Related papers: Compressing Suffix Trees by Path Decompositions
We present algorithms that run in linear time on pointer machines for a collection of problems, each of which either directly or indirectly requires the evaluation of a function defined on paths in a tree. These problems previously had…
Lately, there has been an upsurge of interest in compressed data structures, aiming to pack ever larger quantities of information into constrained memory without sacrificing the efficiency of standard operations, like random access, search,…
A well-known fact in the field of lossless text compression is that high-order entropy is a weak model when the input contains long repetitions. Motivated by this, decades of research have generated myriads of so-called dictionary…
Decision trees are widely-used classification and regression models because of their interpretability and good accuracy. Classical methods such as CART are based on greedy approaches but a growing attention has recently been devoted to…
In highly repetitive strings, like collections of genomes from the same species, distinct measures of repetition all grow sublinearly in the length of the text, and indexes targeted to such strings typically depend only on one of these…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…
We prove a square-root space simulation for deterministic multitape Turing machines, showing $\mathrm{TIME}[t]\subseteq \mathrm{SPACE}[O(\sqrt{t})]$ \emph{measured in tape cells over a fixed finite alphabet}. The key step is a Height…
We present methods to serialize and deserialize tree ensembles that optimize inference latency when models are not already loaded into memory. This arises whenever models are larger than memory, but also systematically when models are…
String matching is the problem of finding all the occurrences of a pattern in a text. It has been intensively studied and the Boyer-Moore string matching algorithm is probably one of the most famous solution to this problem. This algorithm…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
We consider the problem of constructing a sparse suffix tree (or suffix array) for $b$ suffixes of a given text $T$ of size $n$, using only $O(b)$ words of space during construction time. Breaking the naive bound of $\Omega(nb)$ time for…
The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…
In a \emph{weighted sequence}, for every position of the sequence and every letter of the alphabet a probability of occurrence of this letter at this position is specified. Weighted sequences are commonly used to represent imprecise or…
Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…
Over the past decade, we witness an increasing amount of interest in the design of exact exponential-time and parameterized algorithms for problems in Graph Drawing. Unfortunately, we still lack knowledge of general methods to develop such…
In the past thirty years, numerous algorithms for building the suffix array of a string have been proposed. In 2021, the notion of suffix array was extended from strings to DFAs, and it was shown that the resulting data structure can be…
Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…