Related papers: Parallel Computation of Alpha Complex for Biomolec…
As in various fields like scientific research and industrial application, the computation time optimization is becoming a task that is of increasing importance because of its highly parallel architecture. The graphics processing unit is…
Principal component analysis (PCA) is a key statistical technique for multivariate data analysis. For large data sets the common approach to PCA computation is based on the standard NIPALS-PCA algorithm, which unfortunately suffers from…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
In this work, we present an extension of Gaussian process (GP) models with sophisticated parallelization and GPU acceleration. The parallelization scheme arises naturally from the modular computational structure w.r.t. datapoints in the…
Matrix multiplication is a foundational operation in scientific computing and machine learning, yet its computational complexity makes it a significant bottleneck for large-scale applications. The shift to parallel architectures, primarily…
In this paper we show that many sequential randomized incremental algorithms are in fact parallel. We consider algorithms for several problems including Delaunay triangulation, linear programming, closest pair, smallest enclosing disk,…
A finite element method is presented to compute time harmonic microwave fields in three dimensional configurations. Nodal-based finite elements have been coupled with an absorbing boundary condition to solve open boundary problems. This…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
Study of general purpose computation by GPU (Graphics Processing Unit) can improve the image processing capability of micro-computer system. This paper studies the parallelism of the different stages of decimation in time radix 2 FFT…
The Cellular Potts Model (CPM) is a widely used simulation paradigm for systems of interacting cells that has been used to study scenarios ranging from plant development to morphogenesis, tumour growth and cell migration. Despite their wide…
Parallel algorithms on CPU and GPU are implemented for the Unified Gas-Kinetic Scheme and their performances are investigated and compared by a two dimensional channel flow case. The parallel CPU algorithm has a one dimensional block…
We propose a GPU-accelerated distributed optimization algorithm for controlling multi-phase optimal power flow in active distribution systems with dynamically changing topologies. To handle varying network configurations and enable…
Heterogeneity in the cell population of cancer tissues poses many challenges in cancer diagnosis and treatment. Studying the heterogeneity in cell populations from gene expression measurement data in the context of cancer research is a…
In this talk I discuss the general question of the portability of Molecular Dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision arithmetics of the today available APE platforms does…
Modern parallel computing devices, such as the graphics processing unit (GPU), have gained significant traction in scientific and statistical computing. They are particularly well-suited to data-parallel algorithms such as the particle…
This work presents a fully GPU-accelerated algorithm for the polygonal mesh generator known as Polylla. Polylla is a tri-to-polygon mesh generator, which benefits from the half-edge data structure to manage any polygonal shape. The proposed…
As deep neural networks (DNNs) become deeper, the training time increases. In this perspective, multi-GPU parallel computing has become a key tool in accelerating the training of DNNs. In this paper, we introduce a novel methodology to…
Motivated by an application in cell biology, we consider spatial sorting processes defined by particles moving from an initial to a final configuration. We describe an algorithm for constructing a cell complex in space-time, called the…
The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by…
We describe a method for parallelizing the lexicographic enumeration algorithm for the factorization set of an element in a numerical semigroup via bounds. This enables the use of GPU and distributed computing methods. We provide a CUDA…