remote sensing

Article
Exploring the Impact of Noise on Hybrid Inversion of
PROSAIL RTM on Sentinel-2 Data
Nuno César de Sá 1, * , Mitra Baratchi 2 , Leon T. Hauser 1 and Peter van Bodegom 1

1 Institute of Environmental Sciences (CML), Leiden University, P.O. Box 9518,

2300 RA Leiden, The Netherlands; [email protected] (L.T.H.);
[email protected] (P.v.B.)
2 Leiden Institute of Advanced Computer Science (LIACS), Leiden University, P.O. Box 9512,
2300 RA Leiden, The Netherlands; [email protected]
* Correspondence: [email protected]

Abstract: Remote sensing (RS) of biophysical variables plays a vital role in providing the information
necessary for understanding spatio-temporal dynamics in ecosystems. The hybrid approach to retrieve
biophysical variables from RS by combining Machine Learning (ML) algorithms with surrogate data
generated by Radiative Transfer Models (RTM). The susceptibility of the ill-posed solutions to noise
currently constrains further application of hybrid approaches. Here, we explored how noise affects
the performance of ML algorithms for biophysical trait retrieval. We focused on synthetic Sentinel-2
(S2) data generated using the PROSAIL RTM and four commonly applied ML algorithms: Gaussian
Processes (GPR), Random Forests (RFR), and Artificial Neural Networks (ANN) and Multi-task
Neural Networks (MTN). After identifying which biophysical variables can be retrieved from S2
using a Global Sensitivity Analysis, we evaluated the performance loss of each algorithm using the
Mean Absolute Percentage Error (MAPE) with increasing noise levels. We found that, for S2 data,



Carotenoid concentrations are uniquely dependent on band 2, Chlorophyll is almost exclusively

 dependent on the visible ranges, and Leaf Area Index, water, and dry matter contents are mostly
Citation: de Sá, N.C.; Baratchi, M.; dependent on infrared bands. Without added noise, GPR was the best algorithm (<0.05%), followed
Hauser, L.T.; van Bodegom, P. by the MTN (<3%) and ANN (<5%), with the RFR performing very poorly (<50%). The addition of
Exploring the Impact of Noise on noise critically affected the performance of all algorithms (>20%) even at low levels of added noise
Hybrid Inversion of PROSAIL RTM (≈5%). Overall, both neural networks performed significantly better than GPR and RFR when noise
on Sentinel-2 Data. Remote Sens. 2021, was added with the MTN being slightly better when compared to the ANN. Our results imply that
13, 648. https://doi.org/10.3390/
the performance of the commonly used algorithms in hybrid-RTM inversion are pervasively sensitive
rs13040648
to noise. The implication is that more advanced models or approaches are necessary to minimize the
impact of noise to improve near real-time and accurate RS monitoring of biophysical trait retrieval.
Academic Editor: Katja Berger
Received: 7 December 2020
Keywords: radiative transfer models; PROSAIL; sensitivity analysis; inversion; biophysical variables;
Accepted: 8 February 2021
Published: 11 February 2021
machine learning; multi-output; Bayesian optimization; Sentinel-2

Publisher’s Note: MDPI stays neu-

tral with regard to jurisdictional clai-
ms in published maps and institutio- 1. Introduction
nal affiliations. The increasing availability of Earth Observation (EO) solutions to monitor ecosystems
provides a unique opportunity for near real-time monitoring of biodiversity and an in-
creased understanding of spatio-temporal dynamics in ecosystems [1–4]. This opportunity
Copyright: © 2021 by the authors. Li-
benefits from a growing body of research exploring the use of remote sensing to retrieve
censee MDPI, Basel, Switzerland.
the so-called biophysical variables of vegetation [5], alongside advances in satellite sensor
This article is an open access article
technology, availability, and integration [6].
distributed under the terms and con- While a precise definition is somewhat contentious, functional traits of vegetation are
ditions of the Creative Commons At- defined as the characteristics of vegetation that contribute to its fitness and performance [7].
tribution (CC BY) license (https:// Often, in remote sensing, biophysical variables or parameters of vegetation are used instead
creativecommons.org/licenses/by/ to define the physical (e.g., height, leaf mass area) and biochemical (e.g., leaf nitrogen, leaf
4.0/). chlorophyll) characteristics of vegetation [8–10]. The transition from species identification

Remote Sens. 2021, 13, 648. https://doi.org/10.3390/rs13040648 https://www.mdpi.com/journal/remotesensing

Remote Sens. 2021, 13, 648 2 of 20

to monitoring of actual biophysical aspects of vegetation aims to offer additional insights

