GPERF : a perfect hash function generator

gperf is a widely available perfect hash function generator written in C++. It automates a common system software operation: keyword recognition. gperf translates an n element user-specified keyword list keyfile into source code containing a k element lookup table and a pair of functions, phash and in_word_set. phash uniquely maps keywords in keyfile onto the range 0 .. k - 1, where k >/= n. If k = n, then phash is considered a minimal perfect hash function. in_word_set uses phash to determine whether a particular string of characters str occurs in the keyfile, using at most one string comparison.This paper describes the user-interface, options, features, algorithm design and implementation strategies incorporated in gperf. It also presents the results from an empirical comparison between gperf-generated recognizers and other popular techniques for reserved word lookup

Comparison of Perfect Hashing Methods

This study was conducted to compare two minimal perfect hashing method Chang's method and Jaeschke's method. Since hashing is a widely used technique for store data in symbol table and the data are strings of characters, this study f use on the performance of these methods with the letter-oriented set and gives their run time performance curves. Through the analysis of run time and space complexity, an optimal method is given to make each algorithm performance well

Hashing and its applications

This tutorial discusses one of the oldest problems in computing: how to search and retrieve keyed information from a list in the least amount of time. Hashing -- a technique that mathematically converts a key into a storage address -- is one of the best methods of finding and retrieving information associated with a unique identifying key. We briefly survey techniques which have evolved over the past 25 years and then introduce more recent research results for extremely compact and fast methods based on perfect and minimal perfect hashing. Perfect and minimal perfect hashing is useful for rapid lookup of keywords in a compiler, spelling checkers, and database management systems. The results presented here show techniques for constructing long lists which can be searched in one memory reference.KEYWORDS AND PHRASES Key-to-address transformation, hash coding, hash table, scatter table, associative retrieval, associative memory, bucket hashing, perfect hashing, minimal perfect hashing, lookup, indexed retrieval

Data structures

We discuss data structures and their methods of analysis. In particular, we treat the unweighted and weighted dictionary problem, self-organizing data structures, persistent data structures, the union-find-split problem, priority queues, the nearest common ancestor problem, the selection and merging problem, and dynamization techniques. The methods of analysis are worst, average and amortized case

Random hypergraphs for hashing-based data structures

This thesis concerns dictionaries and related data structures that rely on providing several random possibilities for storing each key. Imagine information on a set S of m = |S| keys should be stored in n memory locations, indexed by [n] = {1,…,n}. Each object x [ELEMENT OF] S is assigned a small set e(x) [SUBSET OF OR EQUAL TO] [n] of locations by a random hash function, independent of other objects. Information on x must then be stored in the locations from e(x) only. It is possible that too many objects compete for the same locations, in particular if the load c = m/n is high. Successfully storing all information may then be impossible. For most distributions of e(x), however, success or failure can be predicted very reliably, since the success probability is close to 1 for loads c less than a certain load threshold c^* and close to 0 for loads greater than this load threshold. We mainly consider two types of data structures: • A cuckoo hash table is a dictionary data structure where each key x [ELEMENT OF] S is stored together with an associated value f(x) in one of the memory locations with an index from e(x). The distribution of e(x) is controlled by the hashing scheme. We analyse three known hashing schemes, and determine their exact load thresholds. The schemes are unaligned blocks, double hashing and a scheme for dynamically growing key sets. • A retrieval data structure also stores a value f(x) for each x [ELEMENT OF] S. This time, the values stored in the memory locations from e(x) must satisfy a linear equation that characterises the value f(x). The resulting data structure is extremely compact, but unusual. It cannot answer questions of the form “is y [ELEMENT OF] S?”. Given a key y it returns a value z. If y [ELEMENT OF] S, then z = f(y) is guaranteed, otherwise z may be an arbitrary value. We consider two new hashing schemes, where the elements of e(x) are contained in one or two contiguous blocks. This yields good access times on a word RAM and high cache efficiency. An important question is whether these types of data structures can be constructed in linear time. The success probability of a natural linear time greedy algorithm exhibits, once again, threshold behaviour with respect to the load c. We identify a hashing scheme that leads to a particularly high threshold value in this regard. In the mathematical model, the memory locations [n] correspond to vertices, and the sets e(x) for x [ELEMENT OF] S correspond to hyperedges. Three properties of the resulting hypergraphs turn out to be important: peelability, solvability and orientability. Therefore, large parts of this thesis examine how hyperedge distribution and load affects the probabilities with which these properties hold and derive corresponding thresholds. Translated back into the world of data structures, we achieve low access times, high memory efficiency and low construction times. We complement and support the theoretical results by experiments.Diese Arbeit behandelt Wörterbücher und verwandte Datenstrukturen, die darauf aufbauen, mehrere zufällige Möglichkeiten zur Speicherung jedes Schlüssels vorzusehen. Man stelle sich vor, Information über eine Menge S von m = |S| Schlüsseln soll in n Speicherplätzen abgelegt werden, die durch [n] = {1,…,n} indiziert sind. Jeder Schlüssel x [ELEMENT OF] S bekommt eine kleine Menge e(x) [SUBSET OF OR EQUAL TO] [n] von Speicherplätzen durch eine zufällige Hashfunktion unabhängig von anderen Schlüsseln zugewiesen. Die Information über x darf nun ausschließlich in den Plätzen aus e(x) untergebracht werden. Es kann hierbei passieren, dass zu viele Schlüssel um dieselben Speicherplätze konkurrieren, insbesondere bei hoher Auslastung c = m/n. Eine erfolgreiche Speicherung der Gesamtinformation ist dann eventuell unmöglich. Für die meisten Verteilungen von e(x) lässt sich Erfolg oder Misserfolg allerdings sehr zuverlässig vorhersagen, da für Auslastung c unterhalb eines gewissen Auslastungsschwellwertes c* die Erfolgswahrscheinlichkeit nahezu 1 ist und für c jenseits dieses Auslastungsschwellwertes nahezu 0 ist. Hauptsächlich werden wir zwei Arten von Datenstrukturen betrachten: • Eine Kuckucks-Hashtabelle ist eine Wörterbuchdatenstruktur, bei der jeder Schlüssel x [ELEMENT OF] S zusammen mit einem assoziierten Wert f(x) in einem der Speicherplätze mit Index aus e(x) gespeichert wird. Die Verteilung von e(x) wird hierbei vom Hashing-Schema festgelegt. Wir analysieren drei bekannte Hashing-Schemata und bestimmen erstmals deren exakte Auslastungsschwellwerte im obigen Sinne. Die Schemata sind unausgerichtete Blöcke, Doppel-Hashing sowie ein Schema für dynamisch wachsenden Schlüsselmengen. • Auch eine Retrieval-Datenstruktur speichert einen Wert f(x) für alle x [ELEMENT OF] S. Diesmal sollen die Werte in den Speicherplätzen aus e(x) eine lineare Gleichung erfüllen, die den Wert f(x) charakterisiert. Die entstehende Datenstruktur ist extrem platzsparend, aber ungewöhnlich: Sie ist ungeeignet um Fragen der Form „ist y [ELEMENT OF] S?“ zu beantworten. Bei Anfrage eines Schlüssels y wird ein Ergebnis z zurückgegeben. Falls y [ELEMENT OF] S ist, so ist z = f(y) garantiert, andernfalls darf z ein beliebiger Wert sein. Wir betrachten zwei neue Hashing-Schemata, bei denen die Elemente von e(x) in einem oder in zwei zusammenhängenden Blöcken liegen. So werden gute Zugriffszeiten auf Word-RAMs und eine hohe Cache-Effizienz erzielt. Eine wichtige Frage ist, ob Datenstrukturen obiger Art in Linearzeit konstruiert werden können. Die Erfolgswahrscheinlichkeit eines naheliegenden Greedy-Algorithmus weist abermals ein Schwellwertverhalten in Bezug auf die Auslastung c auf. Wir identifizieren ein Hashing-Schema, das diesbezüglich einen besonders hohen Schwellwert mit sich bringt. In der mathematischen Modellierung werden die Speicherpositionen [n] als Knoten und die Mengen e(x) für x [ELEMENT OF] S als Hyperkanten aufgefasst. Drei Eigenschaften der entstehenden Hypergraphen stellen sich dann als zentral heraus: Schälbarkeit, Lösbarkeit und Orientierbarkeit. Weite Teile dieser Arbeit beschäftigen sich daher mit den Wahrscheinlichkeiten für das Vorliegen dieser Eigenschaften abhängig von Hashing Schema und Auslastung, sowie mit entsprechenden Schwellwerten. Eine Rückübersetzung der Ergebnisse liefert dann Datenstrukturen mit geringen Anfragezeiten, hoher Speichereffizienz und geringen Konstruktionszeiten. Die theoretischen Überlegungen werden dabei durch experimentelle Ergebnisse ergänzt und gestützt

