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Self-organizing mapping based swarm intelligence for secondary and tertiary proteins classification

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Abstract

Proteins have a significant role in animals and human health. Interactions among proteins are complex and large. Proteins separations are challenging process in molecular biology. Computational tools help to simulate the analysis in order to reduce the training data into small testing data. Large proteins have been mapped using self-organizing maps (SOMs). Neural network based SOMs has a significant role in reducing the irregular shapes of proteins interactions. Iterative checking enables the organizations of all proteins. In next stage, particle swarm intelligence is applied to classify the proteins’ families. In the current work, secondary (Two dimensional) and tertiary proteins (Three dimensional) proteins have been grouped. Two dimensional proteins contain fewer hydro-carbons than three dimensional proteins. For faster analysis, the angles of the proteins are taken into account. The SOMs is compared with Bounding Box approach. In final, the experimental evolutions show that swarm intelligence achieved faster processing through enabling less memory consumptions and time. Since PSO combines proteins datasets in fuzzy values, the compactness or integration of similar proteins are strong. On the other hand, Bounding Box uses the Crisp value. Therefore, it needs more space to organize the whole data. Without SOMs, swarm intelligence also results are poor due to the excessive time consuming and required storage area. Moreover, for almost all classification and clustering tools, it is observed that the overall classification task becomes slow, time consuming, space consuming and also less sensitive because of noises, irrelevant data in input datasets. Thus, the proposed SOM based PSO approach achieved less time consuming with efficient classification into secondary and tertiary proteins.

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Authors and Affiliations

  1. East West University Bangladesh, Dhaka, Bangladesh

    Md. Sarwar Kamal, Md. Golam Sarowar & Shamim H. Ripon

  2. Department of Information Technology, Techno India College of Technology, Kolkata, India

    Nilanjan Dey

  3. Department of Electronics and Electrical Communications Engineering, Faculty of Engineering, Tanta University, Tanta, Egypt

    Amira S. Ashour

  4. Department of Electrical Engineering, Indian Institute of Technology, Delhi, India

    B. K. Panigrahi

  5. Departamento de Engenharia Mecânica, Instituto de Ciência e Inovação em Engenharia Mecânica e Engenharia Industrial, Faculdade de Engenharia, Universidade do Porto, Porto, Portugal

    João Manuel R. S. Tavares

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  1. Md. Sarwar Kamal
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Correspondence to Amira S. Ashour.

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Kamal, M.S., Sarowar, M.G., Dey, N. et al. Self-organizing mapping based swarm intelligence for secondary and tertiary proteins classification. Int. J. Mach. Learn. & Cyber. 10, 229–252 (2019). https://doi.org/10.1007/s13042-017-0710-8

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