Feature selection for effective prediction of SARS-COV-2 using machine learning

Ali L, Khan SU, Golilarz NA, Yakubu I, Qasim I, Noor A, Nour R (2019) A feature-driven decision support system for heart failure prediction based on statistical model and gaussian naive bayes. Comput Math Methods Med

Batra R, Olivieri LG, Rubin D, Vallari A, Pearce SK, Olivo A, Prostko JC, Nebbia G, Douthwaite ST, Rodgers MA, Cloherty GA (2020) A comparative evaluation between the abbott panbio™ covid-19 igg/igm rapid test device and abbott architect™ sars cov-2 igg assay. J Clin Virol 132:104645–104645

Article  CAS  PubMed  PubMed Central  Google Scholar 

Berrar DP (2019) Bayes’ theorem and naive bayes classifier. In: Encyclopedia of Bioinformatics and Computational Biology

Cunningham P, Delany SJ (2021) k-nearest neighbour classifiers—a tutorial. ACM Comput Surv (CSUR) 54:1–25

Article  Google Scholar 

de Fátima Cobre A, Stremel DP, Noleto GR, Fachi MM, Surek M, Wiens A, Tonin FS, Pontarolo R (2021) Diagnosis and prediction of covid-19 severity: can biochemical tests and machine learning be used as prognostic indicators? Comput Biol Med 134:104531. https://doi.org/10.1016/j.compbiomed.2021.104531

Article  CAS  Google Scholar 

Duerr R, Dimartino D, Marier C, Zappile P, Levine S, François F, Iturrate E, Wang G, Dittmann M, Lighter J, et al. (2021) Clinical and genomic signatures of rising sars-cov-2 delta breakthrough infections in new york. medRxiv

Duerr R, Dimartino D, Marier C, Zappile P, Levine S, Francois F, Iturrate E, Wang G, Dittmann M, Lighter J, Elbel B, Troxel AB, Goldfeld KS, Heguy A (2022) Clinical and genomic signatures of SARS-CoV-2 Delta breakthrough infections in New York. EBioMedicine 82:104141. https://doi.org/10.1016/j.ebiom.2022.104141

Dutta NK, Mazumdar K, Gordy JT (2020) The nucleocapsid protein of sars-cov-2: a target for vaccine development. J Virol 94(13): e00647–20. https://doi.org/10.1128/JVI.00647-20.

Dutta N, Mazumdar K, Lee B, Baek M, Kim D, Na Y, Park S, Lee H, Kariwa H, Mai L, Park J (2008) Search for potential target site of nucleocapsid gene for the design of an epitope-based sars dna vaccine. Immunol Lett 118(1):65–71. https://doi.org/10.1016/j.imlet.2008.03.003

Article  CAS  PubMed  PubMed Central  Google Scholar 

Emms D, Kelly S (2018) Orthofinder2: fast and accurate phylogenomic orthology analysis from gene sequences. BioRxiv 466201

Geurts P, Ernst D, Wehenkel L (2006) Extremely randomized trees. Mach Learn 36(1):3–42

Article  Google Scholar 

Goraichuk IV, Arefiev V, Stegniy BT, Gerilovych AP (2021) Zoonotic and reverse zoonotic transmissibility of sars-cov-2. Virus Res 302:198473

Article  CAS  PubMed  Google Scholar 

Grant R, Charmet T, Schaeffer L, Galmiche S, Madec Y, Von Platen C, Chény O, Omar F, David C, Rogoff A, Paireau J, Cauchemez S, Carrat F, Septfons A, Levy-Bruhl D, Mailles A, Fontanet A (2022) Impact of sars-cov-2 delta variant on incubation, transmission settings and vaccine effectiveness: Results from a nationwide case-control study in france. Lancet Reg Health - Europe 13:100278. https://doi.org/10.1016/j.lanepe.2021.100278

Article  PubMed  Google Scholar 

Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV (2020) Genomic determinants of pathogenicity in sars-cov-2 and other human coronaviruses. Proc Natl Acad Sci 117(26):15193–15199

