Related papers: High Performance Multiple Sequence Alignment Algor…
High-throughput sequencing (HTS) technologies have revolutionized the field of genomics, enabling rapid and cost-effective genome analysis for various applications. However, the increasing volume of genomic data generated by HTS…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Classification is one of the most important tasks in Machine Learning (ML) and with recent advancements in artificial intelligence (AI) it is important to find efficient ways to implement it. Generally, the choice of classification…
The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Machine learning algorithms have enabled computers to predict things by learning from previous data. The data storage and processing power are increasing rapidly, thus increasing machine learning and Artificial intelligence applications.…
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…
Since the release of human genome sequences, one of the most important research issues is about indexing the genome sequences, and the suffix tree is most widely adopted for that purpose. The traditional suffix tree construction algorithms…
This work proposes a novel approach to evaluate and analyze the behavior of multi-population parallel genetic algorithms (PGAs) when running on a cluster of multi-core processors. In particular, we deeply study their numerical and…
Most machine learning algorithms are configured by one or several hyperparameters that must be carefully chosen and often considerably impact performance. To avoid a time consuming and unreproducible manual trial-and-error process to find…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Sorting is one of the most basic algorithms, and developing highly parallel sorting programs is becoming increasingly important in high-performance computing because the number of CPU cores per node in modern supercomputers tends to…
Scientific investigations that incorporate next generation sequencing involve analyses of high-dimensional data where the need to organize, collate and interpret the outcomes are pressingly important. Currently, data can be collected at the…
Multiple Sequences Alignment (MSA) of biological sequences is a fundamental problem in computational biology due to its critical significance in wide ranging applications including haplotype reconstruction, sequence homology, phylogenetic…
Multiple signal classification algorithm (MUSICAL) provides a super-resolution microscopy method. In the previous research, MUSICAL has enabled data-parallelism well on a desktop computer or a Linux-based server. However, the running time…
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…
One of the most critical issues in machine learning is the selection of appropriate hyper parameters for training models. Machine learning models may be able to reach the best training performance and may increase the ability to generalize…
This work presents a comparison for the performance of sequential sorting algorithms under four different modes of execution, the sequential processing mode, a conventional multi-threading implementation, multi-threading with OpenMP Library…
Design of printed circuit board (PCB) stack-up requires the consideration of characteristic impedance, insertion loss and crosstalk. As there are many parameters in a PCB stack-up design, the optimization of these parameters needs to be…
Sorting is one of the most fundamental problems in the field of computer science. With the rapid development of manycore processors, it shows great importance to design efficient parallel sort algorithm on manycore architecture. This paper…