0000000000230844
AUTHOR
Hoang-vu Dang
showing 7 related works from this author
CUDA-enabled hierarchical ward clustering of protein structures based on the nearest neighbour chain algorithm
2015
Clustering of molecular systems according to their three-dimensional structure is an important step in many bioinformatics workflows. In applications such as docking or structure prediction, many algorithms initially generate large numbers of candidate poses (or decoys), which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates can easily range from thousands to millions, performing the clustering on standard central processing units (CPUs) is highly time consuming. In this paper, we analyse and evaluate different approaches to parallelize the nearest neighbour chain algorithm to perform hierarc…
GEM
2014
The widespread use of digital sensor systems causes a tremendous demand for high-quality time series analysis tools. In this domain the majority of data mining algorithms relies on established distance measures like Dynamic Time Warping (DTW) or Euclidean distance (ED). However, the notion of similarity induced by ED and DTW may lead to unsatisfactory clusterings. In order to address this shortcoming we introduce the Gliding Elastic Match (GEM) algorithm. It determines an optimal local similarity measure of a query time series Q and a subject time series S. The measure is invariant under both local deformation on the measurement-axis and scaling in the time domain. GEM is compared to ED and…
Iterative sparse matrix-vector multiplication for accelerating the block Wiedemann algorithm over GF(2) on multi-graphics processing unit systems
2012
SUMMARY The block Wiedemann (BW) algorithm is frequently used to solve sparse linear systems over GF(2). Iterative sparse matrix–vector multiplication is the most time-consuming operation. The necessity to accelerate this step is motivated by the application of BW to very large matrices used in the linear algebra step of the number field sieve (NFS) for integer factorization. In this paper, we derive an efficient CUDA implementation of this operation by using a newly designed hybrid sparse matrix format. This leads to speedups between 4 and 8 on a single graphics processing unit (GPU) for a number of tested NFS matrices compared with an optimized multicore implementation. We further present…
CUDA-enabled Sparse Matrix–Vector Multiplication on GPUs using atomic operations
2013
We propose the Sliced Coordinate Format (SCOO) for Sparse Matrix-Vector Multiplication on GPUs.An associated CUDA implementation which takes advantage of atomic operations is presented.We propose partitioning methods to transform a given sparse matrix into SCOO format.An efficient Dual-GPU implementation which overlaps computation and communication is described.Extensive performance comparisons of SCOO compared to other formats on GPUs and CPUs are provided. Existing formats for Sparse Matrix-Vector Multiplication (SpMV) on the GPU are outperforming their corresponding implementations on multi-core CPUs. In this paper, we present a new format called Sliced COO (SCOO) and an efficient CUDA i…
Scalable Clustering by Iterative Partitioning and Point Attractor Representation
2016
Clustering very large datasets while preserving cluster quality remains a challenging data-mining task to date. In this paper, we propose an effective scalable clustering algorithm for large datasets that builds upon the concept of synchronization. Inherited from the powerful concept of synchronization, the proposed algorithm, CIPA (Clustering by Iterative Partitioning and Point Attractor Representations), is capable of handling very large datasets by iteratively partitioning them into thousands of subsets and clustering each subset separately. Using dynamic clustering by synchronization, each subset is then represented by a set of point attractors and outliers. Finally, CIPA identifies the…
The Sliced COO Format for Sparse Matrix-Vector Multiplication on CUDA-enabled GPUs
2012
Abstract Existing formats for Sparse Matrix-Vector Multiplication (SpMV) on the GPU are outperforming their corresponding implementations on multi-core CPUs. In this paper, we present a new format called Sliced COO (SCOO) and an effcient CUDA implementation to perform SpMV on the GPU. While previous work shows experiments on small to medium-sized sparse matrices, we perform evaluations on large sparse matrices. We compared SCOO performance to existing formats of the NVIDIA Cusp library. Our resutls on a Fermi GPU show that SCOO outperforms the COO and CSR format for all tested matrices and the HYB format for all tested unstructured matrices. Furthermore, comparison to a Sandy-Bridge CPU sho…
Parallelized Clustering of Protein Structures on CUDA-Enabled GPUs
2014
Estimation of the pose in which two given molecules might bind together to form a potential complex is a crucial task in structural biology. To solve this so-called "docking problem", most algorithms initially generate large numbers of candidate poses (or decoys) which are then clustered to allow for subsequent computationally expensive evaluations of reasonable representatives. Since the number of such candidates ranges from thousands to millions, performing the clustering on standard CPUs is highly time consuming. In this paper we analyze and evaluate different approaches to parallelize the nearest neighbor chain algorithm to perform hierarchical Ward clustering of protein structures usin…