Mutation Probability Research Articles

A Novel Production Scheduling Approach Based on Improved Hybrid Genetic Algorithm

Due to the complexity of the production shop in discrete manufacturing industry, the traditional genetic algorithm (GA) cannot solve the production scheduling problem well. In order to enhance the GA-based method to solve the production scheduling problem effectively, the simulated annealing algorithm (SAA) is used to develop an improved hybrid genetic algorithm. Firstly, the crossover probability and mutation probability of the genetic operation are adjusted, and the elite replacement operation is adopted for simulated annealing operator. Then, a mutation method is used for the comparison and replacement of the genetic operations to obtain the optimal value of the current state. Lastly, the proposed hybrid genetic algorithm is compared with several scheduling algorithms, and the superiority and efficiency of the proposed method are verified in solving the production scheduling.

An optimized solution to the course scheduling problem in universities under an improved genetic algorithm

Abstract The increase in the size of universities has greatly increased the number of teachers, students, and courses and has also increased the difficulty of scheduling courses. This study used coevolution to improve the genetic algorithm and applied it to solve the course scheduling problem in universities. Finally, simulation experiments were conducted on the traditional and improved genetic algorithms in MATLAB software. The results showed that the improved genetic algorithm converged faster and produced better solutions than the traditional genetic algorithm under the same crossover and mutation probability. As the mutation probability in the algorithm increased, the fitness values of both genetic algorithms gradually decreased, and the computation time increased. With the increase in crossover probability in the algorithm, the fitness value of the two genetic algorithms increased first and then decreased, and the computational time decreased first and then increased.

A scheduling route planning algorithm based on the dynamic genetic algorithm with ant colony binary iterative optimization for unmanned aerial vehicle spraying in multiple tea fields.

The complex environments and weak infrastructure constructions of hilly mountainous areas complicate the effective path planning for plant protection operations. Therefore, with the aim of improving the current status of complicated tea plant protections in hills and slopes, an unmanned aerial vehicle (UAV) multi-tea field plant protection route planning algorithm is developed in this paper and integrated with a full-coverage spraying route method for a single region. By optimizing the crossover and mutation operators of the genetic algorithm (GA), the crossover and mutation probabilities are automatically adjusted with the individual fitness and a dynamic genetic algorithm (DGA) is proposed. The iteration period and reinforcement concepts are then introduced in the pheromone update rule of the ant colony optimization (ACO) to improve the convergence accuracy and global optimization capability, and an ant colony binary iteration optimization (ACBIO) is proposed. Serial fusion is subsequently employed on the two algorithms to optimize the route planning for multi-regional operations. Simulation tests reveal that the dynamic genetic algorithm with ant colony binary iterative optimization (DGA-ACBIO) proposed in this study shortens the optimal flight range by 715.8 m, 428.3 m, 589 m, and 287.6 m compared to the dynamic genetic algorithm, ant colony binary iterative algorithm, artificial fish swarm algorithm (AFSA) and particle swarm optimization (PSO), respectively, for multiple tea field scheduling route planning. Moreover, the search time is reduced by more than half compared to other bionic algorithms. The proposed algorithm maintains advantages in performance and stability when solving standard traveling salesman problems with more complex objectives, as well as the planning accuracy and search speed. In this paper, the research on the planning algorithm of plant protection route for multi-tea field scheduling helps to shorten the inter-regional scheduling range and thus reduces the cost of plant protection.

RESISTOR: A New OSPREY Module to Predict Resistance Mutations.

Computational, in silico prediction of resistance-conferring escape mutations could accelerate the design of therapeutics less prone to resistance. This article describes how to use the Resistor algorithm to predict escape mutations. Resistor employs Pareto optimization on four resistance-conferring criteria-positive and negative design, mutational probability, and hotspot cardinality-to assign a Pareto rank to each prospective mutant. It also predicts the mechanism of resistance, that is, whether a mutant ablates binding to a drug, strengthens binding to the endogenous ligand, or a combination of these two factors, and provides structural models of the mutants. Resistor is part of the free and open-source computational protein design software OSPREY.