into ecosystems’ functions, processes and properties [4,5] and functional diversity [11].
Naturally, while different sensors are useful to quantify different biophysical variables
at different scales (e.g., LiDAR for tree canopy structure [12], and optical sensors for
leaf chemistry [13]), while global estimates of most biophysical variables are commonly
dependent on multispectral sensors on-board MODIS, Landsat and increasingly on the
European Space Agency (ESA) Sentinel-2 (S2) twin satellites owing to their short four day
global revisit time and high spatial resolution.
Given the increasing demand for monitoring a changing environment [1–3], the
search for a standard, global approach for monitoring biophysical variables is of particular
importance. Verrelst et al. [14,15] summarized current approaches for retrieving biophysical
variable into four categories: Parametric regressions, Non-parametric regressions, Physically-
based inversion, and Hybrid methods.
Parametric regressions explore known relationships between vegetation indices or specific
bands (or band ratios) and variables of interest, such as height [16] or Chlorophyll [13]. In con-
trast, Non-parametric regressions do not assume any specific relationship between spectral fea-
tures and biophysical variables, but instead retrieve the best features through function-fitting
procedures (e.g., [17]). While these approaches benefit from being data-driven and locally ac-
curate, they have larger data requirements and limited generalization [14,15]. Physically-based
inversion methods use models based on well-known physics laws to simulate the interaction
of electromagnetic radiation with vegetation, known as Radiative Transfer Models (RTM)
(e.g., [18]). The main challenge of Physically-based inversion methods is that they are com-
putationally expensive to generalize to a global scale [14,15]. Hybrid methods combine the
use of physical laws with non-parametric regressions and other Machine Learning (ML) algo-
rithms to develop flexible and computationally efficient retrievals of canopy/leaf properties
(e.g., [19]). Due to their transferability and computational speed, there has been an increasing
interest in Hybrid approaches using ML algorithms such as Gaussian Process [20,21], Random
Forests [19], Support Vector Machines [22], and Artificial Neural Networks [23]. Hybrid ap-
proaches are computationally more efficient than physically-based inversion inversion which
constitutes an important advantage for generating global estimates of biophysical traits [15].
The main challenge for both the Hybrid and Physically-based approaches arises from
the inversion of RTMs being an ill-posed problem, i.e., multiple configurations of leaves
and/or canopy parameters can produce identical or similar spectral responses [10]. This
problem is further amplified when the number of bands is limited or by the presence of
noise [24,25]. Furthermore, the presence of noise in satellite data caused by factors such
as the atmosphere makes the challenge increasingly complex [25–27]. Active learning
methods which integrate new samples based on uncertainty or diversity criteria to improve
the accuracy of the model in the context of Earth observation regression problems [28],
have been shown to enhance retrieval accuracy, which may be due to mitigation of the
ill-posedness within hybrid approaches [10], in particular when field data is available [29].
These limitations pose significant challenges even to advanced ML algorithms, and likely
contribute to a lack of consensus regarding which algorithm generally performs better.
Commonly, ill-posedness is minimized through a reasonable pre-selection of expected
biophysical trait range of values, but this has an obvious implication on the generality and
scalability of the trained models [14,15].
Thus, there is a need to identify which algorithm generally performs better irrespective
of sensor and location. While various explorations exist [26,27,30], this question has so far
not been addressed. Therefore, the aim of this study is to identify the best Hybrid approach
for estimating biophysical parameters of vegetation, irrespective of geographic location or
time, and with a reasonable robustness in treating the effects of noise. To address this aim,
we explore the capabilities and limitations of S2 data to monitor biophysical variables by (1)
identifying which biophysical variables can be measured by S2; (2) identifying the best ML
algorithms to invert simulated S2-like data and (3) explore the effect of noise in the models.
While validation against field data is ultimately needed, it is first essential to explore the
Remote Sens. 2021, 13, 648 3 of 20

best possible inversion of RTMs, which is the focus of our study. This may serve as an
initial step towards global applications for biophysical trait retrieval independent of sensor,
time, and location.

2. Methods
2.1. General Methodology
Our approach consisted of four main steps, and a clear overview is given in Figure 1.
The first step consists of identifying which biophysical variables can potentially be detected
by S2 based on a GSA and band correlation. To perform the GSA, we used an Enhanced
Fourier Amplitude Sensitivity Analysis (EFAST) [31] on the simulated S2-like data to
identify which traits can be detected. The second step was finding the best hyperparameters
of each model to ensure the best possible version of each ML modelling approach. This was
performed using the Tree-structured Parzen Estimator (TPE), which uses Bayesian inference
to search for the best combination of parameters within a pre-set search space [32,33].

Sensitivity Hyperparameter
RTM Inversion Impacts of noise
analysis tuning

Figure 1. The first step consists of identifying which biophysical variables can be detected by S2 while the second step
uses Bayesian optimization to find the best parameters for the various models. Lastly, the third and fourth steps test the
performance of the various algorithms for inverting simulated S2-like data using Radiative Transfer Models in pure and
noisy conditions.

The third part consists of testing the ability of the most commonly used algorithms
for RTM inversion: Random Forests [34], Artificial Neural Networks [35], and Gaussian
Processes [36]. Each of is representative of the different families of algorithms commonly
used for RTM inversion [26]. The final step consists of evaluating the resilience of the above
models to increasing levels of noise. Before describing each of the steps in more detail, we
first describe the selected RTM, i.e., PROSAIL, [37], and the selected algorithms for RTM
inversion.

2.2. PROSAIL
PROSAIL is the most common RTM used for biophysical trait retrievals, and the
most used in Hybrid approaches. PROSAIL is actually the coupling of two core models:
PROSPECT [38–40] and SAIL [37]. PROSPECT uses well-established physical principles
of light-matter interaction to simulate how light interacts with a single leaf. SAIL stands
for Scattering by Arbitrarily Inclined Leaves and is based on the plate model initially proposed
by Suits [41]. The basic principle of SAIL is that vegetation canopy can be represented
by a “plate” that interacts with directional incoming radiation. PROSAIL integrates both
models by characterizing the vegetation canopy using SAIL and the leaves by using
PROSPECT [42]. The result of the model is a description of the reflectance of the vegetation
layer as dependent on the relative positions of the sun, sensor, canopy and soil character-
istics. The ranges of parameters used for this research are described in Table 1 and were
intentionally broader than what is commonly found in other publications (e.g., [42]) to
ensure the full range of possible values of these parameters [43].
Remote Sens. 2021, 13, 648 4 of 20

Table 1. Overview of PROSAIL input parameters used. Trait combinations were sampled representatively using a Latin
hypercube sampling approach across the range identified. For the ML sections, Car was fixed at 10.

