相关论文: From H&M to Gap for Lightweight BWT Merging

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,…

Given a string $T$ on an alphabet of size $\sigma$, we describe a bidirectional Burrows-Wheeler index that takes $O(|T|\log{\sigma})$ bits of space, and that supports the addition \emph{and removal} of one character, on the left or right…

In this paper, we present FLiMS, a highly-efficient and simple parallel algorithm for merging two sorted lists residing in banked and/or wide memory. On FPGAs, its implementation uses fewer hardware resources than the state-of-the-art…

Hypergraphs provide a natural representation for many-to-many relationships in data-intensive applications, yet their scalability is often hindered by high memory consumption. While prior work has improved computational efficiency, reducing…

Extending computational harmonic analysis tools from the classical setting of regular lattices to the more general setting of graphs and networks is very important and much research has been done recently. The Generalized Haar-Walsh…

Bit arrays, or bitmaps, are used to significantly speed up set operations in several areas, such as data warehousing, information retrieval, and data mining, to cite a few. However, bitmaps usually use a large storage space, thus requiring…

Reducing a chain complex (whilst preserving its homotopy-type) using algebraic Morse theory gives the same end-result as Gaussian elimination, but AMT does it only on certain rows/columns and with several pivots (in all matrices…

We describe a simple parallel-friendly lightweight graph reordering algorithm for COO graphs (edge lists). Our ``Batched Order By Attachment'' (BOBA) algorithm is linear in the number of edges in terms of reads and linear in the number of…

Model merging aims to combine multiple task-specific expert models into a single model without joint retraining, offering a practical alternative to multi-task learning when data access or computational budget is limited. Existing methods,…

This paper introduces a novel algorithm combination designed for fast one-to-many multicriteria shortest path search. A preprocessing algorithm excludes irrelevant vertices by building a smaller cover graph. A modified version of…

This paper presents prefix codes which minimize various criteria constructed as a convex combination of maximum codeword length and average codeword length or maximum redundancy and average redundancy, including a convex combination of the…

We reduce the problem of finding an augmenting path in a general graph to a reachability problem in a directed bipartite graph. A slight modification of depth-first search leads to an algorithm for finding such paths. Although this setting…

The compression-complexity trade-off of lossy compression algorithms that are based on a random codebook or a random database is examined. Motivated, in part, by recent results of Gupta-Verd\'{u}-Weissman (GVW) and their underlying…

We aim to speed up approximate keyword matching by storing a lightweight, fixed-size block of data for each string, called a fingerprint. These work in a similar way to hash values; however, they can be also used for matching with errors.…

The Burrows-Wheeler-Transform (BWT) is a reversible string transformation which plays a central role in text compression and is fundamental in many modern bioinformatics applications. The BWT is a permutation of the characters, which is in…

Deep Convolutional Neural Networks (CNNs) are capable of learning unprecedentedly effective features from images. Some researchers have struggled to enhance the parameters' efficiency using grouped convolution. However, the relation between…

The high computational demands of Large Language Models (LLMs) motivate methods that reduce parameter count and accelerate inference. In response, model pruning emerges as an effective strategy, yet current methods typically focus on a…

The Partitioning Min-Max Weighted Matching (PMMWM) problem is an NP-hard problem that combines the problem of partitioning a group of vertices of a bipartite graph into disjoint subsets with limited size and the classical Min-Max Weighted…

The extension of persistent homology to multi-parameter setups is an algorithmic challenge. Since most computation tasks scale badly with the size of the input complex, an important pre-processing step consists of simplifying the input…

Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input strings. The motivations for those results stem from…