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When it comes to solving optimization problems with evolutionary algorithms (EAs) in a reliable and scalable manner, detecting and exploiting linkage information, that is, dependencies between variables, can be key. In this paper, we present the latest version of, and propose substantial enhancements to, the gene-pool optimal mixing evolutionary algorithm (GOMEA): an EA explicitly designed to estimate and exploit linkage information. We begin by performing a large-scale search over several GOMEA design choices to understand what matters most and obtain a generally best-performing version of the algorithm. Next, we introduce a novel version of GOMEA, called CGOMEA, where linkage-based variation is further improved by filtering solution mating based on conditional dependencies. We compare our latest version of GOMEA, the newly introduced CGOMEA, and another contending linkage-aware EA, DSMGA-II, in an extensive experimental evaluation, involving a benchmark set of nine black-box problems that can be solved efficiently only if their inherent dependency structure is unveiled and exploited. Finally, in an attempt to make EAs more usable and resilient to parameter choices, we investigate the performance of different automatic population management schemes for GOMEA and CGOMEA, de facto making the EAs parameterless. Our results show that GOMEA and CGOMEA significantly outperform the original GOMEA and DSMGA-II on most problems, setting a new state of the art for the field.
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http://dx.doi.org/10.1162/evco_a_00338 | DOI Listing |
Water Res
August 2025
College of Environment and Ecology, Chongqing University, Chongqing 400045, China; Key Laboratory of the Three Gorges Reservoir Region's Eco-Environment, Ministry of Education, College of Environment and Ecology, Chongqing University, Chongqing, 400045, China. Electronic address:
This study explores the role of α-Fe₂O₃ in improving extracellular electron transfer (EET) and symbiotic interactions between electroactive Shewanella oneidensis MR-1, its gene-deficient mutants (ΔmtrC, ΔomcA, and ΔcymA), and microalgae (Chlorella vulgaris). The iron oxide facilitates the efficient transfer of electrons generated by MR-1 to microalgal photosystem via the pathway of CymA-MtrC-OmcA to α-Fe₂O₃. This process enhances the removals of TOC, TN, and NH₄⁺-N in the MR-1 bacterial-algal consortium by 9.
View Article and Find Full Text PDFPLoS Pathog
September 2025
Department of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, India.
Host-derived short-chain fatty acids (SCFAs) are essential for Salmonella Typhimurium (STM) virulence. Formate, an SCFA found in the ileum, enhances STM invasion, but the role of the intracellular formate pool in STM pathogenesis remains poorly understood. Deletion of the pflB gene, which encodes pyruvate-formate lyase, depletes this intracellular pool, leading to reduced flagellation and increased expression of pathogenicity island-1 genes (hilA and prgH).
View Article and Find Full Text PDFJ Chromatogr A
October 2025
Tosoh Bioscience LLC, 3604 Horizon Drive, King of Prussia, PA 19406, USA. Electronic address:
Recombinant adeno-associated virus (AAV) vectors have emerged as powerful gene delivery tools for the treatment of genetic disorders. However, the production of high-quality AAV vectors still poses significant challenges. In upstream manufacturing, AAV genome packaging typically results in a diverse pool of empty and partially filled capsids, as well as the desired functional virions.
View Article and Find Full Text PDFJ Mol Model
August 2025
Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126, Pisa, Italy.
Context: hRPE65 is an essential enzyme in the retinoid visual cycle. Numerous missense variants of hRPE65 have been linked to retinal disorders, such as retinitis pigmentosa and Leber congenital amaurosis. Moreover, many hRPE65 missense mutations are currently classified as variants of uncertain significance (VUS) due to insufficient evidence for a definitive pathogenicity classification.
View Article and Find Full Text PDFMethods Mol Biol
August 2025
Neurogenetics Group, University of Leicester, Leicester, UK.
Single-cell RNA-sequencing revolutionized our approach of transcriptomic studies, enabling to analyze gene expression across cell type in a tissue. Here we introduce an optimized cell dissociation and a Split Pool Ligation-based Transcriptome sequencing (SPLiT-seq) protocol to perform single-cell RNA-seq in insects. Up to 400,000 cells can be used as starting material within a single experiment.
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