Computational intelligence to study the importance of characteristics in flood-irrigated rice

Palavras-chave: Oryza sativa L.; multiple regression; computational intelligence; machine learning.

Resumo

The study of traits in crops enables breeders to guide strategies for selecting and accelerating the progress of genetic breeding. Although the simultaneous evaluation of characteristics in the plant breeding programme provides large quantities of information, identifying which phenotypic characteristic is the most important is a challenge facing breeders. Thus, this work aims to quantify the best approaches for prediction and establish a network of better predictive power in flood-irrigated rice via methodologies based on regression, artificial intelligence, and machine learning. Multiple regression, computational intelligence, and machine learning were used to predict the importance of the characteristics. Computational intelligence and machine learning were notable for their ability to extract nonlinear information from model inputs. Predicting the relative contribution of auxiliary characteristics in rice through computational intelligence and machine learning proved to be efficient in determining the relative importance of variables in flood-irrigated rice. The characteristics indicated to assist in decision making are flowering, number of grains filled by panicles and length of panicles for this study. The network with only one hidden layer with 15 neurons was observed to be efficient in determining the relative importance of variables in flooded rice.

Downloads

Não há dados estatísticos.

Referências

Anacleto, R. Cuevas, R. P., Jimenez, R., Llorente, C., Nissila, E., Henry, R., Sreenivasulu, N. (2015). Prospects of breeding high-quality rice using post-genomic tools. Theoretical and Applied Genetics, 128(8), 1449-1466. DOI: https://doi.org/10.1007/s00122-015-2537-6

Beck, M. W. (2018). NeuralNetTools: Visualization and analysis tools for neural networks. Journal of Statistical, 85(11), 1-20. DOI: http://dx.doi.org/10.18637 / jss.v085.i11

Beucher, A., Møller, A. B., & Greve, M. H. (2019). Artificial neural networks and decision tree classification for predicting soil drainage classes in Denmark. Geoderma, 352, 351-359. DOI: https://doi.org/10.1016/j.geoderma.2017.11.004

Cruz, C. D. (2016). Genes Software – extended and integrated with the R, Matlab and Selegen. Acta Scientiarum. Agronomy, 38(4), 547-552. DOI: http://dx.doi.org/10.4025/actasciagron.v38i4.32629

Cruz, C. D., & Nascimento, M. (2018). Inteligência computacional aplicada ao melhoramento genético. Viçosa, MG: Editora UFV.

De Oña, J., & Garrido, C. (2014). Extracting the contribution of independent variables in neural network models: a new approach to handle instability. Neural Computing and Applications, 25(3-4), 859-869. DOI: https://doi.org/10.1007/s00521-014-1573-5

Degenhardt, F., Seifert, S., & Szymczak, S. (2019). Evaluation of variable selection methods for random forests and omics data sets. Briefings in Bioinformatics, 20(2), 492-503. DOI: https://doi.org/10.1093/bib/bbx124

Evans, L. E., & Bhatt, G. M. (1977). Influence of seed size, protein content and cultivar on early seedling vigor in rice. Canadian Journal of Plant Science, 57(3), 929-935. DOI: https://doi.org/10.4141/cjps77-133

Fan, C., Xing, Y., Mao, H., Lu, T., Han, B., Xu, C., … Zhang, Q. (2006). GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 112(6), 1164-1171. DOI: https://doi.org/10.1007/s00122-006-0218-1

Ferreira, M. G., Azevedo, A. M., Siman, L. I., Silva, G. H., Carneiro, C. S., Alves, F. M., … Nick, C. (2017). Automation in accession classification of Brazilian Capsicum germplasm through artificial neural networks. Scientia Agricola, 73(3), 203-207. DOI: http://dx.doi.org/10.1590/1678-992X-2015-0451

Freitas, J. G., Cantarella, H., Salomon, M. V., Malovolta, V. M. A., Castro, L. H. S. M., Gallo, P. B., & Azzini, L. E. (2007). Produtividade de cultivares de arroz irrigado resultante da aplicação de doses de nitrogênio. Bragantia, 66(2), 317-325. DOI: http://dx.doi.org/10.1590/S0006-87052007000200016

Garson, G. D. (1991). Interpreting neural network connection weights. Artificial Intelligence Expert, 6, 46-51.

Gedeon, T. D., Wong, P. M., & Harris, D. (1995). Balancing bias and variance: network topology and pattern set reduction techniques. Berlin, Heidelberg, GE: Springer Berlin Heidelberg.

