arXiv subjects

Giulio Ermanno Pibiri

Publications and source records attributed to Giulio Ermanno Pibiri.

17 recordsLinked to original sources

arXiv2026

Modern Minimal Perfect Hashing: A Survey

Given a set $S$ of $n$ keys, a perfect hash function for $S$ maps the keys in $S$ to the first $m \geq n$ integers without collisions. It may return an arbitrary result for any key not in $S$ and is called minimal if $m = n$. The most important parameters are its space consumption, construction time, and query time. Years of research now enable modern perfect hash functions to be extremely fast to query, very space-efficient, and scale to billions of keys. Different approaches give different trade-offs between these aspects. For example, the smallest constructions get within 0.1% of the space lower bound of $\log_2(e)$ bits per key. Others are particularly fast to query, requiring only one memory access. Perfect hashing has many applications, for example to avoid collision resolution in static hash tables, and is used in databases, bioinformatics, and stringology. Since the last comprehensive survey in 1997, significant progress has been made. This survey covers the latest developments and provides a starting point for getting familiar with the topic. Additionally, our extensive experimental evaluation can serve as a guide to select a perfect hash function for use in applications.

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arXiv2025

U-index: A Universal Indexing Framework for Matching Long Patterns

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index - to accelerate matching. The former solutions thus retain excellent compressed space, but are slow in practice. The latter approaches, like the suffix array, instead sacrifice space for speed. We show that efficient text indexing can be achieved using just a small extra space on top of the original text, provided that the query patterns are sufficiently long. More specifically, we develop a new indexing paradigm in which a sketch of a query pattern is first matched against a sketch of the text. Once candidate matches are retrieved, they are verified using the original text. This paradigm is thus universal in the sense that it allows us to use any solution to index the sketched text, like a suffix array, FM-index, or r-index. We explore both the theory and the practice of this universal framework. With an extensive experimental analysis, we show that, surprisingly, universal indexes can be constructed much faster than their unsketched counterparts and take a fraction of the space, as a direct consequence of (i) having a lower bound on the length of patterns and (ii) working in sketch space. Furthermore, these data structures have the potential of retaining or even improving query time, because matching against the sketched text is faster and verifying candidates can be theoretically done in constant time per occurrence (or, in practice, by short and cache-friendly scans of the text). Finally, we discuss some important applications of this novel indexing paradigm to computational biology. We hypothesize that such indexes will be particularly effective when the queries are sufficiently long, and so demonstrate applications in long-read mapping.

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arXiv2024

PHOBIC: Perfect Hashing with Optimized Bucket Sizes and Interleaved Coding

A minimal perfect hash function (MPHF) maps a set of n keys to {1, ..., n} without collisions. Such functions find widespread application e.g. in bioinformatics and databases. In this paper we revisit PTHash - a construction technique particularly designed for fast queries. PTHash distributes the input keys into small buckets and, for each bucket, it searches for a hash function seed that places its keys in the output domain without collisions. The collection of all seeds is then stored in a compressed way. Since the first buckets are easier to place, buckets are considered in non-increasing order of size. Additionally, PTHash heuristically produces an imbalanced distribution of bucket sizes by distributing 60% of the keys into 30% of the buckets. Our main contribution is to characterize, up to lower order terms, an optimal distribution of expected bucket sizes. We arrive at a simple, closed form solution which improves construction throughput for space efficient configurations in practice. Our second contribution is a novel encoding scheme for the seeds. We split the keys into partitions. Within each partition, we run the bucket distribution and search step. We then store the seeds in an interleaved way by consecutively placing the seeds for the i-th buckets from all partitions. The seeds for the i-th bucket of each partition follow the same statistical distribution. This allows us to tune a compressor for each bucket. Hence, we call our technique PHOBIC - Perfect Hashing with Optimized Bucket sizes and Interleaved Coding. Compared to PTHash, PHOBIC is 0.17 bits/key more space efficient for same query time and construction throughput. We also contribute a GPU implementation to further accelerate MPHF construction. For a configuration with fast queries, PHOBIC-GPU can construct a perfect hash function at 2.17 bits/key in 28 ns per key, which can be queried in 37 ns on the CPU.