Model Domain Description Parameter Units Range

Leaf structure index N - 1
Chlorophyll a + b content Cab ug/cm2 0 120
Total carotenoid content Car ug/cm2 0 60
PROSPECT Leaf
Equivalent water thickness Cw cm 0.001 0.008
Dry matter content Cm g/cm2 0.001 0.008
Brown pigments Cbrown - 0
Total anthocyanin content Canth ug/cm2 0
Leaf area index LAI - 0 10
Average leaf slope LIDFa º −0.35
Canopy Leaf distribution
LIDFb º −0.15
bimodality
Hot spot parameter hspot - 0.01
SAIL Soil reflectance ρsoil - 0.5
Soil
Soil brightness factor αsoi - 0.1
Solar zenith angle tts º 45
Positional Sensor zenith angle tto º 45
Relative azimuth angle phi º 0

2.3. Machine Learning Algorithms

2.3.1. Random Forest
The Random Forest regression (RFR) [34] is a type of ensemble classifier that combines
multiple Classification and regression Trees (CART) through bagging and boosting. In each
iteration, RFR bins the data to different sets and maximizes the “purity” of each through a
given purity index (e.g., Gini index). To formalize the procedure, let s be a candidate split
value at a given node t, then the decrease in impurity is given by:

∆i(s,t) = it − p L i(t L ) − p R i(tR ) (1)

where p R and p L are the proportion of data for each node, it is the node impurity before
splitting and i(t L ) and i(tR ) are the measures of impurity after splitting. While in CART, a
single decision tree (DT) is used, in RFR multiple (K) DT are trained and fitted to a set of
data x, and the final prediction results from either a majority (classification) or the mean
(regression). Formalizing, RFR is an ensemble of K decision trees DT, fitted to a set of data x:

K
1
RF( x) =
K ∑ DTx (2)
k =1

Furthermore, RFR uses the bootstrap aggregating technique to reduce the correlation
between trees and increases the accuracy and stability of the final model [34]. An advantage
of RFR is its ability to provide an estimate of prediction error without the need for external
data since, in each iteration, data non-contributing for model construction is used for
internal testing (out-of-bag error, obb) and to control model overfitting [34].
Remote Sens. 2021, 13, 648 5 of 20

2.3.2. Artificial Neural Networks

Artificial Neural Networks (ANN) were initially proposed as a computational model
for learning inspired by the biological brain [35]. ANN have since been extensively used
in numerous applications due to their particular ability to model non-linear and complex
relationships, and to provide accurate predictions even on unseen data [44]. Two other
important characteristics of neural networks are that they allow the user to adapt the
architecture to the task itself, and that they are fully data-driven approaches that impose no
limitations on the distribution of input data [44,45]. ANN are often represented as graphs
where each node is a neuron and is interconnected with other neurons appearing similar to
a biological brain. Each neuron in an ANN consists of a mapping function:
n
y = f ( ∑ + wi x i + b ) (3)
j =1

where w, b represent the weight and bias of each ith neuron, and x, y represent the input
and output of the hidden layer. Furthermore, the output y of each neuron can also be
plugged into a function, known as activation functions, which can be used to enforce a
specific behavior to each neuron/layer. Each set of interconnected layers of neurons, except
for the input and output sets, are known as hidden layers. The procedure for training a
supervised ANN consists of minimizing the difference of the current model prediction
against the desired outcome by propagating small changes in w and b of all neurons on all
layers in each iteration (epoch).
For this research, we used two different neural networks: a densely connected and
feed-forward ANN with back-propagation training. This is one of the most used archi-
tectures and is used also by the ESA SNAP toolbox [46]. The second architecture is a
feed-forward, Multi-task Neural Network (MTN) with back-propagation training. This
second type of architecture is increasingly more common thanks to the possibility of
partitioning the learning tasks [45].

2.3.3. Gaussian Processes

Gaussian Process Regression (GPR) [36], also known as kriging, is a type of non-
parametric regression modeling. GPR relies on the Bayes method for inference and a
pre-set covariance kernel function that is optimized to fit the given data. A Gaussian
Process is defined as f ( x ), is a set of random variables with a Gaussian distribution that is
normally distributed in the multivariate space. Under these conditions, there exists a mean
(µ) of the multivariate distribution, a covariance function (k) that represents the covariance
between each point and an expected level of Gaussian noise with standard deviation σ:

f ( x ) ∼ GP(µ( x ), k( x, x 0 ) + Iσy2 ) (4)

where x represents sets of observed points, and k a prior covariance function enforced
for designing the covariance matrix. Iσy2 represents noise being added along the diagonal
of the covariance function. This formulation implies that f ( x ) is a linear combination of
underlying sets of Gaussian Processes and predictions on any given location are interpola-
tions of the observed data. The covariance functions are known as kernels and provide the
expected correlation between different observations. The kernel functions tested in this
research were: radial basis function (RBF), rational Quadratic, matérn, and the dot product.
The main benefits of GPR lie in its versatility [47] and the ability to produce good
results even with a limited number of training data [20]. Furthermore, GPR can provide an
empirical estimate of the uncertainty of the prediction given the evidence x and the joint
distribution defined by the covariance matrix k. The caveat is that they are computationally
expensive when using a large data set [15], and that the model requires storing the entire
covariance matrix information which increases the memory load as the covariance matrix
grows quadratically (n2 ) as a function of n data points.
Remote Sens. 2021, 13, 648 6 of 20

2.4. Step 1: Sensitivity Analysis

We explored which biophysical variables can be estimated by S2. We considered
only the most significant leaf and canopy traits of Cab , Car, Cw , Cm and LAI and anal-
ysed them through two different approaches: the first explores the correlations between
any S2 band and a given trait using Spearman’s rank correlation coefficient (ρ). For this,
100 uniformly distributed random samples of traits were generated, and its canopy spectral
response was obtained using PROSAIL and convoluted into S2 bands. Then, the Spear-
man’s correlation between each trait and band was calculated. This analysis quantifies the
association between pairs of bands and biophysical variables and is indicative of the over-
lap in correlations between different variables. However, it does not provide any further
inference relative to combined effects, or a breakdown in direct and indirect interactions,
that variations in biophysical variables can have on the various S2 bands.
The second approach explores the sensitivity of S2 data to variation in biophysical
variables using a GSA index. The GSA was used to quantify the actual sensitivity of each
band to each trait as well as the interactions between bands. This analysis was performed
by using EFAST [31] which is a variance-based global sensitivity analysis that combines
Fourier transformations with Sobol’s method to decompose the various effects [48]. These
effects are decomposed into first-order, interaction and total-order sensitivity indices that
represent the variability associated with single features, interactions between features, and
the sum of all interactions, respectively. This allowed us to explore which S2 bands are
associated with which biophysical trait and if there are significant confounding factors
between them, and is an analysis comparable to what was performed by Gu et al. [49] and
Brede et al. [27]. Since the EFAST provides an estimate of the sensitivity, a conservative
number of samples necessary to provide an accurate estimate must be identified first by
calculating the index with increasing number of samples until the estimate stabilizes.

