25 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…
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…
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…
Ali Asghari, Mohammadhossein Mohammadi, Heming Jia
Metaheuristic algorithms are widely used to find optimal or near-optimal solutions for complex problems by taking inspiration from natural behaviors and processes. Although many different methods have been developed, a common problem in many of them is maintaining a good balance between exploration and exploitation and…
Ahmed F. Ali, Mohamed A. Tawhid
Cuckoo search algorithm is a promising metaheuristic population based method. It has been applied to solve many real life problems. In this paper, we propose a new cuckoo search algorithm by combining the cuckoo search algorithm with the Nelder-Mead method in order to solve the integer and minimax optimization…
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…
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…
Aravind Sankaran, Paolo Bientinesi
—In scientific computing, it is common that a mathematical expression can be computed by many different algorithms (sometimes over hundreds), each identifying a specific sequence of library calls. Although mathematically equivalent, those algorithms might exhibit significant differences in terms of performance. However…
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…
Abdolahad Noori Zehmakan
The Bin Packing Problem is one of the most important optimization problems. In recent years, due to its NP-hard nature, several approximation algorithms have been presented. It is proved that the best algorithm for the Bin Packing Problem has the approximation ratio 3/2 and the time order O(n), unless P=NP. In this…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
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…
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…
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…
Jan H. Jensen
This paper presents a comparison of a graph-based genetic algorithm (GB-GA) and machine learning (ML) results for the optimisation of logP values with a constraint for synthetic accessibility and shows that GA is as good or better than the ML approaches for this particular property. The molecules found by GB-GA bear…
Morihiro Hayashida, Tatsuya Akutsu
Background Comparison of various kinds of biological data is one of the main problems in bioinformatics and systems biology. Data compression methods have been applied to comparison of large sequence data and protein structure data. Since it is still difficult to compare global structures of large biological networks…
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…
Haojing Shao, Jue Ruan
Increasing the accuracy of the nucleotide sequence alignment is an essential issue in genomics research. Although classic dynamic-programming algorithms (e.g., Smith-Waterman and Needleman–Wunsch) guarantee to produce the optimal result, their time complexity hinders the application of large-scale sequence alignment.…
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…
Harsh Ranjan, Sumit Agarwal, Niraj Kumar Singh
This paper introduces a new comparison base stable sorting algorithm, named RS sort. RS Sort involves only the comparison of pair of elements in an array which ultimately sorts the array and does not involve the comparison of each element with every other element. RS sort tries to build upon the relationship…
Abdolahad Noori Zehmakan
Since the Bin Packing Problem (BPP) is one of the main NP-hard problems, a lot of approximation algorithms have been suggested for it. It has been proven that the best algorithm for BPP has the approximation ratio of 3 2 and the time order of (), unless = . In the current paper, a linear 3 2 -approximation algorithm is…
Martin Šošić, Mile Šikić
We present Edlib, an open-source C/C++ library for exact pairwise sequence alignment using edit distance. We compare Edlib to other libraries and show that it is the fastest while not lacking in functionality, and can also easily handle very large sequences. Being easy to use, flexible, fast and low on memory usage, we…
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…