SALoBa: Maximizing Data Locality and Workload Balance for Fast Sequence Alignment on GPUs

Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work has been conducted on GPU acceleration of a sequence alignment, we identify several shortcomings that limit...

An Attention Module for Convolutional Neural Networks

Attention mechanism has been regarded as an advanced technique to capture long-range feature interactions and to boost the representation capability for convolutional neural networks. However, we found two ignored problems in current attentional activations-based models: the approximation problem and the insufficient capacity problem of the...

An Efficient High-Throughput LZ77-Based Decompressor in Reconfigurable Logic

To best leverage high-bandwidth storage and network technologies requires an improvement in the speed at which we can decompress data. We present a “refine and recycle” method applicable to LZ77-type decompressors that enables efficient high-bandwidth designs and present an implementation in reconfigurable logic. The method refines the write...