Ghani, I. M. M., & Ahmad, S. (2010). Stepwise multiple regression method to forecast fish landing. Procedia - Social and Behavioral Sciences, 8, 549-554. DOI: https://doi.org/10.1016/j.sbspro.2010.12.076

Gianola, D., Okut, H., Weigel, K. A., & Rosa, G. J. M. (2011). Predicting complex quantitative traits with Bayesian neural networks: a case study with Jersey cows and wheat. BMC Genetics, 12(87), 1-14. DOI: https://doi.org/10.1186/1471-2156-12-87

Goh, A. T. C. (1995). Back-propagation neural networks for modeling complex systems. Artificial Intelligence in Engineering, 9(3),143-151. DOI: https://doi.org/10.1016/0954-1810(94)00011-S

Gregorutti, B., Michel, B., & Saint-Pierre, P. (2017). Correlation and variable importance in random forests. Statistics and Computing, 27, 659-678. DOI: https://doi.org/10.1007/s11222-016-9646-1

Haddouche, R., Chetate, B., & Said Boumedine, M. (2018). Neural network ARX model for gas conditioning tower. International Journal of Modeling and Simulation, 39(3), 166-177. DOI: https://doi.org/10.1080/02286203.2018.1538848

Hassanzadeh, Z., Ghavami, R., & Kompany-Zareh, M. (2015). Radial basis function neural networks based on the projection pursuit and principal component analysis approaches: QSAR analysis of fullerene[C60]-based HIV-1 PR inhibitors. Medicinal Chemistry Research, 25, 19-29. DOI: https://doi.org/10.1007/s00044-015-1466-x

Hastie, T., Tibshirani, R., & Friedman, J. (2009). The elements of statiscal learning data mining, inference, and prediction (2nd ed.). New York, NY: Springer.

Huang, X., Zhao, Y. Wei, X., Li, C., Wang, A., Zhao, Q., … Han, B. (2012a) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 44, 32-39. DOI: https://doi.org/10.1038/ng.1018

Li, L., & Zha, Y. (2019). Estimating monthly average temperature by remote sensing in China. Advances in Space Research, 63(8), 2345-2357. DOI: https://doi.org/10.1016/j.asr.2018.12.039

Matlab. (2016). Software. Natick, MA: The MathWorks Inc.

Misra, G., Badoni, S., Anacleto, R., Graner, A., Alexandrov, N., & Sreenivasulu, N. (2017). Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice. Scientific Reports, 7(12478), 1-16. DOI: https://doi.org/10.1038/s41598-017-12778-6

Ntanos, D. A., & Koutroubas, S. D. (2002). Dry matter and Naccumulation and translocation for Indica and Japonica riceunder Mediterranean conditions. Field Crops Research, 74(1), 93-101. DOI: https://doi.org/10.1016/S0378-4290(01)00203-9

Olden, J. D., & Jackson, D. A. (2002). Illuminating the “black box”: a randomization approach for understanding variable contributions in artifical neural networks. Ecological Modelling, 154(1–2), 135-150. DOI: https://doi.org/10.1016/s0304-3800(02)00064-9

Osco, L. P., Ramos, A. P. M., Moriya, E. A. S., Bavaresco, L. G., Lima, B. C., Estrabis, N., ... Araújo, F. F. (2019). Modeling hyperspectral response of water-stress induced lettuce plants using artificial neural networks. Remote Sensing, 11(23), 1-15. DOI: https://doi.org/10.3390/rs11232797

Osco, L. P., Ramos, A. P. M., Pinheiro, M. M. F., Moriya, E. A. S., Imai, N. N., Estrabis, N., … Creste, J. E. (2020). A machine learning framework to predict nutrient content in valencia-orange leaf hyperspectral measurement. Remote Sensing, 12(6), 1-21. DOI: http://dx.doi.org/10.3390/rs12060906

Paliwal, M. & Kumar, U. A. (2011). Assessing the contribution of variables in feed forward neural network. Applied Soft Computing, 11, 3690-3696.

