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Article

Using Hybrid Artificial Intelligence and Evolutionary Optimization Algorithms for Estimating Soybean Yield and Fresh Biomass Using Hyperspectral Vegetation Indices

by
Mohsen Yoosefzadeh-Najafabadi
1,
Dan Tulpan
2 and
Milad Eskandari
1,*
1
Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada
2
Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
*
Author to whom correspondence should be addressed.
Remote Sens. 2021, 13(13), 2555; https://doi.org/10.3390/rs13132555
Submission received: 25 April 2021 / Revised: 28 May 2021 / Accepted: 25 June 2021 / Published: 30 June 2021
(This article belongs to the Special Issue Deep Learning Methods for Crop Monitoring and Crop Yield Prediction)
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Abstract

:
Recent advanced high-throughput field phenotyping combined with sophisticated big data analysis methods have provided plant breeders with unprecedented tools for a better prediction of important agronomic traits, such as yield and fresh biomass (FBIO), at early growth stages. This study aimed to demonstrate the potential use of 35 selected hyperspectral vegetation indices (HVI), collected at the R5 growth stage, for predicting soybean seed yield and FBIO. Two artificial intelligence algorithms, ensemble-bagging (EB) and deep neural network (DNN), were used to predict soybean seed yield and FBIO using HVI. Considering HVI as input variables, the coefficients of determination (R2) of 0.76 and 0.77 for yield and 0.91 and 0.89 for FBIO were obtained using DNN and EB, respectively. In this study, we also used hybrid DNN-SPEA2 to estimate the optimum HVI values in soybeans with maximized yield and FBIO productions. In addition, to identify the most informative HVI in predicting yield and FBIO, the feature recursive elimination wrapper method was used and the top ranking HVI were determined to be associated with red, 670 nm and near-infrared, 800 nm, regions. Overall, this study introduced hybrid DNN-SPEA2 as a robust mathematical tool for optimizing and using informative HVI for estimating soybean seed yield and FBIO at early growth stages, which can be employed by soybean breeders for discriminating superior genotypes in large breeding populations.

