competitive with the standard and widely used MWHC technique, which is based on hypergraph peeling. In particular, we introduce broadword programming techniques for fast equation manipulation and a lazy Gaussian elimination algorithm. We also describe a number of technical improvements to the data structure which further reduce space usage and improve lookup speed. Our implementation of these techniques yields a minimal perfect hash function data structure occupying 2.24 bits per element, compared to 2.68 for MWHC-based ones, and a static function data structure which reduces the multiplicative overhead from 1.23 to 1.03

Approximate Range Emptiness in Constant Time and Optimal Space

This paper studies the \emph{$\varepsilon$-approximate range emptiness} problem, where the task is to represent a set $S$ of $n$ points from $\{0,\ldots,U-1\}$ and answer emptiness queries of the form "$[a ; b]\cap S \neq \emptyset$ ?" with a probability of \emph{false positives} allowed. This generalizes the functionality of \emph{Bloom filters} from single point queries to any interval length $L$. Setting the false positive rate to $\varepsilon/L$ and performing $L$ queries, Bloom filters yield a solution to this problem with space $O(n \lg(L/\varepsilon))$ bits, false positive probability bounded by $\varepsilon$ for intervals of length up to $L$, using query time $O(L \lg(L/\varepsilon))$. Our first contribution is to show that the space/error trade-off cannot be improved asymptotically: Any data structure for answering approximate range emptiness queries on intervals of length up to $L$ with false positive probability $\varepsilon$, must use space $\Omega(n \lg(L/\varepsilon)) - O(n)$ bits. On the positive side we show that the query time can be improved greatly, to constant time, while matching our space lower bound up to a lower order additive term. This result is achieved through a succinct data structure for (non-approximate 1d) range emptiness/reporting queries, which may be of independent interest

A Dynamic Space-Efficient Filter with Constant Time Operations

A dynamic dictionary is a data structure that maintains sets of cardinality at most n from a given universe and supports insertions, deletions, and membership queries. A filter approximates membership queries with a one-sided error that occurs with probability at most ?. The goal is to obtain dynamic filters that are space-efficient (the space is 1+o(1) times the information-theoretic lower bound) and support all operations in constant time with high probability. One approach to designing filters is to reduce to the retrieval problem. When the size of the universe is polynomial in n, this approach yields a space-efficient dynamic filter as long as the error parameter ? satisfies log(1/?) = ?(log log n). For the case that log(1/?) = O(log log n), we present the first space-efficient dynamic filter with constant time operations in the worst case (whp). In contrast, the space-efficient dynamic filter of Pagh et al. [Anna Pagh et al., 2005] supports insertions and deletions in amortized expected constant time. Our approach employs the classic reduction of Carter et al. [Carter et al., 1978] on a new type of dictionary construction that supports random multisets

Dynamic Relative Compression, Dynamic Partial Sums, and Substring Concatenation

Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of compression and have recently proved very successful for compressing highly-repetitive massive data sets such as genomes and web-data. We initiate the study of relative compression in a dynamic setting where the compressed source string $S$ is subject to edit operations. The goal is to maintain the compressed representation compactly, while supporting edits and allowing efficient random access to the (uncompressed) source string. We present new data structures that achieve optimal time for updates and queries while using space linear in the size of the optimal relative compression, for nearly all combinations of parameters. We also present solutions for restricted and extended sets of updates. To achieve these results, we revisit the dynamic partial sums problem and the substring concatenation problem. We present new optimal or near optimal bounds for these problems. Plugging in our new results we also immediately obtain new bounds for the string indexing for patterns with wildcards problem and the dynamic text and static pattern matching problem