journal article·2020-11Open access

RETRACTED ARTICLE: A deep learning model and machine learning methods for the classification of potential coronavirus treatments on a single human cell

Nour Eldeen M. Khalifa, Mohamed Hamed N. Taha, Gunasekaran Manogaran, Mohamed Loey

Journal of Nanoparticle Research· Volume 22· Issue 11
This record is marked as retracted by the source. Review the publisher’s notice before using its findings.

Abstract

Coronavirus pandemic is burdening healthcare systems around the world to the full capacity they can accommodate. There is an overwhelming need to find a treatment for this virus as early as possible. Computer algorithms and deep learning can participate positively by finding a potential treatment for SARS-CoV-2. In this paper, a deep learning model and machine learning methods for the classification of potential coronavirus treatments on a single human cell will be presented. The dataset selected in this work is a subset of the publicly online datasets available on RxRx.ai. The objective of this research is to automatically classify a single human cell according to the treatment type and the treatment concentration level. A DCNN model and a methodology are proposed throughout this work. The methodical idea is to convert the numerical features from the original dataset to the image domain and then fed them up into a DCNN model. The proposed DCNN model consists of three convolutional layers, three ReLU layers, three pooling layers, and two fully connected layers. The experimental results show that the proposed DCNN model for treatment classification (32 classes) achieved 98.05% in testing accuracy if it is compared with classical machine learning such as support vector machine, decision tree, and ensemble. In treatment concentration level prediction, the classical machine learning (ensemble) algorithm achieved 98.5% in testing accuracy while the proposed DCNN model achieved 98.2%. The performance metrics strengthen the obtained results from the conducted experiments for the accuracy of treatment classification and treatment concentration level prediction.
Source: europepmc · Quality: candidate unverified · Source record ↗

Research context

OpenAlex topics: COVID-19 diagnosis using AI · SARS-CoV-2 and COVID-19 Research · SARS-CoV-2 detection and testing

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

References (43)