Graphical Abstract

1. Introduction

Soybean (Glycine max (L.) Merr.) is one of the most economically important crops in the world that is used for food, feed and industrial products [1]. Increasing soybean yield has always been the main priority in breeding programs in order to keep pace with the needs of a fast-growing global population [2]. In addition, great attention has been paid to increase soybean fresh biomass (FBIO) due to its biorefinery properties [3]. It would be a significant investment for farmers to make a profit not only from yield but also from FBIO. Therefore, the simultaneous improvement in both yield and FBIO production in soybean seems to be necessary to meet the various demands in the near future. Improving yield and biomass that are considered as complex quantitative traits controlled by several genetic and environmental factors [4] requires significant time and financial investment in breeding programs. Pre-harvest prediction of soybean yield and FBIO will enabled plant breeders to accurately select promising genotypes in large breeding populations at early growth stage while reducing the cost and time in their cultivar development programs [5].
Due to recent advances in the high throughput, non-destructive phenotyping tools such as hyperspectral reflectance, the prediction of complex traits is now available at low cost in early growth stages [6]. Pre-harvest soybean yield and FBIO prediction are not only important for global food security and industrial policy making but also for field management practices [7,8]. Different approaches have been applied for crop yield and FBIO prediction, such as crop modeling and hyperspectral reflectance [7,9].
Proximal and remote sensing of spectral reflectance are known as non-destructive, non-invasive phenotyping approaches for measuring the spectral properties of plants at low cost in large breeding populations [5,10,11,12]. These methods are considered proximal when the spectral properties are collected in crops’ proximities [11]. The use of proximal/remote sensing for discriminating among genotypes with different potential is well documented in different crops such as wheat [12], alfalfa [13], rice [14], sorghum [15] and soybean [16]. The use of spectral properties of crops for predicting complex traits is genotype-specific and depends on the nature of the complex trait [17,18]. Therefore, it is necessary to evaluate and specify the possibilities of using spectral properties to predict complex traits for each plant species [16].
Several vegetation indices are generated from the spectral reflectance and commonly used for estimating important agronomic traits such as plant height, biomass, resistance to different diseases and yield in different plant species, including wheat [19], barley [20], cotton [21] and sorghum [22]. The normalized difference vegetation index (NDVI), for example, is known as an important spectral vegetation index, which is broadly used for monitoring seasonal growth developments in plants and estimating canopy biomass, photosynthesis rate, leaf area index and even yield formation [23,24]. Depending on specific bands used for calculating NDVI, different types of NDVI have been established [13]. The spectral vegetation indices are generally species-specific and, therefore, one of the major obstacles in their applications is their low prediction powers on morphological and physiological processes if they are not calibrated for the target plant species [6]. In addition, analyzing large hyperspectral reflectance data sets requires intensive computational and statistical analyses, which is still challenging in many plant breeding programs [25]. To address the latest issue, machine learning (ML) algorithms are considered as reliable and efficient computational approaches for predicting complex traits [13,26,27].
The functionality of ML algorithms is based upon developing empirical relationships between the target and input variables [13,28]. Therefore, several ML algorithms were implemented for predicting yield in many crops, including artificial neural networks [29], support vector regression [30] and random forests [16]. The successful use of ML algorithms has been documented in several plant species such as chrysanthemum [26], alfalfa [13], wheat [31], soybean [16,32] and maize [33].
As one of the important subsets of ML, deep learning (DL) can automatically learn from a large hierarchical representation of the data by using complex non-linear functions that are trained from the outputs of the previous layers [7,34]. Convolutional neural networks (CNN), deep neural networks (DNN) and long-short term memory (LSTM) are the three most commonly used DL methods that are broadly used in remote sensing [35], medical applications [36] and human activity recognition [37]. Although few studies have exploited DL for crop yield prediction [7,38], the implication of hyperspectral vegetation indices (HVI) for predicting soybean yield and FBIO has not been exploited.
Using only one ML algorithm, especially when the training dataset is small and limited, may result in some level of overfitting in the ultimate prediction [13,39]. In order to address this problem and improve the prediction performance of individual ML algorithms, different methods have been proposed [40]. One of these effective methods is the ensemble method, in which the prediction performance of different ML algorithms is combined to estimate the final prediction [41]. The principle of ensemble methods is built upon the divide-and-conquer paradigm [40]. This idea is usually implemented to find an optimal solution to the proposed problem [42]. The success application of ensemble methods to predict complex traits using related traits is well documented in maize [33], alfalfa [13] and sugarcane [43]. The three most commonly used ensemble algorithms are boosting, bagging and stacking [13,41]. Bagging was first introduced by Breiman [44] as a variance reduction method for several ML algorithms such as radial basis function and random forest [45]. The bagging method is based on the parallel ensemble algorithm, while boosting was introduced by Schapire [46] as a sequential ensemble model of base algorithms by using the dependencies of each ML algorithm [13,41]. Although boosting and bagging methods are commonly used for the combined homogeneous ML algorithms, stacking methods are mostly exploited for heterogeneous ML algorithms and adjust the difference between algorithms to increase the ultimate prediction accuracy [13,41,47].
In addition to the use of ensemble and DL methods for predicting yield and FBIO at early growth stages using HVI, it would be valuable to determine the optimum values of the HVI in genotypes with maximized yield and FBIO production. Therefore, the implementation of optimization algorithms can be beneficial to cultivar development programs. The successful use of optimization algorithms was explored in some areas of plant science such as plant tissue cultures [48,49] but not yet in the field of plant breeding. In order to concurrently maximize two or more traits, multi-objective evolutionary optimization algorithms can be employed for finding the optimal level of inputs for different objective functions [50]. One of the most commonly used multi-objective optimization algorithms is the improved version of the strength Pareto evolutionary algorithm 2 (SPEA2) [51]. To the best of our knowledge, this study is the first report of using the SPEA2 algorithm for optimizing HVI that can be used for selecting soybean genotypes with high yield and FBIO production potential within a breeding program. The main objectives of this study were: (1) investigating the potential benefit of using HVI for predicting soybean yield and FBIO; (2) the comparative analysis of the EB strategy and DNN algorithm to improve yield and FBIO prediction accuracies; and (3) introducing DNN-SPEA2 algorithms as a reliable tool for optimizing the HVI values associated with soybean genotypes with maximized yield and FBIO production. The outcome of this study can provide soybean breeders with new effective methods for selecting genotypes with high yield potential and FBIO production at early growth stages in large breeding populations.

2. Materials and Methods

2.1. Plant Material

In this study, phenotypic data were collected using 250 soybean genotypes, which are the core germplasms of the soybean breeding program at the University of Guelph, Ridgetown and are used for sustainable cultivar development and genetic studies.

2.2. Test Sites and Experimental Designs

The soybean genotypes were cultivated under the field condition at Ridgetown (42°27′14.8′′N 81°52′48.0′′W, 200 m above sea level) and Palmyra (42°25′50.1′′N 81°45′06.9′′W, 195 m above sea level) in 2018 and 2019 in Ontario, Canada (Figure 1). The experiments were conducted using randomized complete block designs (RCBD) with two replications in four environments (two locations and two years), consisting of 2000 research plots in total. Each plot consisted of five rows, 4.2 m long each and 40 cm spacing between each row and the seedling rate was 50–57 seeds per m2. All phenotypic data were adjusted using nearest neighbor analysis (NNA) to remove the possible spatial variation in the field [52,53,54].

