One of the recent significant but challenging research studies in computational biology and bioinformatics is to unveil protein complexes from protein-protein interaction networks (PPINs). However, the development of a reliable algorithm to detect more complexes with high quality is still ongoing in many studies. The main contribution of this paper is to improve the effectiveness of the well-known modularity density ( ) model when used as a single objective optimization function in the framework of the canonical evolutionary algorithm (EA). To this end, the design of the EA is modified with a gene ontology-based mutation operator, where the aim is to make a positive collaboration between the modularity density model and the proposed gene ontology-based mutation operator. The performance of the proposed EA to have a high quantity and quality of the detected complexes is assessed on two yeast PPINs and compared with two benchmarking gold complex sets. The reported results reveal the ability of modularity density to be more productive in detecting more complexes with high quality when teamed up with a gene ontology-based mutation operator.
By definition, the detection of protein complexes that form protein-protein interaction networks (PPINs) is an NP-hard problem. Evolutionary algorithms (EAs), as global search methods, are proven in the literature to be more successful than greedy methods in detecting protein complexes. However, the design of most of these EA-based approaches relies on the topological information of the proteins in the PPIN. Biological information, as a key resource for molecular profiles, on the other hand, acquired a little interest in the design of the components in these EA-based methods. The main aim of this paper is to redesign two operators in the EA based on the functional domain rather than the graph topological domain. The perturb
... Show MoreScheduling Timetables for courses in the big departments in the universities is a very hard problem and is often be solved by many previous works although results are partially optimal. This work implements the principle of an evolutionary algorithm by using genetic theories to solve the timetabling problem to get a random and full optimal timetable with the ability to generate a multi-solution timetable for each stage in the collage. The major idea is to generate course timetables automatically while discovering the area of constraints to get an optimal and flexible schedule with no redundancy through the change of a viable course timetable. The main contribution in this work is indicated by increasing the flexibility of generating opti
... Show MoreIn today's world, the science of bioinformatics is developing rapidly, especially with regard to the analysis and study of biological networks. Scientists have used various nature-inspired algorithms to find protein complexes in protein-protein interaction (PPI) networks. These networks help scientists guess the molecular function of unknown proteins and show how cells work regularly. It is very common in PPI networks for a protein to participate in multiple functions and belong to many complexes, and as a result, complexes may overlap in the PPI networks. However, developing an efficient and reliable method to address the problem of detecting overlapping protein complexes remains a challenge since it is considered a complex and har
... Show MoreThe issue of increasing the range covered by a wireless sensor network with restricted sensors is addressed utilizing improved CS employing the PSO algorithm and opposition-based learning (ICS-PSO-OBL). At first, the iteration is carried out by updating the old solution dimension by dimension to achieve independent updating across the dimensions in the high-dimensional optimization problem. The PSO operator is then incorporated to lessen the preference random walk stage's imbalance between exploration and exploitation ability. Exceptional individuals are selected from the population using OBL to boost the chance of finding the optimal solution based on the fitness value. The ICS-PSO-OBL is used to maximize coverage in WSN by converting r
... Show MoreDepletion of fossil fuel is one of the main reasons why the bioethanol has become popular. It is a renewable energy source. In order to meet the great demand of bioethanol, it is best that the bioethanol production is from cheap raw materials. Since the golden shower fruit is not being utilized and is considered as waste material, hence, this study was conducted to make use of the large volume of the residue as feedstock to test its potential for bioethanol extraction.The main goal of this study is to obtain the most volume of bioethanol from the golden shower fruit liquid residue by the factors, days of fermentation (3, 5, and 7 days) and sugar concentration (15, 20 and 25 brix) of the liquid residue. Also, part of the study is to compu
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