Clinical application of comprehensive genomic profiling panel to thoracic malignancies: A single-center retrospective study.

The usefulness of comprehensive genomic profiling (CGP) panels for thoracic malignancies after completion of the standard treatment is unclear. The results of CGP panels for malignant thoracic diseases performed at our hospital between December 2019 and June 2022 were collected. We examined whether CGP panel results led to new treatment, correlated with the effectiveness of immune checkpoint inhibitors (ICIs), or revealed secondary findings related to hereditary tumors. A total of 60 patients were enrolled, of which 52 (86.6%) had lung cancer. In six (10%) patients, the panel results led to treatment with insurance-listed molecular-targeted agents; four patients had EGFR mutations not detected by the real-time polymerase chain reaction assay and two had MET ex.14 skipping mutations. In small-cell lung cancer, the tumor mutation burden was high in 4/6 (66.7%) patients and pembrolizumab was available. Another MET ex.14 skipping mutation was detected in two cases with EGFR-tyrosine kinase inhibitor resistance. ICI efficacy was ≤1year in patients with STK-11, KEAP1, and NEF2L2 mutations. A BRCA2 mutation with a high probability of germline mutation was detected in one patient. A thymic carcinoma with no detectable oncogenic mutation responded to second-line treatment with Tegafur-Gimeracil-Oteracil Potassium (TS-1) for ≥9 years. CGP panels are useful in thoracic malignancies, especially lung cancer, because they can detect overlooked driver mutations and genetic alterations. We believe that the significance of conducting a CGP panel prior to treatment may also exist, as it may lead to the prediction of ICI treatment efficacy.

Comparative evaluation of the performance of improved genetic algorithms and differential evolution for in-core fuel management of a research reactor

This paper presents a comparative evaluation of the performance of Genetic Algorithm (GA) and Differential Evolution (DE) algorithm applied to in-core fuel management of the DNRR research reactor. Two GA variants corresponding to two selection operators, i.e., tournament (GA1) and roulette wheel (GA2) selections, respectively, with two-point crossover and scramble mutation were implemented for the ICFM problem. A comprehensive survey of the GA control parameters such as population size, crossover-type, mutation probability, and elitist archive size has been conducted to optimize the performance of the GAs. The basic DE was implemented with a standard mutation strategy DE/rand/1/bin. Numerical computations were performed based on the DNRR research reactor core loaded with 100 highly enriched uranium fuel (HEU) bundles for evaluating the performance of the GA and DE algorithms. Two main objectives were included in the fitness function to maximize the fuel cycle length and flatten the power distribution. The performance of the two GA variants and the basic DE was investigated with the same population size, fitness function, and convergence criterion. Each method was performed with 50 independent runs, and the best fitness values were collected for statistical analysis using Kruskal–Wallis and Mann–Whitney tests in comparison among the three methods. The statistical analysis shows that the performance of GA1 with tournament selection and DE are not significantly different and are better than GA2 with roulette wheel selection. DE is stable and efficient in exploring the search space to approach the global optimal solution in most runs. While, GA1 and GA2 were trapped at local optima by about 26% and 38%, respectively. However, the best solutions obtained with GA1 and GA2 after 50 independent runs are better than that obtained with DE in term of fitness values. This suggests an improvement of the basic DE is needed to maintain the potential good solutions during the evolution process.

