17 papers · ranked by Valyu relevance
Julia Golonka, Filip Krużel, Rosario Schiano Lo Moriello
Resource-constrained sensor nodes in Internet-of-Things (IoT) and embedded sensing applications frequently rely on low-cost microcontrollers, where even basic algorithmic choices directly impact latency, energy consumption, and memory footprint. This study evaluates six sorting algorithms-Bubble Sort, Insertion Sort…
Marc Dufay, Roger Wattenhofer
In the online Min-cost Perfect Matching with Delays (MPMD) problem, m requests in a metric space are submitted at different times by an adversary. The goal is to match all requests while (i) minimizing the sum of the distances between matched pairs as well as (ii) how long each request remained unmatched after it…
Finn Moltmann, Tamio-Vesa Nakajima, Sebastian Wild
We give a more space-efficient implementation of adaptive mergesort: Virtual-Memory Powersort. Using internal buffering techniques, we significantly reduce the memory consumption of the algorithm; specifically, for sorting $n$ objects the required buffer area is reduced from space for $n/2$ objects to $O(\sqrt{n \log…
Michael Goodrich, Yan Gu, Ryuto Kitagawa, Yihan Sun
Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied. This framework has received particular attention in the parallel setting, and has…
Qiqi Jason Gu, Mikoláš Janota
Merging is a core operation in version control systems such as Git, but traditional line-based algorithms often yield spurious conflicts, particularly in the presence of refactorings or parallel edits. While syntax- and semantics-aware merging approaches can reduce conflicts, they introduce drawbacks such as loss of…
Mohammad Abdur Rob, Md. Zakir Hossen, Md. Kamal Hossen, Md. Mithun Ali + 2 more
Sorting algorithms play a crucial role in computing, but most are designed with rigid structure that are only efficient under certain conditions. Although some sorting algorithms perform well in some circumstances, they do not perform well on some resistant platforms. This study introduces Wall-L Merge Sort, which…
Leonard Bohnenkämper, Luca Parmigiani, Cedric Chauve, Jens Stoye
Genomic rearrangements are major drivers of evolution and genetic disease. However, studying rearrangements requires segmenting the genomes of interest into conserved regions, called synteny blocks, that highlight structural differences between genomes. Synteny blocks are typically defined from annotated genes or…
Brian Bushnell, Juan C. Villada
Reconstructing genomes from metagenomic assemblies is foundational to microbiome research, yet metagenome binning remains constrained by a persistent trade-off between genome fidelity and deployable throughput. Many high-accuracy approaches rely on GPU-intensive workflows, marker-gene-informed postprocessing, or…
Shimin Li
The problem of maintaining connectivity of a wireless network on a closed cycle is studied in this paper. In the initial input, we have $n$ points located on a closed cycle. The points can move along the cycle, and if the distance between two points is at most a given value $r$, we say these two points are connected.…
Jiyeon Lee, Soonseok Kim, Naveen Chilamkurti
Pipelines that satisfy k-anonymity alone remain vulnerable to attribute disclosure under skewed sensitive attributes. We studied real-time anonymization of high-throughput data streams under strict delay budgets (β). We jointly enforced k-anonymity and l-diversity via a delay-aware Monitor-Trigger-Repair controller…
Miao Yu, Sangman Moh
The development of Unmanned Aerial Vehicle (UAV) formation technology is rapid, and formation flying under complex conditions has also received more attention. However, neighbor selection without reliable radio communication remains challenging because fixed-radius or fixed-topology methods may process redundant…
Clemens Kohl, Martin Vingron, Lihua Zhang
Clustering for single-cell RNA-seq aims at finding similar cells and grouping them into biologically meaningful clusters. Many available clustering algorithms however do not not provide the cluster defining marker genes or are unable to infer the number of clusters in an unsupervised manner as well as lack tools to…
Yoann Dufresne, Francesco Andreace
Sorted lists of elements are particularly good for computing set operations. A single scan of two lists is sufficient to materialize or count the results of the union, intersection, difference, and xor operators. In bioinformatics, only a few tools are designed to perform these operations on k-mers. A fast tool like…
Daniel Anker Hermansen
In the Euclidean travelling salesman problem (Euclidean TSP), a salesman must visit $n$ points in Euclidean space, while minimizing the travel distance, according to the Euclidean distance function. In online Euclidean TSP, introduced by Abrahamsen, Bercea, Beretta, Klausen and Kozma [ESA 2024], the points are revealed…
Mahmudur Rahman Hera, David Koslicki, Conrado Martínez
With the surge in sequencing data generated from an ever-expanding range of biological studies, designing scalable computational techniques has become essential. One effective strategy to enable large-scale computation is to split long DNA or protein sequences into k-mers, and summarize large k-mer sets into compact…
Albert Jiménez-Blanco, Lorién López-Villellas, Juan Carlos Moure, Miquel Moreto + 1 more
Sequence-to-graph alignment is a central problem in bioinformatics, with applications in multiple sequence alignment (MSA) and pangenome analysis, among others. However, current algorithms for optimal affine-gap alignment impose high memory and computational requirements, limiting their scalability to aligning long…
Authors not listed
Atomistic simulations provide essential mechanistic insights into chemical processes, yet many important phenomena in chemistry and materials science occur on timescales that are inaccessible to molecular dynamics. Existing computational approaches force a choice between atomic resolution on relatively short timescales…