23 papers · ranked by Valyu relevance
Lorién López-Villellas, Cristian Iñiguez, Albert Jiménez-Blanco, Quim Aguado-Puig + 4 more
Advances in DNA sequencing have outpaced advances in computation, making sequence alignment a major bottleneck in genome data analyses. Classical dynamic programming (DP) algorithms are particularly memory-intensive, especially when computing gap-affine and dual gap-affine alignments. Existing strategies to reduce…
Mansoor Iqbal, Muhammad Umar Shafiq, Shouzab Khan, Obaidullah + 3 more
'Saad Alahmari' 'Zahid Ullah' 'Massimiliano Fasi'] Efficient task execution is critical to optimize the usage of computing resources in process scheduling. Various task scheduling algorithms ensure optimized and efficient use of computing resources. This article introduces an innovative dual-layer scheduling algorithm…
Ian P. Gent, Ciaran McCreesh, Ian Miguel, Neil C. A. Moore + 3 more
'Peter Nightingale' 'Patrick Prosser' 'Chris Unsworth'] As multicore computing is now standard, it seems irresponsible for constraints researchers to ignore the implications of it. Researchers need to address a number of issues to exploit parallelism, such as: investigating which constraint algorithms are amenable to…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Authors not listed
This comprehensive review examines the evolution of autonomous materials synthesis laboratories that integrate artificial intelligence with advanced robotics to accelerate discovery. Traditional materials development pipelines typically require 10-20 years, but self-driving laboratories (SDLs) and Materials…
Elaine M. Burns, Sofia Lemons, Wheeler Ruml, Rong Zhou
To harness modern multicore processors, it is imperative to develop parallel versions of fundamental algorithms. In this paper, we compare different approaches to parallel best-first search in a shared-memory setting. We present a new method, PBNF, that uses abstraction to partition the state space and to detect…
Andrew J. Page, Thomas M. Keane, Thomas J. Naughton
We present a multi-heuristic evolutionary task allocation algorithm to dynamically map tasks to processors in a heterogeneous distributed system. It utilizes a genetic algorithm, combined with eight common heuristics, in an effort to minimize the total execution time. It operates on batches of unmapped tasks and can…
Mohammad Bakhshalipour, Hamid Sarbazi‐Azad
—Multicore architectures dominate today's processor market. Even though the number of cores and threads are pretty high and continues to grow, inherently serial algorithms do not benefit from the abundance of cores and threads. In this paper, we propose Runahead Computing, a technique which uses idle threads in a…
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
Soumitra Pal, Teresa M. Przytycka
Large-scale data analysis in Bioinformatics requires executing several software in a pipelined fashion. Generally each stage in a pipeline takes considerable computing resources and several workflow management systems (WMS), e.g., Snakemake and Nextflow, have been developed to ensure in case of multiple invocation of…
Olena Doroshenko
Pathfinding in complex topographies poses a challenge with applications extending from urban planning to autonomous navigation. While numerous algorithms offer potential solutions, their comparative efficiency and reliability when confronted with nonlinear terrains remain to be systematically evaluated. This study…
Martina Baiardi, Samuele Burattini, Giovanni Ciatto, Danilo Pianini + 2 more
'Alessandro Ricci' 'Andrea Omicini'] Abstract. The execution of Belief-Desire-Intention (BDI) agents in a Multi-Agent System (MAS) can be practically implemented on top of low-level concurrency mechanisms that impact on efficiency, determinism, and reproducibility. We argue that developers should specify the MAS…
Wilfried Agbeto, Camille Coti, Vladimir Reinharz
Advances in graph algorithmics have allowed in-depth study of many natural objects from molecular biology or chemistry to social networks. Particularly in molecular biology and cheminformatics, understanding complex structures by identifying conserved sub-structures is a key milestone towards the artificial design of…
Bahman Arasteh, Seyed Salar Sefati, Huseyin Kusetogullari, Farzad Kiani + 3 more
Efficient task scheduling remains a key challenge in High-Performance Computing and Internet of Things (IoT) systems, where the sequential execution of nested loops often limits parallelism. This paper proposes a hybrid approach that dynamically parallelizes nested loops in heterogeneous IoT environments. The suggested…
Bérenger Bramas, Gang Mei
Task-based programming models have demonstrated their efficiency in the development of scientific applications on modern high-performance platforms. They allow delegation of the management of parallelization to the runtime system (RS), which is in charge of the data coherency, the scheduling, and the assignment of the…
Robert Utterback, Kunal Agrawal, Jeremy T. Fineman, I-Ting Angelina Lee
'I-Ting Angelina Lee'] This paper addresses the problem of provably efficient and practically good on-the-fly determinacy race detection in task parallel programs that use futures. Prior works on determinacy race detection have mostly focused on either task parallel programs that follow a series-parallel dependence…
Authors not listed
This work establishes theoretical foundations for hierarchical quantum-classical algorithm design, where complex problems are decomposed across multiple spatial, temporal, or organizational scales with quantum and classical computation assigned to appropriate levels. We develop a mathematical framework that…
Shubhendra Pal Singhal, M. Srıdevı
—Optimization of searching the best possible action depending on various states like state of environment, system goal etc. has been a major area of study in computer systems. In any search algorithm, searching best possible solution from the pool of every possibility known can lead to the construction of the whole…
Raja Appuswamy, Jacques Fellay, Nimisha Chaturvedi
Rapid advances in sequencing technologies are producing genomic data on an unprecedented scale. The first, and often one of the most time consuming, step of genomic data analysis is sequence alignment, where sequenced reads must be aligned to a reference genome. Several years of research on alignment algorithms has led…
Authors not listed
Automated chemistry platforms hold the potential to enable large-scale organic synthesis campaigns, such as producing a library of compounds for biological evaluation. The efficiency of such platforms will depend on the schedule according to which the synthesis operations are executed. In this work, we study the…
Authors not listed
Identifying synthesis routes from knowledge graphs poses challenges beyond retrosynthesis, including path–finding artifacts and data issues. We introduce “SynGPS”, a novel algorithm that overcomes these limitations by identifying viable routes even with common artifacts. SynGPS can resolve nonsensical cycles…
Authors not listed
We report the development and application of a scalable machine learning optimisation framework for batched multi-objective reaction optimisation. Through experimental data-derived benchmarks, we demonstrate our approach’s capacity to efficiently handle large parallel batches and high-dimensional search spaces…
Alvaro Estebanez, Diego R. Llanos, David Orden, Belen Palop + 1 more
'Rafael Sachetto Oliveira'] Loops are a rich source of parallelism. Unfortunately, many loops cannot be safely parallelized at compile time because the compiler is not able to guarantee that there will be no dependence violations. Thread-Level Speculation (TLS) techniques, either hardware or software-based, allow the…