Accelerating edit-distance sequence alignment on GPU using the wavefront algorithm

Q Aguado-Puig, S Marco-Sola, JC Moure… - IEEE …, 2022 - ieeexplore.ieee.org
Sequence alignment remains a fundamental problem with practical applications ranging
from pattern recognition to computational biology. Traditional algorithms based on dynamic …

A scalable parallel algorithm for global sequence alignment with customizable scoring scheme

MU Sadiq, MM Yousaf - Concurrency and Computation …, 2023 - Wiley Online Library
Sequence alignment is a critical computational problem in various domains, including
genomics, proteomics, and natural language processing. The Needleman‐Wunsch (NW) …

Data and Process Quality Evaluation in a Textual Big Data Archiving System

M Fugini, J Finocchi - ACM Journal on Computing and Cultural Heritage …, 2022 - dl.acm.org
The article presents a textual Big Data analytics solution developed in a real setting as a part
of a high-capacity document digitization and storage system. A software based on machine …

Space-efficient computation of parallel approximate string matching

MU Sadiq, MM Yousaf - The Journal of Supercomputing, 2023 - Springer
Approximate string matching (ASM) has a number of applications in many disciplines,
ranging from information retrieval to gene matching. Conventional solution to this problem is …

Distributed algorithm for parallel edit distance computation

MU Sadiq, MM Yousaf - Computing and Informatics, 2020 - cai.sk
The edit distance is the measure that quantifies the difference between two strings. It is an
important concept because it has its usage in many domains such as natural language …

Toward Efficient Similarity Search under Edit Distance on Hybrid Architectures

M Khalid, MM Yousaf, MU Sadiq - Information, 2022 - mdpi.com
Edit distance is the most widely used method to quantify similarity between two strings. We
investigate the problem of similarity search under edit distance. Given a collection of …

BIMSA: Accelerating Long Sequence Alignment Using Processing-In-Memory

A Alonso-Marín, I Fernandez, Q Aguado-Puig… - bioRxiv, 2024 - biorxiv.org
Motivation Recent advances in sequencing technologies have stressed the critical role of
sequence analysis algorithms and tools in genomics and healthcare research. In particular …

Accelerating Sequence Alignment Using Processing-In-Memory

A Alonso Marín - 2023 - upcommons.upc.edu
Recent advances in sequencing technologies have made sequencing analysis a
fundamental tool for genomics and healthcare research. Before any biological insights can …

Accelerating pairwise sequence alignment on GPUs using the Wavefront Algorithm

Q Aguado Puig - 2022 - upcommons.upc.edu
Advances in genomics and sequencing technologies demand faster and more scalable
analysis methods that can process longer sequences with higher accuracy. However …

[PDF][PDF] Error correction of semantic mathematical expressions based on bayesian algorithm

X Wang, F Yang, H Liu, Q Shi - Mathematical Biosciences and …, 2022 - aimspress.com
The semantic information of mathematical expressions plays an important role in information
retrieval and similarity calculation. However, a large number of presentational expressions …