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Time series prediction of COVID-19 by mutation rate analysis using recurrent neural network-based LSTM model

Author

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  • Pathan, Refat Khan
  • Biswas, Munmun
  • Khandaker, Mayeen Uddin

Abstract

SARS-CoV-2, a novel coronavirus mostly known as COVID-19 has created a global pandemic. The world is now immobilized by this infectious RNA virus. As of June 15, already more than 7.9 million people have been infected and 432k people died. This RNA virus has the ability to do the mutation in the human body. Accurate determination of mutation rates is essential to comprehend the evolution of this virus and to determine the risk of emergent infectious disease. This study explores the mutation rate of the whole genomic sequence gathered from the patient's dataset of different countries. The collected dataset is processed to determine the nucleotide mutation and codon mutation separately. Furthermore, based on the size of the dataset, the determined mutation rate is categorized for four different regions: China, Australia, the United States, and the rest of the World. It has been found that a huge amount of Thymine (T) and Adenine (A) are mutated to other nucleotides for all regions, but codons are not frequently mutating like nucleotides. A recurrent neural network-based Long Short Term Memory (LSTM) model has been applied to predict the future mutation rate of this virus. The LSTM model gives Root Mean Square Error (RMSE) of 0.06 in testing and 0.04 in training, which is an optimized value. Using this train and testing process, the nucleotide mutation rate of 400th patient in future time has been predicted. About 0.1% increment in mutation rate is found for mutating of nucleotides from T to C and G, C to G and G to T. While a decrement of 0.1% is seen for mutating of T to A, and A to C. It is found that this model can be used to predict day basis mutation rates if more patient data is available in updated time.

Suggested Citation

  • Pathan, Refat Khan & Biswas, Munmun & Khandaker, Mayeen Uddin, 2020. "Time series prediction of COVID-19 by mutation rate analysis using recurrent neural network-based LSTM model," Chaos, Solitons & Fractals, Elsevier, vol. 138(C).
  • Handle: RePEc:eee:chsofr:v:138:y:2020:i:c:s0960077920304161
    DOI: 10.1016/j.chaos.2020.110018
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    Citations

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    Cited by:

    1. Shastri, Sourabh & Singh, Kuljeet & Kumar, Sachin & Kour, Paramjit & Mansotra, Vibhakar, 2020. "Time series forecasting of Covid-19 using deep learning models: India-USA comparative case study," Chaos, Solitons & Fractals, Elsevier, vol. 140(C).
    2. Tayarani N., Mohammad-H., 2021. "Applications of artificial intelligence in battling against covid-19: A literature review," Chaos, Solitons & Fractals, Elsevier, vol. 142(C).
    3. Kafieh, Rahele & Saeedizadeh, Narges & Arian, Roya & Amini, Zahra & Serej, Nasim Dadashi & Vaezi, Atefeh & Javanmard, Shaghayegh Haghjooy, 2020. "Isfahan and Covid-19: Deep spatiotemporal representation," Chaos, Solitons & Fractals, Elsevier, vol. 141(C).
    4. Kalantari, Mahdi, 2021. "Forecasting COVID-19 pandemic using optimal singular spectrum analysis," Chaos, Solitons & Fractals, Elsevier, vol. 142(C).
    5. María Andreína Moros-Ochoa & Gilmer Yovani Castro-Nieto & Anderson Quintero-Español & Carolina Llorente-Portillo, 2022. "Forecasting Biocapacity and Ecological Footprint at a Worldwide Level to 2030 Using Neural Networks," Sustainability, MDPI, vol. 14(17), pages 1-14, August.
    6. Joe Yazbeck & John B. Rundle, 2023. "A Fusion of Geothermal and InSAR Data with Machine Learning for Enhanced Deformation Forecasting at the Geysers," Land, MDPI, vol. 12(11), pages 1-22, October.
    7. Iqra Mehmood & Munazza Ijaz & Sajjad Ahmad & Temoor Ahmed & Amna Bari & Asma Abro & Khaled S. Allemailem & Ahmad Almatroudi & Muhammad Tahir ul Qamar, 2021. "SARS-CoV-2: An Update on Genomics, Risk Assessment, Potential Therapeutics and Vaccine Development," IJERPH, MDPI, vol. 18(4), pages 1-23, February.

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