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Genetic Programming: Efficient Modeling Tool in Hydrology and Groundwater Management

Written By

J. Sreekanth and Bithin Datta

Submitted: November 3rd, 2011 Published: October 18th, 2012

DOI: 10.5772/52102

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1. Introduction

With the advent of computers a wide range of mathematical and numerical models have been developed with the intent of predicting or approximating parts of hydrologic cycle. Prior to the advent of conceptual or process based models, physical hydraulic models, which are reduced scale representations of large hydraulic systems, were used commonly in water resources engineering. Fast development in the computational systems and numerical solutions of complex differential equations enabled development of conceptual models to represent physical systems in almost all arenas of life including hydrological and water resources systems. Thus, in the last two decades large number of mathematical models was developed to represent different processes in the hydrological cycle. Hydrological models can be broadly classified in to three.

  1. Physical models

  2. Conceptual models

  3. Statistical / Black box models

Physical models are reduced scale representations of the actual hydrological system and the responses obtained from these models are up-scaled to estimate the responses of the real system. Conceptual models are based on different individual processes or components of a hydrological process. For example, in modelling the watershed response to a storm event a conceptual model make use of different equations to compute different components like subsurface flow, evapo-transpiration, channel flow, groundwater flow, surface run off etc. The third type of modelling involves using mathematical and statistical techniques to fit a model to a data set which then relates the dependent variable to the independent variables. This type of modelling includes regression models, response matrix, transfer functions, neural networks, support vector machine etc. The most widely used “black box” type modelling approach in hydrology and water resources literature is neural networks. Genetic programming is a potential tool to develop simple and efficient functional relationship between hydrological variables. In spite of the wide range of possible applications in hydrology and water resources, GP has not been widely reported in the hydrology and water resources literature. The focus of this chapter is to discuss the potential applicability of genetic programming to develop simple and computationally efficient hydrological models, in light of a few studies reported in the recent years. The key points discussed are as follows;

  1. GP’s ability to develop simple models with interpretability to overcome the curse of “black box” nature of data intensive models.

  2. Lesser number of parameters used in GP models as compared to parallel neural network architectures.

  3. GP’s ability to parsimoniously identify the significance of the modelling inputs.

1.1. Genetic programming as a modelling tool

Genetic programming belongs to and is one of the latest members in the family of evolutionary computation. Evolutionary computation refers to the group of computational techniques which are inspired by and emulate the natural process of evolution which resulted in the formation of the entire variety of organisms present on earth. Just as the way evolution and natural selection has resulted in the formation of organisms that are competent and best suitable inhabitants to live in any natural environment, the principle has been applied in computational science to evolve solutions to complex engineering problems which are subject to random and chaotic environments similar to the circumstances in which natural evolution has occurred. Evolutionary computation forms the basic principle behind the evolutionary algorithms like genetic algorithm (GA), genetic programming (GP), Evolutionary programming, evolution strategy, differential evolution. Evolutionary algorithms, widely used in mathematical optimization, are in general based on the application of evolutionary principles like selection, cross-over and mutation to a “population” of candidate solutions over a number of generations to find the optimal solutions to an engineering problem. Genetic algorithm is, for example, a widely used optimization techniques using these principles as the basic “operators” of the algorithm. Genetic programming [1] is similar to genetic algorithm in this aspect that it uses these genetic operators selection, cross-over and mutation in its algorithms. However, the uniqueness of genetic programming is that it performs these operators over symbolic expression or formulae or programs rather than over numbers which represent the candidate solutions. Thus, in genetic programming the candidate solutions are symbolic expressions or formulae. In a modelling framework these symbolic expressions or formulae or programs are candidate models to simulate a physical phenomenon. The parse tree notations of two parent and offspring genetic programs are shown in figure 1. Thus the optimal formula that is evolved by genetic programming can be used as a best fit model for predicting the physical phenomenon under consideration.

Figure 1.

Symbolic representation of parent and offspring genetic programs

In figure 1, two parent programs to model a physical phenomenon are shown. After testing these programs for their modelling performance, they are operated by cross-over operator. That is, parts of the programs are crossed over at the dashed locations to generate the offspring programs. Also, mutation is illustrated by arbitrarily changing the parameter 2 to 6.