Non-genetic resistance facilitates survival while hindering the evolution of drug resistance due to intraspecific competition

Rising rates of resistance to antimicrobial drugs threaten the effective treatment of infections across the globe. Drug resistance has been established to emerge from non-genetic mechanisms as well as from genetic mechanisms. However, it is still unclear how non-genetic resistance affects the evolution of genetic drug resistance. We develop deterministic and stochastic population models that incorporate resource competition to quantitatively investigate the transition from non-genetic to genetic resistance during the exposure to static and cidal drugs. We find that non-genetic resistance facilitates the survival of cell populations during drug treatment while hindering the development of genetic resistance due to competition between the non-genetically and genetically resistant subpopulations. Non-genetic resistance in the presence of subpopulation competition increases the fixation times of drug resistance mutations, while increasing the probability of mutation before population extinction during cidal drug treatment. Intense intraspecific competition during drug treatment leads to extinction of susceptible and non-genetically resistant subpopulations. Alternating between drug and no drug conditions results in oscillatory population dynamics, increased resistance mutation fixation timescales, and reduced population survival. These findings advance our fundamental understanding of the evolution of resistance and may guide novel treatment strategies for patients with drug-resistant infections.

Suppressors of fixation can increase average fitness beyond amplifiers of selection

Evolutionary dynamics on graphs has remarkable features: For example, it has been shown that amplifiers of selection exist that-compared to an unstructured population-increase the fixation probability of advantageous mutations, while they decrease the fixation probability of disadvantageous mutations. So far, the theoretical literature has focused on the case of a single mutant entering a graph-structured population, asking how the graph affects the probability that a mutant takes over a population and the time until this typically happens. For continuously evolving systems, the more relevant case is that mutants constantly arise in an evolving population. Typically, such mutations occur with a small probability during reproduction events. We thus focus on the low mutation rate limit. The probability distribution for the fitness in this process converges to a steady state at long times. Intuitively, amplifiers of selection are expected to increase the population's mean fitness in the steady state. Similarly, suppressors of selection are expected to decrease the population's mean fitness in the steady state. However, we show that another set of graphs, called suppressors of fixation, can attain the highest population mean fitness. The key reason behind this is their ability to efficiently reject deleterious mutants. This illustrates the importance of the deleterious mutant regime for the long-term evolutionary dynamics, something that seems to have been overlooked in the literature so far.

A Variant Genetic Algorithm for a Specific Examination Timetabling Problem in a Japanese University

Background: Examination Timetabling Problem which tries to find an optimal examination schedule for schools, colleges, and universities, is a well-known NP-hard problem. This paper presents a Genetic Algorithm variant approach to solve a specific examination timetabling problem common in Japanese colleges and universities. Methods: The proposed algorithm uses direct chromosome representation Genetic Algorithm and implements constraint-based initialization and constraint-based crossover operations to satisfy the hard and soft constraints. An Island model with varying crossover and mutation probabilities and an improvement approach called pre-training are applied to the algorithm to further improve the result quality. Results: The proposed model is tested on synthetic as well as real datasets obtained from Sophia University, Japan and shows acceptable results. The algorithm was fine-tuned with different penalty points combinations and improvement combinations. Conclusion: The comparison results support the idea that the initial population pre-training and the island model are effective approaches to improve the result quality of the proposed model. Although the current island model used only four islands, incorporating greater number of islands, and some other diversity maintenance approaches such as memetic structures are expected to further improve the diversity and the result quality of the proposed algorithm on large scale problems.

Interactive genetic color matching design of cultural and creative products considering color image and visual aesthetics

To optimize the colors used in cultural and creative products, this paper proposes a color matching design method that considers the color image and visual aesthetics. First, 99 color samples are identified based on Chinese traditional colors, and user preferences for 30 image semantic terms are measured by the semantic differential method. This leads to six color image factors being extracted by factor analysis. Second, quantitative analysis of the color visual aesthetics is applied, and formulas for calculating the harmony, balance, and symmetry are derived. On this basis, an interactive genetic algorithm is developed to promote and optimize the color scheme of cultural and creative products, and a fitness function based on subjective image evaluation and objective visual aesthetics is constructed. The subjective image evaluation adopts interval numbers, and a grayscale approach is used to measure the uncertainty of the subjective evaluation. Through grayscale analysis of the interval fitness values, information reflecting the evolutionary distribution of the population is extracted, before adaptive crossover and mutation probabilities are applied to the evolutionary individuals. Finally, the proposed method is verified through the example of color matching design for a speaker box. The results demonstrate that the proposed approach can effectively assist industrial designers.