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jackins V, Vimal S, Kaliappan M, Lee MY (2021) Ai-based smart prediction of clinical disease using random forest classifier and naive bayes. J Supercomput 77(5):5198–5219

Article  Google Scholar 

Jiang G, Wang W (2017) Error estimation based on variance analysis of k-fold cross-validation. Pattern Recognit. 69:94–106

Article  Google Scholar 

Johnson MC, Lyddon TD, Suarez R, Salcedo B, LePique M, Graham M, Ricana C, Robinson C, Ritter DG (2020) Optimized pseudotyping conditions for the sars-cov-2 spike glycoprotein. J Virol 94(21):e01062-20

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kang S, Yang M, Hong Z, Zhang L, Huang Z, Chen X, He S, Zhou Z, Zhou Z, Chen Q, Yan Y, Zhang C, Shan H, Chen S (2020) Crystal structure of sars-cov-2 nucleocapsid protein rna binding domain reveals potential unique drug targeting sites. Acta Pharm Sin B 10(7):1228–1238. https://doi.org/10.1016/j.apsb.2020.04.009

Article  CAS  PubMed  PubMed Central  Google Scholar 

Katoh K, Standley DM (2016) A simple method to control over-alignment in the mafft multiple sequence alignment program. Bioinformatics 32(13):1933–1942

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laatifi M, Douzi S, Bouklouz A, Ezzine H, Jaafari J, Zaid Y, El Ouahidi B, Naciri M (2022) Machine learning approaches in covid-19 severity risk prediction in morocco. J Big Data 9(1):1–21

Article  Google Scholar 

Marrocco C, Tortorella F (2016) Exploiting coding theory for classification: an ldpc-based strategy for multiclass-to-binary decomposition. Inf Sci 357:88–107

Article  Google Scholar 

Miao F, Cai YP, Zhang YX, Fan XM, Li Y (2018) Predictive modeling of hospital mortality for patients with heart failure by using an improved random survival forest. IEEE Access 6:7244–7253. https://doi.org/10.1109/ACCESS.2018.2789898

Article  Google Scholar 

Mlcochova P, Kemp S, Dhar M, Papa G, Meng B, Ferreira I, Datir R, Collier D, Albecka A, Singh S, et al (2021) Cov-2 genomics consortium (insacog). In: Genotype to Phenotype Japan (G2P-Japan) Consortium, pp 114–119

Oronsky B, Larson C, Caroen S, Hedjran F, Sanchez A, Prokopenko E, Reid T (2022) Nucleocapsid as a next-generation covid-19 vaccine candidate. Int J Infect Dis 122:529–530. https://doi.org/10.1016/j.ijid.2022.06.046

Article  CAS  PubMed  PubMed Central  Google Scholar 

Palimkar P, Shaw RN, Ghosh A (2022) Machine learning technique to prognosis diabetes disease: Random forest classifier approach. In: Bianchini M, Piuri V, Das S, Shaw RN (eds) Advanced Computing and Intelligent Technologies, Singapore. Springer, Singapore, pp 219–244

Chapter  Google Scholar 

Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS (2021) Sars-cov-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 102(4)

Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E (2011) Scikit-learn: machine learning in Python. J Mach Learn Res 12:2825–2830

Google Scholar 

Pisner D, Schnyer DM (2020) Support vector machine. Mach Learn

Prasad AM, Iverson LR, Liaw A, Liaw A (2006) Newer classification and regression tree techniques: Bagging and random forests for ecological prediction

Preto AJ, Moreira IS (2020) Spotone: Hot spots on protein complexes with extremely randomized trees via sequence-only features. Int J Mol Sci 21(19). https://doi.org/10.3390/ijms21197281

Saito T, Rehmsmeier M (2015) The precision-recall plot is more informative than the roc plot when evaluating binary classifiers on imbalanced datasets. PLoS ONE 10(3):e0118432

