26 papers · ranked by Valyu relevance
Zhimeng Zhou, Yang Nan, Minjie Mou, Yuntao Qian + 16 more
Artificial intelligence (AI) is increasingly permeating the drug development pipeline. Numerous algorithms for accelerating this multi-stage and multi-task process have been constructed, which depends heavily on expert design and labor-intensive task-specific optimization. Given that AI-driven acceleration of drug…
Gang Liu, Yihan Zhu, Jie Chen, Meng Jiang
Large language models hold promise as scientific assistants, yet existing agents either rely solely on algorithm evolution or on deep research in isolation, both of which face critical limitations. Pure algorithm evolution, as in AlphaEvolve, depends only on the internal knowledge of LLMs and quickly plateaus in…
Anja Surina, Amin Mansouri, Lars Quaedvlieg, Amal Seddas + 3 more
'Maryna Viazovska' 'Emmanuel Abbe' 'Caglar Gulcehre'] Discovering efficient algorithms for solving complex problems has been an outstanding challenge in mathematics and computer science, requiring substantial human expertise over the years. Recent advancements in evolutionary search with large language models (LLMs)…
Kaichen Ouyang, Yu, Mingyang, Ke + 11 more
This paper introduces a novel framework linking evolutionary computation to statistical physics by formulating optimization as a statistical phase transition. We propose Wasserstein Evolution (WE), an algorithm based on the Wasserstein gradient flow of a free energy functional, translating the physical competition…
Alexander Novikov, Nhat Vu, Eisenberger, Marvin + 15 more
Alexander Novikov \ , Ngân Vu˜ \ , Marvin Eisenberger \ , Emilien Dupont \ , Po-Sen Huang \ , Adam Zsolt Wagner \ , Sergey Shirobokov \ , Borislav Kozlovskii \ , Francisco J. R. Ruiz, Abbas Mehrabian, M. Pawan Kumar, Abigail See, Swarat Chaudhuri, George Holland, Alex Davies, Sebastian Nowozin, Pushmeet Kohli and Matej…
Minghao Yan, Bo Peng, Benjamin Coleman, Ziqi Chen + 10 more
Large language models have become drivers of evolutionary search, but most systems rely on a fixed, prompt-elicited policy to sample next candidates. This limits adaptation in practical engineering and research tasks, where evaluations are expensive, and progress depends on learning task-specific search dynamics. We…
Franz Kuchling, Chris Fields, Michael Levin, Ryota Kanai + 2 more
'Pablo A. Morales' 'Fernando E. Rosas'] Evolution is full of coevolving systems characterized by complex spatio-temporal interactions that lead to intertwined processes of adaptation. Yet, how adaptation across multiple levels of temporal scales and biological complexity is achieved remains unclear. Here, we formalize…
Iztok Fister, Iztok Fister
The main deficiency of the algorithms running on digital computers nowadays is their inability to change themselves during the execution. In line with this, the paper introduces the so-called replicated algorithms, inspired by the concept of developing a human brain. Similar to the human brain, where the process of…
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…
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.…
Inès Benito, Johannes F. Lutzeyer, Benjamin Doerr
Baldwinian and Lamarckian evolution have existed for a long time in evolutionary algorithms (EAs) without ever dominating the academic literature or practical applications. In this work, we use modern empirical and theoretical methods to revisit Lamarckian and Baldwinian evolution and rigorously compare them with the…
Prasad U. Bandodkar, Razeen R. Shaikh, Gregory T. Reeves
Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a…
Sizhe Yuen, Thomas H. G. Ezard, Adam J. Sobey
Evolutionary computation is a group of biologically inspired algorithms used to solve complex optimization problems. It can be split into evolutionary algorithms, which take inspiration from genetic inheritance, and swarm intelligence algorithms, that take inspiration from cultural inheritance. However, much of the…
Bilal Khurshid, Shahid Maqsood, Muhammad Salman Habib, Muhammad Omair + 1 more
'Muhammad Omair' 'Seung-June Hwang'] Flow shop scheduling has garnered significant attention from researchers over the past ten years, establishing itself as a prominent area of study within the field of scheduling. Nevertheless, there exists a paucity of research dedicated to addressing Non-Permutation Flow Shop…
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…
Innocent Sibanda, Geoff Nitschke
The goal of bioengineering in synthetic biology is to redesign, reprogram, and rewire biological systems for specific applications using standardized parts such as promoters and ribosomes. For example, bioengineered micro-organisms capable of cleaning up environmental pollution or producing antibodies de novo to defend…
Authors not listed
Finding the most stable adsorption geometry of a flexible molecule on a catalytic surface remains a key challenge due to the high dimensionality and ruggedness of the potential energy surface. We present a Gradient-Enhanced Genetic Algorithm (GE-GA) for the global optimization of adsorbate–surface configurations…
Michael Tetteh, Douglas Mota Dias, Conor Ryan
The evolution of complex circuits remains a challenge for the Evolvable Hardware field in spite much effort. There are two major issues: the amount of testing required and the low evolvability of representation structures to handle complex circuitry, at least partially due to the destructive effects of genetic…
Alexander O. Gusev, Leonid M. Martyushev, Robert Niven, Hisashi Ozawa
'Hisashi Ozawa'] The simplest evolutionary model for catching prey by an agent (predator) is considered. The simulation is performed on the basis of a software-emulated Intel i8080 processor. Maximizing the number of catches is chosen as the objective function. This function is associated with energy dissipation and…
Steven A. Frank, Antonio M. Scarfone
Diverse learning algorithms, optimization methods, and natural selection share a common mathematical structure despite their apparent differences. Here, I show that a simple notational partitioning of change by the Price equation reveals a universal force-metric-bias (FMB) law: $Δθ=(Mf+b+ξ)$. The force $f$ drives…
Authors not listed
Fluoride-ion batteries (FIBs) present a promising alternative to lithium-ion technologies, offering superior theoretical energy densities and improved sustainability. However, fluoride's high reactivity rapidly degrades traditional organic solvents via nucleophilic attack, limiting practical use. Here, we…
Authors not listed
Strong coupling and environmental memory render many open quantum systems intractable to classical computation. To overcome this barrier, we present a variational quantum algorithm capable of solving generalized form time-local quantum master equations directly on Noisy Intermediate-Scale Quantum (NISQ) processors. Our…
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
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
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
Machine olfaction—the artificial replication of the sense of smell—faces significant challenges due to the absence of large, standardized training datasets. Unlike vision, language, and audio models, which benefit from extensive corpora such as ImageNet, GLUE, and AudioSet, olfaction lacks scaled equivalents and…