Scientific Machine Learning to simplify hydrological modelling in a changing climate


Joost Iwema


January 16, 2023


vadose zone, modelling

Machine Learning and Scientific Machine Learning in Vadose Zone Hydrology

In literature a commonly used word for the unsaturated, or better said, the variably saturated part of the soil, is the vadose zone. On this website we use this term.

The movement of water in the vadose zone is often modelled with the Richardson-Richards’ equation (“Weather Prediction by Numerical Process” 1922; Richards 1931). This equation is based on the Buckingham-Darcy equation and assumes conservation of mass, an incompressable porous medium (which is not always acceptable in clay soils and peat soils) and a constant liquid density (acceptable in most cases in agriculture and other environments). Solving the the Richardson-Richards’ equation (numerically) is non-trivial and computationally expensive.

Recently Ghanbarian and Pachepsky (2022) shared a communication on the use of machine learning in vadose zone hydrology. They mentioned that hydrologists and soil scientists were early adopters of machine learning techniques. The application has been mostly regarding pedotransfer functions. Pedotransfer functions are formulas that translate soil properties like soil composition information (e.g. sand, silt, clay, and organic matter contents) to soil hydraulic properties, like hydraulic conductivity and water retention capacity. A well-known example is the Rosetta model (Schaap, Leij, and van Genuchten 2001; Zhang and Schaap 2017), which was constructed using an artificial neural network.

Another application of machine learning targeted relatively often in modelling the vadose zone, is the construction of metamodels. Metamodels, both based on machine learning and other techniques, have been applied in vadose zone hydrology to limit the high computational costs of running physics based soil hydrologcal models when applied at for instance regional scale. An example of a metamodel that includes the vadose zone to an important extend, and that uses machine learning is part of ‘WaterVision Agriculture’ (Hack-ten Broeke et al. 2016). It is based on the vadose zone model SWAP (Dam et al. 2008) and the plant physiological model WOFOST (Boogaard et al. 1998).


WaterVision Agriculture was developed to calculate the effects of hydrological measures on annual average agricultural production in the Netherlands. This model allows to compute effects under both the current climate and future climate. It can do so while distinguishing between effects on agricultural production from drought, too wet conditions (oxygen stress), and salinity in the root zone. Besides different climate scenarios, the metamodel takes as input 72 different soil units typical of The Netherlands, multiple crop types, and groundwater dynamics. Groundwater dynamics input is provided as a yearly average largest and a yearly average smallest groundwater table depth, which the user can set with a precision of 1 cm. The model then searches a database to find the closest model run available within it. This database was build with a random forest (Breiman 2001) of regression trees. A random forest is a machine learning technique that employs the decision tree technique, using IF-ELSE statements.

More recently, beyond common machine learning, SciML has been explored in vadose zone hydrology (Ghorbani, Sadeghi, and Jones 2021; Bandai and Ghezzehei 2021; Tartakovsky et al. 2020). Especially, the PINN method (Maziar Raissi, Perdikaris, and Karniadakis 2017a; Maziar Raissi, Perdikaris, and Karniadakis 2017b) has been investigated. However, different techniques have been used as well. In the next sections we provide an overview of what has been done on this matter.

PINN-approach in vadose zone hydrology

Tartakovsky et al. (2020) applied the physics-informed deep learning (PINN) method established by Maziar Raissi, Perdikaris, and Karniadakis (2017a) and Maziar Raissi, Perdikaris, and Karniadakis (2017b) to approximate partial differential equations and the pedotranfer functions used within them. They estimated saturated and unsaturated hydraulic conductivity and hydraulic pressure. They used measurements of saturated hydraulic conductivity and hydraulic head for saturated flow and capillary pressure head for unsaturated flow. The partial differential equations used were Darcy for saturated flow and Richardson-Richards’ for unsaturated flow. These PDEs were constrained by minimising the PDE-error at selected points. The PINN-method yielded more accurate approximations of partial differential equation estimates than traditional deep learning. Saturated hydraulic conductivity was estimated with higher accuracy when the PINN-method was used, compared to more traditional approaches. The relationship between hydraulic pressure and conductivity was estimated accurately with the PINN-method when employing only (noisy) matric pressure measurements.

While soil hydrological parameter values from laboratory experiments are available, these can not simply be transferred to field scale, at which soil hydrological modelling usually takes place. More accurate parameter value estimates at field scale can however be estimated with inverse modelling, using field scale observations. Bandai and Ghezzehei (2021) applied the PINN-method to estimating soil water retention curves, hydraulic conductivity functions, and to solving the Richardson-Richards’ equation. One advantage of using the PINN-approach in this case was that no explicit boundary or initial conditions are needed. Another advantage was that no good prior estimations of the soil hydraulic functions are needed. Yet another advantage was that the shapes of the soil hydraulic functions do not need to be defined beforehand. Using only synthetic soil volumetric water content data from HYDRUS1D simulations (Šimnek et al. 2008) with synthetic noise added, they obtained functions that could simulate the true volumetric water content dynamics. Both the soil water retention curves and hydraulic conductivity functions were simulated accurately by the PINNs at mid-range soil water content, in nonparametric form. At the dry and wet ends however, both soil hydraulic functions were not estimated well, due to non-linearity not captured by the neural networks. The PINNs simulated soil water flow well with noisy synthetic soil moisture flow data.

