20 papers · ranked by Valyu relevance
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
C. Addison Stone, Melissa O'Neill, Sonja A. Bohr, Adam M. Cozzette + 4 more
'M. Joe DeBlasio' 'Julia Matsieva' 'Stuart Pernsteiner' 'Ari D. Schumer'] Programmers benefit because they can reason largely sequentially. Remaining interthread interactions are far less chaotic than in other models, permitting easier reasoning and debugging. Programmers can also defer the choice of…
Maximilian Hanussek, Felix Bartusch, Jens Krüger, Christos A. Ouzounis
'Christos A. Ouzounis'] The large amount of biological data available in the current times, makes it necessary to use tools and applications based on sophisticated and efficient algorithms, developed in the area of bioinformatics. Further, access to high performance computing resources is necessary, to achieve results…
Kato Mivule, Benjamin Harvey, Crystal Cobb, H El Ashry El Sayed
– The advent of high performance computing (HPC) and graphics processing units (GPU), present an enormous computation resource for Large data transactions (big data) that require parallel processing for robust and prompt data analysis. While a number of HPC frameworks have been proposed, parallel programming models…
Elham Sagheb Hossein Pour
Digital image analysis has made a big advance in many areas of enterprise applications including medicine, industry, and entertainment by assisting the extraction of semantic information from digital images. However, its large computational complexity has been a trouble to most real-time developments. While image…
Mischael Schill, Sebastian Nanz, Bertrand Meyer
Programming models for concurrency are optimized for dealing with nondeterminism, for example to handle asynchronously arriving events. To shield the developer from data race errors effectively, such models may prevent shared access to data altogether. However, this restriction also makes them unsuitable for…
Michail Patsakis, Kimonas Provatas, Aris Karatzikos, Charalampos Koilakos + 2 more
'Charalampos Koilakos' 'Ioannis Mouratidis' 'Ilias Georgakopoulos-Soares'] Motivation With the rapid expansion of large-scale biological datasets, DNA and protein sequence alignments have become essential for comparative genomics and proteomics. These alignments facilitate the exploration of sequence similarity…
Saugata Ghose
The first years of the 2000s led to an inflection point in computer architectures: while the number of available transistors on a chip continued to grow, crucial transistor scaling properties started to break down and result in increasing power consumption, while aggressive single-core performance optimizations were…
J.A. Bergstra
| 1 | Introduction, PMTh | | 2 | | --- | --- | --- | --- | | | 1.1 | Concurrency, multi-tasking, multi-threading, arbitrary interleav | | | | | ing, and strategic interleaving | 3 | | | 1.2 | Multi-threading in psychology versus multi-threading in computing | 4 | | | 1.3 | Designing a story on PMTh | 6 | | | 1.4 | A…
Michael Doube
Sequential region labelling, also known as connected components labelling, is a standard image segmentation problem that joins contiguous foreground pixels into blobs. Despite its long development history and widespread use across diverse domains such as bone biology, materials science, and geology, connected…
Zsuzsanna Sükösd, Bjarne Knudsen, Morten Værum, Jørgen Kjems + 1 more
'Ebbe S Andersen'] Background The prediction of the structure of large RNAs remains a particular challenge in bioinformatics, due to the computational complexity and low levels of accuracy of state-of-the-art algorithms. The pfold model couples a stochastic context-free grammar to phylogenetic analysis for a high…
Basheera M. Mahmmod, Wameedh Nazar Flayyih, Zainab Hassan Fakhri, Sadiq H. Abdulhussain + 3 more
'Sadiq H. Abdulhussain' 'Wasiq Khan' 'Abir Hussain' 'Viacheslav Kovtun'] Orthogonal polynomials and their moments have significant role in image processing and computer vision field. One of the polynomials is discrete Hahn polynomials (DHaPs), which are used for compression, and feature extraction. However, when the…
Xing Liu, Kun Mean Hou, Christophe de Vaulx, Jun Xu + 4 more
'Haiying Zhou' 'Hongling Shi' 'Peng Zhou'] Memory and energy optimization strategies are essential for the resource-constrained wireless sensor network (WSN) nodes. In this article, a new memory-optimized and energy-optimized multithreaded WSN operating system (OS) LiveOS is designed and implemented. Memory cost of…
Saurabh Hukerikar, Keita Teranishi, Pedro C. Diniz, Robert F. Lucas
In the presence of accelerated fault rates, which are projected to be the norm on future exascale systems, it will become increasingly difficult for highperformance computing (HPC) applications to accomplish useful computation. Due to the fault-oblivious nature of current HPC programming paradigms and execution…
Jacob Porter
Fast Neighbor-Net is a command-line Java program that has fast implementations of the popular Neighbor-Net phylo-genetic split network approach. This allows more efficiency in computationally intensive tasks such as larger scale data analysis and bootstrapping. The canonical search phase iteratively finds a pair of…
Fahd Yazin, Gargi Majumdar, Neil Bramley, Paul Hoffman
Reliance on internal predictive models of the world is central to many theories of human cognition. Yet it is unknown whether humans acquired multiple separate internal models, each evolved for a specific domain, or maintain a globally unified representation. Using fMRI during naturalistic experiences (movie watching…
Susanne Kunkel, Maximilian Schmidt, Jochen M. Eppler, Hans E. Plesser + 7 more
'Hans E. Plesser' 'Gen Masumoto' 'Jun Igarashi' 'Shin Ishii' 'Tomoki Fukai' 'Abigail Morrison' 'Markus Diesmann' 'Moritz Helias'] Brain-scale networks exhibit a breathtaking heterogeneity in the dynamical properties and parameters of their constituents. At cellular resolution, the entities of theory are neurons and…
Felix Van der Jeugt, Peter Dawyndt, Bart Mesuere
FragGeneScanRs is a better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads. Its command line interface is backward compatible and adds extra features for more flexible usage. Compared to the original C implementation, shotgun metagenomic reads are processed up to…
Himaghna Bhattacharjee, Jackson Burns, Dionisios Vlachos
The recent advances in deep learning, generative modeling, and statistical learning have ushered in a renewed interest in traditional cheminformatics tools and methods. Quantifying molecular similarity is essential in molecular generative modeling, exploratory molecular synthesis campaigns, and drug-discovery…
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…