Related papers: Accelerating DNA Sequence Analysis using Intel Xeo…
Recently Graphics Processing Units (GPUs) have been used to speed up very CPU-intensive gravitational microlensing simulations. In this work, we use the Xeon Phi coprocessor to accelerate such simulations and compare its performance on a…
In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides…
To study the performance of multi-threaded Geant4 for high-energy physics experiments, an application has been developed which generalizes and extends previous work. A highly-complex detector geometry is used for benchmarking on an Intel…
DNA pattern matching is essential for many widely used bioinformatics applications. Disease diagnosis is one of these applications, since analyzing changes in DNA sequences can increase our understanding of possible genetic diseases. The…
Nowadays, subsequence similarity search is required in a wide range of time series mining applications: climate modeling, financial forecasts, medical research, etc. In most of these applications, the Dynamic TimeWarping (DTW) similarity…
Discord is a refinement of the concept of anomalous subsequence of a time series. The task of discords discovery is applied in a wide range of subject domains related to time series: medicine, economics, climate modeling, etc. In this…
We implement the Lanczos algorithm on an Intel Xeon Phi coprocessor and compare its performance to a multi-core Intel Xeon CPU and an NVIDIA graphics processor. The Xeon and the Xeon Phi are parallelized with OpenMP and the graphics…
Frequent itemset mining leads to the discovery of associations and correlations among items in large transactional databases. Apriori is a classical frequent itemset mining algorithm, which employs iterative passes over database combining…
Genomics is changing our understanding of humans, evolution, diseases, and medicines to name but a few. As sequencing technology is developed collecting DNA sequences takes less time thereby generating more genetic data every day. Today the…
This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate…
For a deep learning model, efficient execution of its computation graph is key to achieving high performance. Previous work has focused on improving the performance for individual nodes of the computation graph, while ignoring the…
Intel Xeon Phi many-integrated-core (MIC) architectures usher in a new era of terascale integration. Among emerging killer applications, parallel graph processing has been a critical technique to analyze connected data. In this paper, we…
With the increasing size and complexity of data produced by large scale numerical simulations, it is of primary importance for scientists to be able to exploit all available hardware in heterogenous High Performance Computing environments…
Co-expression network is a critical technique for the identification of inter-gene interactions, which usually relies on all-pairs correlation (or similar measure) computation between gene expression profiles across multiple samples.…
In this article we discuss our implementation of a polyphase filter for real-time data processing in radio astronomy. We describe in detail our implementation of the polyphase filter algorithm and its behaviour on three generations of…
We develop methods for accelerating metric similarity search that are effective on modern hardware. Our algorithms factor into easily parallelizable components, making them simple to deploy and efficient on multicore CPUs and GPUs. Despite…
Breadth First Search (BFS) is a building block for graph algorithms and has recently been used for large scale analysis of information in a variety of applications including social networks, graph databases and web searching. Due to its…
Electrical power requirements will be a constraint on the future growth of Distributed High Throughput Computing (DHTC) as used by High Energy Physics. Performance-per-watt is a critical metric for the evaluation of computer architectures…
Motif discovery in DNA sequences is a challenging task in molecular biology. In computational motif discovery, Planted (l, d) motif finding is a widely studied problem and numerous algorithms are available to solve it. Both hardware and…
Computing $k$-Nearest Neighbors (KNN) is one of the core kernels used in many machine learning, data mining and scientific computing applications. Although kd-tree based $O(\log n)$ algorithms have been proposed for computing KNN, due to…