12 papers · ranked by Valyu relevance
John Kruper, Ariel Rokem
Tractography based on diffusion-weighted MRI (dMRI) is the predominant in vivo method for mapping the brain’s white matter. However, it is also one of the most computationally demanding steps in neuroimaging data analysis-requiring the generation and filtering of millions of streamlines per subject. Over the past…
Mohammed Alaa Ala’anzy, Nurdaulet Tolendi, Baizhan Baubek, Abdulmohsen Algarni + 1 more
Sorting can be approached in two main ways: sequentially and in parallel. In sequential sorting, data is processed in a single-threaded manner, which can be slow for large datasets. However, parallel sorting divides the task across multiple processing units, enabling faster results by processing data simultaneously.…
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Jose L Figueroa, Richard Allen White
We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC)…
Lin Chen, Yuhan Chen, Ziqi Cheng, Jing Guo + 20 more
MHPC512 is a massively parallel, special-purpose supercomputer designed primarily for atomic-level molecular dynamics (MD) simulations of biomolecular systems. It comprises 512 processor units interconnected by a high-speed three-dimensional torus network and employs a custom chip architecture that uses 35-bit…
Kecong Tang, Ardalan Naseri, Degui Zhi, Shaojie Zhang + 1 more
At each site indexed by k, the algorithm maintains a prefix array $P_{k}$, which encodes the co-lexicographic ordering of haplotypes based on their reversed prefixes up to the current site. Formally, let ${x_{i}}$, where $i=1$ to M, denote M haplotype sequences over N sites. At site k, the prefix array $P_{k}$ is…
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…
Sumesh Kumar, Joseph Zambreno, Ashfaq Khokhar, Shoaib Akram + 1 more
Improving the speed and efficiency of database search algorithms that deduce peptides from mass spectrometry (MS) data has been an active area of research for more than three decades. The significance of the need for faster database search methods has rapidly increased due to the growing interest in studying non-model…
Kevin Garner, Polykarpos Thomadakis, Nikos Chrisochoides
This paper presents a distributed memory method for anisotropic mesh adaptation that is designed to avoid the use of collective communication and global synchronization techniques. In the presented method, meshing functionality is separated from performance aspects by utilizing a separate entity for each - a multicore…
Nhan Ly-Trong, Samuel Martin, Nick Goldman, Nicola De Maio + 1 more
Phylogenetic analysis is essential to genomic epidemiology, for example in tracing the origin and evolution of SARS-CoV-2 variants during the COVID-19 pandemic. We previously introduced CMAPLE, a single-threaded implementation of the MAPLE algorithm designed for large-scale epidemiological genomic datasets. CMAPLE can…
Chun Gong, Qi Yang, Ruiwen Wan, Shengkang Li + 2 more
Joint variant calling is a crucial step in population-scale sequencing analysis. While population-scale sequencing is a powerful tool for genetic studies, achieving fast and accurate joint variant calling on large cohorts remains computationally challenging. To meet this challenge, we developed Distributed Population…
Renée A. Sirbu, Luciano Floridi
Biological computing (biocomputing) leverages biologically derived materials and processes, such as DNA and protein synthesis, to perform computational tasks. Biocomputing offers significant advantages over traditional silicon-based systems in terms of scalability, energy efficiency, computational flexibility, and…