In the last decade a few studies in the broad area of hydrology have utilized genetic programming based models for making hydrological predictions. The utility of GP in developing rainfall-runoff models, which are highly non-linear models was addressed in [2] They combined the use of GP based models with other conceptual models in deriving useful hydro-climatic models. It was concluded that GP was able to develop more robust models in that the functional relationships between different model inputs could be easily identified thus resulting in more transparency of the “black box” type of modelling. Another study [3] applied genetic programming and artificial neural networks in hydrology to model the effect of rain on the runoff flow in an urban basin. This study also illustrated the possibility of including the physical basis of the problem in the GP based model. Another research in this direction [4] compared three different artificial intelligence techniques viz, neural networks, adaptive neuro-fuzzy inference system (ANFIS), and genetic programming for discharge routing of a river in Turkey. The study revealed that GP displayed a better edge over the other two modelling approaches in all the statistics compared like the mean absolute error (MAE), mean squared relative error (MSRE) and correlation coefficient. Kisi et al (2010) [5] developed a wavelet gene expression programming (WGEP) for forecasting daily precipitation and compared it with wavelet neuro-fuzzy models (WNF). The results showed that WGEP models are effective in forecasting daily precipitation with better performance over WNF models. Selle [6] utilized genetic programming to systematically develop alternative model structures with different complexity levels for hydrological modelling with the objective of testing whether GP can be used to identify the dominant processes within the hydrological system. Models were developed for predicting the deep percolation responses under surface irrigated pastures to different soil types, water table depths and water ponding times during surface irrigation. The dominant process in the model prediction as determined from the models generated using genetic programming was found to be comparable to those determined using conceptual models. Thus it was concluded that Genetic programming can be used to evaluate the structure of hydrological models. A common aspect of GP based modelling that all these studies reported is the fact that the GP modelling resulted in fairly simpler models which could be easily interpreted for the physical significance of the input variables in making a prediction. Jyothiprakash and Magar (2012) [12] performed a comparative study of reservoir inflow models developed using ANN, ANFIS and linear GP for lumped and distributed data. The study reported superior performance of GP models over ANN and ANFIS models.


2. Simple and interpretable hydrological models using genetic programming

The major drawback of all the data driven modelling approaches is the black box nature of these models, i.e., the user cannot easily identify what is happening in model which computes the outputs corresponding to the inputs supplied to the model. One of the key advantages of genetic programming as a modelling tool is its ability to develop simple hydrological models. The simplicity of the models is close associated with their interpretability. The simpler the models are the better they can be interpreted. This in turn helps in assessing the contributions of different members of the predictor set or inputs in making a particular prediction. Selle and Muttil (2011) utilized this capability of GP to test the structure of hydrological models to predict deep percolation response in surface irrigated pastures. Data obtained using lysimeter experiments were used to develop simple models using genetic programming. The developed models were simple and interpretable which helped in identifying the dominant processes involved in the deep percolation process. Often the developed models could be expressed as simple algebraic equations. The dominant processes identified compared well with the same as used in conceptual models. The study also investigated the recurrence of the models developed using GP in multiple runs and found out that they were consistently coming up with the same model for a given level of complexity of the model. However, the study also reported that as the level of complexity increases recurrence of the generated model were affected and the physical interpretability of the models decreases and hence careful understanding of the complexity of the system is to be considered before a level of complexity is chosen for the GP models.

This however, illustrates that carefully developed GP models remain mathematically simple and are readily interpretable to the extent that the dominant processes which influence the prediction could be readily identified from the model structure. When carefully implemented models can throw light into and identify the key physical processes contributing to the phenomenon predicted and hence the development of the model. This is an important feature lacking from many of the data mining based prediction models resulting from which these modelling approaches are often earmarked as “black-box” models. “Black-box” nature of the prediction models often result in the limited use of such models for practical predictive applications.

2.1. Model complexity of GP and neural networks – Comparative study

The authors had conducted a study [7] to evaluate the complexity of predictive models developed using Genetic programming in comparison with models developed using neural networks. The models based on GP and neural network were developed as potential surrogate models to a complex numerical groundwater flow and transport model. The saltwater intrusion levels at monitoring locations resulting due to the excitation of the aquifer by pumping from a number of groundwater pumping wells were modelled by using GP and neural networks. The pumping rates at these groundwater well locations for three different stress periods were the inputs or independent variables for the model. The resulting salinity levels at the monitoring locations were the dependent variables or outputs.