Application of LSTM model optimized by individual-ordering-based adaptive genetic algorithm in stock forecasting

PurposeTo improve the accuracy of stock price trend prediction in the field of quantitative financial trading, this paper takes the prediction accuracy as the goal and avoid the enormous number of network structures and hyperparameter adjustments of long-short-term memory (LSTM).Design/methodology/approachIn this paper, an adaptive genetic algorithm based on individual ordering is used to optimize the network structure and hyperparameters of the LSTM neural network automatically.FindingsThe simulation results show that the accuracy of the rise and fall of the stock outperform than the model with LSTM only as well as other machine learning models. Furthermore, the efficiency of parameter adjustment is greatly higher than other hyperparameter optimization methods.Originality/value(1) The AGA-LSTM algorithm is used to input various hyperparameter combinations into genetic algorithm to find the best hyperparameter combination. Compared with other models, it has higher accuracy in predicting the up and down trend of stock prices in the next day. (2) Adopting real coding, elitist preservation and self-adaptive adjustment of crossover and mutation probability based on individual ordering in the part of genetic algorithm, the algorithm is computationally efficient and the results are more likely to converge to the global optimum.

An Improved Arithmetic Optimization Algorithm and Its Application to Determine the Parameters of Support Vector Machine

The arithmetic optimization algorithm (AOA) is a new metaheuristic algorithm inspired by arithmetic operators (addition, subtraction, multiplication, and division) to solve arithmetic problems. The algorithm is characterized by simple principles, fewer parameter settings, and easy implementation, and has been widely used in many fields. However, similar to other meta-heuristic algorithms, AOA suffers from shortcomings, such as slow convergence speed and an easy ability to fall into local optimum. To address the shortcomings of AOA, an improved arithmetic optimization algorithm (IAOA) is proposed. First, dynamic inertia weights are used to improve the algorithm’s exploration and exploitation ability and speed up the algorithm’s convergence speed; second, dynamic mutation probability coefficients and the triangular mutation strategy are introduced to improve the algorithm’s ability to avoid local optimum. In order to verify the effectiveness and practicality of the algorithm in this paper, six benchmark test functions are selected for the optimization search test verification to verify the optimization search ability of IAOA; then, IAOA is used for the parameter optimization of support vector machines to verify the practical ability of IAOA. The experimental results show that IAOA has a strong global search capability, and the optimization-seeking capability is significantly improved, and it shows excellent performance in support vector machine parameter optimization.

Effectiveness of Network Classroom Teaching Based on Genetic Algorithm

In online classroom teaching, the function of teaching system can play an important role in the effectiveness of classroom teaching. How to use genetic algorithm to optimize online classroom teaching system has become a research hotspot. Based on genetic algorithm, this paper proposes an adaptive genetic algorithm model based on the traditional algorithm. After setting the appropriate mutation probability, the model can improve the convergence speed. Moreover, based on adaptive genetic algorithm, combined with the direct value method and BT neural network theory, this paper constructs the online classroom teaching quality evaluation model and the teaching system test paper data model, and optimizes adaptive mutation genetic algorithm and BP neural network to evaluate the teaching effectiveness. Simulation experiments are carried out based on the algorithm model, and the visual parameter values are obtained. After experimental comparison, the initial value of the mutation rate is set between 0.002 and 0.004. For the network classroom teaching system, this paper introduces the system demand analysis, function module design, and database design in detail. Finally, through the questionnaire survey, this paper understands the network situation of students in class and the use of online classroom teaching platform in detail, analyzes the problems and influencing factors of online teaching, and finally puts forward the strategies to improve the effectiveness of online classroom teaching.

Cancer risk assessment models versus National Comprehensive Cancer Network guidelines: What is the most comprehensive method to assess cancer risk and triage for genetic testing? (373)

Cancer risk assessment models versus National Comprehensive Cancer Network guidelines: What is the most comprehensive method to assess cancer risk and triage for genetic testing? (373)

Pervasive conditional selection of driver mutations and modular epistasis networks in cancer.

