Genetic algorithms
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This paper presents an implementation of the parallelization of genetic algorithms. Three models of parallelized genetic algorithms are presented, namely the Master-Slave genetic algorithm, the Coarse-Grained genetic algorithm, and the Fine-Grained genetic algorithm. Furthermore, these models are compared with the basic serial genetic algorithm model. Four modules, Multiprocessing, Celery, PyCSP, and Scalable Concurrent Operation in Python, were investigated among the many parallelization options in Python. The Scalable Concurrent Operation in Python was selected as the most favorable option, so the models were implemented using the Python programming language, RabbitMQ, and SCOOP. Based on the implementation results and testing performed, a comparison of the hardware utilization of each deployed model is provided. The results' implementation using SCOOP was investigated from three aspects. The first aspect was the parallelization and integration of the SCOOP module into the resulting Python module. The second was the communication within the genetic algorithm topology. The third aspect was the performance of the parallel genetic algorithm model depending on the hardware.
- Klíčová slova
- Coarse-Grained, Fine-Grained, Master–Slave, SCOOP, parallelized genetic algorithms,
- MeSH
- algoritmy * MeSH
- počítače * MeSH
- Publikační typ
- časopisecké články MeSH
The analysis and segmentation of articular cartilage magnetic resonance (MR) images belongs to one of the most commonly routine tasks in diagnostics of the musculoskeletal system of the knee area. Conventional regional segmentation methods, which are based either on the histogram partitioning (e.g., Otsu method) or clustering methods (e.g., K-means), have been frequently used for the task of regional segmentation. Such methods are well known as fast and well working in the environment, where cartilage image features are reliably recognizable. The well-known fact is that the performance of these methods is prone to the image noise and artefacts. In this context, regional segmentation strategies, driven by either genetic algorithms or selected evolutionary computing strategies, have the potential to overcome these traditional methods such as Otsu thresholding or K-means in the context of their performance. These optimization strategies consecutively generate a pyramid of a possible set of histogram thresholds, of which the quality is evaluated by using the fitness function based on Kapur's entropy maximization to find the most optimal combination of thresholds for articular cartilage segmentation. On the other hand, such optimization strategies are often computationally demanding, which is a limitation of using such methods for a stack of MR images. In this study, we publish a comprehensive analysis of the optimization methods based on fuzzy soft segmentation, driven by artificial bee colony (ABC), particle swarm optimization (PSO), Darwinian particle swarm optimization (DPSO), and a genetic algorithm for an optimal thresholding selection against the routine segmentations Otsu and K-means for analysis and the features extraction of articular cartilage from MR images. This study objectively analyzes the performance of the segmentation strategies upon variable noise with dynamic intensities to report a segmentation's robustness in various image conditions for a various number of segmentation classes (4, 7, and 10), cartilage features (area, perimeter, and skeleton) extraction preciseness against the routine segmentation strategies, and lastly the computing time, which represents an important factor of segmentation performance. We use the same settings on individual optimization strategies: 100 iterations and 50 population. This study suggests that the combination of fuzzy thresholding with an ABC algorithm gives the best performance in the comparison with other methods as from the view of the segmentation influence of additive dynamic noise influence, also for cartilage features extraction. On the other hand, using genetic algorithms for cartilage segmentation in some cases does not give a good performance. In most cases, the analyzed optimization strategies significantly overcome the routine segmentation methods except for the computing time, which is normally lower for the routine algorithms. We also publish statistical tests of significance, showing differences in the performance of individual optimization strategies against Otsu and K-means method. Lastly, as a part of this study, we publish a software environment, integrating all the methods from this study.
