Machine learning techniques in disease forecasting: a case study on rice blast prediction

Abstract

Background: Diverse modeling approaches viz. neural networks and multiple regression have been followed to date for disease prediction in plant populations. However, due to their inability to predict value of unknown data points and longer training times, there is need for exploiting new prediction softwares for better understanding of plant-pathogen-environment relationships. Further, there is no online tool available which can help the plant researchers or farmers in timely application of control measures. This paper introduces a new prediction approach based on support vector machines for developing weather-based prediction models of plant diseases.

Results: Six significant weather variables were selected as predictor variables. Two series of models (cross-location and cross-year) were developed and validated using a five-fold cross validation procedure. For cross-year models, the conventional multiple regression (REG) approach achieved an average correlation coefficient (r) of 0.50, which increased to 0.60 and percent mean absolute error (%MAE) decreased from 65.42 to 52.24 when back-propagation neural network (BPNN) was used. With generalized regression neural network (GRNN), the r increased to 0.70 and %MAE also improved to 46.30, which further increased to r = 0.77 and %MAE = 36.66 when support vector machine (SVM) based method was used. Similarly, cross-location validation achieved r = 0.48, 0.56 and 0.66 using REG, BPNN and GRNN respectively, with their corresponding %MAE as 77.54, 66.11 and 58.26. The SVM-based method outperformed all the three approaches by further increasing r to 0.74 with improvement in %MAE to 44.12. Overall, this SVM-based prediction approach will open new vistas in the area of forecasting plant diseases of various crops.

Conclusion: Our case study demonstrated that SVM is better than existing machine learning techniques and conventional REG approaches in forecasting plant diseases. In this direction, we have also developed a SVM-based web server for rice blast prediction, a first of its kind worldwide, which can help the plant science community and farmers in their decision making process. The server is freely available at http://www.imtech.res.in/raghava/rbpred/.

Figure 1

Observed and predicted mean disease severity based comparison of prediction accuracy of multiple regression (REG), backpropagation neural network (BPNN), generalized regression neural network (GRNN) and support vector machine (SVM) approaches for 'cross-location models' during year(s) 2000 (A); 2001 (B); 2002 (C); 2003 (D); and during 2004 (E).

Figure 2

Observed and predicted mean disease severity based comparison of prediction accuracy of multiple regression (REG), backpropagation neural network (BPNN), generalized regression neural network (GRNN) and support vector machine (SVM) approaches for 'cross-year models' at Palampur-I (early transplanting) (A); at Palampur-II (normal transplanting) (B); at Palampur-III (late transplanting) (C); at Rice Research Station, Malan (D); and at farmers' fields, Pharer (E).

Figure 3

An overview of submission form for online prediction of rice blast severity with 'RB-Pred' web server.