Cancer driver mutations often display mutual exclusion or co-occurrence, underscoring the key role of epistasis in carcinogenesis. However, estimating the magnitude of epistasis and quantifying its effect on tumor evolution remains a challenge. We develop a method (Coselens) to quantify conditional selection on the excess of nonsynonymous substitutions in cancer genes. Coselens infers the number of drivers per gene in different partitions of a cancer genomics dataset using covariance-based mutation models and determines whether coding mutations in a gene affect selection for drivers in any other gene. Using Coselens, we identify 296 conditionally selected gene pairs across 16 cancer types in the TCGA dataset. Conditional selection affects 25%-50% of driver substitutions in tumors with >2 drivers. Conditionally co-selected genes form modular networks, whose structures challenge the traditional interpretation of within-pathway mutual exclusivity and across-pathway synergy, suggesting a more complex scenario where gene-specific across-pathway epistasis shapes differentiated cancer subtypes.

Prediction of Rapid Chloride Penetration Resistance of Metakaolin Based Concrete Using Multi-Expression Programming

This study investigates the resistance of concrete to Rapid Chloride ions Penetration (RCP) as an indirect measure of the concrete’s durability. The RCP resistance of concrete is modelled in multi-expression programming approach using different input variables, such as, age of concrete, amount of binder, fine aggregate, coarse aggregate, water to binder ratio, metakaolin content and the compressive strength (CS) of concrete. The parametric investigation was carried out by varying the hyperparameters, i.e., number of subpopulations Nsub, subpopulation size Ssize, crossover probability Cprob, mutation probability Mprob, tournament size Tsize, code length Cleng, and number of generations Ngener to get an optimum model. The performance of all the 29 number of trained models were assessed by comparing mean absolute error (MAE) values. The optimum model was obtained for Nsub = 50, Ssize = 100, Cprob = 0.9, Mprob = 0.01, Tsize = 9, Cleng = 100, and Ngener = 300 with MAE of 279.17 in case of training (TR) phase, whereas 301.66 for testing (TS) phase. The regression slope analysis revealed that the predicted values are in good agreement with the experimental values, as evident from their higher R and R2 values equaling 0.96 and 0.93 (for the TR phase), and 0.92 and 0.90 (for the TS phase), respectively. Similarly, parametric and sensitivity analyses revealed that the RCP resistance is governed by the age of concrete, amount of binder, concrete CS, and aggregate quantity in the concrete mix. Among all the input variables, the RCP resistance sharply increased within the first 28 days age of the concrete specimen and similarly plummeted with increasing the quantity of fine aggregate, thus validating the model results.

Product Shape Design Scheme Evaluation Method Based on Spatial Data Mining

The stage of product modeling design implies a lot of complex tacit knowledge, which is the embodiment of the design concept centered on product modeling design and is also the hot spot and difficulty of modern design theory and method research. Aiming at the evaluation and decision of product modeling design scheme, a decision-making method of approaching ideal solution ranking based on grey relational analysis was proposed, which realized the convergence of tacit knowledge. The empty association rule is an important knowledge content of spatial data mining. A fuzzy genetic algorithm can solve the characteristics of random and nonlinear problems and solve the data mining problems of spatial association rules. The fuzzy genetic algorithm of discrete crossover probability and mutation probability is applied to data mining of spatial association rules in a spatial database, the coding method of the fuzzy genetic algorithm and the construction of fitness function are discussed, and the process of mining spatial association rules is given. The results show that the method of mining s association rules with the fuzzy genetic algorithm is feasible and has higher mining efficiency. This paper discusses the construction method of designing a decision support database based on linear regression and neural network and then proposes a decision method combining TOPSIS and grey relational analysis, which comprehensively considers the position and shape of the scheme data curve.

Integration of artificial intelligence and plasma steroidomics with laboratory information management systems: application to primary aldosteronism.