2.5. Step 2: Hyperparameter Tuning

A critical first step in any ML is hyperparameter tuning. This step thus consists
of identifying the best combination of the ML model hyperparameters for the task of
RTM inversion. As mentioned in Section 2.3, each of the aforementioned algorithms have
different sets of parameters that should be tuned. Therefore, hyperparameter tuning is
particularly important when comparing such different ML algorithms to ensure fairness.
Thus, and in contrast to [50], Bayesian optimization was applied for hyperparameter
optimization instead of on the RTM inversion itself (Step 3). Table 2 shows the range of
hyperparameters used for this procedure.
The hyperparameter tuning task was performed using the TPE approach with the hy-
peropt package in Python [32]. This method consists of a sequential optimization procedure
that uses Bayesian inferences to explore the potential solution space and identify the best
combination of hyperparameters. This procedure was performed using 1800 samples with
a 10-k fold cross-validation evaluation of the training error and 200 sequential evaluations
of the parameters. Once the hyperparameters for the models were selected, we identified
the number of training epochs for the ANN. We tested this by analysing the effect of the
number of epochs on the prediction error and concluded that 500 epochs was reasonable
number between the over-fitting risk and training time (see Figure A1).
Remote Sens. 2021, 13, 648 7 of 20

Table 2. Overview of the hyperparameters tested during the optimization. The final set of parameters used are given in
Tables 4 and 5.

Model Parameter Data Type Range

Number of trees Integer {50, 100, 150, ..., 1000}
Random Forests Minimum samples node split Continuous [0; 0.5]
Minimum samples leaf node Continuous [0; 0.5]
Number of optimizer restarts Integer {10, 20, 30, 40, 50, 60, 70, 80, 90, 100}
Gaussian Processes radial basis function, rational quadratic,
Kernel functions Categorical
matérn, dot product
Number of hidden layers Integer 1 to 3
Number of neurons Integer {5, 10, 15, 20}
Artificial Neural Network Linear, Sigmoid, Tanh, Exponential,
Activation functions Categorical
Softplus, ReLU, Softsign
Optimizer Categorical Adam, RMSprop, Adadelta
Number of shared layers Categorical {1, 2}
Number of single task layers Integer {1, 2}
Number of neurons (shared) Integer {5, 10, 15, 20}
Multi-task Neural Network
Number of neurons (single) Integer {1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
Linear, Sigmoid, Tanh, Exponential,
Activation functions Categorical
Softplus, ReLU, Softsign
Optimizer Categorical Adam, RMSprop, Adadelta

2.6. Step 3: RTM Inversion

The inversion of RTM data followed a hybrid approach, as proposed by Verrelst et al. [26].
Trait data was generated using a Latin hypercube sampling approach based on the trait space
and parameters as shown in Table 1. The data generated with PROSAIL represents the canopy
reflectance from 400 to 2500 nm with a resolution of 1 nm. However, the S2 data only measure
reflectance in specific bands. Therefore, to convert the PROSAIL data to S2 resolution, we
used a weighted sum spectral convolution approach:

∑2500
i =400 wi · Ri
RS2 = (5)
∑2500
i =400 wi

where for each independent RS2 band, the weights (w) were obtained from the spectral
responses provided by ESA for S2A [51], and the Ri represents the reflectance values
obtained from PROSAIL for each band at wavelength i. Finally, only the band products
provided at 10–20 m in the final level 2A product were used: i.e., bands 2, 3, 4, 5, 6, 7, 8A,
11 and 12.
To evaluate the performance of the models, we opted to use the Mean Absolute
Percentage Error (MAPE) because it provides an intuitive interpretation and is easily
comparable between all traits. This is important for this case since the different biophysical
variables have very different ranges of values (see Table 1), and this way we ensure a
proper and intuitive interpretation of the results across the board. MAPE is calculated by:
n
1 Re f i − Predi
MAPE =
n ∑ Re f i
(6)
i =1

where Re f and Pred are the reference and predicted data, respectively, and n the number
of data points used for validation. In the absence of noise, the next step was to partition
the data into the three sets needed for cross-validation: 10% of the total data was left out
Remote Sens. 2021, 13, 648 8 of 20

for estimating the validation error; the remaining 90% of the total data was used for both
the algorithm training and to estimate the training error through a 10 k-fold leave-one-out
approach. All tested algorithms were trained under identical conditions and using the
same training data in each run. To identify how many samples are needed for inverting
PROSAIL RTM, we incremented from a minimum of 50 samples to 4000 samples by steps
of 250. This experiment allowed us to identify both the best algorithm for PROSAIL RTM
inversion as well as their data needs.

2.7. Impacts of Noise

To assess the impact of noise on the accuracy of each model, we explored how increas-
ing levels of correlated Gaussian noise affected the accuracy of the models as shown in
Figure 2. Two noise models were tested, as defined by Locherer et al [25]:

Combined : Rnoise (λ) = Rsim (λ)[1 + N (0, 2σ (λ)] + N (0, σ (λ)) (7)

Inverted : Rnoise (λ) = 1 − (1 − Rsim (λ))[1 + N (0, 2σ(λ)] + N (0, σ (λ)) (8)
where Rnoise , Rsim represent the noisy signal and pure simulated spectra, and λ the wave-
length. While both models add noise as a function of wavelength, the Inverted model will
affect more bands on the visible and SWIR regions of the spectra, while the Combined
model will affect more the IR region. Using both types of Gaussian models, we tested the
effect of the following increasing levels of noise added to the training data: 1%, 3%, 5%, 10%,
15%, 20%, 25%, 30%, 40%, and 50%. This experiment aims to explore the pervasiveness of
noisy data in the performance of the ML RTM inversion.