2.3. Data Acquisition

2.3.1. Field Data Collection

Seed yield (kg ha−1) for each plot was measured by harvesting three middle rows and adjusted to 13% moisture. The above-ground biomass samples (g m−2) for each plot were collected at the beginning seed (R5) growth stage [55] in 1.0 m sections per row that were randomly selected among designated sections. The best linear unbiased prediction (BLUP) was implemented in order to estimate the average phenotyping plots for each soybean genotype [56].

2.3.2. Hyperspectral Reflectance Data Collection

In each plot, the hyperspectral reflectance properties were acquired at the R5 growth stage using UniSpec-DC Spectral Analysis System (PP Systems International, Inc. 110 Haverhill Road, Suite 301, Amesbury, MA, USA). The device covers 250 reflectance bands ranging between 350–1100 nm with a bandwidth of 3 nm. The sensors were able to cover a sample area of 0.25 m2 due to their 25° field-of-view properties. The “proximal sensing” method was used for measuring hyperspectral reflectance due to the proximity of the sensor to the canopy. For calibrating and reducing the incoming solar radiation, the dark reference and the Spectralon panels were used for the dual and basal channels, respectively. In addition, all hyperspectral reflectance data were collected as close to solar noon as possible for minimizing the signal noise associated with the environment.

2.4. Data Pre-Processing and Statistical Analyses

Several random noises occurring across the whole spectra can lead to misinterpretation of the results. This is mainly caused by electronic and sensor fluctuations [57]. Therefore, three hyperspectral reflectance measurements were conducted for each plot and the BLUP values were calculated for hyperspectral reflectance bands. In addition, hyperspectral reflectance data at the upper (1005–1100 nm) and lower (350–395 nm) edges of the spectra were eliminated from the original data. Data centering, scaling and a Savitzky–Golay filter were applied for improving spectral properties and signal-to-noise ratio [58,59]. All the pre-processing procedures were conducted using the R software, version 3.6.1.

2.5. Hyperspectral Vegetation Index (HVI) Extraction

In order to reduce the hyperspectral data dependency, the vegetation indices were used to predict the soybean yield and FBIO instead of using the original reflectance bands. Therefore, 34 vegetation indices were selected based on the published papers (Table 1), each characterizing two spectral bands. The used vegetation indices were categorized into the two most well-known indices, the normalized difference vegetation index (NDVI) and the simple ratio index (SRI). In this study, the 34 vegetation indices were considered as the input variables and yield or FBIO was tagged as the target variable. The Pearson correlation coefficients among input and output variables was evaluated in order to estimate the relevancy of each HVI to the soybean yield and FBIO.

2.6. Variable Selection

One of the important approaches to determine the relationship between input and output variables is sensitivity analysis [60]. Several methods were developed and used for sensitivity analysis in different fields of studies such as predicting crash frequency [60], crash injury severity prediction [61], computer science [62] and plant science [16]. Recently developed sensitivity analysis methods for variable or feature selection techniques are usually used to determine important input variables in predicting given target traits. In this study, recursive feature elimination (RFE), as one of the most common wrapper methods, was applied for estimating the importance of selected HVI for predicting yield and FBIO. Due to its easy to configure property [63], RFE has the ability to effectively extract important variables in a short time. More detail about the RFE can be found in Yoosefzadeh-Najafabadi, et al. [16]. All the RFE analyses were carried out through the caret package [64] in R software, version 3.6.1.

2.7. Yield and FBIO Prediction Model Calibration and Validation

2.7.1. Ensemble Method (Ensemble-Bagging Algorithm)

Three of the most common used ML algorithms, i.e., the radial basis function (RBF), support vector regression (SVR) and random forest (RF), were selected as the base learners for the ensemble method. RBF is a neural network algorithm, which applies approximate multivariate functions to predict the output variable using multi-dimensional input variables [87,88]. SVR is a regression version of the support vector machine algorithm that uses hyperplanes to discover the optimal separation of values in output variables [89]. In SVR, the input and output variables are transformed based on kernel functions from the original space to a support vectors space and the linear function is used to eliminate errors between the insensitive loss function and the training data [13,90]. The third ML algorithm used in this study was RF, which is based on generating a series of trees representing a subset of independent observations [91] and estimates the final prediction by averaging the production of all determined trees [48]. We implemented an EB based on the bagging strategy to improve the prediction performance of individual algorithms as described by Ye, et al. [90]. For this aim, we combined all the prediction performance of the tested ML algorithms and selected the one with the highest performance as the MetaClassifier for the EB. Each parameter in the tested ML algorithms was tuned and adjusted based on the input/output variables. All ML and EB analyses were conducted using the workbench for machine learning (Weka) software version 3.9.4 [92].