Mass spectrometry-based steroidomics combined with machine learning (ML) provides a potentially powerful approach in endocrine diagnostics, but is hampered by limitations in the conveyance of results and interpretations to clinicians. We address this shortcoming by integration of the two technologies with a laboratory information management systems (LIMS) model. The approach involves integration of ML algorithm-derived models with commercially available mathematical programming software and a web-based LIMS prototype. To illustrate clinical utility, the process was applied to plasma steroidomics data from 22 patients tested for primary aldosteronism (PA). Once mass spectrometry data are uploaded into the system, automated processes enable generation of interpretations of steroid profiles from ML models. Generated reports include plasma concentrations of steroids in relation to age- and sex-specific reference intervals along with results of ML models and narrative interpretations that cover probabilities of PA. If PA is predicted, reports include probabilities of unilateral disease and mutations of KCNJ5 known to be associated with successful outcomes of adrenalectomy. Preliminary results, with no overlap in probabilities of disease among four patients with and 18 without PA and correct classification of all four patients with unilateral PA including three of four with KCNJ5 mutations, illustrate potential utility of the approach to guide diagnosis and subtyping of patients with PA. The outlined process for integrating plasma steroidomics data and ML with LIMS may facilitate improved diagnostic-decision-making when based on higher-dimensional data otherwise difficult to interpret. The approach is relevant to other diagnostic applications involving ML.

Association between squamous cell carcinoma antigen level and EGFR mutation status in Chinese lung adenocarcinoma patients.

BackgroundTo investigate the association between squamous cell carcinoma antigen (SCCAg) level and epidermal growth factor receptor (EGFR) mutation status in Chinese lung adenocarcinoma patients.MethodsWe retrospectively analyzed 293 patients with lung adenocarcinoma, divided into EGFR mutant group (n = 178) and EGFR wild‐type group (n = 115). The general data and laboratory parameters of the two groups were compared. We used univariable and multivariable logistic regression to analyze the association between SCCAg level and EGFR mutation. Generalized additive model was used for curve fitting, and a hierarchical binary logistic regression model was used for interaction analysis.ResultsSquamous cell carcinoma antigen level in the EGFR wild‐type group was significantly higher than that in the mutant group (p < 0.001). After adjusting for confounding factors, we found that elevated SCCAg was associated with a lower probability of EGFR mutation, with an OR of 0.717 (95% CI: 0.543–0.947, p = 0.019). For the tripartite SCCAg groups, the increasing trend of SCCAg was significantly associated with the decreasing probability of EGFR mutation (p for trend = 0.015), especially for Tertile 3 versus Tertile 1 (OR = 0.505; 95% CI: 0.258–0.986; p = 0.045). Curve fitting showed that there was an approximate linear negative relationship between continuous SCCAg and EGFR mutation probability (p = 0.020), which was first flattened and then decreased (p < 0.001). The association between the two was consistent among different subgroups, suggesting no interaction (all p > 0.05).ConclusionThere is a negative association between SCCAg level and EGFR mutation probability in Chinese lung adenocarcinoma patients.

Enhancing the fuzzy inference system using genetic algorithm for predicting the optimum production of a scientific publishing house

As a scientific publishing house, Indonesian Institute of Sciences (LIPI) Press' encountered some problems in publication planning, mainly predicting the optimum production of publications. This study aimed to enhance a fuzzy inference system (FIS) parameters using the genetic algorithm (GA). The enhancements led to optimally predict the number of LIPI Press publications for the following year. The predictors used were the number of work units, the number of workers, and the publishing process duration. The dataset covered a five years range of total production of LIPI Press. Firstly, an expert set up the parameters of the fuzzy inference system denoted as a FIS expert. Next, we performed a FIS GA by applying the genetic algorithm and K-fold validation in splitting the training data and testing data. The FIS GA revealed optimum prediction with parameters that were composed of both population size (30), the probability of crossover (0.75), the probability of mutation (0.01), and the number of generations (150). The experiment results show that our enhanced FIS GA outperformed FIS expert approach.