Biophysical trait
table

kth fold Algorithm Training

cal/val pairs training error
PROSAIL

90%
Spectral K-fold
convolution procedure
10%

Noise model
Holdout-out Validation
set error

Simulated S2
data

Figure 2. Flowchart representing the training and validating procedure of the experiments. All
algorithms were trained with the same data to exclude any random effect. The noise is only added in
the second part of the experiment when testing its effect on the error.

3. Results
3.1. Sensitivity Analysis
The Spearman rank correlation coefficients are shown in Table 3, while the scatterplots
are shown in Figure 3. Many significant ρ were found between multiple pairs of bands and
traits. These relationships are, however, not linear as seen in Figure 3. Cab was shown to
have a negative correlation with all visible bands and had a negligible correlation with the
remaining biophysical parameters (Table 3). Somewhat inversely, Cw is strongly negatively
correlated with the two bands in the longest wavelengths (B11 and B12). Cm and LAI are
both strongly correlated with the NIR and SWIR bands, while Cm has a positive correlation
(Table 3). It is also seen that LAI has a negative correlation, indicating a high potential for
interaction in these bands (Table 3). Finally, Car is only significantly correlated with the
Remote Sens. 2021, 13, 648 9 of 20

blue band. Cw was found to be almost exclusively associated with B11 and B12, which
indicates that there might be also some degree of correlation between Cw and Cm (Figure 3
and Table 3).

Table 3. Summary of Spearman’s ρ correlation coefficients for different biophysical variables and S2
bands. The significance levels are represented as: p ≤ 0.001 (***); p ≤ 0.01 (**); p ≤ 0.05 (*); p ≤ 0.1 (.);
p > 0.1: no symbol.

Band Cab Cw Cm LAI Car

B2 −0.10 (***) 0.00 −0.04 (.) 0.2 (***) −0.46 (***)
B3 −0.95 (***) 0.03 −0.02 −0.04 (.) −0.10 (***)
B4 −0.56 (***) 0.02 −0.02 0.01 −0.02
B5 −0.97 (***) 0.03 −0.02 −0.04 −0.01
B6 −0.61 (***) 0.00 −0.19 (***) 0.49 (***) 0.01
B7 −0.01 −0.01 −0.47 (***) 0.82 (***) 0.01
B8A 0.01 −0.02 −0.47 (***) 0.82 (***) 0.01
B11 0.04 −0.65 (***) −0.49 (***) 0.46 (***) −0.01
B12 0.02 −0.67 (***) −0.69 (***) 0.03 −0.02

B2 B3 B4 B5 B6 B7 B8A B11 B12

0.04
0.05 0.2 0.5 0.6
0.10 0.6 0.4 0.20
0.04 0.4 0.5 0.5
Cab 0.03 0.06 0.1 0.3 0.15
0.03 0.3 0.4 0.4
0.3 0.3 0.10
0.02 0.02 0.2 0.2
0.02 0.0
60 120 60 120 60 120 60 120 60 120 60 120 60 120 60 120 60 120

0.04
0.05 0.2 0.5 0.6 0.4
0.10 0.6 0.20
0.04 0.4 0.5 0.5
Cw 0.03 0.3 0.15
0.06 0.03 0.1 0.3 0.4 0.4
0.3 0.3 0.10
0.02 0.2 0.2
0.02 0.02
0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010

0.04
0.05 0.2 0.5 0.6 0.4
0.10 0.6 0.20
0.04 0.4 0.5 0.5
Cm 0.03 0.3 0.15
0.06 0.03 0.1 0.3 0.4 0.4
0.3 0.3 0.10
0.02 0.2 0.2
0.02 0.02
0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010 0.005 0.010

0.04
0.05 0.2 0.5
0.10 0.6 0.6 0.4 0.20
0.04 0.4
LAI 0.03 0.5 0.5
0.3 0.15
0.06 0.03 0.1 0.3 0.4 0.4
0.02 0.3 0.3 0.10
0.02 0.2 0.2
0.02
5 10 5 10 5 10 5 10 5 10 5 10 5 10 5 10 5 10

0.04
0.05 0.2 0.5 0.6 0.4
0.10 0.6 0.20
0.04 0.4 0.5 0.5
Car 0.03
0.06 0.4 0.3 0.15
0.03 0.1 0.3 0.4
0.3 0.3 0.10
0.02 0.2 0.2
0.02 0.02
30 60 30 60 30 60 30 60 30 60 30 60 30 60 30 60 30 60

Figure 3. Scatterplot between each trait and band. To improve visualization, only a fraction of 100 samples were used in
this plot.
We found that for around 2000 samples the variation on the estimate of GSA stabilized;
therefore, we used this number of samples to analyse the sensitivity (Figure 4). The final
GSA estimates (Figure 5) show that LAI was most associated with the three bands on
Remote Sens. 2021, 13, 648 10 of 20

the red-edge region B6, B7 and B8A, and most of the sensitivity on each band was of
first-order. Cw was strongly dependent on bands B11 and B12, with some interaction effects
occurring on B12. Cm was shown to be sensitive to variations in multiple bands from the
infrared region (B06, B07 and B8A) to the short-wave infrared region (B11 and B12). Some
interaction between Cm and Cw can be observed in B12. Car was found to be exclusively
dependent on the blue band (B2), which is of concern due to the high degree of interaction
with Cab . This, combined with the lack of variation in reflectance (see Figure A2), indicates
that Car cannot be detected by S2 data simulated by PROSAIL; therefore, we excluded it
from the remainder of the analysis.

