23 papers · ranked by Valyu relevance
Unitsa Sangket, Surakameth Mahasirimongkol, Wasun Chantratita, Pichaya Tandayya + 1 more
'Pichaya Tandayya' 'Yurii S Aulchenko'] Background Genome-Wide Association (GWA) analysis is a powerful method for identifying loci associated with complex traits and drug response. Parts of GWA analyses, especially those involving thousands of individuals and consuming hours to months, will benefit from parallel…
Timothy A. Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao
In precision medicine, genomic data needs to be processed as fast as possible to arrive at treatment decisions in a timely fashion. We developed mmbam, a library to allow sequence analysis informatics software to access raw sequencing data stored in BAM files extremely fast. Taking advantage of memory mapped file…
Francois Besnier, Kevin A. Glover, Maria Anisimova
This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to…
Donald S. Ene, V.I.E Anireh
- Evaluating how well a whole system or set of subsystems performs is one of the primary objectives of performance testing. We can tell via performance assessment if the architecture implementation meets the design objectives. Performance evaluations of several parallel algorithms are compared in this study. Both…
Julia L Turner, Scott T Kelley, James S Otto, Faramarz Valafar + 1 more
'Andrew J Bohonak'] Background The Isolation by Distance Web Service (IBDWS) is a user-friendly web interface for analyzing patterns of isolation by distance in population genetic data. IBDWS enables researchers to perform a variety of statistical tests such as Mantel tests and reduced major axis regression (RMA), and…
G.R. van der Ploeg, J.A. Westerhuis, A. Heintz-Buschart, A.K. Smilde
Recently, studies that investigate microbial temporal dynamics have become more frequent. In a longitudinal microbiome study design, microbial abundance data are collected across multiple time points from the same subjects. In this context, exploratory analysis of longitudinal microbiome data using Principal Component…
V. Schwambach, S. Cleyet-Merle, Alain Issard, Stéphane Mancini
—Computer vision applications constitute one of the key drivers for embedded multicore architectures. Although the number of available cores is increasing in new architectures, designing an application to maximize the utilization of the platform is still a challenge. In this sense, parallel performance prediction tools…
Alessandro Petrini, Marco Mesiti, Max Schubach, Marco Frasca + 7 more
The idea on which multi-core parSMURF builds is that all operations performed on the different parts of the partition can be assigned to multiple core/threads and processed in parallel. Namely, given q threads, the data parts N1, …, Nn are equally distributed among threads so that thread i receives a subset (chunk) Ci…
Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo + 3 more
'Tao Tang' 'Yingbo Cui'] Background The advent of Single Molecule Real-Time (SMRT) sequencing has overcome many limitations of second-generation sequencing, such as limited read lengths, PCR amplification biases. However, longer reads increase data volume exponentially and high error rates make many existing alignment…
Authors not listed
Protein conformational landscapes contain the functionally relevant information useful for understanding biological processes. Mapping out conformational landscapes provides valuable insights into protein behaviors and biological phenomena, and has relevance to therapeutic design. While experimental structural biology…
Rishi Sharma, Shreyansh Kulshreshtha, Manas Thakur
With the advent of multi-core systems, GPUs and FPGAs, loop parallelization has become a promising way to speedup program execution. In order to stay up with time, various performance-oriented programming languages provide a multitude of constructs to allow programmers to write parallelizable loops. Correspondingly…
S. Katharina Schmitz, Philipp P. Hasselbach, Boris Ebisch, Anja Klein + 2 more
'Anja Klein' 'Gordon Pipa' 'Ralf A. W. Galuske'] The identification of important features in multi-electrode recordings requires the decomposition of data in order to disclose relevant features and to offer a clear graphical representation. This can be a demanding task. Parallel Factor Analysis (PARAFAC; Hitchcock…
Hüsser Alejandra, Caron-Desrochers Laura, Tremblay Julie, Vannasing Phetsamone + 2 more
Functional near infrared spectroscopy (fNIRS) is a neuroimaging technique that uses light at two different wavelengths in the near infrared spectrum to estimate cerebral hemodynamic response, based on concentration changes in both oxygenated and deoxygenated hemoglobin. A multi-dimensional decomposition technique…
Kecong Tang, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang
Durbin’s positional Burrows-Wheeler transform (PBWT) enables algorithms with the optimal time complexity of O(MN) for reporting all vs all haplotype matches in a population panel with M haplotypes and N variant sites. However, even this efficiency may still be too slow when the number of haplotypes reaches millions. To…
Amirhossein Shahbazinia, Saber Salehkaleybar, Matin Hashemi
—One of the key objectives in many fields in machine learning is to discover causal relationships among a set of variables from observational data. In linear non-Gaussian acyclic models (LiNGAM), it can be shown that the true underlying causal structure can be identified uniquely from merely observational data.…
Elias Stehle, Hans‐Arno Jacobsen
Parsing is essential for a wide range of use cases, such as stream processing, bulk loading, and in-situ querying of raw data. Yet, the compute-intense step often constitutes a major bottleneck in the data ingestion pipeline, since parsing of inputs that require more involved parsing rules is challenging to…
Suejb Memeti, Sabri Pllana
—Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for large problem sizes. In this paper, we describe a novel algorithm for parallel…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Authors not listed
As demand rises for scalable and sustainable energy storage, fast and low-cost diagnostics capable of identifying cell-to-cell variations are urgently needed, particularly for factory-produced sorting and second-life assessment. Electrochemical impedance spectroscopy (EIS) is widely used but remains slow, expensive and…
Authors not listed
Background: Pharmaceutical batch scheduling in multi-reactor configurations presents complex optimization challenges under operational uncertainty, yet limited research addresses how parallel processing capacity affects heuristic performance and predictive modeling. Objectives: This study investigated scheduling…
Andrew Simmonett, Bernard Brooks, Thomas Darden
Evaluation of noncovalent electrostatic interactions is the dominant bottleneck in classical molecular dynamics simulations, and evaluation of Coulombic matrix elements similarly limits quantum mechanical self consistent field calculations. These difficulties are a result of the Coulomb operator’s slow decay, which…
Caroline Arnoux, Luis-Adrian Perez-Covarrubias, Alexandre Khaldi, Quentin Carlier + 4 more
Although additive manufacturing using multi-photon direct laser writing is nowadays considered as a major tool in the fabrication of future nano/micro-objects and optical components, it is currently limited by the low throughput of the writing process. To circumvent this issue, massive parallelization of the write…
Authors not listed
Raman spectroscopy is an increasingly powerful and fast-growing analytical technique across diverse disciplines, from materials science and chemistry to biology and medicine, thanks to advances in Raman instrumentation and greatly supported by the flourishing of chemometrics and artificial intelligence (AI). However…