Related papers: Accelerating the Understanding of Life's Code Thro…

In this paper we describe SYNERGY, which is a highly parallelizable, linear planning system that is based on the genetic programming paradigm. Rather than reasoning about the world it is planning for, SYNERGY uses artificial selection,…

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…

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…

With an ever-growing number of parameters defining increasingly complex networks, Deep Learning has led to several breakthroughs surpassing human performance. As a result, data movement for these millions of model parameters causes a…

Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing…

Because of unmatched improvements in CPU performance, memory transfers have become a bottleneck of program execution. As discovered in recent years, this also affects sorting in internal memory. Since partitioning around several pivots…

String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…

The tremdendous advances in high-throughput sequencing technologies have made population-scale sequencing as performed in the 1000 Genomes project and the Genome of the Netherlands project possible. Next-generation sequencing has allowed…

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…

Neuromorphic computing is henceforth a major research field for both academic and industrial actors. As opposed to Von Neumann machines, brain-inspired processors aim at bringing closer the memory and the computational elements to…

Objective: Spike sorting is a fundamental step in analysing extracellular recordings, enabling the isolation of single-neuron activity. However, it remains a challenging problem because extracellular traces mix overlapping spikes from…

Finding out the computational redundant part of a trained Deep Neural Network (DNN) is the key question that pruning algorithms target on. Many algorithms try to predict model performance of the pruned sub-nets by introducing various…

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…

Spiking neural networks (SNNs) are the third generation of neural networks and can explore both rate and temporal coding for energy-efficient event-driven computation. However, the decision accuracy of existing SNN designs is contingent…

In this paper we propose a novel parallel stochastic coordinate descent (SCD) algorithm with convergence guarantees that exhibits strong scalability. We start by studying a state-of-the-art parallel implementation of SCD and identify…

For a given dataset $\mathcal{D}$ and structured label $f$, the goal of Filtered Approximate Nearest Neighbor Search (FANNS) algorithms is to find top-$k$ points closest to a query that satisfy label constraints, while ensuring both recall…

In this paper we introduce a novel parallel pipeline for fast and accurate mapping of RNA sequences on servers equipped with multicore processors. Our software, named HPG-Aligner, leverages the speed of the Burrows-Wheeler Transform to map…

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…

Program similarity is a fundamental concept, central to the solution of software engineering tasks such as software plagiarism, clone identification, code refactoring and code search. Accurate similarity estimation between programs requires…

Spiking Neural Networks (SNNs) hold great potential to realize brain-inspired, energy-efficient computational systems. However, current SNNs still fall short in terms of multi-scale temporal processing compared to their biological…