Parmley, K. A., Higgins, R. H., Ganapathysubramanian, B., Sarkar, S., & Singh, A. K. (2019). Machine learning approach for prescriptive plant breeding. Scientific Reports, 9(1), 1-12. DOI: https://doi.org/10.1038/s41598-019-53451-4

Paruelo, J. M., & Tomasel, F. (1997). Prediction of functional characteristics of ecosystems: a comparison of artificial neural networks and regression models. Ecological Modelling, 98(2-3), 173-186. DOI: https://doi.org/10.1016/s0304-3800(96)01913-8

Porwal, A., Carranza, E. J. M., & Hale, M. (2003). Artificial neural networks for mineral potential mapping; a case study from Aravalli Province, Western India. Natural Resources Research, 12(3), 155-171. DOI: https://doi.org/10.1023/A:1025171803637

Quinlan, J. R. (1996). Learning decision tree classifiers. ACM Computing Surveys, 28(1), 71-72. DOI: https://doi.org/10.1145/234313.234346

Roy, P. P., & Roy, K. (2008). On some aspects of variable selection for partial least squares regression models. QSAR & Combinatorial Science, 27(3), 302-313. DOI: https://doi.org/10.1002/qsar.200710043

Sant’Anna, I. C., Ferreira, R. A. D. C., Nascimento, M., Carneiro, V. Q., Silva, G. N., Cruz, C. D., ... Chagas, F. E. O. (2019). Multigenerational prediction of genetic values using genome-enabled prediction. PLoS ONE, 14(1), 1-14. DOI: https://doi.org/10.1371/journal.pone.0210531

Santos, R. P, Dean, D. L., Weaver, J. M., & Hovanski, Y. (2018). Identifying the relative importance of predictive variables in artificial neural networks based on data produced through a discrete event simulation of a manufacturing environment. International Journal of Modelling and Simulation, 39(4), 234-245. DOI: https://doi.org/10.1080/02286203.2018.1558736

Silva, G. N., Nascimento, M., Sant’Anna, I. C., Cruz, C. D., Caixeta, E. T., Carneiro, P. C. S., ... Oliveira, M. S. (2017). Artificial neural networks compared with Bayesian generalized linear regression for leaf rust resistance prediction in Arabica coffee. Pesquisa Agropecuária Brasileira, 52(3), 186-193. DOI: http://dx.doi.org/10.1590/s0100-204x2017000300009

Silva, G. N., Tomaz, R. S., Sant’anna, I. C., Nascimento, M., Bhering, L. L., & Cruz, C. D. (2014). Neural networks for predicting breeding values and genetic gains. Scientia Agricola, 71(6), 494-498. DOI: http://dx.doi.org/10.1590/0103-9016-2014-0057

Skawsang, S., Nagai, M., Nitin, K., & Soni, P. (2019). Predicting rice pest population occurrence with satellite-derived crop phenology, ground meteorological observation, and machine learning: A case study for the central plain of Thailand. Applied Sciences, 9(22), 1-19. DOI: https://doi.org/10.3390/app9224846

Somers, M. J., & Casal, J.C. (2009). Using artificial neural networks to model nonlinearity: The case of the job satisfaction-job performance relationship. Organizational Research Methods, 12(3), 403-417. DOI: https://doi.org/10.1177/1094428107309326

Sousa, I. C., Nascimento, M., Silva, G. N., Nascimento, A. C. C., Cruz, C. D., Fonseca, F., ... Caixeta, E. T. (2020). Genomic prediction of leaf rust resistance to Arabica coffee using machine learning algorithms. Scientia Agricola, 78(4), 1-8. DOI: http://dx.doi.org/10.1590/1678-992x-2020-0021

Tan, K., Li, E., Du, Q., & Du, P. (2014). An efficient semi-supervised classification approach for hyperspectral imagery. ISPRS Journal of Photogrammetry and Remote Sensing, 97, 36-45. http://dx.doi.org/10.1016/j.isprsjprs.2014.08.003.

Tsang, M., Cheng, D., & Liu, Y. (2017). Detecting statistical interactions from neural network weights. In 6th International Conference on Learning Representations (p. 1-21). Vancouver, CA: ICLR. DOI: https://doi.org/10.48550/arXiv.1705.04977

Yu, H., Campbell, M. T., Zhang, Q., Walia, H., & Morota, G. (2019). Genomic Bayesian confirmatory factor analysis and Bayesian network to characterize a wide spectrum of rice phenotypes. G3: Genes, Genomes, Genetics, 9(6), 1975-1986. DOI: https://doi.org/10.1534/g3.119.400154

Publicado
2022-11-22
Como Citar
Silva Junior, A. C. da, Sant’Anna, I. C., Silva, G. N., Cruz, C. D., Nascimento, M., Lopes, L. B., & Soares, P. C. (2022). Computational intelligence to study the importance of characteristics in flood-irrigated rice . Acta Scientiarum. Agronomy, 45(1), e57209. https://doi.org/10.4025/actasciagron.v45i1.57209
Seção
Melhoramento Vegetal

 

2.0
2019CiteScore
 
 
60th percentile
Powered by  Scopus

 

2.0
2019CiteScore
 
 
60th percentile
Powered by  Scopus