Despite the limitations shown by the outcomes, the fact that the PINN-method can provide useful nonparametric soil hydraulic functions with only volumetric soil content and no initial or boundary conditions, is interesting at least. There are multiple ways forward from this finding. First of all, the approach has been limited to synthetic data and homogeneous soil profiles. Applying it to vertically heterogeneous soils and using real observations is considerably more complicated. To cater for heterogeneity, monotonicity needs to be build in according to Bandai and Ghezzehei (2021), as elaborated on by Daniels and Velikova (2010). Another limitation is that the PINN implementation of Bandai and Ghezzehei (2021) cannot handle well sharp gradients and strong non-linearity. Bandai and Ghezzehei (2021) propose the residual-based refinement method from Lu et al. (2019) to meet this challenge. Another issue is the optimisation of the neural network architecture (number of hidden layers and number of nodes). Within this study, the soil water flux was used for this purpose, but this variable is not usually observed in the real world. As a solution to this, Bandai and Ghezzehei (2021) proposed to use the training error, which is defined in terms of the volumetric water content, to optimise the architecture (Mishra and Molinaro 2020). So, to use the PINN-approach in field-scale soil hydrology in practice, further work needs to be done.

Bandai and Ghezzehei (2021) built further on the work of Tartakovsky et al. (2020), by using (synthetic) volumetric water content data instead of (synthetic) soil matric potential (i.e. soil hydraulic pressure) data. The advantage of using volumetric water content is that such data is more readily available. That is despite that soil water pressure observations should actually be the preferred option, if available. Soil water flow is directly related to differences in spatial soil hydraulic head. Physical knowledge is added to the neural network approach through the PINN loss function, which contains two separate terms for both the comparison with observational data and for the comparison with the physics-based differential equation(M. Raissi, Perdikaris, and Karniadakis 2019). Moreover, Bandai and Ghezzehei (2021) successfully tested and applied the monotonicity constraint on both soil water retention functions. Monotonicity means that a function can yield increasing or decreasing values only, for increasing or decreasing input values. In other words, the derivative does not change sign (plus versus minus). This constraint makes physical sense because, soil hydraulic conductivity and soil hydraulic head (which goes from strongly negative to small negative values) only increase (monotonically) with increasing soil water content. Technically, Bandai and Ghezzehei (2021) used three fully forward connected neural networks. One network was to estimate soil hydraulic pressure head from vertical space coordinates and time coordinates, thereby simulating the Richardson-Richards’ equation. The output of this network was then fed to both a neural network that yielded soil hydraulic conductivity and a neural network that yielded soil water content. Applying automatic differentiation, first and second order differentials were computed. These differentials are terms of the Richardson-Richards’ equation. The residual function of this equation is the physics-based loss term of the PINN loss function. On the neural network architecture side, another interesting detail is the choice of activation and output function types. The activation function of the first neural network part (with output hydraulic pressure) was chosen to be a hyperbolic because the Richardson-Richards’ function is a second-order partial differential equation. The matric potential (i.e. pressure head) must be negative and therefore a negative exponential was chosen as output function The tangent hyperbolic function was used as activation function of both soil hydraulic functions. Their output function of the soil water retention function was chosen to be a sigmoid, to assure output values between zero and one. The output function of the soil hydraulic conductivity function was an exponential function to obtain positive values.

Other SciML-approaches in vadose zone hydrology

Ghorbani, Sadeghi, and Jones (2021) took another step to develop scientific machine learning in vadose zone modelling. They developed a machine learning based second order partial differential equation, similar in shape to the Richardson-Richards’ equation. To do so, they assumed a fourth order partial differential equation and let the training of the machine learning algorithm determine which order terms were significant (i.e. non-zero) and which non-zero parameter values these got. The algorithm yielded an equation with only the first and second order derivaties, the same terms as the basic Richardson-Richards’ equation contains. Which terms come out as non-zero is interesting as such, because it is known that the first and second order derivatives relate to gravity-induced flow and moisture diffusion, and that for instance the fourth-order derivative relates to wetting from instability and gravitational fingering (Cueto-Felgueroso and Juanes 2009).

Employing the sparse regression method, Ghorbani, Sadeghi, and Jones (2021) solved an equation with observed soil moisture and modeled soil moisture time-derivatives. Thereby, coefficients for the different space-derivatives of the observed soil moisture were obtained. Like Bandai and Ghezzehei (2021), Ghorbani, Sadeghi, and Jones (2021) used synthetic soil moisture data and a homogeneous soil profile. To produce the synthetic data, they used actually observed near-surface soil moisture data as input for a HYDRUS1D-model. They used the HYDRUS1D output as a reference against the outcomes of the machine learning approach. THe HYDRUS1D soil moisture output was also used as synthetic training data for the machine learning algorithm.

