23 papers · ranked by Valyu relevance
Alexander V. Spirov, Ekaterina M. Myasnikova, Josh Bongard
Evolutionary computing (EC) is an area of computer sciences and applied mathematics covering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches…
Alexander Lalejini, Emily Dolson, Anya E. Vostinar, Luis Zaman
Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses the principles of Darwinian evolution as a…
Eugene Eberbach
Evolution by natural selection, which is one of the most compelling themes of modern science, brought forth evolutionary algorithms and evolutionary computation, applying mechanisms of evolution in nature to various problems solved by computers. In this paper we concentrate on evolutionary automata that constitute an…
Beichen Huang, Ran Cheng, Yaochu Jin, Kay Chen Tan
—Inspired by natural evolutionary processes, Evolutionary Computation (EC) has established itself as a cornerstone of Artificial Intelligence. Recently, with the surge in data-intensive applications and large-scale complex systems, the demand for scalable EC solutions has grown significantly. However, most existing EC…
Alexander Lalejini, Emily Dolson, Anya E Vostinar, Luis Zaman + 2 more
'C Brandon Ogbunugafor' 'Christian R Landry'] Directed microbial evolution harnesses evolutionary processes in the laboratory to construct microorganisms with enhanced or novel functional traits. Attempting to direct evolutionary processes for applied goals is fundamental to evolutionary computation, which harnesses…
Rustam Eynaliyev, Huai Liu
Evolutionary computing (EC) has proven to be effective in solving complex optimization and robotics problems. Unfortunately, typical Evolutionary Algorithms (EAs) are constrained by the computational capacity available to researchers. More recently, GPUs have been extensively used in speeding up workloads across a…
Olga Speck, Thomas Speck, Sabine Baur, Michael Herdy + 3 more
'Laith Abualigah' 'Xuewen Xia'] With a focus on education and teaching, we provide general background information on bioinspired optimization methods by comparing the concept of optimization and the search for an optimum in engineering and biology. We introduce both the principles of Darwinian evolution and the basic…
Bowen Zhao, Wei‐Neng Chen, Xiaoguo Li, Ximeng Liu + 2 more
'Jun Zhang'] Abstract—Recently, evolutionary computation (EC) has been promoted by machine learning, distributed computing, and big data technologies, resulting in new research directions of EC like distributed EC and surrogate-assisted EC. These advances have significantly improved the performance and the application…
Lillian T. Tatka, Lucian P. Smith, Herbert M. Sauro
Evolutionary algorithms, a class of optimization techniques inspired by biological evolution, have emerged as powerful tools for the optimization of complex systems, including the evolution of mass-action chemical reaction networks. This work explores the application of evolutionary algorithms in this domain…
Licheng Jiao, Jiaxuan Zhao, Chao Wang, Xu Liu + 6 more
'Lingling Li' 'Ronghua Shang' 'Yangyang Li' 'Wenping Ma' 'Shuyuan Yang'] Nature, with its numerous surprising rules, serves as a rich source of creativity for the development of artificial intelligence, inspiring researchers to create several nature-inspired intelligent computing paradigms based on natural mechanisms.…
Paolo Pagliuca
The mutual relationship between evolution and learning is a controversial argument among the artificial intelligence and neuro-evolution communities. After more than three decades, there is still no common agreement on the matter. In this paper the author investigates whether combining learning and evolution permits to…
Y. Ma, Tan Chye Cheah
problem Authors: ['Y. Ma' 'Tan Chye Cheah'] This paper implements a new way of solving a problem called the traveling salesman problem (TSP) using quantum genetic algorithm (QGA). We compared how well this new approach works to the traditional method known as a classical genetic algorithm (CGA). The TSP is a…
Stefano Nolfi, Paolo Pagliuca
We investigate the use of competitive co-evolution for synthesizing progressively better solutions. Specifically, we introduce a set of methods to measure historical and global progress. We discuss the factors that facilitate genuine progress. Finally, we compare the efficacy of four qualitatively different algorithms.…
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…
Authors not listed
Designing molecules with specific target properties remains a fundamental challenge in computational chemistry. While existing approaches show promise, most rely on simplified representations like SMILES strings or 2D graphs that lack essential three-dimensional geometric information. We present EvoDiffMol, a…
Kangbien Park
Humans have long employed directed evolution (DE) to engineer desired biological traits. In this paper, I introduce an algebraic framework that provides a quantitative representation of the general phenotypic traits of asexual populations, enabling the systematic modeling of DE processes. Within this framework, key…
Ali Fozooni, Osman Kamari, Mostafa Pourtalebiyan, Masoud Gorgich + 2 more
'Mohammad Khalilzadeh' 'Amin Valizadeh'] In this study, we evaluate several nongradient (evolutionary) search strategies for minimizing mathematical function expressions. We developed and tested the genetic algorithms, particle swarm optimization, and differential evolution in order to assess their general efficacy in…
Daniel Gaissmaier, Matthias van den Borg, Donato Fantauzzi, Timo Jacob
In this work, we demonstrate the superior exploration capabilities of the population-based methods over the sequential one-parameter parabolic interpolation (SOPPI) approach to optimise ReaxFF force field parameters. Evolutionary algorithms (EAs) are heuristic-based approaches using a population of concurrent models in…
Sudhir Kumar
Molecular evolutionary analyses require computationally intensive steps such as aligning multiple sequences, optimizing substitution models, inferring evolutionary trees, testing phylogenies by bootstrap analysis, and estimating divergence times. With the rise of large genomic data sets, phylogenomics is imposing a big…
Andre KY Low, Flore Mekki-Berrada, Aleksandr Ostudin, Jiaxun Xie + 7 more
The development of automated high-throughput experimental platforms has enabled fast sampling of high-dimensional decision spaces. To reach target properties efficiently, these platforms are increasingly paired with intelligent experimental design. When solving optimization problems, Bayesian-based optimizers are often…
Authors not listed
Organic molecular crystals offer a broad spectrum of potential applications. The vast number of possible molecules is both an opportunity and a challenge, because of the prohibitive expense of exhaustively searching chemical space to find novel molecules with promising solid-state properties. Computational methods can…
Dariia Yehorova, Rory Crean, Peter Kasson, Shina Caroline Lynn Kamerlin
Protein structure (and thus function) is dictated by non-covalent interaction networks. These can be highly evolutionarily conserved across protein families, the members of which can diverge in sequence and evolutionary history. Here we present KIN, a tool to identify and analyze conserved non-covalent interaction…
Qi Zhang, Chang Liu, Stephen Wu, Ryo Yoshida
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods…