Related papers: More efficient PBWT prefix-array access via batchi…
The research on indexing repetitive string collections has focused on the same search problems used for regular string collections, though they can make little sense in this scenario. For example, the basic pattern matching query "list all…
In multiple-choice data structures each element $x$ in a set $S$ of $m$ keys is associated with a random set $e(x) \subseteq [n]$ of buckets with capacity $\ell \geq 1$ by hash functions. This setting is captured by the hypergraph $H =…
We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…
A near-field simultaneous wireless information and power transfer (SWIPT) network is investigated, where the hybrid beamforming architecture is employed at the base station (BS) for information transmission while charging energy harvesting…
Searching on bipartite graphs is basal and versatile to many real-world Web applications, e.g., online recommendation, database retrieval, and query-document searching. Given a query node, the conventional approaches rely on the similarity…
We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of…
We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…
The most popular framework for distributed training of machine learning models is the (synchronous) parameter server (PS). This paradigm consists of $n$ workers, which iteratively compute updates of the model parameters, and a stateful PS,…
Perfect hash functions give unique "names" to arbitrary keys requiring only a few bits per key. This is an essential building block in applications like static hash tables, databases, or bioinformatics. This paper introduces the PHast…
We propose a novel framework for fast integral operations by uncovering hidden geometries in the row and column structures of the underlying operators. This is accomplished through the \texttt{Questionnaire} algorithm, an iterative…
We propose a multistage method for making inference at all levels of a Bayesian hierarchical model (BHM) using natural data partitions to increase efficiency by allowing computations to take place in parallel form using software that is…
For an even integer t \geq 2, the Matchings Connecivity matrix H_t is a matrix that has rows and columns both labeled by all perfect matchings of the complete graph K_t on t vertices; an entry H_t[M_1,M_2] is 1 if M_1\cup M_2 is a…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
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 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…
We study how the application of injective morphisms affects the number $r$ of equal-letter runs in the Burrows-Wheeler Transform (BWT). This parameter has emerged as a key repetitiveness measure in compressed indexing. We focus on the…
Many hard graph problems, such as Hamiltonian Cycle, become FPT when parameterized by treewidth, a parameter that is bounded only on sparse graphs. When parameterized by the more general parameter clique-width, Hamiltonian Cycle becomes…
We develop fast approximation algorithms for the minimum-cost version of the Bounded-Degree MST problem (BD-MST) and its generalization the Crossing Spanning Tree problem (Crossing-ST). We solve the underlying LP to within a $(1+\epsilon)$…
To harness modern multicore processors, it is imperative to develop parallel versions of fundamental algorithms. In this paper, we compare different approaches to parallel best-first search in a shared-memory setting. We present a new…