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

Sparse Matrix-Matrix Multiplication (SpMM) is a fundamental operation in graph computing and analytics. However, the irregularity of real-world graphs poses significant challenges to achieving efficient SpMM operation for graph data on…

State-of-the-art multiple sequence alignment (MSA) algorithms are based on progressive approaches that rely on pairwise sequence alignment (PSA) to generate guide trees to align all sequences. Given an evidenced explosion in genomic data…

A Multigrid Full Approximation Storage algorithm for solving Deep Residual Networks is developed to enable neural network parallelized layer-wise training and concurrent computational kernel execution on GPUs. This work demonstrates a 10.2x…

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given…

We propose a parallel graph-based data clustering algorithm using CUDA GPU, based on exact clustering of the minimum spanning tree in terms of a minimum isoperimetric criteria. We also provide a comparative performance analysis of our…

Many mission-critical systems are based on GPU for inference. It requires not only high recognition accuracy but also low latency in responding time. Although many studies are devoted to optimizing the structure of deep models for efficient…

The focus of my PhD thesis is on exploring parallel approaches to efficiently solve problems modeled by constraints and presenting a new proposal. Current solvers are very advanced; they are carefully designed to effectively manage the…

The surge in availability of genomic data holds promise for enabling determination of genetic causes of observed individual traits, with applications to problems such as discovery of the genetic roots of phenotypes, be they molecular…

We present a GPU solution for exact maximal clique enumeration (MCE) that performs a search tree traversal following the Bron-Kerbosch algorithm. Prior works on parallelizing MCE on GPUs perform a breadth-first traversal of the tree, which…

FPGA-based hardware accelerators for convolutional neural networks (CNNs) have obtained great attentions due to their higher energy efficiency than GPUs. However, it is challenging for FPGA-based solutions to achieve a higher throughput…

This Article presents two optimized multi-GPU algorithms for Fock matrix construction, building on the work of Ufimtsev et al. and Barca et al. The novel algorithms, opt-UM and opt-Brc, introduce significant enhancements, including improved…

General sparse matrix-matrix multiplication (SpGEMM) is a fundamental building block for numerous applications such as algebraic multigrid method (AMG), breadth first search and shortest path problem. Compared to other sparse BLAS routines,…

We design, implement, and evaluate GPU-based algorithms for the maximum cardinality matching problem in bipartite graphs. Such algorithms have a variety of applications in computer science, scientific computing, bioinformatics, and other…

Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…

Nowadays, several industrial applications are being ported to parallel architectures. In fact, these platforms allow acquire more performance for system modelling and simulation. In the electric machines area, there are many problems which…

We examine the problem of optimizing classification tree evaluation for on-line and real-time applications by using GPUs. Looking at trees with continuous attributes often used in image segmentation, we first put the existing algorithms for…

Process mapping asks to assign vertices of a task graph to processing elements of a supercomputer such that the computational workload is balanced while the communication cost is minimized. Motivated by the recent success of GPU-based graph…

We present the Cuckoo Trie, a fast, memory-efficient ordered index structure. The Cuckoo Trie is designed to have memory-level parallelism -- which a modern out-of-order processor can exploit to execute DRAM accesses in parallel -- without…

We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…

The gamma-index dose comparison tool has been widely used to compare dose distributions in cancer radiotherapy. The accurate calculation of gamma-index requires an exhaustive search of the closest Euclidean distance in the high-resolution…