2.7.2. Deep Neural Network (DNN)

Thanks to recent advances in the performance of complex computational procedures, several DNN approaches have been introduced with multiple processing hidden layers [93]. The DNN algorithm has the ability to learn the multivariate mapping function between the output and input variables. The scheme of the used DNN algorithm is illustrated in Figure 2. In this study, the multilayer perceptron (MLP) as one of the feed-forward neural networks was used to predict the soybean yield and FBIO at an early growth stage using HVI. The structure and function of MLP were explained in detail by Pal and Mitra [94]. In brief, MLP contains input, output and hidden layers of M interconnected neurons. Each layer in the MLP algorithm has full connections to the next layer, so the output of layer M would be the input of the M +1 layer [95]. In this study, optimizing MLP parameters was conducted using GUI editors in Weka software version 3.9.4. In general, there were four hidden layers with 17 nodes in each layer, a learning rate of 0.3 and a momentum of 0.2 (Figure 2).

2.8. Optimization Process (SPEA2 Algorithm)

Multi-objective optimization algorithms are usually implemented for two or more than two outputs that sometimes are in conflict with each other. SPEA2 is a sophisticated optimization algorithm that can be successfully implemented for finding the optimum Pareto front solutions (Figure 3). In this study, based on the best algorithms for soybean yield and FBIO predictions, we used SPEA2 to find the optimum levels of HVI for maximizing yield and FBIO as objective functions. The main steps of SPEA2 were summarized in Figure 3. To achieve the best results, population size along with three of the most important parametric mechanisms in the SPEA2 algorithm (i.e., crossover, selection and mutation operations) were determined [96]. The overall population size, generation number, uniform crossover and mutation rate were respectively set to 400, 1000, 0.8 and 0.6. The two-point crossover method was used to select elite populations for crossover and obtain the appropriate fitness. More details about the SPEA2 environmental selection methods and fitness assignment can be found in [97].

2.9. Quantification of Model Performance and Error Estimations

In order to quantify the performance of EB and DNN for predicting soybean yield and FBIO using HVI, the 250 soybean genotypes were randomly split into testing and training sets by using five k-fold cross-validations (80–20% splits) with ten repetitions (Figure 4) and root mean square error (RMSE, Equation (1)), mean absolute errors (MAE, Equation (2)) and coefficient of determination (R2, Equation (3)) were measured as follows:
R M S E = ∑ ( Y ′ − Y ) 2 n
M A E = ∑ i = 1 n | Y ′ i − Y i | n
R 2 = S S T − S S E S S T
where, Y′ and Y are the predicted and measured values, respectively, n is the number of observations, SST stands for the sum of squares for total and SSE stands for the sum of the squares for error.

3. Results

3.1. Yield, FBIO and HVI Properties

In this study, the average FBIO of the 250 soybean genotypes grown in four environments had the range of 1366.9 to 2548.5 g m−2 with a mean and standard deviation of 1948.9 and 336.36 g m−2, respectively. The average yield of the 250 soybean genotypes ranged from 2.38 to 5.71 ton ha−1 with a mean of 4.19 ton ha−1 and a standard deviation of 0.58 ton ha−1. The distributions of soybean yield and FBIO production for each genotype across the four environments are shown in Figure 5. In general, the variation in the yield was larger than for the FBIO among soybean genotypes across the environments.

3.2. Correlation Analysis of HVI vs. Soybean Yield and FBIO

The linear associations of HVI with yield and FBIO was measured using Pearson correlation coefficients (Figure 6 and Table S1). All HVI showed significant correlations with both soybean yield and fresh biomass. Among all the tested HVI, three of them had positive correlations and 31 HVI showed negative correlations with both soybean yield and FBIO. While S14 showed the highest positive correlation (0.71) with yield, the highest negative correlation was found to be between N5 and yield (−0.84). S1 showed the lowest positive correlation with the soybean yield (0.60) and the lowest negative correlation was with N1 (−0.15). Regarding the correlation of HVI with soybean FBIO, S9 had the highest positive correlation (0.75) and N5 had the highest negative correlation (−0.90). The lowest positive and negative correlations with FBIO were found with S1 (0.62) and N1 (−0.18). Since all the tested HVI were significantly correlated with soybean yield and FBIO, all HVI was used as the input variables in EB and DNN algorithms (Table S1).