The GP and ANN based surrogate models were trained based on the training and validation data generated using a three dimensional coupled flow and transport simulation model FEMWATER. The GP models were developed using a software Discipulus, which uses a linear genetic programming algorithm. The ANN surrogate models were developed using a feed forward back propagation algorithm implemented in the software neuroshell. The input data considered were the pumping rates at eleven well locations over three different time periods, constituting 33 input variables. Since pumping at each location can take any real value between the prescribed minimum and maximum these input variables constitute a 33 dimensional continuous space, each dimension representative of a pumping rate at a particular location in a particular stress period. Hence efficient training of the GP and ANN models required carefully chosen input data which is representative of the entire input space. Latin hypercube sampling was performed to choose uniformly distributed input samples from the 33 dimensional input space. An input sample is a vector of 33 values of pumping rate at 11 well locations during three stress periods. The salinity level at each observation location is the dependent variable or output. The values of the outputs required for training the GP and ANN models were generated by running the FEMWATER model. The numerical simulation model was run numerous times to generate the output data set corresponding to each input vector. The input-output data set generated following this procedure was divided into two sets with three quarters of the data in one set and the rest in the other. The larger set was used for training GP and ANN models and the smaller one was used for validating the models. The members of the training and validation sets for both GP and ANN were chosen randomly.

The ANN used in the study was trained in the supervised training mode using a back propagation algorithm. The objective function considered for both the GP and ANN training was minimization of the total root mean square error (RMSE) of the prediction. The prediction error was calculated as the difference between the model (GP or ANN) predicted values and the actual from the numerical model generated data set.

The input-hidden-output layer architecture for the ANN model was optimized by trial and error. Both GP and ANN models had 33 input variables and 3 outputs. The number of hidden neurons in the ANN model was determined by adding 1 hidden neuron during each trial. A sigmoid transfer function and a learning rate of 0.1 were used. In developing the model the back propagation algorithm modifies the connection weights connecting the input-hidden and output neurons by an amount proportional to the prediction error in each iteration and repeats this procedure numerous times till the prediction errors are minimized to a pre-specified level. Thus for any given model architecture (model structure) the neural network model optimizes the connection weights to accomplish satisfactory model predictions. Where as the genetic programming modelling approach is different in that it evolves the optimal model architecture and their respective parameters in achieving satisfactory predictions.

The GP models developed used a population size of 500, mutation and cross over frequencies of respectively 95 and 50 percent. The number of generations were not specified a priory, instead the evolutionary process was stopped when the fitness function was less than a critical value. In order to achieve the simplest models, the mathematical operators where initially kept a minimum and then further operators were added into the functional set. In this manner, initially addition and subtraction were alone added in this set and later the operators multiplication, arithmetic and data transfer were added into the set.

The predictive performance of the GP and ANN models on an independent set of data were found to be satisfactory in terms of the correlation coefficient and minimized RMSE. Figure 2 and 3 respectively shows the ANN and GP predictions of salinity levels at three monitoring locations corresponding to the their corresponding values from the numerical simulation model A dissection of the GP and ANN models were performed to evaluate the model complexity. The modelling framework of the GP models essentially has a functional set and a terminal set. The functional set comprises of the mathematical operations like addition, subtraction, division, multiplication, trigonometric functions etc. The terminal set of GP comprises of the model parameters which are also optimized simultaneously as the model structure is optimized. In our study the developed GP models used a maximum terminal set size of 30. i.e., satisfactory model predictions could be achieved with only 30 parameters for the GP model.

The functional operators essentially develop the structure of the GP models by operating on the input variables. In the GP modelling framework this model structure is not pre-specified unlike the ANN models. Instead, the model structure is evolved in the course of model development by testing numerous different model structures. This approach definitely provides scope for the development of improved model structures as against the ANN method. In the ANN approach where comparatively only a few models are tested in the trial and error approach which does not implement an organized search for better model architectures. The only components that are optimized during the development of the ANN model are the connection weights. Thus the model structure is rigid and is retained as determined by the trial and error procedure. This gives lesser flexibility in adapting the model structure with respect to the process being modelled. In our study it was found that while GP models required only 30 parameters in developing the model the number of connection weights in the ANN models was 1224. This is a metric of the simplicity of the GP models as against the ANN models. From figures 2 and 3 it is observed that despite the simplicity of the model and much lesser number of parameters used GP predictions are very similar to the ANN model predictions. For each hidden neuron added into the ANN architecture the number of connection weights increases by a number equal to the total number of inputs and outputs. Hence there is a geometric increase in the number of connection weights with increase in the number of hidden neurons in ANN architecture.

The comparison of the number of parameters in itself testifies the ability of the genetic programming framework to develop simpler models. The impact of the number of parameters on the model is on the uncertainty of the predictions made using the model. The more the number of parameters, the more uncertainty in them and hence this uncertainty propagates into the predictions made.


