23 papers · ranked by Valyu relevance
de Ronde, Folkert, Knapen, Alexander + 4 more
This paper introduces a novel approach to enhance the execution of quantum algorithms on distributed quantum systems. The proposed method involves the development of a hardware design that supports parallel instruction execution and a compiler that modifies the order of instructions to increase parallelism…
Authors not listed
Recent advances in machine learning force fields (MLFF) have significantly extended the reach of atomistic simulations. Continuous progress in this field requires reliable reference datasets, accurate MLFF architectures, and efficient active learning strategies to enable robust modeling of complex molecular and…
Ge Zhang
bcftools is the standard toolkit for handling VCF and BCF variant files, but it processes records on a single core; its --threads option speeds up only compression of the output, not the work done on variant records. Processing large call sets is therefore slow, and users often divide the genome and reassemble the…
Haymo Kutschbach
This work introduces a self-optimizing virtual processor (VP) for numerical array programs that shifts parallelization from a manual developer task to a cooperative, agent-like runtime mechanism. Instead of relying on centralized task-graph scheduling, static compiler optimization, or explicitly annotated parallel…
Rafael Terra, Diego Carvalho, Denis Jacob Machado, Carla Osthoff + 1 more
Advances in High-Performance Computing (HPC) have enabled increasingly complex genomic analyses, including those in phylogenomics. These analyses contribute to understanding the evolution of viruses and pathogens, improving our knowledge of disease transmission, and supporting targeted public health strategies.…
Aleix Roca, Vicenç Beltran
The convergence of high-performance computing (HPC) and artificial intelligence (AI) is driving the emergence of increasingly complex parallel applications and workloads. These workloads often combine multiple parallel runtimes within the same application or across co-located jobs, creating scheduling demands that…
Kecong Tang, Ardalan Naseri, Degui Zhi, Shaojie Zhang + 1 more
To support memory-efficient execution without compromising the all-vs.-all nature of IBD detection, RaPID2 adopts a partitioning strategy that operates on haplotype pairs () rather than subpanels. All pairs are normalized such that $A<B$ to ensure consistent key assignment, and each pair is deterministically assigned…
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…
Harry Fitchett, Charles M. Fox
While transistor density is still increasing, clock speeds are not, motivating the search for new parallel architectures. One approach is to completely abandon the concept of CPU – and thus serial imperative programming – and instead to specify and execute tasks in parallel, compiling from programming languages to data…
Zhejian Yu
Fast simulation of next-generation sequencing (NGS) data is vital for software development and benchmarking. Here we describe art_modern, an accelerated ART simulator that can simulate various NGS data. We accelerated ART using updated sampling algorithms, single-instruction multiple-data (SIMD) instruction-set…
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.…
Rob Patro, Siddhant Bharti, Prajwal Singhania, Rakrish Dhakal + 2 more
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compressed fastq.gz files has become a substantial scalability bottleneck in the modern world of fast and massively parallel…
Alexander Strack, Alexander Van Craen, Dirk Pflüger
Fork-join parallelism, popularized by OpenMP, remains the dominant model for shared-memory parallel programming, but its implicit synchronization barriers can penalize algorithms with inhomogeneous workloads. Asynchronous many-task (AMT) runtimes sidestep these barriers by expressing work as a dependency graph of…
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…
Noam Teyssier, Alexander Dobin
Single-cell genomics is rapidly scaling toward billion-cell atlases, but computational analysis has become a critical bottleneck. Processing multiplexed datasets with existing tools requires substantial computational resources and runtime that become prohibitive at scale. Here we present cyto, an ultra highthroughput…
Mateusz Gruzewski, Marek Palkowski, Ramon Antonio Rodriges Zalipynis
In this article, we present an efficient and concise OpenMP implementation of the Nussinov RNA folding algorithm, a well-known representative of non-serial polyadic dynamic programming (NPDP). Our goal is to develop an optimized implementation that can serve as a template for related dynamic programming applications.…
Ismail Melik Turker, Isa Yildirim
3.3.1#### Experimental setup All experiments were conducted on a laptop running Ubuntu 24.04 LTS, equipped with an Intel Core i7-12700H processor (12th generation, Alder Lake hybrid architecture with 6 performance and 8 efficient cores) and 64 GB of DDR4 memory. The code was written entirely in C++17 and parallelized…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Anders Pitman, Cathy Yang, Yi Qiao
Next-generation sequencing now produces whole-genome data in hours, but downstream variant calling remains a multi-hour to multi-day bottleneck that excludes genomic analysis from time-critical clinical settings. GPU acceleration offers a natural path forward — variant calling is inherently parallelizable across…
Authors not listed
Self-driving laboratories (SDLs) promise accelerated scientific discovery and product development by closing the loop between robotic execution and AI/ML-driven decision making. In practice, however, SDL orchestration remains fragmented; workflows are typically encoded as laboratory-specific scripts or bespoke…
Authors not listed
This comprehensive review examines the evolution of autonomous materials synthesis laboratories that integrate artificial intelligence with advanced robotics to accelerate discovery. Traditional materials development pipelines typically require 10-20 years, but self-driving laboratories (SDLs) and Materials…
Authors not listed
The analysis of molecular dynamics (MD) simulations is a critical but fragmented process, often requiring researchers to chain together multiple software tools and write bespoke scripts for routine structural and dynamic analyses. This workflow complexity creates a significant barrier to efficiency, standardization…
Authors not listed
We describe a collaborative research project spanning the disciplines of quantum hardware, quantum algorithms, conventional computational chemistry, synthetic medicinal chemistry and life sciences. Our project seeks to demonstrate an impact of quantum computing on human health. It is one of several funded by Wellcome…