3.3. Comparative Analysis of the EB and DNN Algorithms

One of the objectives of this study was to compare the efficacy of EB and DNN algorithms for predicting soybean yield and FBIO from HVI data collected at the R5 growth stage. Among all the tested ML algorithms used for establishing the EB method, the SVR algorithm outperformed the other algorithms (Tables S2 and S3) and, therefore, was selected as the MetaClassifier for the EB strategy. The results of this study showed that the EB method had a slightly, but not significantly, higher R2 values (0.77) over DNN (0.76) in predicting yield from HVI (Figure 7A), with the lowest RMSE and MAE values of 224.97 and 149.28 kg ha−1, respectively (Figure 7B,C). Regarding the FBIO prediction results, the highest R2 was obtained using DNN with the value of 0.91 (Figure 7D). The DNN algorithm also had the lowest RMSE and MAE values of 102.66 and 80.09 g m−2, respectively (Figure 7E,F).

3.4. Variable Selection

In this study, RFE as one of the common variable selection methods was used in order to select the top 10 important HVI in predicting the yield and FBIO. The results (Figure 8) showed that N5 had the highest importance value in predicting both yield (11.24) and FBIO (12.49), followed by the RNDVI, S8, N2 and S6 indices as the most important HVI in explaining soybean yield and FBIO. While the least important HVI for predicting yield was found to be S1 (0.014), N10 (0.70) was the least important HVI for predicting FBIO. The prediction accuracy of both EB and DNN for predicting the soybean seed yield and FBIO using the selected 10 HVI was found not to be significantly lower than what were obtained using all the 35 HVI (data were not shown).

3.5. The DNN-SPEA2 Optimization Algorithm

The DNN algorithm, with the highest prediction accuracies for predicting both soybean yield and FBIO from HVI, was selected and linked to the SPEA2 optimization algorithm for estimating the optimized values of HVI in soybean genotypes with maximized yield, 4445.2 kg·ha−1 and FBIO, 2254.8 g·m−2 (Figure 9).

