24 papers · ranked by Valyu relevance
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…
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…
Csenge Petak, Lapo Frati, Renske M. A. Vroomans, Melissa H. Pespeni + 1 more
Title: Significance The speed and direction of evolution depend on the availability of phenotypic variation. Genotype-to-phenotype maps can, over time, bias phenotypic variability to more readily produce alternative adaptive phenotypes in fluctuating environments. However, because properties of the fitness landscapes…
Léo Pio‐Lopez, Benedikt Hartl, Michael Levin
Although substantial advancements are made in manipulating lifespan in model organisms, the fundamental mechanisms driving aging remain elusive. No comprehensive computational platform is capable of making predictions on aging in multicellular systems. Focus is placed on the processes that build and maintain complex…
Matthew Aquilina, Florian Katzmeier, Minke A.D. Nijenhuis, Siyuan Stella Wang + 8 more
Crisscross polymerization enables the assembly of hundreds of unique DNA origami ‘slats’ into micron-sized structures with nanoscale precision. To design these megastructures, thousands of handle sequences from a fixed library must be assigned to individual slats to encode the desired binding architecture. This…
Alireza Rezaee
This paper presents a genetic algorithm (GA) approach to cost-optimal task scheduling in a production line. The system consists of a set of serial processing tasks, each with a given duration, unit execution cost, and precedence constraints, which must be assigned to an unlimited number of stations subject to a…
Mohamed Issa
The effective tuning of Proportional-Integral-Derivative (PID) controllers is crucial for industrial process control, but achieving optimal parameters for complex systems remains challenging. The recent Artificial Satellite Search Algorithm (ASSA) is strong in exploration but suffers from an imbalance between global…
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…
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
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…
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…
João Sartori, Eduardo Krempser, Ana Carolina Ramos Guimarães, Lucas de Almeida Machado
The optimization of protein sequences for enhanced binding and stability remains a formidable challenge in bioengineering due to the vastness of sequence space. Existing state-of-the-art methods, including traditional structure-based design and protein language models, use fitness estimators as objective functions to…
Stephan Lukasczyk, Gordon Fraser
Search-based test-generation algorithms have countless configuration options. Users rarely adjust these options and usually stick to the default values, which may not lead to the best possible results. Tuning an algorithm's hyperparameters is a method to find better hyperparameter values, but it typically comes with a…
Maxim Sakharov, Heming Jia
Memetic algorithms achieve strong optimization performance by combining population-based global search with local refinement operators, yet their effectiveness critically depends on the design and management of memes. Local search strategies are typically handcrafted, problem-specific, and fixed prior to execution.…
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…
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…
Dhananjai VS, Sathi Sailesh Reddy, K Abhimanyu Kumar Patro, Soumya Ranjan Das
The planning of future sixth-generation (6G) wireless networks needs efficient node placement algorithms that can handle heterogeneous network deployment, high connectivity density, and competing performance requirements. Current node placement algorithms mostly use single-layer graph models and traditional…
Authors not listed
Compositionally complex materials, e.g. high-entropy alloys/oxides, have long been of research interest for their unique mechanical and functional properties thanks to the synergistic effects between the large number of components. More recently, they have emerged as a promising platform for the development of novel…
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…
Vaibhav Mohanty, Anna Sappington, Eugene I. Shakhnovich, Bonnie Berger
Classical population genetics has largely relied on the same stochastic differential equations (SDEs) for over 60 years to describe evolutionary dynamics. However, these SDEs ignore the fact that phenotype heterogeneity and noise are ubiquitous in biological systems from bacteria to cancers. Here, we develop…
Jiayi Zhang, Yongfeng Gu, Jianhao Ruan, Maojia Song + 9 more
Agentic evolution has emerged as a powerful paradigm for improving programs, workflows, and scientific solutions by iteratively generating candidates, evaluating them, and using feedback to guide future search. However, existing methods are typically instantiated either as fixed hand-designed procedures that are…
Authors not listed
Molecular generation for pharmaceutical and agrochemical development remains computationally expensive and statistically under-validated. We conducted a comprehensive benchmark of five molecular generation methods—Genetic Algorithm, Proximal Policy Optimization (PPO), REINFORCE, Transformer-based generation, and random…
Kangbien Park, Jiapeng Liu
Directed evolution of asexual populations is expected to offer a wide range of benefits to humanity. Achieving efficient directed evolution (DE) requires a quantitative formulation of experimental methodologies-or logics-that can address potential challenges throughout the evolutionary process. In this article, ten…
Zeki Doruk Erden
Sexual selection is among the most pervasive and costly features of biological reproduction, reaching its greatest elaboration in lineages of greater complexity and capability—costs that signal a structural function not adequately accounted for by only the existing explanations focused on immediate adaptive benefits. I…