Related papers: FPGA Acceleration of Short Read Alignment

Modern data-intensive applications demand high computation capabilities with strict power constraints. Unfortunately, such applications suffer from a significant waste of both execution cycles and energy in current computing systems due to…

With the emerging big data applications of Machine Learning, Speech Recognition, Artificial Intelligence, and DNA Sequencing in recent years, computer architecture research communities are facing the explosive scale of various data…

Pairwise sequence alignment is one of the most computationally intensive kernels in genomic data analysis, accounting for more than 90% of the runtime for key bioinformatics applications. This method is particularly expensive for…

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics.…

Motivation: Recent advances in sequencing technologies promise ultra-long reads of $\sim$100 kilo bases (kb) in average, full-length mRNA or cDNA reads in high throughput and genomic contigs over 100 mega bases (Mb) in length. Existing…

BarraCUDA is a C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. The genetically improved (GI) code is up to three times faster on short paired end…

With the rapidly-developing high-speed wireless communications, the 60 GHz millimeter-wave frequency range and radio-over-fiber systems have been investigated as a promising solution to deliver mm-wave signals. Neural networks have been…

Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…

Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is…

This study presents advanced neural network architectures including Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN), Long Short-Term Memory Networks (LSTMs), and Deep Belief Networks (DBNs) for enhanced ECG signal…

Neural Networks (NN) provide a solid and reliable way of executing different types of applications, ranging from speech recognition to medical diagnosis, speeding up onerous and long workloads. The challenges involved in their…

Field-programmable gate array (FPGA) based accelerators are being widely used for acceleration of convolutional neural networks (CNNs) due to their potential in improving the performance and reconfigurability for specific application…

Spiking neural networks (SNNs) recently gained momentum due to their low-power multiplication-free computing and the closer resemblance of biological processes in the nervous system of humans. However, SNNs require very long spike trains…

Multipliers are widely-used arithmetic operators in digital signal processing and machine learning circuits. Due to their relatively high complexity, they can have high latency and be a significant source of power consumption. One strategy…

This research delves into sophisticated neural network frameworks like Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN), Long Short-Term Memory Networks (LSTMs), and Deep Belief Networks (DBNs) for improved analysis of…

The rapidly changing landscape of sequencing technologies brings new opportunities to genomics research. Longer sequence reads and higher sequence throughput coupled with ever-improving base accuracy and decreasing per-base cost is now…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

FPGA-based heterogeneous architectures provide programmers with the ability to customize their hardware accelerators for flexible acceleration of many workloads. Nonetheless, such advantages come at the cost of sacrificing programmability.…

We have recently used genetic programming to automatically generate an improved version of Langmead's DNA read alignment tool Bowtie2 Sect.5.3 RN/12/09. We find it runs more than four times faster than the Bioinformatics sequencing tool…

FPGA accelerators for lightweight neural convolutional networks (LWCNNs) have recently attracted significant attention. Most existing LWCNN accelerators focus on single-Computing-Engine (CE) architecture with local optimization. However,…