Related papers: Burrows-Wheeler transform and LCP array constructi…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
We present a new fast Chase decoding algorithm for binary BCH codes. The new algorithm reduces the complexity in comparison to a recent fast Chase decoding algorithm for Reed--Solomon (RS) codes by the authors (IEEE Trans. IT, 2022), by…
We set new speed records for multiplying long polynomials over finite fields of characteristic two. Our multiplication algorithm is based on an additive FFT (Fast Fourier Transform) by Lin, Chung, and Huang in 2014 comparing to previously…
A bit catastrophe, loosely defined, is when a change in just one character of a string causes a significant change in the size of the compressed string. We study this phenomenon for the Burrows-Wheeler Transform (BWT), a string transform at…
Multi-robot path planning is difficult due to the combinatorial explosion of the search space with every new robot added. Complete search of the combined state-space soon becomes intractable. In this paper we present a novel form of…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB…
Conformal prediction provides distribution-free prediction intervals with finite-sample coverage guarantees, and recent work by Snell \& Griffiths reframes it as Bayesian Quadrature (BQ-CP), yielding powerful data-conditional guarantees via…
Data centers are increasingly using high-speed circuit switches to cope with the growing demand and reduce operational costs. One of the fundamental tasks of circuit switches is to compute a sparse collection of switching configurations to…
Complex Logical Query Answering (CLQA) over incomplete knowledge graphs is a challenging task. Recently, Query Embedding (QE) methods are proposed to solve CLQA by performing multi-hop logical reasoning. However, most of them only consider…
We survey the different methods used for extending the BWT to collections of strings, following largely [Cenzato and Lipt\'ak, CPM 2022, Bioinformatics 2024]. We analyze the specific aspects and combinatorial properties of the resulting BWT…
The recent rise of generative artificial intelligence (AI), powered by Transformer networks, has achieved remarkable success in natural language processing, computer vision, and graphics. However, the application of Transformers in…
A wavelet forest for a text $T [1..n]$ over an alphabet $\sigma$ takes $n H_0 (T) + o (n \log \sigma)$ bits of space and supports access and rank on $T$ in $O (\log \sigma)$ time. K\"arkk\"ainen and Puglisi (2011) implicitly introduced…
A standard format used for storing the output of high-throughput sequencing experiments is the FASTQ format. It comprises three main components: (i) headers, (ii) bases (nucleotide sequences), and (iii) quality scores. FASTQ files are…
In this paper, we study the ensemble average of boundary CFT (BCFT) data consistent with the bootstrap equations. We apply the results to computing ensemble average of copies of multi-point correlation functions of boundary changing…
Traditional algorithms for multiway join computation are based on rewriting the order of joins and combining results of intermediate subqueries. Recently, several approaches have been proposed for algorithms that are "worst-case optimal"…
In this paper, a novel real-time acceleration-continuous path-constrained trajectory planning algorithm is proposed with an appealing built-in tradability mechanism between cruise motion and time-optimal motion. Different from existing…
The Windows Scheduling Problem, also known as the Pinwheel Problem, is to schedule periodic jobs subject to their processing frequency demands. Instances are given as a set of jobs that have to be processed infinitely often such that the…
The sheer sizes of modern datasets are forcing data-structure designers to consider seriously both parallel construction and compactness. To achieve those goals we need to design a parallel algorithm with good scalability and with low…
Computing all-pairs shortest paths is a fundamental and much-studied problem with many applications. Unfortunately, despite intense study, there are still no significantly faster algorithms for it than the $\mathcal{O}(n^3)$ time algorithm…