Meraculous: De Novo Genome Assembly with Short Paired-End Reads

We describe a new algorithm, meraculous, for whole genome assembly of deep paired-end short reads, and apply it to the assembly of a dataset of paired 75-bp Illumina reads derived from the 15.4 megabase genome of the haploid yeast Pichia stipitis. More than 95% of the genome is recovered, with no errors; half the assembled sequence is in contigs longer than 101 kilobases and in scaffolds longer than 269 kilobases. Incorporating fosmid ends recovers entire chromosomes. Meraculous relies on an efficient and conservative traversal of the subgraph of the k-mer (deBruijn) graph of oligonucleotides with unique high quality extensions in the dataset, avoiding an explicit error correction step as used in other short-read assemblers. A novel memory-efficient hashing scheme is introduced. The resulting contigs are ordered and oriented using paired reads separated by ∼280 bp or ∼3.2 kbp, and many gaps between contigs can be closed using paired-end placements. Practical issues with the dataset are described, and prospects for assembling larger genomes are discussed

Signature file access methodologies for text retrieval: a literature review with additional test cases

Signature files are extremely compressed versions of text files which can be used as access or index files to facilitate searching documents for text strings. These access files, or signatures, are generated by storing hashed codes for individual words. Given the possible generation of similar codes in the hashing or storing process, the primary concern in researching signature files is to determine the accuracy of retrieving information. Inaccuracy is always represented by the false signaling of the presence of a text string. Two suggested ways to alter false drop rates are: 1) to determine if either of the two methologies for storing hashed codes, by superimposing them or by concatenating them, is more efficient; and 2) to determine if a particular hashing algorithm has any impact. To assess these issues, the history of suprimposed coding is traced from its development as a tool for compressing information onto punched cards in the 1950s to its incorporation into proposed signature file methodologies in the mid-1980\u27 s. Likewise, the concept of compressing individual words by various algorithms, or by hashing them is traced through the research literature. Following this literature review, benchmark trials are performed using both superimposed and concatenated methodologies while varying hashing algorithms. It is determined that while one combination of hashing algorithm and storage methodology is better, all signature file mehods can be considered viable

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Engineering Aggregation Operators for Relational In-Memory Database Systems

In this thesis we study the design and implementation of Aggregation operators in the context of relational in-memory database systems. In particular, we identify and address the following challenges: cache-efficiency, CPU-friendliness, parallelism within and across processors, robust handling of skewed data, adaptive processing, processing with constrained memory, and integration with modern database architectures. Our resulting algorithm outperforms the state-of-the-art by up to 3.7x