- Klíčová slova
- ABC, DPSO, K-means clustering, Otsu thresholding, PSO, articular cartilage, medical image segmentation, regional segmentation,
- MeSH
- algoritmy MeSH
- artefakty MeSH
- kloubní chrupavka * diagnostické zobrazování MeSH
- magnetická rezonanční tomografie metody MeSH
- počítačové zpracování obrazu metody MeSH
- shluková analýza MeSH
- Publikační typ
- časopisecké články MeSH
PURPOSE: Genetic testing in consanguineous families advances the general comprehension of pathophysiological pathways. However, short stature (SS) genetics remain unexplored in a defined consanguineous cohort. This study examines a unique pediatric cohort from Sulaimani, Iraq, aiming to inspire a genetic testing algorithm for similar populations. METHODS: Among 280 SS referrals from 2018-2020, 64 children met inclusion criteria (from consanguineous families; height ≤ -2.25 SD), 51 provided informed consent (30 females; 31 syndromic SS) and underwent investigation, primarily via exome sequencing. Prioritized variants were evaluated by the American College of Medical Genetics and Genomics standards. A comparative analysis was conducted by juxtaposing our findings against published gene panels for SS. RESULTS: A genetic cause of SS was elucidated in 31 of 51 (61%) participants. Pathogenic variants were found in genes involved in the GH-IGF-1 axis (GHR and SOX3), thyroid axis (TSHR), growth plate (CTSK, COL1A2, COL10A1, DYM, FN1, LTBP3, MMP13, NPR2, and SHOX), signal transduction (PTPN11), DNA/RNA replication (DNAJC21, GZF1, and LIG4), cytoskeletal structure (CCDC8, FLNA, and PCNT), transmembrane transport (SLC34A3 and SLC7A7), enzyme coding (CYP27B1, GALNS, and GNPTG), and ciliogenesis (CFAP410). Two additional participants had Silver-Russell syndrome and 1 had del22q.11.21. Syndromic SS was predictive in identifying a monogenic condition. Using a gene panel would yield positive results in only 10% to 33% of cases. CONCLUSION: A tailored testing strategy is essential to increase diagnostic yield in children with SS from consanguineous populations.
- Klíčová slova
- Consanguinity, Genetic testing algorithm, Pediatric endocrinology, Short stature, Short stature genes,
- MeSH
- algoritmy MeSH
- dítě MeSH
- genetické testování * metody MeSH
- lidé MeSH
- mladiství MeSH
- nanismus * genetika epidemiologie diagnóza MeSH
- pokrevní příbuzenství MeSH
- předškolní dítě MeSH
- rodokmen MeSH
- sekvenování exomu MeSH
- tělesná výška genetika MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Irák epidemiologie MeSH
In genetic programming (GP), computer programs are often coevolved with training data subsets that are known as fitness predictors. In order to maximize performance of GP, it is important to find the most suitable parameters of coevolution, particularly the fitness predictor size. This is a very time-consuming process as the predictor size depends on a given application, and many experiments have to be performed to find its suitable size. A new method is proposed which enables us to automatically adapt the predictor and its size for a given problem and thus to reduce not only the time of evolution, but also the time needed to tune the evolutionary algorithm. The method was implemented in the context of Cartesian genetic programming and evaluated using five symbolic regression problems and three image filter design problems. In comparison with three different CGP implementations, the time required by CGP search was reduced while the quality of results remained unaffected.
- Klíčová slova
- Cartesian genetic programming, coevolutionary algorithms, evolutionary design, fitness prediction, image processing., symbolic regression,
- MeSH
- algoritmy * MeSH
- biologická evoluce * MeSH
- genetická zdatnost MeSH
- lidé MeSH
- počítačová simulace MeSH
- počítačové zpracování obrazu metody MeSH
- poměr signál - šum MeSH
- regresní analýza MeSH
- software * MeSH
- vylepšení obrazu metody MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The evaluation of an animal is based on production records, adjusted for environmental effects, which gives a reliable estimation of its breeding value. Highly reliable daughter yield deviations are used as inputs for genetic marker evaluation. Genetic variability is explained by particular loci and background polygenes, both of which are described by the genomic breeding value selection index. Automated genotyping enables the determination of many single-nucleotide polymorphisms (SNPs) and can increase the reliability of evaluation of young animals (from 0.30 if only the pedigree value is used to 0.60 when the genomic breeding value is applied). However, the introduction of SNPs requires a mixed model with a large number of regressors, in turn requiring new algorithms for the best linear unbiased prediction and BayesB. Here, we discuss a method that uses a genomic relationship matrix to estimate the genomic breeding value of animals directly, without regressors. A one-step procedure evaluates both genotyped and ungenotyped animals at the same time, and produces one common ranking of all animals in a whole population. An augmented pedigree-genomic relationship matrix and the removal of prerequisites produce more accurate evaluations of all connected animals.
