2 research outputs found

    Providing SSPCO Algorithm to Construct Static Protein-Protein Interaction (PPI) Networks

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    Protein-Protein Inter-action Networks are dynamic in reality; i.e. Inter-actions among different proteins may be ineffective in different circumstances and times. One of the most crucial parameters in the conversion of a static network into a temporal graph is the well-tuning of transformation threshold. In this part of the article, using additional data, like gene expression data in different times and circumstances and well-known protein complexes, it is tried to determine an appropriate threshold. To accomplish this task, we transform the problem into an optimization one and then we solve it using a meta-heuristic algorithm, named Particle Swarm Optimization (SSPCO). One of the most important parts in our work is the determination of interestingness function in the SSPCO. It is defined as a function of standard complexes and gene co-expression data. After producing a threshold per each gene, in the following section we will discuss how using these thresholds, active proteins are determined and then temporal graph is created. For final assessment of the produced graph quality, we use graph clustering algorithms and protein complexes determination algorithms. For accomplishing this task, we use MCL, Cluster One, MCODE algorithms. Due to high number of the obtained clusters, the obtained results, if they have some special conditions, will filter out or be merged with each other. Standard performance criteria like Recal, Precision, and F-measure are employed. There is a new proposed criterion named Smoothness. Our experimental results show that the graphs produced by the proposed method outperform the previous methods

    Comprehensive Taxonomies of Nature- and Bio-inspired Optimization: Inspiration versus Algorithmic Behavior, Critical Analysis and Recommendations

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    In recent years, a great variety of nature- and bio-inspired algorithms has been reported in the literature. This algorithmic family simulates different biological processes observed in Nature in order to efficiently address complex optimization problems. In the last years the number of bio-inspired optimization approaches in literature has grown considerably, reaching unprecedented levels that dark the future prospects of this field of research. This paper addresses this problem by proposing two comprehensive, principle-based taxonomies that allow researchers to organize existing and future algorithmic developments into well-defined categories, considering two different criteria: the source of inspiration and the behavior of each algorithm. Using these taxonomies we review more than three hundred publications dealing with nature-inspired and bio-inspired algorithms, and proposals falling within each of these categories are examined, leading to a critical summary of design trends and similarities between them, and the identification of the most similar classical algorithm for each reviewed paper. From our analysis we conclude that a poor relationship is often found between the natural inspiration of an algorithm and its behavior. Furthermore, similarities in terms of behavior between different algorithms are greater than what is claimed in their public disclosure: specifically, we show that more than one-third of the reviewed bio-inspired solvers are versions of classical algorithms. Grounded on the conclusions of our critical analysis, we give several recommendations and points of improvement for better methodological practices in this active and growing research field.Comment: 76 pages, 6 figure
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