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arXiv2024

Verifiable Boosted Tree Ensembles

Verifiable learning advocates for training machine learning models amenable to efficient security verification. Prior research demonstrated that specific classes of decision tree ensembles -- called large-spread ensembles -- allow for robustness verification in polynomial time against any norm-based attacker. This study expands prior work on verifiable learning from basic ensemble methods (i.e., hard majority voting) to advanced boosted tree ensembles, such as those trained using XGBoost or LightGBM. Our formal results indicate that robustness verification is achievable in polynomial time when considering attackers based on the $L_\infty$-norm, but remains NP-hard for other norm-based attackers. Nevertheless, we present a pseudo-polynomial time algorithm to verify robustness against attackers based on the $L_p$-norm for any $p \in \mathbb{N} \cup \{0\}$, which in practice grants excellent performance. Our experimental evaluation shows that large-spread boosted ensembles are accurate enough for practical adoption, while being amenable to efficient security verification.

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arXiv2023

Verifiable Learning for Robust Tree Ensembles

Verifying the robustness of machine learning models against evasion attacks at test time is an important research problem. Unfortunately, prior work established that this problem is NP-hard for decision tree ensembles, hence bound to be intractable for specific inputs. In this paper, we identify a restricted class of decision tree ensembles, called large-spread ensembles, which admit a security verification algorithm running in polynomial time. We then propose a new approach called verifiable learning, which advocates the training of such restricted model classes which are amenable for efficient verification. We show the benefits of this idea by designing a new training algorithm that automatically learns a large-spread decision tree ensemble from labelled data, thus enabling its security verification in polynomial time. Experimental results on public datasets confirm that large-spread ensembles trained using our algorithm can be verified in a matter of seconds, using standard commercial hardware. Moreover, large-spread ensembles are more robust than traditional ensembles against evasion attacks, at the cost of an acceptable loss of accuracy in the non-adversarial setting.

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arXiv2023

Parallel and External-Memory Construction of Minimal Perfect Hash Functions with PTHash

A function $f : U \to \{0,\ldots,n-1\}$ is a minimal perfect hash function for a set $S \subseteq U$ of size $n$, if $f$ bijectively maps $S$ into the first $n$ natural numbers. These functions are important for many practical applications in computing, such as search engines, computer networks, and databases. Several algorithms have been proposed to build minimal perfect hash functions that: scale well to large sets, retain fast evaluation time, and take very little space, e.g., 2 - 3 bits/key. PTHash is one such algorithm, achieving very fast evaluation in compressed space, typically several times faster than other techniques. In this work, we propose a new construction algorithm for PTHash enabling: (1) multi-threading, to either build functions more quickly or more space-efficiently, and (2) external-memory processing to scale to inputs much larger than the available internal memory. Only few other algorithms in the literature share these features, despite of their big practical impact. We conduct an extensive experimental assessment on large real-world string collections and show that, with respect to other techniques, PTHash is competitive in construction time and space consumption, but retains 2 - 6$\times$ better lookup time.