Show source-provided references
1. Ardakani AA, Kanafi AR, Acharya UR, Khadem N, Mohammadi A (Jun. 2020) Application of deep learning technique to manage COVID-19 in routine clinical practice using CT images: results of 10 convolutional neural networks. Comput Biol Med 121:103795. https://doi.org/10.1016/j.compbiomed.2020.10379510.1016/j.compbiomed.2020.103795 ↗
2. Bagasta AR, Rustam Z, Pandelaki J, Nugroho WA (2019) Comparison of cubic SVM with Gaussian SVM: classification of infarction for detecting ischemic stroke, in IOP Conference Series: Materials Science and Engineering, vol. 546, no. 5, p. 05201610.1088/1757-899X/546/5/052016 ↗
3. Banfield RE, Hall LO, Bowyer KW, Kegelmeyer WP (2006) A comparison of decision tree ensemble creation techniques. IEEE Trans Pattern Anal Mach Intell 29(1):173–18010.1109/TPAMI.2007.250609 ↗
4. Çayir A, Yenidoğan I, Dağ H (2018) Feature extraction based on deep learning for some traditional machine learning methods, in 2018 3rd International Conference on Computer Science and Engineering (UBMK), 2018, pp. 494–497, https://doi.org/10.1109/UBMK.2018.856638310.1109/UBMK.2018.8566383 ↗
5. Chamola V, Hassija V, Gupta V, Guizani M (2020) A comprehensive review of the COVID-19 pandemic and the role of IoT, drones, AI, blockchain, and 5G in managing its impact. IEEE Access 8:90225–90265. https://doi.org/10.1109/ACCESS.2020.299234110.1109/ACCESS.2020.2992341 ↗
6. Chang Y-W, Lin C-J (2008) Feature ranking using linear SVM. In: Causation and prediction challenge, pp 53–64
7. Chang L, Yan Y, Wang L (2020) Coronavirus disease 2019: coronaviruses and blood safety. Transfus Med Rev. https://doi.org/10.1016/j.tmrv.2020.02.00310.1016/j.tmrv.2020.02.003 ↗
8. Civit-Masot J, Luna-Perejón F, Domínguez Morales M, Civit A (2020) Deep learning system for COVID-19 diagnosis aid using X-ray pulmonary images. Appl Sci 10(13):13. https://doi.org/10.3390/app1013464010.3390/app10134640 ↗
9. Coronavirus (COVID-19) map (2020). https://www.google.com/covid19-map/ (accessed Apr. 26, 2020)
10. Damrongsakmethee T, Neagoe V-E (2019) Principal component analysis and relieff cascaded with decision tree for credit scoring, in Computer Science On-line Conference, pp. 85–9510.1007/978-3-030-19810-7_9 ↗
11. El-Sawy A, Loey M, EL-Bakry H (2017a) Arabic handwritten characters recognition using convolutional neural network. WSEAS Trans Comput Res 5 Accessed: Apr. 01, 2020. [Online]. Available: http://www.wseas.org/multimedia/journals/computerresearch/2017/a045818-075.php
12. El-Sawy A, El-Bakry H, Loey M (2017b) CNN for handwritten Arabic digits recognition based on LeNet-5 BT - Proceedings of the International Conference on Advanced Intelligent Systems and Informatics 2016, Cham, pp. 566–57510.1007/978-3-319-48308-5_54 ↗
13. Giovanetti M, Benvenuto D, Angeletti S, Ciccozzi M (May 2020) The first two cases of 2019-nCoV in Italy: where they come from? J Med Virol 92(5):518–521. https://doi.org/10.1002/jmv.2569910.1002/jmv.25699 ↗
14. C. Goutte and E. Gaussier, A probabilistic interpretation of precision, recall and F-score, with implication for evaluation, 2010
15. Hang R, Liu Q, Song H, Sun Y (2015) Matrix-based discriminant subspace ensemble for hyperspectral image spatial–spectral feature fusion. IEEE Trans Geosci Remote Sens 54(2):783–79410.1109/TGRS.2015.2465899 ↗
16. Heiser K et al (2020) Identification of potential treatments for COVID-19 through artificial intelligence-enabled phenomic analysis of human cells infected with SARS-CoV-2. bioRxiv10.1101/2020.04.21.054387 ↗
17. Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H, Spitters C, Ericson K, Wilkerson S, Tural A, Diaz G, Cohn A, Fox L, Patel A, Gerber SI, Kim L, Tong S, Lu X, Lindstrom S, Pallansch MA, Weldon WC, Biggs HM, Uyeki TM, Pillai SK, Washington State 2019-nCoV Case Investigation Team (2020) First case of 2019 novel coronavirus in the United States. N Engl J Med 382(10):929–936. https://doi.org/10.1056/NEJMoa200119110.1056/NEJMoa2001191 ↗
18. Jogin M, Mohana, Madhulika MS, Divya GD, Meghana RK, Apoorva S (2018) Feature extraction using convolution neural networks (CNN) and deep learning, in 2018 3rd IEEE International Conference on Recent Trends in Electronics, Information Communication Technology (RTEICT), pp. 2319–2323, https://doi.org/10.1109/RTEICT42901.2018.901250710.1109/RTEICT42901.2018.9012507 ↗
19. Khalifa NEM, Taha MHN, Hassanien AE (2018) Aquarium family fish species identification system using deep neural networks. In: International Conference on Advanced Intelligent Systems and Informatics, pp 347–356
20. Khalifa N, Loey M, Taha M, Mohamed H (2019a) Deep transfer learning models for medical diabetic retinopathy detection. Acta Inform Med 27(5):327. https://doi.org/10.5455/aim.2019.27.327-33210.5455/aim.2019.27.327-332 ↗
21. Khalifa NEM, Taha MHN, Hassanien AE, Hemedan AA (2019b) Deep bacteria: robust deep learning data augmentation design for limited bacterial colony dataset. Int J Reason Based Intell Syst 11(3):256–264