4. Discussion

Several studies have reported significant associations between HVI and the two important agronomic traits of yield and FBIO production in several crop species, such as sorghum [98], corn [99], rice [100], potato [101] and wheat [102]. In this study, we also confirmed significant correlations between HVI and both yield and FBIO by evaluating 250 soybean genotypes across four environments. All the tested HVI were extracted based on the previous studies and their correlations with the tested variables (yield and FBIO). Similarly, the tested HVI were selected from different spectral regions (e.g., blue, green, red, red-edge and near-infrared regions) to investigate the potential use of different spectral regions in predicting soybean seed yield and FBIO. The visible region of the spectra (blue, green and red) region is absorbed by the epidermis and palisade mesophyll due to the presence of chloroplast and plant pigments that use the light to drive photosynthesis [103,104]. Chlorophyll a, chlorophyll b and plant pigments absorb light to drive photosynthesis [105]. The near-infrared (700–1300 nm) region is mainly absorbed by spongy mesophyll in the plant, which is known as a good stress indicator [104]. One of the most vital portions of the reflectance spectra is the red edge because, in this region, plant pigments stopped absorbing light and began to reflect it [106]. Generally, with these measurements of the light that is reflected by the plant canopy, chlorophyll content, biomass, yield, abiotic stress and disease can be estimated [107,108,109].
Among all the tested HVI, N5 had the highest negative correlation with both yield and FBIO. The N5 index consists of two specific wavelengths, 800 nm and 670 nm [68]. The 670 nm band located in the red region of the spectral was previously introduced as one of the most important reflectance bands in agricultural studies [110,111,112,113]. This reflectance band has shown strong correlation with the chlorophyll contents in plants, which is considered as one of the most pivotal components in determining the ultimate yield and FBIO production [114]. The 800 nm band is placed within the near-infrared region of the spectrum [110,115] and has been previously reported to be involved in characterizing the structure of the leaves in plants. More specifically, this band is associated with different levels of liquid water in the inter-cellular spaces of leaves [116]. Changes in the balance of water and air in the inter-cellular space in leaves have significant impact on ultimate yield and FBIO production [117]. Based on our previous report [16], the red region, which is ranged mostly from 655 to 675 nm, had the highest association with the soybean yield formation. In this study, we found the importance of red wavelength in predicting FBIO as well. Therefore, N5 can be considered as one of the most informative indices for predicting the final yield and FBIO production in soybean and, therefore, for discriminating genotypes with different genetic potential for the two traits.
Among all the tested HVI, the S14 and S9 indices had the highest positive correlations with yield and FBIO, respectively. The S14 index, introduced by Mutanga and Skidmore [72], has consisted of only red-edge reflectance bands. The S9 index, which was proposed by Chappelle, et al. [83], is built upon both red and red-edge reflectance regions. The red-edge reflectance bands have been reported to have strong correlations with the chlorophyll contents and used as an explanatory indicator for senescence and stress in plants [110,118]. Several studies reported the efficiency of using red and red-edge regions in discriminating plant characteristics such as yield [119], biomass [120] and disease [121]. The potential yield and FBIO production of a given genotype can be estimated by the level of chlorophyll and the senescence rate, especially at the later development stages [122]. In this study, the hyperspectral reflectance data were collected at the R5 growth and development stage, in which pods and seeds are developing, and plants have initiated the senescence from the lower leaves. These special properties of the two indices can explain their high positive correlations with yield and FBIO. In addition, RFE analysis indicated the high importance score for N5 in predicting soybean yield and FBIO. N5 consisted of two reflectance bands, 670 and 800 nm, which were placed in red and near-infrared regions, respectively. Our previous study also obtained the high importance score for the near-infrared regions and red regions in predicting soybean yield classes, specifically the high yielding class [16]. Here, the efficiency of using these two reflectance bands in predicting soybean yield and FBIO was verified as single hyperspectral vegetation indices.
In general, qualitative traits can be analyzed using conventional statistical methods [123,124]; however, estimating complex quantitative traits such as yield and FBIO from HVI data sets in large breeding populations require more sophisticated statistical methods such as machine or deep learning algorithms [89]. Recently, the use of ML algorithms was successfully reported in many crop species such as soybean [16], wheat [12], chrysanthemum [49], alfalfa [13] and rice [30]. However, in some cases, the potential issue of overfitting through using individual ML algorithms is inevitable [125]. To overcome this shortage, different ensemble algorithms have been introduced, in which the outcomes of different ML algorithms are combined for better predictive performance [126]. In this study, the RBF, SVR and RF algorithms were used as individual ML algorithms to construct the ensemble strategy based on the bagging principles and SVR with the highest accuracy was selected as the MetaClassifier.
The superior accuracy performance of SVR, compared to other ML algorithms tested in this study, can be due to the use of structural than empirical risk minimization inductive principles [26,127]. In addition to EB, the DNN algorithm was also used to predict soybean yield and FBIO production using HVI. Recently, DNN algorithms have attracted the attention from several researchers in different areas such as object detection [128], image processing [129], disease detection [130] and various engineering areas [131]. The DNN algorithms are commonly used in non-linear problems because they are easy to implement and can overcome the adverse effect of data dimensionality [132]. Although there are some ambiguities around considering MLP as a type of DNN, several studies reported MLP as a subset of DNN [95,133,134]. In this study, the DNN algorithm outperformed the EB algorithm since DNN has the ability to learn the weights between nodes through unsupervised learning instead of generating weights randomly in the initialization stage [135]. After that, DNN tries to adjust weights during the learning process. This property can improve the prediction accuracy of DNN in compared to other ML algorithms.
One of the most important objectives for plant breeders is to improve the discrimination ability among plant genotypes with different yield and FBIO potentials in large breeding populations, directly or indirectly [136]. Direct selection methods are focused on selecting the superior genotypes based on the average performance of the target trait across many locations and over several years, while indirect selections are based upon selecting for high heritable secondary traits that are strongly associated with the target trait [137]. Therefore, efficient plant breeding programs are established based on combined direct and indirect selection strategies to maximize the accuracy of the selections [12,137,138]. In order to move toward efficient breeding, it is important to have an estimation of the optimized level of each secondary trait in superior genotypes. This goal can be accomplished by using optimization algorithms such as the improved strength Pareto evolutionary algorithm (SPEA2). SPEA2 is used for multi-objective optimization problems to figure out the Pareto-optimal set [97]. In this study, the DNN as the superior algorithm in predicting the soybean yield and FBIO production was linked to SPEA2 to optimize the HVI for maximizing yield and FBIO production (Figure 9). The successful use of SPEA2 was reported in different areas such as engineering [139], material science [140] and economics [141], but not in plant science. To the best of our knowledge, this is the first report of using SPEA2 in the plant science area. The advantages of SPEA2, over other multi-objective optimization algorithms, is built upon its improved fitness assignment scheme that results in understanding of the number of individuals that dominant or are dominated by others in the data sets [97]. This technique empowers SPEA2 to optimize all HVI, precisely, in soybean genotypes with maximized yield and FBIO production. By having this information, soybean breeders could be able to design the “ideotype” genotypes with optimum values for hyperspectral vegetation indices, which are potentially high seed yield and FBIO genotypes in large breeding populations and set up their selection strategies based on these criteria.