- MeSH
- chov * MeSH
- genetická variace * MeSH
- genetické markery MeSH
- genom * MeSH
- genotyp MeSH
- jednonukleotidový polymorfismus MeSH
- kvantitativní znak dědičný MeSH
- lokus kvantitativního znaku * MeSH
- modely genetické MeSH
- rodokmen MeSH
- skot genetika MeSH
- zvířata MeSH
- Check Tag
- skot genetika MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- přehledy MeSH
- Názvy látek
- genetické markery MeSH
Objective.The current practices of designing neural networks rely heavily on subjective judgment and heuristic steps, often dictated by the level of expertise possessed by architecture designers. To alleviate these challenges and streamline the design process, we propose an automatic method, a novel approach to enhance the optimization of neural network architectures for processing intracranial electroencephalogram (iEEG) data.Approach.We present a genetic algorithm, which optimizes neural network architecture and signal pre-processing parameters for iEEG classification.Main results.Our method improved the macroF1 score of the state-of-the-art model in two independent datasets, from St. Anne's University Hospital (Brno, Czech Republic) and Mayo Clinic (Rochester, MN, USA), from 0.9076 to 0.9673 and from 0.9222 to 0.9400 respectively.Significance.By incorporating principles of evolutionary optimization, our approach reduces the reliance on human intuition and empirical guesswork in architecture design, thus promoting more efficient and effective neural network models. The proposed method achieved significantly improved results when compared to the state-of-the-art benchmark model (McNemar's test,p≪ 0.01). The results indicate that neural network architectures designed through machine-based optimization outperform those crafted using the subjective heuristic approach of a human expert. Furthermore, we show that well-designed data preprocessing significantly affects the models' performance.
- Klíčová slova
- deep learning, genetic algorithms, intracranial EEG, neural network, optimization,
- MeSH
- elektroencefalografie metody MeSH
- elektrokortikografie * MeSH
- lidé MeSH
- neuronové sítě * MeSH
- počítačové zpracování signálu MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
In this paper, a permanent magnet synchronous machine (PMSM) with an auxiliary winding (AW) on the rotor is analyzed by two-dimensional approach. This PMSM with AW (AWPMSM) can be used in many applications such as propulsion system, aircraft and traction because it includes rotor flux control capability. First, the magnetic field in different parts of AWPMSM is calculated based on Maxwell equations. Then, as a consequence of the magnetic field, the torque components, including cogging, reluctance, electromagnetic and instantaneous torque are computed. Next, torque-speed characteristic has been investigated. This AWPMSM can be located in the flux weakening mode in two ways, first one is to attenuate the rotor field by changing the direction of the AW field and the other one is to adjust the armature current angle, both of them have been investigated. After that, the overload capability and temperature effects have been analyzed. Finally, using the meta-heuristic algorithms such as genetic algorithm, particle swarm optimization, differential evolution and teaching learn base optimization the dimensions of AWPMSM and the initial angle of the rotor are determined in such a way that the torque-to-volume ratio is maximized. The influences of the type of armature winding and the magnetization patterns have also been investigated. The results obtained by the two-dimensional method have been confirmed numerically.
- Klíčová slova
- Armature reaction, Auxiliary winding, Excitation coil, Meta-heuristic algorithms, Permanent magnet,
- Publikační typ
- časopisecké články MeSH
In this paper, we analysed the steady state fluorescence spectra of cell suspensions containing healthy and carcinoma fibroblast mouse cells, using a genetic-algorithm-spectra-decomposition software (GASpeD). In contrast to other deconvolution algorithms, such as polynomial or linear unmixing software, GASpeD takes into account light scatter. In cell suspensions, light scatter plays an important role as it depends on the number of cells, their size, shape, and coagulation. The measured fluorescence spectra were normalized, smoothed and deconvoluted into four peaks and background. The wavelengths of intensities' maxima of lipopigments (LR), FAD, and free/bound NAD(P)H (AF/AB) of the deconvoluted spectra matched published data. In deconvoluted spectra at pH = 7, the fluorescence intensities of the AF/AB ratio in healthy cells was always higher in comparison to carcinoma cells. In addition, the AF/AB ratio in healthy and carcinoma cells were influenced differently by changes in pH. In mixtures of healthy and carcinoma cells, AF/AB decreases when more than 13% of carcinoma cells are present. Expensive instrumentation is not required, and the software is user friendly. Due to these attributes, we hope that this study will be a first step in the development of new cancer biosensors and treatments with the use of optical fibers.
