Related papers: FPGA Acceleration of Short Read Alignment

Computational complexity and storage requirements are crucial factors influencing the performance and efficiency of convolutional neural networks (CNNs) in resource-constrained environments. This paper presents a high-performance embedded…

FPGAs are increasingly gaining traction in cloud and edge computing environments due to their hardware flexibility, low latency, and low energy consumption. However, the existing hardware stack of FPGA and the host-FPGA connectivity does…

We propose Frequency-Guided Attention (FGA), a lightweight upsampling module for single image super-resolution. Conventional upsamplers, such as Sub-Pixel Convolution, are efficient but frequently fail to reconstruct high-frequency details…

Floorplanning problem has been extensively explored for homogeneous FPGAs. Most modern FPGAs consist of heterogeneous resources in the form of configurable logic blocks, DSP blocks, BRAMs and more. Very little work has been done for…

Spiking Neural Networks (SNNs) can reduce energy consumption compared to conventional Artificial Neural Networks (ANNs) when spiking activity is sparse and the neuron model is hardware-friendly. However, biologically faithful models are…

Motivation: Antifungal resistance has become an increasing global concern in both clinical and environmental health. Detecting known resistance mutations directly from sequencing reads, in special metagenomic samples, remains a major…

Sequence alignment has had an enormous impact on our understanding of biology, evolution, and disease. The alignment of biological {\em networks} holds similar promise. Biological networks generally model interactions between biomolecules…

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that…

To satisfy the growing throughput demand of data-intensive applications, the performance of optical communication systems increased dramatically in recent years. With higher throughput, more advanced equalizers are crucial, to compensate…

Deep convolutional neural networks (CNNs) obtain outstanding results in tasks that require human-level understanding of data, like image or speech recognition. However, their computational load is significant, motivating the development of…

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…

We demonstrate an FPGA implementation of a parallel and reconfigurable architecture for sparse neural networks, capable of on-chip training and inference. The network connectivity uses pre-determined, structured sparsity to significantly…

The current over-provisioned heterogeneous multi-cores require effective run-time optimization strategies, and the run-time power monitoring subsystem is paramount for their success. Several state-of-the-art methodologies address the design…

Field-Programmable Gate Arrays (FPGAs) have evolved from uniform logic arrays into heterogeneous fabrics integrating digital signal processors (DSPs), memories, and specialized accelerators to support emerging workloads such as machine…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

A new field programmable gate array (FPGA)-based emulation platform is proposed to accelerate fault tolerance analysis of inference accelerators of convolutional neural networks (CNN). For a given CNN model, hardware accelerator…

Reconfigurable architectures like Field Programmable Gate Arrays (FPGAs) have been used for accelerating computations in several domains because of their unique combination of flexibility, performance, and power efficiency. However, FPGAs…

In natural language processing (NLP), the "Transformer" architecture was proposed as the first transduction model replying entirely on self-attention mechanisms without using sequence-aligned recurrent neural networks (RNNs) or convolution,…

Simulated annealing (SA) is a well-known algorithm for solving combinatorial optimization problems. However, the computation time of SA increases rapidly, as the size of the problem grows. Recently, a stochastic simulated annealing (SSA)…

DNA read mapping is a ubiquitous task in bioinformatics, and many tools have been developed to solve the read mapping problem. However, there are two trends that are changing the landscape of readmapping: First, new sequencing technologies…