22. Khalifa NEM, Taha MHN, Ali DE, Slowik A, Hassanien AE (2020) Artificial intelligence technique for gene expression by tumor RNA-Seq data: a novel optimized deep learning approach. IEEE Access 8:22874–2288310.1109/ACCESS.2020.2970210 ↗
23. Khattar A, Jain PR, Quadri SMK (2020) Effects of the disastrous pandemic COVID 19 on learning styles, activities and mental health of young Indian students - a machine learning approach, in 2020 4th International Conference on Intelligent Computing and Control Systems (ICICCS), pp. 1190–1195, https://doi.org/10.1109/ICICCS48265.2020.912095510.1109/ICICCS48265.2020.9120955 ↗
24. Kleinbaum DG, Klein M (2002) Logistic regression: a self-learning text, 2nd edn. Springer-Verlag, New York
25. Lai C-C, Shih T-P, Ko W-C, Tang H-J, Hsueh P-R (2020) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): the epidemic and the challenges. Int J Antimicrob Agents 55(3):105924. https://doi.org/10.1016/j.ijantimicag.2020.10592410.1016/j.ijantimicag.2020.105924 ↗
26. Li J, Li J(J), Xie X, Cai X, Huang J, Tian X, Zhu H (Mar. 2020) Game consumption and the 2019 novel coronavirus. Lancet Infect Dis 20(3):275–276. https://doi.org/10.1016/S1473-3099(20)30063-310.1016/S1473-3099(20)30063-3 ↗
27. Loey M, Smarandache F, Khalifa NEM (2020a) Within the lack of chest COVID-19 X-ray dataset: a novel detection model based on GAN and deep transfer learning. Symmetry 12(4):4. https://doi.org/10.3390/sym1204065110.3390/sym12040651 ↗
28. Loey M, ElSawy A, Afify M (2020b) Deep learning in plant diseases detection for agricultural crops: a survey. Int J Serv Sci Manag Eng Technol (IJSSMET) www.igi-global.com/article/deep-learning-in-plant-diseases-detection-for-agricultural-crops/248499 (accessed Apr. 11, 2020)10.4018/IJSSMET.2020040103 ↗
29. Loey M, Naman MR, Zayed HH (2020c) A survey on blood image diseases detection using deep learning. Int J Serv Sci Manag Eng Technol (IJSSMET) www.igi-global.com/article/a-survey-on-blood-image-diseases-detection-using-deep-learning/256653 (accessed Jun. 17, 2020)
30. Loey M, Naman M, Zayed H (2020d) Deep transfer learning in diagnosing leukemia in blood cells. Computers 9(2):2. https://doi.org/10.3390/computers902002910.3390/computers9020029 ↗
31. Mangalova E, Agafonov E (Apr. 2014) Wind power forecasting using the k-nearest neighbors algorithm. Int J Forecast 30(2):402–406. https://doi.org/10.1016/j.ijforecast.2013.07.00810.1016/j.ijforecast.2013.07.008 ↗
32. Narayan Das N, Kumar N, Kaur M, Kumar V, Singh D (2020, IRBM) Automated deep transfer learning-based approach for detection of COVID-19 infection in chest X-rays. https://doi.org/10.1016/j.irbm.2020.07.00110.1016/j.irbm.2020.07.001 ↗
33. Naseem I, Togneri R, Bennamoun M (Nov. 2010) Linear regression for face recognition. IEEE Trans Pattern Anal Mach Intell 32(11):2106–2112. https://doi.org/10.1109/TPAMI.2010.12810.1109/TPAMI.2010.128 ↗
34. Navada A, Ansari AN, Patil S, Sonkamble BA (2011) Overview of use of decision tree algorithms in machine learning, in 2011 IEEE Control and System Graduate Research Colloquium, pp. 37–42, https://doi.org/10.1109/ICSGRC.2011.599182610.1109/ICSGRC.2011.5991826 ↗
35. Polikar R (2012) Ensemble learning. In: Zhang C, Ma Y (eds) Ensemble machine learning: methods and applications. Springer US, Boston, MA, pp 1–34
36. Rothe C, Schunk M, Sothmann P, Bretzel G, Froeschl G, Wallrauch C, Zimmer T, Thiel V, Janke C, Guggemos W, Seilmaier M, Drosten C, Vollmar P, Zwirglmaier K, Zange S, Wölfel R, Hoelscher M (2020) Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. N Engl J Med 382(10):970–971. https://doi.org/10.1056/NEJMc200146810.1056/NEJMc2001468 ↗
37. Sharfstein JM, Becker SJ, Mello MM (2020) Diagnostic testing for the novel coronavirus. JAMA. https://doi.org/10.1001/jama.2020.386410.1001/jama.2020.3864 ↗
38. Shorten C, Khoshgoftaar TM (2019) A survey on image data augmentation for deep learning. J Big Data 6(1):6010.1186/s40537-019-0197-0 ↗
39. Singhal T (2020) A review of coronavirus disease-2019 (COVID-19). Indian J Pediatr 87(4):281–286. https://doi.org/10.1007/s12098-020-03263-610.1007/s12098-020-03263-6 ↗
40. Tu P-L, Chung J-Y (1992) A new decision-tree classification algorithm for machine learning, in Proceedings Fourth International Conference on Tools with Artificial Intelligence TAI ‘92, pp. 370–377, https://doi.org/10.1109/TAI.1992.24643110.1109/TAI.1992.246431 ↗
41. Waheed A, Goyal M, Gupta D, Khanna A, Al-Turjman F, Pinheiro PR (2020) CovidGAN: data augmentation using auxiliary classifier GAN for improved Covid-19 detection. IEEE Access 8:91916–91923. https://doi.org/10.1109/ACCESS.2020.299476210.1109/ACCESS.2020.2994762 ↗
42. Worldometer (2020) Countries where Coronavirus has spread – Worldometer. https://www.worldometers.info/coronavirus/countries-where-coronavirus-has-spread/ (accessed Jul. 10, 2020)
43. Xiao Y, Wu J, Lin Z, Zhao X (2018) A deep learning-based multi-model ensemble method for cancer prediction. Comput Methods Prog Biomed 153:1–9. https://doi.org/10.1016/j.cmpb.2017.09.00510.1016/j.cmpb.2017.09.005 ↗