The training showed that three to six years of soil moisture data was needed to obtain convergence on the soil hydraulic conductivity and soil water diffusivity parameters. However, when surface boundary conditions were replaced with sinusoidal functions, just a few weeks of data was needed for training. The original top boundary was taken from rather noisy surface flux measurements fed into HYDRUS1D. From comparing different scenarios with observations at different depths, Ghorbani, Sadeghi, and Jones (2021) found that high temporal variability in soil moisture (like near the soil surface) should be accompanied with a large spatial extent of the data. The method computes temporal and spatial derivatives and therefore sufficient observations in both space and time are needed. Vertical interpolation was found to successfully establish a partial differential equation.

Ghorbani, Sadeghi, and Jones (2021) propose to use more advanced differentiation techniques, like automatic differentiation. The approach of Ghorbani, Sadeghi, and Jones (2021) can be used to reduce the nonlinearity of vadose zone models. This can be achieved by establishing a physically consistent, linear or quasilinear partial differential equation that is able to describe spatiotemporal soil moisture variability accurately, under different boundary conditions.

Ghanbarian and Pachepsky (2022) argued that with a large expansion of machine learning use in vadose zone hydrology, there has been less attention to certain important aspects of applying this technique. Accuracy and uncertainty of machine learning are database-dependent, i.e. they differ between datasets to which the same machine learning technique is applied. Reproducibility is often insufficient, with data, models, and computer code often not publicly available (lack of delivery).

In disciplines including (vadose zone) hydrology and soil science, data are (spatial) scale-dependent. Therefore, applying a machine learning model built with data at a certain scale cannot simply be applied at another scale (Ghanbarian and Pachepsky 2022). Comparing different types of machine learning algorithms on the same problem is often not done, while this would help assess quality of study outcomes. Fundamental protocols for machine learning, including on data, are required for earth sciences, following examples like proposed for environmental sciences by Heil et al. (2021). Ghanbarian and Pachepsky (2022) conclude with a call to address fundamental questions about the application of machine learning in research. For instance, they mention the questions why machine learning models exist and if there is a limit to machine learning model accuracy and reliability and what that depends on.

Concluding, there is considerable space and need for SciML in vadose zone research. While the PINNs-method has been tested in a few cases (M. Raissi, Perdikaris, and Karniadakis 2019), we have not found a vadose zone study with the UDE-approach (Rackauckas et al. 2020). This might be due to the more recent development of this method, but also due to the complexity of solving the Richardson-Richards’ equation. While UDE-solutions for different partial differential equations are available online, we could not locate one for the Richardson-Richards’.

What is currently needed to advance scientific machine learning in (vadose zone) hydrology?

Our literature study on SciML in (vadose zone) hydrology shows the research so far has been limited, due to the novelty of the technique. Fundamental machine learning questions need to be addressed and different machine learning algorithms should be compared (Ghanbarian and Pachepsky 2022) Studies that employed SciML-approaches like PINNs, show there is work to be done, especially with regard to using real observations and heterogeneous soils. To our knowledge, no study has so far used the UDE-approach to solve the Richardson-Richards’ equation for vadose zone modelling. Due to the complexity of solving this formula numerically, this poses an interesting challenge to explore.

Besides solving the soil physics itself, the relation with other processes can be addressed by SciML. Upper (meteorology) and lower boundary conditions (groundwater level dynamics) could be approached with SciML-techniques. Complex and poorly understood soil features like macropores could be addressed with for instance hybrid modelling (replacing part of a physics-based model with a machine learning module). Developing SciML-based metamodels for vadose zone models like SWAP and HYDRUS1D could be interesting from the viewpoint of reducing computational costs.

Karniadakis et al. (2021) listed some challenges relevant to developing SciML for vadose zone hydrology:

  • High-frequency patterns hard for PINNs to solve
  • Learning multiphysics-systems simultaneously is computationally expensive. This cost could be reduced by learning the different processes separately first and then coupling the different networks.
  • Neural Networks physics-informed loss-functions may fail in specific low-dimensional cases, like diffusion with irregular conductivity. This could be the case in hydrology and soil science.
  • During training, different terms of the complex loss function of a physically-informed neural network compete and therefore convergence to the global minimum cannot be guaranteed.
  • Lack of theoretical foundation of physics informed learning models.

So, it seems there are plenty of research opportunities.

When exploring a new topic, it makes sense to start easy. Willard et al. (2022) provided us with some direction from this perspective. Hybrid modelling is easiest to implement, whereas physics-guided loss functions and physics-guided architecture need more expertise. Given the complexity of the vadose zone and the Richardson-Richards’ equation, it seems easiest to start with model boundary conditions. Therefore, we started with a use case on replacing the Penman-Monteith evapotranspiration formula (an upper boundary condition to the Richardson-Richards’ equation). Further steps we intend to take are: to dive into solving the Richardson-Richards’ equation with SciML-techniques, to address macropore flow, to replace lower boundary conditions with SciML, and to build a metamodel for SWAP (Dam et al. 2008).


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