26 papers · ranked by Valyu relevance
Aravind Sankaran, Paolo Bientinesi
—Linear algebra expressions, which play a central role in countless scientific computations, are often computed via a sequence of calls to existing libraries of building blocks (such as those provided by BLAS and LAPACK). A sequence identifies a computing strategy, i.e., an algorithm, and normally for one linear…
Anupam Biswas
—The performance of individual evolutionary optimization algorithms are mostly measured in terms of statistics such as mean, median and standard deviation etc., computed over the best solutions obtained with few trails of the algorithm. To compare the performance of two algorithms, the values of these statistics are…
Liad Nagi, Moriya Elgrabli
A fair division algorithm is an algorithm that divides a set of resources among several people who have an entitlement to them so that each person receives their due share. The algorithm takes into account the utilities of the items to each person. This paper compares fair division algorithms in minimum utility and the…
Jialing Yan, Gang Hu, Jiulong Zhang, Heming Jia + 2 more
'Xuewen Xia'] To address the shortcomings of the recently proposed Fick’s Law Algorithm, which is prone to local convergence and poor convergence efficiency, we propose a multi-strategy improved Fick’s Law Algorithm (FLAS). The method combines multiple effective strategies, including differential mutation strategy…
Qihang Yuan, Yongde Zhang, Xuesong Dai, Shu Zhang
The reptile search algorithm (RSA) is a swarm-based metaheuristic algorithm inspired by the encirclement and hunt mechanisms of crocodiles. Compared with other algorithms, RSA is competitive but still suffers from low population diversity, unbalanced exploitation and exploration, and the tendency to fall into local…
Samuel Genheden, Esben Bjerrum
We introduce a framework for benchmarking multi-step retrosynthesis methods, i.e. route predictions, called PaRoutes. The framework consists of two sets of 10,000 synthetic routes extracted from the patent literature, a list of stock compounds, and a curated set of reactions on which one-step retrosynthesis models can…
Authors not listed
Accurately predicting the diverse bound-state conformations of small molecules is crucial for successful drug discovery and design, particularly when detailed protein-ligand interactions are unknown. Established tools exist, but efficiently exploring the vast conformational space remains challenging. This work…
Ran Wang, Weiquan Huang, Junyu Wu, Chen Chen + 3 more
To address the rapid population diversity loss and premature convergence of the Artificial Lemming Algorithm (ALA) in complex optimization problems, this paper proposes an Improved Artificial Lemming Algorithm (IALA) with multi-strategy enhancements inspired by lemming behavior. First, a non-uniform mutation operator…
Bilal Khurshid, Shahid Maqsood, Yahya Khurshid, Khawar Naeem + 1 more
This study investigates the no-wait flow shop scheduling problem and proposes a hybrid (HES-IG) algorithm that utilizes makespan as the objective function. To address the complexity of this NP-hard problem, the HES-IG algorithm combines evolution strategies (ES) and iterated greedy (IG) algorithm, as hybridizing…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Wang, Haibo, Alidaee, Bahram
This paper addresses the single-assignment uncapacitated multi-level facility location (MFL) problem, which has numerous applications, including tactical and strategic supply chain management. We consider four- and five-level facilities (4-LFL and 5-LFL). Although the MFL has been addressed in the literature in various…
You-hang Liu, Zai-dong Qi, Qiang Liu
Comparing the similarity between digital images is an important subroutine in various image processing algorithms. In this study, we present three quantum algorithms for comparing the similarity between two quantum images. These algorithms are applied to binary, grey and color images for the first time. Without…
Siyi Xu, Wenwen Liu, Chengpei Wu, Junli Li + 1 more
The No Free Lunch Theorem tells us that no algorithm can beat other algorithms on all types of problems. The algorithm selection structure is proposed to select the most suitable algorithm from a set of algorithms for an unknown optimization problem. This paper introduces an innovative algorithm selection approach…
Esteban Arias-Méndez, Diego Barquero-Morera, Francisco J. Torres-Rojas, Bernhard Schuster
'Francisco J. Torres-Rojas' 'Bernhard Schuster'] Metabolic pathways provide key information for achieving a better understanding of life and all its processes; this is useful information for the improvement of medicine, agronomy, pharmacy, and other similar areas. The main analysis tool used to study these pathways is…
Rahmani, Mohammad Khalid Imam
Due to the abundance of large number of data repositories with ever-growing volume of online and offline data which are being maintained by enterprise houses, research institutions, medical & healthcare organizations, finding a key is a time-consuming task. For taking a strategic decision, the managers of such…
Jordan M. Eizenga, Benedict Paten
Modern genomic sequencing data is trending toward longer sequences with higher accuracy. Many analyses using these data will center on alignments, but classical exact alignment algorithms are infeasible for long sequences. The recently proposed WFA algorithm demonstrated how to perform exact alignment for long, similar…
Jonas Verhellen
Computer-assisted design of small molecules has experienced a resurgence in academic and indus- trial interest due to the widespread use of data-driven techniques such as deep generative models. While the ability to generate molecules that fulfill required chemical properties is encouraging, the use of deep learning…
Benjamin Ries, Irfan Alibay, David W H Swenson, Hannah M Baumann + 3 more
Relative binding free energy (RBFE) calculations have emerged as a powerful tool supporting ligand optimization in drug discovery. Despite many successes, the use of RBFEs can often be limited by automation problems, in particular the setup of such calculations. Atom mapping algorithms are an essential component in…
Akhil Shajan, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open- source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
Zhengyang Guo, Yang Wang, Guangshuo Ou
Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for…
Lionel Zoubritzky, François-Xavier Coudert
We present here an open-source Julia library for the topological identification of crystalline materials, with algorithmic and computational improvements over the previously available software in the field, resulting in a speed increase of one order of magnitude. This new algorithm and implementation can therefore be…
Yidi Hao, Baodong Qin, Yitian Sun, Jose Manuel Molina López
Due to the rapid development of machine-learning technology, companies can build complex models to provide prediction or classification services for customers without resources. A large number of related solutions exist to protect the privacy of models and user data. However, these efforts require costly communication…
Rahul Varki, Christina Boucher
Relative Lempel–Ziv (RLZ) is an effective compression method for large, repetitive collections; however, the fundamental primitives required to elevate it from a passive archival format to a tractable representation for compressed construction have yet to be fully established. In this paper, we introduce an algorithmic…
Randolph T. Bushman, Tanya M. Tebcherani, Alhassan S. Yasin
In this paper, we introduce and prove QR Sort, a novel non-comparative integer sorting algorithm. This algorithm uses principles derived from the Quotient-Remainder Theorem and Counting Sort subroutines to sort input sequences stably. QR Sort exhibits the general time and space complexity O ( + + ), where denotes the…
Daniel J. van Zyl, Marcel Dunaiski, Houriiyah Tegally, Cheryl Baxter + 2 more
The rapid increase in nucleotide sequence data generated by next-generation sequencing (NGS) technologies demands efficient computational tools for sequence comparison. Alignment-based methods, such as BLAST, are increasingly overwhelmed by the scale of contemporary datasets due to their high computational demands for…
Zhenghao Wu, Tianhang Zhou
In the realm of multiscale molecular simulations, structure-based coarse graining is a prominent approach for creating efficient coarse-grained (CG) representations of soft matter systems such as polymers. This involves optimizing CG interactions by matching static correlation functions of corresponding degrees of…