5. Conclusions

Having reliable estimations of the optimum values for highly heritable secondary traits such as HVI that are strongly associated with yield and FBIO can guide breeders to construct efficient breeding programs focused on designing and selecting “ideotype” genotypes for their target traits. In this study, we demonstrate the significant correlations of several HVI, including the red region, especially the 670 nm and 800 nm wavelengths in the near-infrared region, with soybean seed yield and FBIO production. We also developed EB and DNN algorithms as reliable tools for predicting the soybean seed yield and FBIO from HVI data collected at early growth stages. Furthermore, for the first time, we linked DNN to the SPEA2 to estimate the optimum values of HVI in soybean genotypes with maximized yield and FBIO. These optimum values of HVI are suggested to be validated in new and independent breeding populations before being used by soybean breeders in their cultivar development programs for selecting high-yielding genotypes with high FBIO potential.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/rs13132555/s1, Table S1: Tabular format of Pearson correlation analyses of hyperspectral vegetation indices (HVI), soybean seed yield and fresh biomass (FBIO), Table S2: Analysis performance of random forest (RF), radial basis function (RBF) and support vector regression (SVR) algorithms for soybean yield prediction using yield component traits, Table S3: Analysis performance of random forest (RF), radial basis function (RBF) and support vector regression (SVR) algorithms for soybean fresh biomass (FBIO) prediction using yield component traits.

Author Contributions

Conceptualization, M.E.; methodology, M.E.; software, M.Y.-N.; validation, M.Y.-N., D.T. and M.E.; formal analysis, M.Y.-N.; investigation, M.Y.-N.; resources, M.E.; data curation, M.Y.-N., D.T.; writing—original draft preparation, M.Y.-N. and M.E.; writing—review and editing, M.Y.-N., D.T. and M.E.; visualization, M.Y.-N.; supervision, M.E.; project administration, M.E.; funding acquisition, M.E. All authors have read and agreed to the published version of the manuscript.

Funding

This project was funded in part by Grain Farmers of Ontario (GFO) and SeCan. The funding bodies did not play any role in the design of the study and collection, analysis and interpretation of data and in writing the manuscript.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

All datasets will be freely available upon request.

Acknowledgments

The authors are grateful to the past and current members of Eskandari laboratory at the University of Guelph, Ridgetown Campus, including Sepideh Torabi, Bryan Stirling, John Kobler and Robert Brandt for their technical support. We would also like to thank Maryam Vazin for her assistance with the field data collection.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