3. Parsimonious selection of input variables

Another key feature of the genetic programming based modelling approach is the ability of genetic programming to identify the relative importance of the independent variables chosen as the modelling inputs. Many often in hydrological applications it is uncertain which variables are important to be included as inputs in modelling a physical phenomenon. Similarly time series models are used quite often in predicting or forecasting hydrological variables. For example the river stages measured on a few consecutive days can be used to forecast the river stage for the following days. In doing so the number of past days’ flow to be included as inputs into the time series model depends on the size and shape of the catchment and many similar parameters. Most often rigorous statistical tests like auto-correlation studies are conducted to determine whether an independent variable is significant to be included in the model development or not. Once included most often it is not possible to eliminate from most of the modelling frameworks because of the earlier mentioned rigidity of the model structure. For example, in neural networks an insignificant model input should be ideally assigned zero connection weights to the output. However, these connection weights most often don’t assume the zero value but converge to very small values near zero. This results in the insignificant variable being influencing the predictions made by a small amount. These results in uncertainties in the predictions made.

The evolutionary process of determining the optimum model structure helps GP to identify and eliminate insignificant variables from the model development. The authors conducted a study dissecting the neural network and GP models developed in the same study described above to evaluate the parsimony in the selection of inputs for model development. GP evolves the best model structure and parameters by testing millions of alternate model structures. The relative importance of the each independent variable in the model development was computed by the recurrence of each independent variable in the best 30 models developed by GP. Thus, if an input appears in all the 30 models its impact factor is 1 and if one independent variable appears in none of the best 30 models its impact factor is 0.

Figure 2.

Salinity predictions at three locations by the ANN models

To determine the significance of the inputs in the neural network model a connection weights method was used [7]. In this method the significance of each input is computed as a function of the connection weights which connects it to the output through the hidden layer. The formulae used in [7] were used to compute this;

  1. First step in this approach was to compute the product of the input-hidden layer and hidden output layer weights. The, divide this by the sum of products of absolute values of the input-hidden and hidden output layer weights of all input neurons. This is given by Qih in (2)

  1. Divide the sum of the Qih for each hidden neuron by the sum for each hidden neuron of the sum for each input neuron ofQih, for each i. The relative importance of all output weights attributable to the given input variable is then obtained. The relative importance is then mapped to a 0-1 scale with the most important variables assuming a value of 1. A RI value of 0 indicates an insignificant variable.


In this manner, the significance of each independent variable (input) to the model was quantified in a 0-1 range as impact factor and relative importance respectively for GP and ANN models. These values for GP and ANN models are plotted in figures 4,5 and 6.

Figure 3.

Salinity predictions at three locations by the ANN models

Figure 4.

Impact factors of input variables in predicting Salinity at location 1.

Figure 5.

Impact factors of input variables in predicting Salinity at location 2.

From these figures it can be observed that all the variables considered has a non-zero impact in the developed ANN models. Whereas, GP is able to assign zero impact factor to those inputs which are not significant and thus able to eliminate them from the model. This helps in developing simpler models and reducing the predictive uncertainty. In figure 4 it can be seen that GP identified 13 inputs with zero impact factor. This implies that the pumping values corresponding to these inputs have negligible effect on the salinity levels at the observation location. Thus 13 out of the 33 inputs considered are eliminated from the GP models resulting in much simpler models compared to the ANN models where all the 33 inputs take part in predicting the salinity even though some of them are having very less impact on the predictions made. The ability of GP to eliminate insignificant variables is because of the evolutionary nature of model structure optimization. By performing cross-over, mutation and selection of candidate models over a number of generations GP is able to derive the optimum model structure with the most important input variables which are relevant to the model prediction. This inturn help in developing simpler models with fewer uncertainties in the model prediction.

Figure 6.

Impact factors of input variables in predicting Salinity at location 3.


4. Multiple predictive model structures using GP

The advent of GP as a modelling tool has paved the way for researches exploring the possibility of multiple optimal models for predicting hydrological processes. Genetic programming, in its evolutionary approach to derive optimal model structures and parameters, tests millions of model structures which can mimic the physical process under consideration. Researches have found that multiple models can be identified using GP which are considerably different in model structures but able to make consistently good predictions. Parasuraman and Elshorbagy [8] developed genetic programming based models for predicting the evapo-transporation. In doing so, multiple optimal GP models were trained and tested and they were applied to quantify the uncertainty in those models. Another study by the authors [9] developed ensemble surrogate models for predicting the aquifer responses to pumping in terms of salinity levels at observation locations. An ensemble of surrogate models based on GP was developed and the ensemble was used to get model predictions with improved reliability levels. The variance of the model predictions were used as the measure of uncertainty in the modelling process.


