Related papers: Toward an Automated HPC Pipeline for Processing La…
When physical testbeds are out of reach for evaluating a networked system, we frequently turn to simulation. In today's datacenter networks, bottlenecks are rarely at the network protocol level, but instead in end-host software or hardware…
Single particle cryo-electron microscopy (EM) is an increasingly popular method for determining the 3-D structure of macromolecules from noisy 2-D images of single macromolecules whose orientations and positions are random and unknown. One…
Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…
In the field of connectomics, neuroscientists seek to identify cortical connectivity comprehensively. Neuronal boundary detection from the Electron Microscopy (EM) images is often done to assist the automatic reconstruction of neuronal…
This short report describes the scaling, up to 1024 software processes and hardware cores, of a distributed simulator of plastic spiking neural networks. A previous report demonstrated good scalability of the simulator up to 128 processes.…
Scanning transmission electron microscopy (STEM) is an extremely versatile method for studying materials on the atomic scale. Many STEM experiments are supported or validated with electron scattering simulations. However, using the…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
Automated cardiac image interpretation has the potential to transform clinical practice in multiple ways including enabling low-cost serial assessment of cardiac function in the primary care and rural setting. We hypothesized that advances…
The use of FPGAs for efficient graph processing has attracted significant interest. Recent memory subsystem upgrades including the introduction of HBM in FPGAs promise to further alleviate memory bottlenecks. However, modern multi-channel…
Many scientific and medical researchers are working towards the creation of a virtual human - a personalised digital copy of an individual - that will assist in a patient's diagnosis, treatment and recovery. The complex nature of living…
Particle picking is a crucial first step in the computational pipeline of single-particle cryo-electron microscopy (cryo-EM). Selecting particles from the micrographs is difficult especially for small particles with low contrast. As…
We present the first automated pipeline to create an atlas of in situ hybridization gene expression in the adult marmoset brain in the same stereotaxic space. The pipeline consists of segmentation of gene expression from microscopy images…
The construction industry represents a major sector in terms of resource consumption. Recycled construction material has high reuse potential, but quality monitoring of the aggregates is typically still performed with manual methods.…
An increasing amount of research is being devoted to applying machine learning methods to electronic health record (EHR) data for various clinical purposes. This growing area of research has exposed the challenges of the accessibility of…
Curating, processing, and combining large-scale medical imaging datasets from national studies is a non-trivial task due to the intense computation and data throughput required, variability of acquired data, and associated financial…
Neural networks have emerged as a powerful tool for solving complex tasks across various domains, but their increasing size and computational requirements have posed significant challenges in deploying them on resource-constrained devices.…
Large-scale modelling of three-dimensional controlled-source electromagnetic (CSEM) surveys used to be feasible only for large companies and research consortia. This has changed over the last few years, and today there exists a selection of…
There are many science applications that require scalable task-level parallelism and support for flexible execution and coupling of ensembles of simulations. Most high-performance system software and middleware, however, are designed to…
Big science initiatives are trying to reconstruct and model the brain by attempting to simulate brain tissue at larger scales and with increasingly more biological detail than previously thought possible. The exponential growth of parallel…
The aim of this paper is to develop an approach to visualizations that benefits from distributed computing. Three schemes of process distribution are considered: parallel, pipeline, and expanding pipeline computations. Expanding pipeline…