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arXiv2023

Locality-Preserving Minimal Perfect Hashing of k-mers

Minimal perfect hashing is the problem of mapping a static set of $n$ distinct keys into the address space $\{1,\ldots,n\}$ bijectively. It is well-known that $n\log_2(e)$ bits are necessary to specify a minimal perfect hash function (MPHF) $f$, when no additional knowledge of the input keys is to be used. However, it is often the case in practice that the input keys have intrinsic relationships that we can exploit to lower the bit complexity of $f$. For example, consider a string and the set of all its distinct $k$-mers as input keys: since two consecutive $k$-mers share an overlap of $k-1$ symbols, it seems possible to beat the classic $\log_2(e)$ bits/key barrier in this case. Moreover, we would like $f$ to map consecutive $k$-mers to consecutive addresses, as to also preserve as much as possible their relationship in the codomain. This is a useful feature in practice as it guarantees a certain degree of locality of reference for $f$, resulting in a better evaluation time when querying consecutive $k$-mers. Motivated by these premises, we initiate the study of a new type of locality-preserving MPHF designed for $k$-mers extracted consecutively from a collection of strings. We design a construction whose space usage decreases for growing $k$ and discuss experiments with a practical implementation of the method: in practice, the functions built with our method can be several times smaller and even faster to query than the most efficient MPHFs in the literature.

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arXiv2021

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 $\{0,\ldots,n-1\}$ 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 $2-4\times$ better lookup time.

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arXiv2021

Rank/Select Queries over Mutable Bitmaps

The problem of answering rank/select queries over a bitmap is of utmost importance for many succinct data structures. When the bitmap does not change, many solutions exist in the theoretical and practical side. In this work we consider the case where one is allowed to modify the bitmap via a flip(i) operation that toggles its i-th bit. By adapting and properly extending some results concerning prefix-sum data structures, we present a practical solution to the problem, tailored for modern CPU instruction sets. Compared to the state-of-the-art, our solution improves runtime with no space degradation. Moreover, it does not incur in a significant runtime penalty when compared to the fastest immutable indexes, while providing even lower space overhead.

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arXiv2020

Practical Trade-Offs for the Prefix-Sum Problem

Given an integer array A, the prefix-sum problem is to answer sum(i) queries that return the sum of the elements in A[0..i], knowing that the integers in A can be changed. It is a classic problem in data structure design with a wide range of applications in computing from coding to databases. In this work, we propose and compare several and practical solutions to this problem, showing that new trade-offs between the performance of queries and updates can be achieved on modern hardware.

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arXiv2020

Techniques for Inverted Index Compression

The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent performance requirements imposed by the heavy load of queries, the inverted index stores billions of integers that must be searched efficiently. In this scenario, index compression is essential because it leads to a better exploitation of the computer memory hierarchy for faster query processing and, at the same time, allows reducing the number of storage machines. The aim of this article is twofold: first, surveying the encoding algorithms suitable for inverted index compression and, second, characterizing the performance of the inverted index through experimentation.

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arXiv2020

Efficient and Effective Query Auto-Completion

Query Auto-Completion (QAC) is an ubiquitous feature of modern textual search systems, suggesting possible ways of completing the query being typed by the user. Efficiency is crucial to make the system have a real-time responsiveness when operating in the million-scale search space. Prior work has extensively advocated the use of a trie data structure for fast prefix-search operations in compact space. However, searching by prefix has little discovery power in that only completions that are prefixed by the query are returned. This may impact negatively the effectiveness of the QAC system, with a consequent monetary loss for real applications like Web Search Engines and eCommerce. In this work we describe the implementation that empowers a new QAC system at eBay, and discuss its efficiency/effectiveness in relation to other approaches at the state-of-the-art. The solution is based on the combination of an inverted index with succinct data structures, a much less explored direction in the literature. This system is replacing the previous implementation based on Apache SOLR that was not always able to meet the required service-level-agreement.

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arXiv2020

Succinct Dynamic Ordered Sets with Random Access

The representation of a dynamic ordered set of $n$ integer keys drawn from a universe of size $m$ is a fundamental data structuring problem. Many solutions to this problem achieve optimal time but take polynomial space, therefore preserving time optimality in the \emph{compressed} space regime is the problem we address in this work. For a polynomial universe $m = n^{Θ(1)}$, we give a solution that takes $\textsf{EF}(n,m) + o(n)$ bits, where $\textsf{EF}(n,m) \leq n\lceil \log_2(m/n)\rceil + 2n$ is the cost in bits of the \emph{Elias-Fano} representation of the set, and supports random access to the $i$-th smallest element in $O(\log n/ \log\log n)$ time, updates and predecessor search in $O(\log\log n)$ time. These time bounds are optimal.