5. GP as surrogate model for simulation-optimization

A very important application of data intensive modelling approaches is to develop surrogate models to computationally complex numerical simulation models. As detailed elsewhere in this article, the authors have utilized GP in developing potential surrogates to a complex density dependent groundwater flow and transport simulation model. The potential utility of the surrogates is to replace the numerical simulation model in simulation-optimization frameworks. Simulation-optimization models are used to derive optimal management decisions using optimization algorithms in which a numerical simulation models is run to predict the outcome of implementing the alternative management options. For example, the authors developed simulation-optimization models to develop optimal management decisions for coastal aquifers. The optimal pumping from the coastal aquifer can be decided only by considering the impact of any alternative pumping strategy on saltwater intrusion. For this the numerical simulation model needs to be integrated with the optimization algorithm and the impact of each candidate pumping strategy is predicted by using the simulation model iteratively. This involve a lot of computational burden as thousands of numerical model runs are required before an optimal pumping strategy is identified.

GP was used a surrogate model within the optimization algorithm as a substitute of the numerical simulation model in our study (Sreekanth and Datta, 2010). Previous studies have used artificial neural networks as surrogate models to replace groundwater numerical simulation models. Emily et a1 (2005) used genetic programming based surrogate models for groundwater pollution source identification. In our study (Sreekanth and Datta, 2010), it was found that genetic programming could be used as a superior surrogate model in such application with definite advantages. The study intended to develop optimal pumping strategies for coastal aquifers in which the total pumping could be maximized and at the same time limiting the saltwater intrusion at pre-specified limits. In doing so, the effect of pumping on the salinity levels was predicted using trained and tested GP models. The GP models were externally coupled to a genetic algorithm based optimization model to derive the optimal management strategies. The results of the GP based simulation-optimization was then compared to the results obtained using an ANN-based simulation-optimization model. The ability of GP in parsimoniously identifying the model inputs helped in reducing the dimension of the decision space in which modelling and optimization was carried out. The smaller dimension of the modelling space helped in reducing the training and testing required to develop the surrogate models. The study identified that GP has potential applicability in developing surrogate models with potential application in simulation-optimization methodology to solve environmental management problems.


6. Conclusion

The aim of this chapter is to introduce genetic programming as a potential modelling tool for hydrology and water resources applications. Genetic programming belongs to the broad class of evolutionary computational tools developed in recent years. Compared to the vast number of data mining and artificial intelligence applications in hydrology and water resources, the application of GP has been limited in spite of its potential applicability in a wide range of modelling applications. This chapter illustrates a few applications of GP as a modelling tool in the broad area of water resources modelling and management. The studies have found GP to be a useful tool for such applications with some advantages over other artificial intelligence techniques. The major findings reported in this chapter are enumerated as follows;

  1. Genetic programming is able to develop simple models for developing the time series forecast models. When compared to the complex architecture of neural networks the GP models are simpler and easy to analyse. This is particularly relevant in developing transparent models for predicting natural phenomena. Complex neural network architectures make ANN model more or less “black-box” in nature, where as simpler GP models makes it easy to analyse the physical significance of each input in the model development.

  2. In GP modeling, the optimum model architecture is evolved by GP after testing, most often, millions of alternate model structures and parameters as against the trial and error approach being followed by other artificial intelligence modeling approaches like neural networks. This helps in converging to global optimal solutions in minimizing the error criteria used for model development. Thus GP is able to develop global optimum models for predicting/forecasting hydrological processes and time series.

  3. Genetic programming has the capability of parsimoniously selecting the variables for model development from the potential inputs. This helps to prevent redundancy in model development in terms of unnecessary inputs and parameters. In course of the model development GP determines the significance of each input in the model development in an efficient way so that the totally insignificant inputs are eliminated from the model. As shown in the results approaches like neural network models are also able to identify the relative significance of the inputs, they are less efficient in achieving this because of the rigidity of the model structure and connection weights.

These key advantages of GP modeling are illustrated using realistic example in the broad area of hydrology and groundwater management for time series model development and conclusions are drawn which establishes the potential of genetic programming as a modeling and prediction tool for hydrology and water resources application.


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Written By

J. Sreekanth and Bithin Datta

Submitted: November 3rd, 2011 Published: October 18th, 2012