Article  PubMed  PubMed Central  Google Scholar 

Schwenker F, Trentin E (2014) Pattern classification and clustering: a review of partially supervised learning approaches. Pattern Recognit Lett 37:4–14. https://doi.org/10.1016/j.patrec.2013.10.017

Article  Google Scholar 

Sigal A (2022) Milder disease with omicron: is it the virus or the pre-existing immunity? Nat Rev Immunol 22(2):69–71

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tallei TE, Alhumaid S, AlMusa Z, Kusumawaty D, Alynbiawi A, Alshukairi AN, Rabaan AA (2022) Update on the omicron sub-variants ba. 4 and ba. 5. Rev Med Virol e2391

Tang F, Hammel IS, Andrew MK, Ruiz JG (2022) Covid-19 mrna vaccine effectiveness against hospitalisation and death in veterans according to frailty status during the sars-cov-2 delta (b. 1.617. 2) variant surge in the usa: a retrospective cohort study. Lancet Healthy Longev

Torres-Vásquez M, Chávez-Bosquez O, Hernández-Ocaña B, Hernández-Torruco J (2020) Classification of guillain-barré syndrome subtypes using sampling techniques with binary approach. Symmetry 12(3). https://doi.org/10.3390/sym12030482

Tuekprakhon A, Nutalai R, Dijokaite-Guraliuc A, Zhou D, Ginn HM, Selvaraj M, Liu C, Mentzer AJ, Supasa P, Duyvesteyn HM et al (2022) Antibody escape of sars-cov-2 omicron ba. 4 and ba. 5 from vaccine and ba. 1 serum. Cell 185(14):2422–2433

Article  CAS  PubMed  PubMed Central  Google Scholar 

van den Hoogen LL, Smits G, van Hagen CC, Wong D, Vos ER, van Boven M, de Melker HE, van Vliet J, Kuijer M, Woudstra L, Wijmenga-Monsuur AJ, GeurtsvanKessel CH, Stoof SP, Reukers D, Wijsman LA, Meijer A, Reusken CB, Rots NY, van der Klis FR, van Binnendijk RS, den Hartog G (2022) Seropositivity to nucleoprotein to detect mild and asymptomatic sars-cov-2 infections: a complementary tool to detect breakthrough infections after covid-19 vaccination? Vaccine 40(15):2251–2257. https://doi.org/10.1016/j.vaccine.2022.03.009

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang K, Zuo P, Liu Y, Zhang M, Zhao X, Xie S, Zhang H, Chen X, Liu C (2020) Clinical and laboratory predictors of in-hospital mortality in patients with coronavirus disease-2019: a cohort study in Wuhan, China. Clin Infect Dis 71(16):2079–2088

Article  CAS  PubMed  Google Scholar 

Wu C, Qavi AJ, Hachim A, Kavian N, Cole AR, Moyle AB, Wagner ND, Sweeney-Gibbons J, Rohrs HW, Gross ML et al (2021) Characterization of sars-cov-2 nucleocapsid protein reveals multiple functional consequences of the c-terminal domain. Iscience 24(6):102681

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu P, Ye H, Cai X, Li C, Li S, Chen M, Wang M, Heidari AA, Chen M, Li J et al (2021) An effective machine learning approach for identifying non-severe and severe coronavirus disease 2019 patients in a rural chinese population: the wenzhou retrospective study. Ieee Access 9:45486–45503

Article  PubMed  Google Scholar 

Zareapoor M, Shamsolmoali P (2015) Application of credit card fraud detection: Based on bagging ensemble classifier. Procedia Comput Sci 48:679–685

Article  Google Scholar 

Zeng H, Edwards MD, Liu G, Gifford DK (2016) Convolutional neural network architectures for predicting dna-protein binding. Bioinformatics 32(12):i121–i127

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhou JT, Tsang IWH, Ho SS, Müller KR (2019) N-ary decomposition for multi-class classification. Mach Learn 108:809–830

Article  Google Scholar 

Comments (0)

No login
gif