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Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-05-29 Jiajie Li , Jan-Niklas Schmelzle , Yixiao Du , Simon Heumos , Andrea Guarracino , Giulia Guidi , Pjotr Prins , Erik Garrison , Zhiru Zhang

Three approaches to implement genetic programming on GPU hardware are compilation, interpretation and direct generation of machine code. The compiled approach is known to have a prohibitive overhead compared to other two. This paper…

Neural and Evolutionary Computing · Computer Science 2017-05-23 Hakan Ayral , Songül Albayrak

For large-scale graph analytics on the GPU, the irregularity of data access and control flow, and the complexity of programming GPUs, have presented two significant challenges to developing a programmable high-performance graph library.…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-01-06 Yangzihao Wang , Yuechao Pan , Andrew Davidson , Yuduo Wu , Carl Yang , Leyuan Wang , Muhammad Osama , Chenshan Yuan , Weitang Liu , Andy T. Riffel , John D. Owens

Parallel computing can offer an enormous advantage regarding the performance for very large applications in almost any field: scientific computing, computer vision, databases, data mining, and economics. GPUs are high performance many-core…

Distributed, Parallel, and Cluster Computing · Computer Science 2015-11-24 Bogdan Oancea , Tudorel Andrei , Raluca Mariana Dragoescu

The problem of solving a system of polynomial equations is one of the most fundamental problems in applied mathematics. Among them, the problem of solving a system of binomial equations form a important subclass for which specialized…

Algebraic Geometry · Mathematics 2015-03-03 Tianran Chen , Dhagash Mehta

Tree-based Genetic Programming (TGP) is a widely used evolutionary algorithm for tasks such as symbolic regression, classification, and robotic control. Due to the intensive computational demands of running TGP, GPU acceleration is crucial…

Neural and Evolutionary Computing · Computer Science 2026-02-17 Zhihong Wu , Lishuang Wang , Kebin Sun , Zhuozhao Li , Ran Cheng

Due to their highly parallel multi-cores architecture, GPUs are being increasingly used in a wide range of computationally intensive applications. Compared to CPUs, GPUs can achieve higher performances at accelerating the programs'…

Distributed, Parallel, and Cluster Computing · Computer Science 2021-10-05 Frédéric Magoulès , Abal-Kassim Cheik Ahamed , Alban Desmaison , Jean-Christophe Léchenet , François Mayer , Haifa Ben Salem , Thomas Zhu

The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…

Molecular Networks · Quantitative Biology 2026-04-22 Joyce Reimer , Pranta Saha , Chris Chen , Neeraj Dhar , Brook Byrns , Steven Rayan , Gordon Broderick

In recent years graphical processing units (GPUs) have become a powerful tool in scientific computing. Their potential to speed up highly parallel applications brings the power of high performance computing to a wider range of users.…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-04-26 Uldis Locans , Andreas Adelmann , Andreas Suter , Jannis Fischer , Werner Lustermann , Gunther Dissertori , Qiulin Wang

Graphics Processing Units (GPUs) are high performance co-processors originally intended to improve the use and quality of computer graphics applications. Once, researchers and practitioners noticed the potential of using GPU for general…

Numerical Analysis · Computer Science 2016-07-12 K. Parand , Saeed Zafarvahedian , Sayyed A. Hossayni

Dynamic programming (DP) is a cornerstone of combinatorial optimization, yet its inherently sequential structure has long limited its scalability in scenario-based stochastic programming (SP). This paper introduces a GPU-accelerated…

Optimization and Control · Mathematics 2025-11-25 Jingyi Zhao , Linxin Yang , Haohua Zhang , Tian Ding

Beagle is a new software framework that enables execution of Genetic Programming tasks on the GPU. Currently available for symbolic regression, it processes individuals of the population and fitness cases for training in a way that…

Neural and Evolutionary Computing · Computer Science 2026-03-16 Nathan Haut , Ilya Basin , Marzieh Kianinejad , Ruchika Gupta , Elijah Smith , Zachary Perrico , Wolfgang Banzhaf

The ability to train large-scale neural networks has resulted in state-of-the-art performance in many areas of computer vision. These results have largely come from computational break throughs of two forms: model parallelism, e.g. GPU…

Computer Vision and Pattern Recognition · Computer Science 2013-12-24 Thomas Paine , Hailin Jin , Jianchao Yang , Zhe Lin , Thomas Huang

Recent years have witnessed a rapid advancement in GPU technology, establishing it as a formidable high-performance parallel computing technology with superior floating-point computational capabilities compared to traditional CPUs. This…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-04-18 Xinyao Yi , Yuxin Qiao

General Purpose Graphic Processing Unit(GPGPU) is used widely for achieving high performance or high throughput in parallel programming. This capability of GPGPUs is very famous in the new era and mostly used for scientific computing which…

Distributed, Parallel, and Cluster Computing · Computer Science 2018-10-10 Vajira Thambawita , Roshan G. Ragel , Dhammike Elkaduwe

The vision of super computer at every desk can be realized by powerful and highly parallel CPUs or GPUs or APUs. Graphics processors once specialized for the graphics applications only, are now used for the highly computational intensive…

Distributed, Parallel, and Cluster Computing · Computer Science 2012-04-16 Chittampally Vasanth Raja , Srinivas Balasubramanian , Prakash S Raghavendra

Graph coloring has been broadly used to discover concurrency in parallel computing. To speedup graph coloring for large-scale datasets, parallel algorithms have been proposed to leverage modern GPUs. Existing GPU implementations either have…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-01-22 Xuhao Chen , Pingfan Li , Jianbin Fang , Tao Tang , Zhiying Wang , Canqun Yang

With the advent of high-performance computing techniques, the data for analysis has grown significantly. Here, graphic processing unit (GPU) based program kernels are discussed to exploit parallelism in the analysis codes specific to…

Computational Physics · Physics 2018-11-07 Gourav Shrivastav , Manish Agarwal

In this work we propose an accelerated stochastic learning system for very large-scale applications. Acceleration is achieved by mapping the training algorithm onto massively parallel processors: we demonstrate a parallel, asynchronous GPU…

Machine Learning · Computer Science 2017-02-24 Thomas Parnell , Celestine Dünner , Kubilay Atasu , Manolis Sifalakis , Haris Pozidis

Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…