First−order First−order First−order First−order First−order First−order First−order First−order First−order

B02 B03 B04 B05 B06 B07 B11 B12 B8A
1.00 ●
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Sensitivity index

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Total−order Total−order Total−order Total−order Total−order Total−order Total−order Total−order Total−order

B02 B03 B04 B05 B06 B07 B11 B12 B8A
1.00 ●● ● ● ● ● ●● ● ● ● ●
●
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0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000 0 1000 2000 3000
Samples
● Cab ● Car ● Cm ● Cw ● LAI

Figure 4. Global sensitivity index EFAST as function of the number of samples.

First−order Interactions Total−order

LAI

Cw
Biophysical traits

Cm

Car

Cab

0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00 0.00 0.25 0.50 0.75 1.00
Sensitivity index
B02 B04 B06 B8A B12
B03 B05 B07 B11

Figure 5. The sensitivity index as a function of each trait. The first-order sensitivity is the sensitivity associated with each
trait while the total order is the sum of the first order with the interactions.

3.2. Hyperparameter Tuning

The final hyperparameter obtained for each model are shown in Tables 4 and 5. While
the first shows the overall parameters for the RFR, GPR, and both ANN, the second
Remote Sens. 2021, 13, 648 11 of 20

shows the task-specific parameters for the MTN. For the RFR, 850 trees were selected with a
negligible minimum number of sample being used for node or leaf splitting. For GPR, it was
found that 80 optimization procedures were necessary, using a rational quadratic kernel.

Table 4. Summary of selected hyperparameters. * on the multi-task network are related to the shared
layers; task-specific parameters are given in Table 5.

Model Parameter Selected

Number of trees 850
Random Forests Minimum samples node split 0.00053
Minimum samples leaf node 0.00286
Number of optimizer restarts 80
Gaussian Processes
Kernel functions Rational Quadratic
Number of hidden layers 3

Artificial Neural Network Number of neurons (20, 20, 15)

Activation functions Softsign, Softsign, ReLU
Optimizer Adam
Number of shared layers 2
Trait-specific layers 2
Multi-task Neural network Number of neurons * (15, 20)
Activation functions * Tanh, Exponential
Optimizer Adam

Table 5. Summary of selected hyperparameters for the trait-specific layers

Model Trait Parameter Selected

Number of neurons (3, 6)
Cab
Activation functions Softplus, Sigmoid
Number of neurons (3, 4)
Cw
Multi-task Neural network Activation functions Softplus, Tanh
Number of neurons (8, 6)
Cm
Activation functions ReLU, Sigmoid
Number of neurons (6,10)
LAI
Activation functions Softsign, Softsign

In the case of the neural networks, for all cases, the maximum number of hidden layers
was selected and with a high number of neurons (Tables 4 and 5). Non-linear activation
functions were selected with different functions for the ANN and MTN (shared layers).
For the MTN, less complexity was found on the layers associated with Cab and Cw , while
more complexity was needed for Cm , and especially for LAI, as shown by the need for
more neurons in each hidden layer (Tables 4 and 5). This is of particular interest since it is
well established that reflectance often saturates at higher levels of LAI (Tables 4 and 5).

3.3. RTM Inversion

When inverting PROSAIL spectra without any added noise (Figures 6 and 7, see
Tables 4 and 5 for details), the RFR was overall the worst performing model by converging
on Cm and Cw at approximately 45% and 50% MAPE. Only for Cab did RFR approximate
the performance of the other models. The worst performance of ANN was in LAI esti-
mation where MAPE converged at 5%, while on all other variables it achieved a MAPE
Remote Sens. 2021, 13, 648 12 of 20

of approximately 2%. The MTN converged faster and showed a significant improvement
in accuracy in all biophysical variables by achieving approximately 2% error in all target
traits. GPR was by far the best performing model with a negligible MAPE in all biophysical
variables, even with fewer than 1000 samples.

Pure RTM inversion

Cab Cm Cw LAI
80
Mean absolute percentage error (%)

60

40

20

0
0 1000 2000 3000 4000 0 1000 2000 3000 4000 0 1000 2000 3000 4000 0 1000 2000 3000 4000
Nr of samples
ANN Training error GPR Training error MTN Training error RFR Training error
ANN Validation error GPR Validation error MTN Validation error RFR Validation error

Figure 6. Model performance on pure PROSAIL RTM simulation. While each model has its own color, the darker colors
represent the training error. The data used for these plots is accessible in the Github repository provided at the end of
this manuscript.

Pure RTM inversion

Cab Cm Cw LAI
5
Mean absolute percentage error (%)

0
0 1000 2000 3000 4000 0 1000 2000 3000 4000 0 1000 2000 3000 4000 0 1000 2000 3000 4000
Nr of samples
ANN Training error GPR Training error MTN Training error RFR Training error
ANN Validation error GPR Validation error MTN Validation error RFR Validation error

Figure 7. Detail of Figure 6 between 0 and 5%.

While most models produced errors below 2.5% on Cab , the RFR was the worst overall
model by being unable to properly predict Cm or Cw , and not being able to predict LAI
with less than 10% error (Figure 7). The GSA analysis showed that these three biophysical
variables are likely correlated and interacting (see Table 3 and Figure 5) and thus RFR
was not able to address this effect. MTN outperformed ANN both in terms of the MAPE
error as well as in terms of the number of samples necessary for accurate predictions.
Remote Sens. 2021, 13, 648 13 of 20

Although the actual MAPE error is small for both ANN and MTN, it was also several
orders of magnitude larger than the MAPE error of GPR. For the remainder of the analysis,
2000 samples were used given that the error margins did not improve significantly with a
larger sample size (Figure 7).

3.4. Impacts of Noise

Adding noise to the models had a noticeable impact on the model performance, with
all of them showing quick and significant degradation of performance. In particular, GPR
was no longer the best performing model for the entire range of noise levels tested, and
instead, MTN showed slightly better results (Figure 8). Increasing noise levels resulted in
saturation of the prediction error for all traits, with LAI getting the highest MAPE error.
Interestingly, for Cm and Cw , the RFR error rate did not change significantly and all models
eventually converged to the same error level.

