19 papers · ranked by Valyu relevance
Carbonell Juan Pablo, Solsona, José E., Szasz + 3 more
We provide full certifications of two versions of merge sort of arrays in the verification-aware programming language Dafny. We start by considering schemas for applying the divide-and-conquer or partition method of solution to specifications given by pre- and post-conditions involving linear arrays. We then derive the…
Glodny, Niels
Despite being widely used, the algorithms that enable collaboration with Git are not well understood. The diff and merge algorithms are particularly interesting, as they could be applied in other contexts. In this thesis, I document the main functionalities of Git: how diffs are computed, how they are used to run…
William Cawley Gelling, Markus E. Nebel, Benjamin Smith, Sebastian Wild
'Sebastian Wild'] We present a stable mergesort variant, Multiway Powersort, that exploits existing runs and finds nearly-optimal merging orders for k-way merges with negligible overhead. This builds on Powersort (Munro &Wild, ESA 2018), which has recently replaced Timsort's suboptimal merge policy in the CPython…
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…
Gene Myers
Merging T sorted, non-redundant lists containing M elements into a single sorted, non-redundant result of size N ≥ M/T is a classic problem typically solved practically in O(M log T ) time with a priority-queue data structure the most basic of which is the simple heap. We revisit this problem in the situation where the…
Alexander Ponomarenko
This paper addresses the challenge of merging hierarchical navigable small world (HNSW) graphs, a critical operation for distributed systems, incremental indexing, and database compaction. We propose three algorithms for this task: Naive Graph Merge (NGM), Intra Graph Traversal Merge (IGTM), and Cross Graph Traversal…
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…
Willi Mann, Nikolaus Augsten, Christian S. Jensen, Mateusz Pawlik
We provide efficient support for applications that aim to continuously find pairs of similar sets in rapid streams, such as Twitter streams that emit tweets as sets of words. Using a sliding window model, the top-k result changes as new sets enter the window or existing ones leave the window. Specifically, when a set…
Guang Wu, Xinbiao Gan, Zhengbin Pang, Bo Huang + 1 more
—Finding the maximum matching in bipartite graphs is a fundamental graph operation widely used in various fields. To expedite the acquisition of the maximum matching, Karp and Sipser introduced two data reduction rules aimed at decreasing the input size. However, the KaSi algorithm, which implements the two data…
Giulio Ermanno Pibiri
We consider the problem of representing a set of $k$-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a $k$-mer is efficient. The representation is called a weighted dictionary of $k$-mers and finds application in numerous tasks in Bioinformatics…
Aaron S. Brewster, Daniel W. Paley, Asmit Bhowmick, David W. Mittan-Moreau + 5 more
The cctbx.xfel suite of processing programs and tools allows fast, visual analysis of serial diffraction images from synchrotrons and XFELs. Built on DIALS and cctbx, cctbx.xfel is designed for real-time and post-experiment processing with a fully featured graphical user interface. Users can quickly identify hitrates…
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…
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…
Adam C. English, Vipin K. Menon, Richard Gibbs, Ginger A. Metcalf + 1 more
For multi-sample structural variant analyses like merging, benchmarking, and annotation, the fundamental operation is to identify when two SVs are the same. Commonly applied approaches for comparing SVs were developed alongside technologies which produce ill-defined boundaries. As SV detection becomes more exact…
Benjamin D. Redelings, Mark T. Holder
The Open Tree of Life (OToL) project produces a supertree that summarizes phylogenetic knowledge from tree estimates published in the primary literature. The supetree construction algorithm iteratively calls Aho’s Build algorithm thousands of times in order to assess the compatability of different phylogenetic…
Noah Brown, Charles Danis, Vazira Ahmedjanova, Jennifer L. Guler
Structural variants (SVs) are abundant across all life, and have major impacts on the genome and transcriptome. However, it is difficult to appreciate the individual significance of SVs when they are heterogeneously distributed across a genomic neighborhood. Further, low-input sequencing technologies or sequencing of…
Gene Myers, Richard Durbin, Chenxi Zhou
FastGA finds alignments between two genome sequences more than an order of magnitude faster than previous methods that have comparable sensitivity. Its speed is due to (a) a carefully engineered architecture involving only cache-coherent MSD radix sorts and merges, (b) a novel algorithm for finding adaptive seed hits…
Charu Manivannan, Jakub Krukar, Angela Schwering, Saeid Norouzian-Maleki
'Saeid Norouzian-Maleki'] Sketch maps are valuable tools used across various disciplines including spatial cognition, environmental psychology, and spatial reasoning. A common approach to evaluate sketch maps in research is to align and compare them with metric maps. However, sketch maps are highly abstract and contain…
Trevor Gokey, David L. Mobley
Molecular mechanics force fields require a chemical perception model to assign parameters to molecules. A recent advancement in force fields is the use of the SMARTS substructure query language as the perception model. Although it is straightforward to write SMARTS patterns to define new force field parameters, it is…