Related papers: Faster and More Accurate Sequence Alignment with S…

Motivation: High throughput DNA sequencing (HTS) technologies generate an excessive number of small DNA segments -- called short reads -- that cause significant computational burden. To analyze the entire genome, each of the billions of…

Spiking Neural Networks (SNNs) provide a promising framework for energy-efficient and biologically grounded computation; however, scalable learning in deep recurrent architectures with sparse connectivity remains a major challenge. In this…

We propose Stochastic Weight Averaging in Parallel (SWAP), an algorithm to accelerate DNN training. Our algorithm uses large mini-batches to compute an approximate solution quickly and then refines it by averaging the weights of multiple…

Background: Identifying all possible mapping locations of next-generation sequencing (NGS) reads is highly essential in several applications such as prediction of genomic variants or protein binding motifs located in repeat regions, isoform…

Spiking Neural Networks (SNNs) have emerged as a promising substitute for Artificial Neural Networks (ANNs) due to their advantages of fast inference and low power consumption. However, the lack of efficient training algorithms has hindered…

Recent strides in low-latency spiking neural network (SNN) algorithms have drawn significant interest, particularly due to their event-driven computing nature and fast inference capability. One of the most efficient ways to construct a…

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…

Programs based on hash tables and Burrows-Wheeler are very fast for mapping short reads to genomes but have low accuracy in the presence of mismatches and gaps. Such reads can be aligned accurately with the Smith-Waterman algorithm but it…

In this paper, we propose Broad Neural Architecture Search (BNAS) where we elaborately design broad scalable architecture dubbed Broad Convolutional Neural Network (BCNN) to solve the above issue. On one hand, the proposed broad scalable…

It is demonstrated earlier that the exact Smith-Waterman algorithm yields more accurate results than the members of the heuristic BLAST family of algorithms. Unfortunately, the Smith-Waterman algorithm is much slower than the BLAST and its…

The efficiency of modern machine intelligence depends on high accuracy with minimal computational cost. In spiking neural networks (SNNs), synaptic delays are crucial for encoding temporal structure, yet existing models treat them as fully…

Genome sequence analysis is a powerful tool in medical and scientific research. Considering the inevitable sequencing errors and genetic variations, approximate string matching (ASM) has been adopted in practice for genome sequencing.…

High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…

Spiking Neural Networks (SNNs) have emerged as a promising approach to improve the energy efficiency of machine learning models, as they naturally implement event-driven computations while avoiding expensive multiplication operations. In…

Spiking Neural Networks (SNNs) event-driven nature enables efficient encoding of spatial and temporal features, making them suitable for dynamic time-dependent data processing. Despite their biological relevance, SNNs have seen limited…

Summary: We present an extension of CUSHAW2 for fast and accurate alignments of SOLiD color-space short-reads. Our extension introduces a double-seeding approach to improve mapping sensitivity, by combining maximal exact match seeds and…

Spiking Neural Networks (SNNs) have been attached great importance due to the distinctive properties of low power consumption, biological plausibility, and adversarial robustness. The most effective way to train deep SNNs is through…

Spiking Neural Networks (SNNs) are extensively utilized in brain-inspired computing and neuroscience research. To enhance the speed and energy efficiency of SNNs, several many-core accelerators have been developed. However, maintaining the…

Spiking neural networks (SNNs) have closer dynamics to the brain than current deep neural networks. Their low power consumption and sample efficiency make these networks interesting. Recently, several deep convolutional spiking neural…

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…