Cab Cm Cw LAI

100
Mean absolute percentage error (%)

Combined
50

100

Inverted
50

0
0 10 20 30 40 50 0 10 20 30 40 50 0 10 20 30 40 50 0 10 20 30 40 50
Noise level (%)
ANN Training error GPR Training error MTN Training error RFR Training error
ANN Validation error GPR Validation error MTN Validation error RFR Validation error

Figure 8. Effect of noise on model performance. While each model has its own color, the darker colors represent the training
error. The data used for these plots is accessible in the Github repository provided at the end of this manuscript.

Cab Cm Cw LAI
50
40
Mean absolute percentage error (%)

Combined

30
20
10
0

50
40
Inverted

30
20
10
0
0.0 2.5 5.0 7.5 10.0 0.0 2.5 5.0 7.5 10.0 0.0 2.5 5.0 7.5 10.0 0.0 2.5 5.0 7.5 10.0
Noise level (%)
ANN Training error GPR Training error MTN Training error RFR Training error
ANN Validation error GPR Validation error MTN Validation error RFR Validation error

Figure 9. Detail of Figure 8 between 0 and 10% added noise.

Remote Sens. 2021, 13, 648 14 of 20

Inverted noise affected the prediction accuracy more than Combined noise. This effect
is particularly evident for LAI, Cm and Cw , even at low levels of noise (Figure 9). For
low values of added noise, the neural networks were the best performing model for most
traits/noise models, even if the absolute error increased significantly. Furthermore, MTN
performed better than ANN and showed more resilience to noise.

4. Discussion
The results of our sensitivity analysis provided clear insights into which biophysical
variables can be measured using S2 data (see Figure 5 and Table 3), and furthermore,
provided insights into the effects of their interaction with spectral responses. Our results
on the band correlation (Table 3) and sensitivity analysis (Figure 5) are in line with previous
results [52], and in particular, when compared with recent results by Brede et al. [27] also
on S2 data, and Gu et al. [49] on Landsat TM data. Similarly, both studies found that Cab
was associated with the visible range in Landsat TM bands, and that Cm , Cw and LAI was
associated with NIR and SWIR bands (see Figure 5). The GSA analysis also shows that Cm ,
Cw and LAI have a degree of interaction between, them which has also been experienced
in previous research [15,52,53]. These interactions can have serious implications for the
accuracy of the retrievals, as specific traits can be more easily inverted due to a higher
number of dedicated bands (e.g., Cab ), while others are more vulnerable to interactions (e.g.,
Cm and Cw ). On top of that, from a biological perspective, it is also likely that some traits
vary together (e.g., Cab and LAI). The main difference for S2 is on which bands are sensitive
to which biophysical variables: in our case, the red-edge (5 and 6) and NIR (8A) were most
strongly associated with LAI, which can be indicative of this sensor being more suited for
LAI estimates but also possessing a higher potential for correlations and interactions. A
significant output of this analysis is that Car is hardly measurable by S2 because only band
B2 showed sensitivity with a high degree of interaction with Cab (Figure 5), and almost no
variation is detectable (see Figure A2).
The use of the Tree-structured Parzen Estimator showed that deeper and more complex
architectures yield better results. This is notable when comparing the ANN with MTN and
observing that a different number of neurons and activation functions were selected as
a function of the objective trait (see Tables 4 and 5). In the case of MTN, and consistent
with sensitivity analysis (Figure 5), more complex architectures were selected by the op-
timization procedure for the traits with higher degrees of interactions (see Figure 5 and
Table 5). This is also in line with other results in other fields of ML where it has been
shown that automatic procedures can greatly improve the model performance and infer
specific domain knowledge [49]. Together, these results can have significant implications
for the commonly used architectures, which are often simpler (e.g., ESA SNAP) and sug-
gest that more complex architectures can improve the retrieval of biophysical variables.
Furthermore, encoding hyperparameter tuning approaches into retrieval procedures can
increase the model versatility by adapting it to specific location or trait-spaces. In addition,
although these adaptations would be hindered by the high computational cost of hyper-
parameter tuning [54], recent developments in the field of AutoML are addressing this
through the concept of meta-learning [55] and multi-layer stacking [56] which minimize
the computational costs for finding suitable models.
Not all ML algorithms were found to be equally capable of hybrid inversion of pure
S2 data (Figures 6 and 7). As with most recent research, [10,20,57] found the Gaussian
Processes produced the best results for pure signals by significant levels of magnitude. This
is of particular importance when considering that the use of Gaussian Processes for this task
is less common than the use of other methods such as ANN [15] or RFR [17]. While in our
case, we found that RFR is unfit for hybrid inversion of S2 data, Campos-Taberner et al. [19]
successfully mapped biophysical variables using this algorithm on MODIS data, implying
that these results are dependent also on the sensors used - and intersecting with the
concept of meta-learning [55], model pipelines trained on sensors with different bands can
potentially provide pre-set model hyperparameters that are transferable between sensors.
Remote Sens. 2021, 13, 648 15 of 20

