相关论文: Ultra-fast Multiple Genome Sequence Matching Using…

Matrix factorization (MF) is employed by many popular algorithms, e.g., collaborative filtering. The emerging GPU technology, with massively multicore and high intra-chip memory bandwidth but limited memory capacity, presents an opportunity…

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…

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…

Many techniques in program synthesis, superoptimization, and array programming require parallel rollouts of general-purpose programs. GPUs, while capable targets for domain-specific parallelism, are traditionally underutilized by such…

We present a multi-purpose genetic algorithm, designed and implemented with GPGPU / CUDA parallel computing technology. The model was derived from a multi-core CPU serial implementation, named GAME, already scientifically successfully…

Graph Neural Networks (GNNs) have shown great superiority on non-Euclidean graph data, achieving ground-breaking performance on various graph-related tasks. As a practical solution to train GNN on large graphs with billions of nodes and…

Bloom filters are a fundamental data structure for approximate membership queries, with applications ranging from data analytics to databases and genomics. Several variants have been proposed to accommodate parallel architectures. GPUs,…

Our formulation reveals that the reduction across the sequence axis can be efficiently computed in parallel through a tree reduction. Our algorithm, called Tree Attention, for parallelizing exact attention computation across multiple GPUs…

Applications in many domains require processing moving object trajectories. In this work, we focus on a trajectory similarity search that finds all trajectories within a given distance of a query trajectory over a time interval, which we…

Structural parameters are normally extracted from observed galaxies by fitting analytic light profiles to the observations. Obtaining accurate fits to high-resolution images is a computationally expensive task, requiring many model…

Sequence alignment is a fundamental process in computational biology which identifies regions of similarity in biological sequences. With the exponential growth in the volume of data in bioinformatics databases, the time, processing power,…

Over the past decade there has been a growing interest in the development of parallel hardware systems for simulating large-scale networks of spiking neurons. Compared to other highly-parallel systems, GPU-accelerated solutions have the…

While it is well-known and acknowledged that the performance of graph algorithms is heavily dependent on the input data, there has been surprisingly little research to quantify and predict the impact the graph structure has on performance.…

Connected components and spanning forest are fundamental graph algorithms due to their use in many important applications, such as graph clustering and image segmentation. GPUs are an ideal platform for graph algorithms due to their high…

With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…

GPU has a significantly higher performance in single-precision computing than that of double precision. Hence, it is important to take a maximal advantage of the single precision in the CG inverter, using the mixed precision method. We have…

Subgraph matching has garnered increasing attention for its diverse real-world applications. Given the dynamic nature of real-world graphs, addressing evolving scenarios without incurring prohibitive overheads has been a focus of research.…

There is increasing interest in using multicore processors to accelerate stream processing. For example, indexing sliding window content to enhance the performance of streaming queries is greatly improved by utilizing the computational…

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…

Rapid analysis of DNA sequences is important in preventing the evolution of different viruses and bacteria during an early phase, early diagnosis of genetic predispositions to certain diseases (cancer, cardiovascular diseases), and in DNA…