10 papers · ranked by Valyu relevance
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…
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…
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.…
Kangbien Park
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 the experimental methodologies—or logics—that can address potential challenges throughout the evolutionary process. In this article, I…
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…
Juliette Luiselli, David P. Parsons, Romain Gallé, Paul Banse + 2 more
Aevol is a forward-in-time simulator of genome architecture. It simulates a population of individuals, each with an explicit genome whose sequence and architecture can be modified by various mutational operators, including substitutions, indels, and large-scale chromosomal rearrangements. This enables performing in…
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…
Vladimir Nikolić, Moriah Echlin, Boris Aguilar, Ilya Shmulevich
The capacity of cells to process information is currently used to design cell-based tools for ecological, industrial, and biomedical applications such as detecting dangerous chemicals or for bioremediation. In most applications, individual cells are used as the information processing unit. However, single cell…
Laura E. Suárez, Agoston Mihalik, Filip Milisav, Kenji Marshall + 4 more
The connection patterns of neural circuits form a complex network. How signaling in these circuits manifests as complex cognition and adaptive behaviour remains the central question in neuroscience. Concomitant advances in connectomics and artificial intelligence open fundamentally new opportunities to understand how…
Hongwei Cai, Zheng Ao, Chunhui Tian, Zhuhao Wu + 5 more
Brain-inspired hardware emulates the structure and working principles of a biological brain and may address the hardware bottleneck for fast-growing artificial intelligence (AI). Current brain-inspired silicon chips are promising but still limit their power to fully mimic brain function for AI computing. Here, we…