Related papers: String Partition for Building Long Burrows-Wheeler…
A parameterized string (p-string) is a string over an alphabet $(\Sigma_{s} \cup \Sigma_{p})$, where $\Sigma_{s}$ and $\Sigma_{p}$ are disjoint alphabets for static symbols (s-symbols) and for parameter symbols (p-symbols), respectively.…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
Structural planning is important for producing long sentences, which is a missing part in current language generation models. In this work, we add a planning phase in neural machine translation to control the coarse structure of output…
The problem of reconstructing strings from their substring spectra has a long history and in its most simple incarnation asks for determining under which conditions the spectrum uniquely determines the string. We study the problem of coded…
Many problems in Computer Science can be abstracted to the following question: given a set of objects and rules respectively, which new objects can be produced? In the paper, we consider a succinct version of the question: given a set of…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
The suffix tree is a very important data structure in string processing, but it suffers from a huge space consumption. In large-scale applications, compressed suffix trees (CSTs) are therefore used instead. A CST consists of three…
We introduce a method to reduce constituent parsing to sequence labeling. For each word w_t, it generates a label that encodes: (1) the number of ancestors in the tree that the words w_t and w_{t+1} have in common, and (2) the nonterminal…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…
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…
Suffix tree (and the closely related suffix array) are fundamental structures capturing all substrings of a given text essentially by storing all its suffixes in the lexicographical order. In some applications, we work with a subset of $b$…
The issue of internal fragmentation in data structures is a fundamental challenge in database design. A seminal result of Yao in this field shows that evenly splitting the leaves of a B-tree against a workload of uniformly random insertions…
We propose an external memory algorithm for the computation of the BWT and LCP array for a collection of sequences. Our algorithm takes the amount of available memory as an input parameter, and tries to make the best use of it by splitting…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…
In this paper, a novel modulation scheme called set partition modulation (SPM) is proposed. In this scheme, set partitioning and ordered subsets in the set partitions are used to form codewords. We define different SPM variants and depict a…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
The Transformer architecture has shown significant success in many language processing and visual tasks. However, the method faces challenges in efficiently scaling to long sequences because the self-attention computation is quadratic with…