scESI: evolutionary sparse imputation for single-cell transcriptomes from nearest neighbor cells.

The ubiquitous dropout problem in single-cell RNA sequencing technology causes a large amount of data noise in the gene expression profile. For this reason, we propose an evolutionary sparse imputation (ESI) algorithm for single-cell transcriptomes, which constructs a sparse representation model based on gene regulation relationships between cells. To solve this model, we design an optimization framework based on nondominated sorting genetics. This framework takes into account the topological relationship between cells and the variety of gene expression to iteratively search the global optimal solution, thereby learning the Pareto optimal cell-cell affinity matrix. Finally, we use the learned sparse relationship model between cells to improve data quality and reduce data noise. In simulated datasets, scESI performed significantly better than benchmark methods with various metrics. By applying scESI to real scRNA-seq datasets, we discovered scESI can not only further classify the cell types and separate cells in visualization successfully but also improve the performance in reconstructing trajectories differentiation and identifying differentially expressed genes. In addition, scESI successfully recovered the expression trends of marker genes in stem cell differentiation and can discover new cell types and putative pathways regulating biological processes.

A decomposition-based multiobjective evolutionary algorithm using Simulated Annealing for the ambulance dispatching and relocation problem during COVID-19.

The outbreak of the COVID-19 epidemic has had a significant impact in increasing the number of emergency calls, which causes significant problems to emergency medical services centers (EMS) in many countries around the world, such as Saudi Arabia, which attracts a huge number of pilgrims during pilgrimage seasons. Among these issues, we address real-time ambulance dispatching and relocation problems (real-time ADRP). This paper proposes an improved MOEA/D algorithm using Simulated Annealing (G-MOEA/D-SA) to handle the real-time ADRP issue. The simulated annealing (SA) seeks to obtain optimal routes for ambulances to cover all emergency COVID-19 calls through the implementation of convergence indicator based dominance relation (CDR). To prevent the loss of good solutions once they are found in the G-MOEA/D-SA algorithm, we employ an external archive population to store the non-dominated solutions using the epsilon dominance relationship. Several experiments are conducted on real data collected from Saudi Arabia during the Covid-19 pandemic to compare our algorithm with three relevant state-of-art algorithms including MOEA/D, MOEA/D-M2M and NSGA-II. Statistical analysis of the comparative results obtained using ANOVA and Wilcoxon test demonstrate the merits and the outperformance of our G-MOEA/D-SA algorithm.

Computational design and analysis of modular cells for large libraries of exchangeable product synthesis modules.

Microbial metabolism can be harnessed to produce a large library of useful chemicals from renewable resources such as plant biomass. However, it is laborious and expensive to create microbial biocatalysts to produce each new product. To tackle this challenge, we have recently developed modular cell (ModCell) design principles that enable rapid generation of production strains by assembling a modular (chassis) cell with exchangeable production modules to achieve overproduction of target molecules. Previous computational ModCell design methods are limited to analyze small libraries of around 20 products. In this study, we developed a new computational method, named ModCell-HPC, that can design modular cells for large libraries with hundreds of products with a highly-parallel and multi-objective evolutionary algorithm and enable us to elucidate modular design properties. We demonstrated ModCell-HPC to design Escherichia coli modular cells towards a library of 161 endogenous production modules. From these simulations, we identified E. coli modular cells with few genetic manipulations that can produce dozens of molecules in a growth-coupled manner with different types of fermentable sugars. These designs revealed key genetic manipulations at the chassis and module levels to accomplish versatile modular cells, involving not only in the removal of major by-products but also modification of branch points in the central metabolism. We further found that the effect of various sugar degradation on redox metabolism results in lower compatibility between a modular cell and production modules for growth on pentoses than hexoses. To better characterize the degree of compatibility, we developed a method to calculate the minimal set cover, identifying that only three modular cells are all needed to couple with all compatible production modules. By determining the unknown compatibility contribution metric, we further elucidated the design features that allow an existing modular cell to be re-purposed towards production of new molecules. Overall, ModCell-HPC is a useful tool for understanding modularity of biological systems and guiding more efficient and generalizable design of modular cells that help reduce research and development cost in biocatalysis.

Simultaneous extraction of Cu2+ and Cd2+ ions in water, wastewater, and food samples using solvent-terminated dispersive liquid-liquid microextraction: optimization by multiobjective evolutionary algorithm based on decomposition.

Solvent-terminated dispersive liquid-liquid microextraction (ST-DLLME) as a simple, fast, and low-cost technique was developed for simultaneous extraction of Cd2+ and Cu2+ ions in aqueous solutions. Multiobjective evolutionary algorithm based on decomposition with the aid of artificial neural networks (ANN-MOEA/D) was used for the first time in chemistry, environment, and food sciences to optimize several independent variables affecting the extraction efficiency, including disperser volume and extraction solvent volume, pH, and salt addition. To perform the ST-DLLME operations, xylene, methanol, and dithizone were utilized as an extraction solvent, disperser solvent, and chelating agent, respectively. Non-dominated sorting genetic algorithm versions II and III (NSGA II and NSGA III) as multiobjective metaheuristic algorithms and in addition central composite design (CCD) were studied as comparable optimization methods. A comparison of results from these techniques revealed that ANN-MOEA/D model was the best optimization technique owing to its highest efficiency (97.6% for Cd2+ and 98.3% for Cu2+). Under optimal conditions obtained by ANN-MOEAD, the detection limit (S/N = 3), the quantitation limit(S/N = 10), and the linear range for Cu2+ were 0.05, 0.15, and 0.15-1000 µg L-1, respectively, and for Cd2+ were 0.07, 0.21, and 0.21-750 µg L-1, respectively. The real sample recoveries at a spiking level of 0.05, 0.1, and 0.3 mg L-1 of Cu2+ and Cd2+ ions under the optimal conditions obtained by ANN-MOEA/D ranged from 94.8 to 105%.

Prediction of Effective Lens Position Using Multiobjective Evolutionary Algorithm.

PURPOSE: The purpose of this study was to evaluate the prediction accuracy of effective lens position (ELP) after cataract surgery using a multiobjective evolutionary algorithm (MOEA). METHODS: Ninety-six eyes of 96 consecutive patients (aged 73.9 ± 8.6 years) who underwent cataract surgery were retrospectively studied; the eyes were randomly distributed to a prediction group (55 eyes) and a verification group (41 eyes). The procedure was repeated randomly 30 times to create 30 data sets for both groups. In the prediction group, based on the parameters of preoperative optical coherence tomography (OCT), biometry, and anterior segment (AS)-OCT, the prediction equation of ELP was created using MOEA and stepwise multiple regression analysis (SMR). Subsequently, the prediction accuracy of ELPs was evaluated and compared with conventional formulas, including SRK/T and the Haigis formula. RESULTS: The rate of mean absolute prediction error of 0.3 mm or higher was significantly lower in MOEA (mean 4.9% ± 3.2%, maximum 9.8%) than SMR (mean 7.3% ± 4.8%, maximum 24.4%) (P = 0.0323). The median of the correlation coefficient (R 2 = 0.771) between the MOEA predicted and measured ELP was higher than the SRK/T (R 2 = 0.412) and Haigis (R 2 = 0.438) formulas. CONCLUSIONS: The study demonstrated that ELP prediction by MOEA was more accurate and was a method of less fluctuation than that of SMR and conventional formulas. TRANSLATIONAL RELEVANCE: MOEA is a promising method for solving clinical problems such as prediction of ocular biometry values by simultaneously optimizing several conditions for subjects affected by various complex factors.