- Klíčová slova
- cancer biosensor, cell suspension auto-fluorescence, endogenous fluorophores, genetic algorithm, steady state fluorescence,
- MeSH
- algoritmy * MeSH
- buněčné kultury MeSH
- fluorescence MeSH
- fluorescenční spektrometrie MeSH
- karcinom * MeSH
- myši MeSH
- software MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Social networks have greatly expanded in the last ten years the need for sharing multimedia data. However, on open networks such as the Internet, where security is frequently compromised, it is simple for eavesdroppers to approach the actual contents without much difficulty. Researchers have created a variety of encryption methods to strengthen the security of this transmission and make it difficult for eavesdroppers to get genuine data. However, these conventional approaches increase computing costs and communication overhead and do not offer protection against fresh threats. The problems with current algorithms encourage academics to further investigate the subject and suggest new algorithms that are more effective than current methods, that reduce overhead, and which are equipped with features needed by next-generation multimedia networks. In this paper, a genetic operator-based encryption method for multimedia security is proposed. It has been noted that the proposed algorithm produces improved key strength results. The investigations using attacks on data loss, differential assaults, statistical attacks, and brute force attacks show that the encryption technique suggested has improved security performance. It focuses on two techniques, bitplane slicing and followed by block segmentation and scrambling. The suggested method first divides the plaintext picture into several blocks, which is then followed by block swapping done by the genetic operator used to combine the genetic information of two different images to generate new offspring. The key stream is produced from an iterative chaotic map with infinite collapse (ICMIC). Based on a close-loop modulation coupling (CMC) approach, a three-dimensional hyperchaotic ICMIC modulation map is proposed. By using a hybrid model of multidirectional circular permutation with this map, a brand-new colour image encryption algorithm is created. In this approach, a multidirectional circular permutation is used to disrupt the image's pixel placements, and genetic operations are used to replace the pixel values. According to simulation findings and security research, the technique can fend off brute-force, statistical, differential, known-plaintext, and chosen-plaintext assaults, and has a strong key sensitivity.
The open-pollinated (OP) family testing combines the simplest known progeny evaluation and quantitative genetics analyses as candidates' offspring are assumed to represent independent half-sib families. The accuracy of genetic parameter estimates is often questioned as the assumption of "half-sibling" in OP families may often be violated. We compared the pedigree- vs. marker-based genetic models by analysing 22-yr height and 30-yr wood density for 214 white spruce [Picea glauca (Moench) Voss] OP families represented by 1694 individuals growing on one site in Quebec, Canada. Assuming half-sibling, the pedigree-based model was limited to estimating the additive genetic variances which, in turn, were grossly overestimated as they were confounded by very minor dominance and major additive-by-additive epistatic genetic variances. In contrast, the implemented genomic pairwise realized relationship models allowed the disentanglement of additive from all nonadditive factors through genetic variance decomposition. The marker-based models produced more realistic narrow-sense heritability estimates and, for the first time, allowed estimating the dominance and epistatic genetic variances from OP testing. In addition, the genomic models showed better prediction accuracies compared to pedigree models and were able to predict individual breeding values for new individuals from untested families, which was not possible using the pedigree-based model. Clearly, the use of marker-based relationship approach is effective in estimating the quantitative genetic parameters of complex traits even under simple and shallow pedigree structure.
- Klíčová slova
- GenPred, Mendelian sampling term, genetic variance decomposition, genomic selection, open-pollinated families, pedigree- and marker-based relationships, shared data resource,
- MeSH
- algoritmy MeSH
- fenotyp MeSH
- genetická variace MeSH
- genom rostlinný * MeSH
- genomika * metody MeSH
- genotyp MeSH
- genotypizační techniky MeSH
- kvantitativní znak dědičný MeSH
- modely genetické MeSH
- opylení genetika MeSH
- smrk klasifikace genetika MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