Model performance was severely affected even at low levels of noise (Figures 8 and 9).
This is of particular concern given that every data has noise, and previous research has
shown that the Sen2Cor atmospheric correction algorithm produces between 5% and 10%
noise [27,52]. Moreover, and in contrast to results obtained on pure data, both neural
networks generally performed better than GPR when noise was added, which indicates
that further developments with GPR are needed to be able to deal effectively with noisy
observations. Recently, Svendsen et al. [58] showed how GPR can be extended to more
complex, structures similar deep learning neural networks and is worth exploring in
future research.
As expected, noise did not affect all bands equally [52], which is consistent with the
different band selection and interactions according to the sensitivity analysis (see Figure 5).
In line with this, Cab estimates were shown to be more resilient to noise, which can be
explained by the high number of bands associated with this trait as well as their lack of
interaction. The opposite was observed for LAI, Cm and Cw , which share many of the same
band sensitivities and behaved similarly when noise was added. Nevertheless, the error
dependence on each trait implies that specific care to each trait should be given when using
a hybrid approach for RTM inversion in S2. Two potential approaches to minimize the trait
specific error are (1) to encode more hyperparameter optimization effort towards inverting
the more vulnerable traits (2) to when using neural networks, enforce task-sharing and
task specific layers on these known interactions.
For practical purposes, in the case of global predictions of biophysical variables,
both GPR and the two neural networks (ANN and MTN) have specific advantages and
disadvantages. For example, ANN are models that can be continuously updated without
significant increases in terms memory requirements as new training implies only changing
the weights and biases of the neurons and hidden layers. This implies that it is trivial to
share pre-trained neural networks for the entire globe which can be used as meta-learning
models for warm-starting the hyperparameter tuning optimization procedures tailored
for each location/sensor. On the other hand, GPR requires a very low number of samples
to stabilize its prediction and offers Active Learning opportunities that combine field
measurements with hybrid inversion within the model itself [20,59]. The caveats regarding
GPR are its tendency to overfit if given too much data, its training time scaling cubically in
function of the number samples [47,60], thus increasing its computational load and cost.
Another important aspect regarding GPR is that optimizing this model for tasks implies
either prior knowledge to impose a specific behaviour to the model or complex methods
for structure discovery due to the additive and multiplicative properties of the kernels [47].
A possible solution to address these challenges which has not yet been fully explored
could be to combine Decision Trees or Random Forests with Gaussian Processes [60], by
clustering the data into similar groups and applying GPR on the leaf nodes.
A final concern is that most approaches for hybrid inversion work on the assumption
that there are no known correlations between the biophysical variables. In nature, it is
virtually impossible to observe random combinations of traits as were used for model
training, e.g., a leaf with LAI of 10 but no Cab . The lack of real-world correlations between
biophysical variables likely aggravates the ill-posedness problem and future research on
exploring approaches that can include known correlations between biophysical variables or
exclude unrealistic combinations will likely contribute to improvements without necessarily
losing generalization [61].
Further potential avenues for improving the retrieval of biophysical parameters using
RTM inversion include the ingestion of a priori knowledge of the ecosystem and trait-space
understudy. Such ancillary information can help reduce the range of input parameters
used which in turn limits the solution space and related degree of ill-posedness [62]. In
dealing with ill-posedness, Rivera et al., 2013 [63] has suggested the use of an ensemble
approach which could prove helpful in reducing uncertainties in real-world applications.
Band selection methods and the use of spectral indices (ratio) in addition to spectral bands
to train inversion models can be also be explored as earlier results have shown [10,64].
Remote Sens. 2021, 13, 648 16 of 20

In many cases, RTMs are used as surrogate information given the lack of field data
due to these campaigns being particularly labour intensive and costly. If more data were
available, more data-driven approaches could be implemented, and the requirement of
RTM-based inversions can be minimized. While plant trait database conglomerates such as
TRY [43] or continental-scale observatory networks such as NEON [65] are a vital step in
the right direction, further steps are needed to make use of the unprecedented availability
of EO data and cloud computing solutions that are increasingly available for researchers.

5. Conclusions
This study shows that biophysical variables can be obtained successfully from S2 data
using a hybrid inversion of PROSAIL RTM. Within such inversion, Gaussian Processes
outperform all other models when using pure data. However, with added noise, this is
no longer true, and ANN, MTN, and GPR have similar results, with the neural networks
being slightly better. Moreover, while GPR can be trained quicker and with less data,
neural network architectures offer a lot of opportunities for improvement and less compu-
tational load. Therefore, more complex neural network architectures should be explored
to improve the accuracy and generality of biophysical trait retrieval on global scale. Such
future explorations may also benefit from the integration of ecological knowledge into the
training procedure, e.g., by imposing these relationships on the training data itself and
from automatic hyperparameter tuning based on sensor, location, and objects. Other future
opportunities can arise with the increasing number of publicly available trait databases and
sensors which can allow the development of meta-learning approaches that could improve
both the model performance as well as reduce the computational cost. In combination,
this study provides a major encouragement for using hybrid RTM inversion to retrieve
biophysical variables from satellite data, e.g., for monitoring global change impacts.

Author Contributions: N.C.d.S. was responsible for the conceptualization, implementation, execu-
tion and preparation of this manuscript. M.B. was responsible for the conceptualization, assisted in
the implementation and contributed for the preparation of this manuscript. L.T.H. contributed for
the conceptualization and preparation of the manuscript. P.v.B. contributed for the conceptualization
and preparation of the manuscript. All authors have read and agreed to the published version of
the manuscript.
Funding: This research was partly funded through the Leiden University Data Science Research
Program.
Code Availability: https://github.com/nunocesarsa/RTM_Inversion (accessed on 2 December 2020).
Acknowledgments: The authors would like to acknowledge the three reviewers for their valuable
comments and suggestions that greatly improved the manuscript. The authors would also like to
acknowledge Andrew Sorensen for his review of the English quality of this manuscript.
Conflicts of Interest: The authors declare no conflict of interest.
Remote Sens. 2021, 13, 648 17 of 20

Appendix A
Appendix A.1. Spectral Variability in Response to Trait Variability

Cab Cm

●
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7.5 ●
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20
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5.0
Mean absolute percentage error (%)

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Cw LAI
25

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15 20 ● ●
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10 ●
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0 0
0 1000 2000 3000 4000 0 1000 2000 3000 4000
Epochs
●
ANN Training ●
ANN Validation ●
MTN Training ●
MTN Validation

Figure A1. Neural networks training and validation error in function of epochs. Error bars represent the standard deviation
of a 5-fold cross-validation procedure.

Appendix A.2. Artificial Neural Networks Mean Absolute Percentage Error in Function of
Training Epochs

Figure A2. With this figure it is possible to visualize the variation in PROSAIL simulated S2-like data reflectance spectra
when stabilizing all traits except for one. This shows that variations in Car are likely not measurable by Sentinel-2.
Remote Sens. 2021, 13, 648 18 of 20

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