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Figure 1. Test site location in 2018 and 2019.
Figure 1. Test site location in 2018 and 2019.
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Figure 2. The schematic view of the Deep Neural Network (DNN) algorithm.
Figure 2. The schematic view of the Deep Neural Network (DNN) algorithm.
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Figure 3. The schematic diagram of the Improved version of the strength Pareto evolutionary algorithms-2 (SPEA2) as multi-objective optimization algorithm.
Figure 3. The schematic diagram of the Improved version of the strength Pareto evolutionary algorithms-2 (SPEA2) as multi-objective optimization algorithm.
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Figure 4. The experimental workflow of algorithm selection and validation to predict the soybean fresh biomass (FBIO) and seed yield using hyperspectral vegetation indices (HVI). DNN; deep neural network, EB; ensemble bagging.
Figure 4. The experimental workflow of algorithm selection and validation to predict the soybean fresh biomass (FBIO) and seed yield using hyperspectral vegetation indices (HVI). DNN; deep neural network, EB; ensemble bagging.
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Figure 5. The variation of (A) yield and (B) fresh biomass (FBIO) across four environments.
Figure 5. The variation of (A) yield and (B) fresh biomass (FBIO) across four environments.
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Figure 6. Pearson correlation analysis of hyperspectral vegetation indices (HVI), soybean seed yield and fresh biomass (FBIO).
Figure 6. Pearson correlation analysis of hyperspectral vegetation indices (HVI), soybean seed yield and fresh biomass (FBIO).
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Figure 7. Violin plots representing the coefficient of determination (R2), mean absolute errors (MAE), root mean square error (RMSE) of yield (A–C) and fresh biomass (D–F) performance of the deep neural network (DNN) algorithm and ensemble-bagging (EB) strategy for soybean yield and fresh biomass prediction using hyperspectral vegetation indices (HVI).
Figure 7. Violin plots representing the coefficient of determination (R2), mean absolute errors (MAE), root mean square error (RMSE) of yield (A–C) and fresh biomass (D–F) performance of the deep neural network (DNN) algorithm and ensemble-bagging (EB) strategy for soybean yield and fresh biomass prediction using hyperspectral vegetation indices (HVI).
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Figure 8. The importance of the tested hyperspectral vegetation indices (HVI) based on the recursive feature elimination (RFE) strategy for predicting soybean seed yield and fresh biomass (FBIO).
Figure 8. The importance of the tested hyperspectral vegetation indices (HVI) based on the recursive feature elimination (RFE) strategy for predicting soybean seed yield and fresh biomass (FBIO).
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Figure 9. Optimized hyperspectral vegetation indices (HVI) values in soybeans with maximized seed yield and fresh biomass (FBIO).
Figure 9. Optimized hyperspectral vegetation indices (HVI) values in soybeans with maximized seed yield and fresh biomass (FBIO).
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Table
Table 1. Summary of the selected hyperspectral vegetation indices (HVI) used in this study.
Table 1. Summary of the selected hyperspectral vegetation indices (HVI) used in this study.
Index CategoryAbbreviationFormulaReference
Normalized difference vegetation index
(NDVI)		N1[584 nm − 471 nm]/[584 nm + 471 nm][65]
N2[689 nm − 521 nm]/[689 nm + 521 nm][65]
N3[760 nm − 550 nm]/[760 nm + 550 nm][66]
N4[740 nm − 667 nm]/[740 nm + 667 nm][67]
N5[800 nm − 670 nm]/[800 nm + 670 nm][68]
N6[750 nm − 705 nm]/[750 nm + 705 nm][69]
N7[750 nm − 710 nm]/[750 nm + 710 nm][70]
N8[780 nm − 710 nm]/[780 nm + 710 nm][71]
N9[750 nm − 710 nm]/[750 nm + 710 nm][72]
N10[732 nm − 717 nm]/[732 nm + 717 nm][72]
N11[820 nm − 720 nm]/[820 nm + 720 nm][73]
N12[750 nm − 735 nm]/[750 nm + 734 nm][72]
Normalized difference red edge (NDRE)NDRE[790 nm − 720 nm]/[790 nm + 720 nm][74]
Green normalized difference vegetation index (GNDVI)GNDVI[750 nm − 550 nm]/[750 nm + 550 nm][75]
Renormalized difference vegetation index (RDVI)RDVI[800 nm − 670 nm]/[800 nm + 670 nm][76]
Simple ratio index
(SRI)		S1[565 nm/533 nm][77]
S2[750 nm/550 nm][78]
S3[760 nm/550 nm][66]
S4[810 nm/560 nm][79]
S5[734 nm/629 nm][67]
S6[810 nm/660 nm][80]
S7[700 nm/670 nm][81]
S8[800 nm/670 nm][82]
S9[675 nm/700 nm][83]
S10[800 nm/680 nm][84]
S11[752 nm/690 nm][78]
S12[750 nm/700 nm][78]
S13[750 nm/705 nm][69]
S14[706 nm/755 nm][72]
S15[747 nm/708 nm][85]
S16[750 nm/710 nm][86]
S17[741 nm/717 nm][85]
S18[735 nm/720 nm][85]
S19[738 nm/720 nm][85]
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Yoosefzadeh-Najafabadi, M.; Tulpan, D.; Eskandari, M. Using Hybrid Artificial Intelligence and Evolutionary Optimization Algorithms for Estimating Soybean Yield and Fresh Biomass Using Hyperspectral Vegetation Indices. Remote Sens. 2021, 13, 2555. https://doi.org/10.3390/rs13132555

AMA Style

Yoosefzadeh-Najafabadi M, Tulpan D, Eskandari M. Using Hybrid Artificial Intelligence and Evolutionary Optimization Algorithms for Estimating Soybean Yield and Fresh Biomass Using Hyperspectral Vegetation Indices. Remote Sensing. 2021; 13(13):2555. https://doi.org/10.3390/rs13132555

Chicago/Turabian Style

Yoosefzadeh-Najafabadi, Mohsen, Dan Tulpan, and Milad Eskandari. 2021. "Using Hybrid Artificial Intelligence and Evolutionary Optimization Algorithms for Estimating Soybean Yield and Fresh Biomass Using Hyperspectral Vegetation Indices" Remote Sensing 13, no. 13: 2555. https://doi.org/10.3390/rs13132555

APA Style

Yoosefzadeh-Najafabadi, M., Tulpan, D., & Eskandari, M. (2021). Using Hybrid Artificial Intelligence and Evolutionary Optimization Algorithms for Estimating Soybean Yield and Fresh Biomass Using Hyperspectral Vegetation Indices. Remote Sensing, 13(13), 2555. https://doi.org/10.3390/rs13132555

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