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arXiv2020

On Optimally Partitioning Variable-Byte Codes

The ubiquitous Variable-Byte encoding is one of the fastest compressed representation for integer sequences. However, its compression ratio is usually not competitive with other more sophisticated encoders, especially when the integers to be compressed are small that is the typical case for inverted indexes. This paper shows that the compression ratio of Variable-Byte can be improved by 2x by adopting a partitioned representation of the inverted lists. This makes Variable-Byte surprisingly competitive in space with the best bit-aligned encoders, hence disproving the folklore belief that Variable-Byte is space-inefficient for inverted index compression. Despite the significant space savings, we show that our optimization almost comes for free, given that: we introduce an optimal partitioning algorithm that does not affect indexing time because of its linear-time complexity; we show that the query processing speed of Variable-Byte is preserved, with an extensive experimental analysis and comparison with several other state-of-the-art encoders.

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arXiv2020

Compressed Indexes for Fast Search of Semantic Data

The sheer increase in volume of RDF data demands efficient solutions for the triple indexing problem, that is devising a compressed data structure to compactly represent RDF triples by guaranteeing, at the same time, fast pattern matching operations. This problem lies at the heart of delivering good practical performance for the resolution of complex SPARQL queries on large RDF datasets. In this work, we propose a trie-based index layout to solve the problem and introduce two novel techniques to reduce its space of representation for improved effectiveness. The extensive experimental analysis conducted over a wide range of publicly available real-world datasets, reveals that our best space/time trade-off configuration substantially outperforms existing solutions at the state-of-the-art, by taking 30-60% less space and speeding up query execution by a factor of 2-81x.

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arXiv2020

Handling Massive N-Gram Datasets Efficiently

This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and estimation, that is computing the probability distribution of the strings from a large textual source. Regarding the problem of indexing, we describe compressed, exact and lossless data structures that achieve, at the same time, high space reductions and no time degradation with respect to state-of-the-art solutions and related software packages. In particular, we present a compressed trie data structure in which each word following a context of fixed length k, i.e., its preceding k words, is encoded as an integer whose value is proportional to the number of words that follow such context. Since the number of words following a given context is typically very small in natural languages, we lower the space of representation to compression levels that were never achieved before. Despite the significant savings in space, our technique introduces a negligible penalty at query time. Regarding the problem of estimation, we present a novel algorithm for estimating modified Kneser-Ney language models, that have emerged as the de-facto choice for language modeling in both academia and industry, thanks to their relatively low perplexity performance. Estimating such models from large textual sources poses the challenge of devising algorithms that make a parsimonious use of the disk. The state-of-the-art algorithm uses three sorting steps in external memory: we show an improved construction that requires only one sorting step thanks to exploiting the properties of the extracted n-gram strings. With an extensive experimental analysis performed on billions of n-grams, we show an average improvement of 4.5X on the total running time of the state-of-the-art approach.

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arXiv2019

On Slicing Sorted Integer Sequences

Representing sorted integer sequences in small space is a central problem for large-scale retrieval systems such as Web search engines. Efficient query resolution, e.g., intersection or random access, is achieved by carefully partitioning the sequences. In this work we describe and compare two different partitioning paradigms: partitioning by cardinality and partitioning by universe. Although the ideas behind such paradigms have been known in the coding and algorithmic community since many years, inverted index compression has extensively adopted the former paradigm, whereas the latter has received only little attention. As a result, an experimental comparison between these two is missing for the setting of inverted index compression. We also propose and implement a solution that recursively slices the universe of representation of a sequence to achieve compact storage and attain to fast query execution. Albeit larger than some state-of-the-art representations, this slicing approach substantially improves the performance of list intersections and unions while operating in compressed space, thus offering an excellent space/time trade-off for the problem.

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