Cache-Oblivious Peeling of Random Hypergraphs

The computation of a peeling order in a randomly generated hypergraph is the most time-consuming step in a number of constructions, such as perfect hashing schemes, random $r$-SAT solvers, error-correcting codes, and approximate set encodings. While there exists a straightforward linear time algorithm, its poor I/O performance makes it impractical for hypergraphs whose size exceeds the available internal memory. We show how to reduce the computation of a peeling order to a small number of sequential scans and sorts, and analyze its I/O complexity in the cache-oblivious model. The resulting algorithm requires $O(\mathrm{sort}(n))$ I/Os and $O(n \log n)$ time to peel a random hypergraph with $n$ edges. We experimentally evaluate the performance of our implementation of this algorithm in a real-world scenario by using the construction of minimal perfect hash functions (MPHF) as our test case: our algorithm builds a MPHF of $7.6$ billion keys in less than $21$ hours on a single machine. The resulting data structure is both more space-efficient and faster than that obtained with the current state-of-the-art MPHF construction for large-scale key sets

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

A resource-frugal probabilistic dictionary and applications in (meta)genomics

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.Comment: Submitted to PSC 201

Efficient Gauss Elimination for Near-Quadratic Matrices with One Short Random Block per Row, with Applications

In this paper we identify a new class of sparse near-quadratic random Boolean matrices that have full row rank over F_2 = {0,1} with high probability and can be transformed into echelon form in almost linear time by a simple version of Gauss elimination. The random matrix with dimensions n(1-epsilon) x n is generated as follows: In each row, identify a block of length L = O((log n)/epsilon) at a random position. The entries outside the block are 0, the entries inside the block are given by fair coin tosses. Sorting the rows according to the positions of the blocks transforms the matrix into a kind of band matrix, on which, as it turns out, Gauss elimination works very efficiently with high probability. For the proof, the effects of Gauss elimination are interpreted as a ("coin-flipping") variant of Robin Hood hashing, whose behaviour can be captured in terms of a simple Markov model from queuing theory. Bounds for expected construction time and high success probability follow from results in this area. They readily extend to larger finite fields in place of F_2. By employing hashing, this matrix family leads to a new implementation of a retrieval data structure, which represents an arbitrary function f: S -> {0,1} for some set S of m = (1-epsilon)n keys. It requires m/(1-epsilon) bits of space, construction takes O(m/epsilon^2) expected time on a word RAM, while queries take O(1/epsilon) time and access only one contiguous segment of O((log m)/epsilon) bits in the representation (O(1/epsilon) consecutive words on a word RAM). The method is readily implemented and highly practical, and it is competitive with state-of-the-art methods. In a more theoretical variant, which works only for unrealistically large S, we can even achieve construction time O(m/epsilon) and query time O(1), accessing O(1) contiguous memory words for a query. By well-established methods the retrieval data structure leads to efficient constructions of (static) perfect hash functions and (static) Bloom filters with almost optimal space and very local storage access patterns for queries

Fast and Scalable Minimal Perfect Hashing for Massive Key Sets

Minimal perfect hash functions provide space-efficient and collision-free hashing on static sets. Existing algorithms and implementations that build such functions have practical limitations on the number of input elements they can process, due to high construction time, RAM or external memory usage. We revisit a simple algorithm and show that it is highly competitive with the state of the art, especially in terms of construction time and memory usage. We provide a parallel C++ implementation called BBhash. It is capable of creating a minimal perfect hash function of 10^{10} elements in less than 7 minutes using 8 threads and 5 GB of memory, and the resulting function uses 3.7 bits/element. To the best of our knowledge, this is also the first implementation that has been successfully tested on an input of cardinality 10^{12}. Source code: https://github.com/rizkg/BBHas

Constructing Minimal Perfect Hash Functions Using SAT Technology

Minimal perfect hash functions (MPHFs) are used to provide efficient access to values of large dictionaries (sets of key-value pairs). Discovering new algorithms for building MPHFs is an area of active research, especially from the perspective of storage efficiency. The information-theoretic limit for MPHFs is 1/(ln 2) or roughly 1.44 bits per key. The current best practical algorithms range between 2 and 4 bits per key. In this article, we propose two SAT-based constructions of MPHFs. Our first construction yields MPHFs near the information-theoretic limit. For this construction, current state-of-the-art SAT solvers can handle instances where the dictionaries contain up to 40 elements, thereby outperforming the existing (brute-force) methods. Our second construction uses XOR-SAT filters to realize a practical approach with long-term storage of approximately 1.83 bits per key.Comment: Accepted for AAAI 202

Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data

A key problem in processing raw optical mapping data (Rmaps) is finding Rmaps originating from the same genomic region. These sets of related Rmaps can be used to correct errors in Rmap data, and to find overlaps between Rmaps to assemble consensus optical maps. Previous Rmap overlap aligners are computationally very expensive and do not scale to large eukaryotic data sets. We present SELKIE, an Rmap overlap aligner based on a spaced (l,k)-mer index which was pioneered in the Rmap error correction tool ELMER. Here we present a space efficient version of the index which is twice as fast as prior art while using just a quarter of the memory on a human data set. Moreover, our index can be used for filtering candidates for Rmap overlap computation, whereas ELMERI used the index only for error correction of Rmaps. By combining our filtering of Rmaps with the exhaustive, but highly accurate, algorithm of Valouev etal. (2006), SELKIE maintains or increases the accuracy of finding overlapping Rmaps on a bacterial dataset while being at least four times faster. Furthermore, for finding overlaps in a human dataset, SELKIE is up to two orders of magnitude faster than previous methods.Peer reviewe

PTHash: Revisiting FCH Minimal Perfect Hashing

Given a set S of n distinct keys, a function f that bijectively maps the keys of S into the range (0,...,n-1) is called a minimal perfect hash function for S. Algorithms that find such functions when n is large and retain constant evaluation time are of practical interest; for instance, search engines and databases typically use minimal perfect hash functions to quickly assign identifiers to static sets of variable-length keys such as strings. The challenge is to design an algorithm which is efficient in three different aspects: time to find f (construction time), time to evaluate f on a key of S (lookup time), and space of representation for f. Several algorithms have been proposed to trade-off between these aspects. In 1992, Fox, Chen, and Heath (FCH) presented an algorithm at SIGIR providing very fast lookup evaluation. However, the approach received little attention because of its large construction time and higher space consumption compared to other subsequent techniques. Almost thirty years later we revisit their framework and present an improved algorithm that scales well to large sets and reduces space consumption altogether, without compromising the lookup time. We conduct an extensive experimental assessment and show that the algorithm finds functions that are competitive in space with state-of-the art techniques and provide 2-4x better lookup time

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

Dense peelable random uniform hypergraphs

We describe a new family of k-uniform hypergraphs with independent random edges. The hypergraphs have a high probability of being peelable, i.e. to admit no sub-hypergraph of minimum degree 2, even when the edge density (number of edges over vertices) is close to 1. In our construction, the vertex set is partitioned into linearly arranged segments and each edge is incident to random vertices of k consecutive segments. Quite surprisingly, the linear geometry allows our graphs to be peeled "from the outside in". The density thresholds f_k for peelability of our hypergraphs (f_3 ~ 0.918, f_4 ~ 0.977, f_5 ~ 0.992, ...) are well beyond the corresponding thresholds (c_3 ~ 0.818, c_4 ~ 0.772, c_5 ~ 0.702, ...) of standard k-uniform random hypergraphs. To get a grip on f_k, we analyse an idealised peeling process on the random weak limit of our hypergraph family. The process can be described in terms of an operator on [0,1]^Z and f_k can be linked to thresholds relating to the operator. These thresholds are then tractable with numerical methods. Random hypergraphs underlie the construction of various data structures based on hashing, for instance invertible Bloom filters, perfect hash functions, retrieval data structures, error correcting codes and cuckoo hash tables, where inputs are mapped to edges using hash functions. Frequently, the data structures rely on peelability of the hypergraph or peelability allows for simple linear time algorithms. Memory efficiency is closely tied to edge density while worst and average case query times are tied to maximum and average edge size. To demonstrate the usefulness of our construction, we used our 3-uniform hypergraphs as a drop-in replacement for the standard 3-uniform hypergraphs in a retrieval data structure by Botelho et al. [Fabiano Cupertino Botelho et al., 2013]. This reduces memory usage from 1.23m bits to 1.12m bits (m being the input size) with almost no change in running time. Using k > 3 attains, at small sacrifices in running time, further improvements to memory usage