Related papers: Scalable Construction of Text Indexes

Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…

Document clustering as an unsupervised approach extensively used to navigate, filter, summarize and manage large collection of document repositories like the World Wide Web (WWW). Recently, focuses in this domain shifted from traditional…

The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…

The suffix tree is arguably the most fundamental data structure on strings: introduced by Weiner (SWAT 1973) and McCreight (JACM 1976), it allows solving a myriad of computational problems on strings in linear time. Motivated by its large…

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…

Suffix arrays encode the lexicographical order of all suffixes of a text and are often combined with the Longest Common Prefix array (LCP) to simulate navigational queries on the suffix tree in reduced space. In space-critical applications…

Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…

Sparse suffix sorting is the problem of sorting $b=o(n)$ suffixes of a string of length $n$. Efficient sparse suffix sorting algorithms have existed for more than a decade. Despite the multitude of works and their justified claims for…

Graph structure learning is a core problem in graph-based machine learning, essential for uncovering latent relationships and ensuring model interpretability. However, most existing approaches are ill-suited for large-scale and dynamically…

String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least)…

We consider strategies to organize easily updatable associative arrays in external memory. These arrays are used for full-text search. We study indexes with different keys: single word form, two word forms, and sequences of word forms. The…

The suffix array is arguably one of the most important data structures in sequence analysis and consequently there is a multitude of suffix sorting algorithms. However, to this date the GSACA algorithm introduced in 2015 is the only known…

A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…

Different from the traditional benchmarking methodology that creates a new benchmark or proxy for every possible workload, this paper presents a scalable big data benchmarking methodology. Among a wide variety of big data analytics…

We consider construction of the suffix tree and the directed acyclic word graph (DAWG) indexing data structures for a collection $\mathcal{T}$ of texts, where a new symbol may be appended to any text in $\mathcal{T} = \{T_1, \ldots, T_K\}$,…

Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…

We present a structural clustering algorithm for large-scale datasets of small labeled graphs, utilizing a frequent subgraph sampling strategy. A set of representatives provides an intuitive description of each cluster, supports the…

Large language models (LLMs) are powerful tools that have found applications beyond human-machine interfaces and chatbots. In particular, their ability to generate reasoning traces motivated their use in many prediction tasks like math…

The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…

This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…