相关论文: A New Lightweight Algorithm to compute the BWT and…

Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input genome string into short, exactly matching substrings (e.g.,…

We present two variations of Duval's algorithm for computing the Lyndon factorization of a word. The first algorithm is designed for the case of small alphabets and is able to skip a significant portion of the characters of the string, for…

Grammar compression is, next to Lempel-Ziv (LZ77) and run-length Burrows-Wheeler transform (RLBWT), one of the most flexible approaches to representing and processing highly compressible strings. The main idea is to represent a text as a…

Given strings $P$ and $Q$ the (exact) string matching problem is to find all positions of substrings in $Q$ matching $P$. The classical Knuth-Morris-Pratt algorithm [SIAM J. Comput., 1977] solves the string matching problem in linear time…

We study algorithms for solving the problem of constructing a text (long string) from a dictionary (sequence of small strings). The problem has an application in bioinformatics and has a connection with the Sequence assembly method for…

A deterministic BSP algorithm for constructing the suffix array of a given string is presented, based on a technique which we call accelerated sampling. It runs in optimal O(n/p) local computation and communication, and requires a near…

Large language models (LLMs) have driven major progress in NLP, yet their substantial memory and compute demands still hinder practical deployment. Binarization can compress weights to 1 bit, fundamentally lowering compute and bandwidth…

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…

Computing the LZ factorization (or LZ77 parsing) of a string is a computational bottleneck in many diverse applications, including data compression, text indexing, and pattern discovery. We describe new linear time LZ factorization…

In the reordering buffer problem (RBP), a server is asked to process a sequence of requests lying in a metric space. To process a request the server must move to the corresponding point in the metric. The requests can be processed slightly…

The Transformer model is widely successful on many natural language processing tasks. However, the quadratic complexity of self-attention limit its application on long text. In this paper, adopting a fine-to-coarse attention mechanism on…

A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is,…

In this paper we develop a theory describing how the extended Burrows-Wheeler Transform (eBWT) of a collection of DNA fragments tends to cluster together the copies of nucleotides sequenced from a genome G. Our theory accurately predicts…

The prevalent use of Byte Pair Encoding (BPE) in Large Language Models (LLMs) facilitates robust handling of subword units and avoids issues of out-of-vocabulary words. Despite its success, a critical challenge persists: long tokens, rich…

Counting distinct permutations with replacement, especially when involving multiple subwords, is a longstanding challenge in combinatorial analysis, with critical applications in cryptography, bioinformatics, and statistical modeling. This…

The Bag-of-Words (BoW) representation is well applied to recent state-of-the-art image retrieval works. Typically, multiple vocabularies are generated to correct quantization artifacts and improve recall. However, this routine is corrupted…

Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

We consider two closely related problems of text indexing in a sub-linear working space. The first problem is the Sparse Suffix Tree (SST) construction of a set of suffixes $B$ using only $O(|B|)$ words of space. The second problem is the…

We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes…