Slide 1 John Paul Gosling University of Sheffield GEM-SA: a tutorial

mucm.group.shef.ac.ukSlide 2 Overview GEM-SA: Gaussian Emulation Machine for Sensitivity Analysis It’s a Windows based program that has a graphical interface created by Marc Kennedy during his time in CTCD It does emulation for prediction, uncertainty analysis and sensitivity analysis It also has a facility to create experimental designs for the analysis of computer models.

mucm.group.shef.ac.ukSlide 3 Starting the program On the desktop, there is a folder, opening it will reveal two other folders: Inside the folder is the program: Double-clicking this will start the program

mucm.group.shef.ac.ukSlide 4 Main window menu toolbar log window Sensitivity Analysis output grid

mucm.group.shef.ac.ukSlide 5 Generating input designs There are two designs available: LP-TAU and Maximin Latin Hypercube. Both have good space filling properties. Press this button to create a file of inputs for your computer model

mucm.group.shef.ac.ukSlide 6 Generating input designs Then we specify ranges over which the input will be of interest These must cover your beliefs about the range of each input

mucm.group.shef.ac.ukSlide 7 The design Here’s a 50-point LP-TAU design for three inputs You’ll also find they’ve been written to the file you specified (LP_TAU50.txt) in GEM-SA’s working directory

mucm.group.shef.ac.ukSlide 8 Creating/Editing a project Now, we’ll run through some of the options available to us for emulator building. We can create a new project or edit an existing project by selecting the appropriate item from the project menu. Or we can use these toolbar buttons. NewEdit

mucm.group.shef.ac.ukSlide 9 Edit Project - Files Names of input files Names of output files

mucm.group.shef.ac.ukSlide 10 Edit Project - Options How many inputs? Edit input names

mucm.group.shef.ac.ukSlide 11 Edit Project - Options What should be calculated, and how? Which joint effects should be calculated?

mucm.group.shef.ac.ukSlide 12 Edit Project - Options Are the inputs uncertain? What prior mean for the output?

mucm.group.shef.ac.ukSlide 13 Edit Project - Options What kind of predictions and cross validation?

mucm.group.shef.ac.ukSlide 14 Edit Project - Simulations MCMC control parameters Number of realisations for prediction and ME/JE How many points used to calculate main effects, joint effects

mucm.group.shef.ac.ukSlide 15 Input names By clicking the button, a window opens that allows us to name each of the inputs. This can be handy when viewing the variance decomposition results and main effects plots.

mucm.group.shef.ac.ukSlide 16 Distributions for inputs When we click the button, the following window opens. This windows allows us to specify our beliefs about the inputs.

mucm.group.shef.ac.ukSlide 17 A first run through Consider the simple nonlinear model we saw earlier y = sin(x 1 )/{1+exp(x 1 +x 2 )} We have 2 inputs, x 1 and x 2, and we assume they both must be valued in the range [0,1]. 20 points will give us a decent coverage of the unit square that is the input space here. Two files have already been saved in the folder to help save us time.

mucm.group.shef.ac.ukSlide 18 Monte Carlo method Here’s the result of a Monte Carlo analysis using 30 input pairs. Mean = 0.139, median = Std. dev. = Variance =

mucm.group.shef.ac.ukSlide 19 Monte Carlo method Mean = 0.114, median = Std. dev. = Variance = Here’s the result of a Monte Carlo analysis using 10,000 input pairs.

mucm.group.shef.ac.ukSlide 20 Prediction Predictions can be Correlated realisations of outputs at the prediction inputs Similar to main effect outputs Marginal means and variances of outputs at the prediction inputs Faster to compute, especially with many prediction points Easy to interpret

mucm.group.shef.ac.ukSlide 21 A plot of the predictions Here is the prediction output files plotted with the real function with x 2 fixed at 0.5.

mucm.group.shef.ac.ukSlide 22 Cross validation Choice of none, leave-one-out or leave final 20% out Leave-one-out Hyperparameters use all data and are then fixed when prediction is carried out for each omitted point Leave final 20% out Hyperparameters are estimated using the reduced data subset

mucm.group.shef.ac.ukSlide 23 A real example A dynamic vegetation model is being used to predict the NBP of deciduous broadleaf woodland in the vicinity of Whitby, North Yorkshire. The scientists are uncertain about ten inputs of the model and want to know how this uncertainty affects the NBP output of the model – Monte Carlo methods are out of the question as the model is too complex. When they used their best guesses for these inputs, the model returned a NBP of 146.4gC/m 2.

mucm.group.shef.ac.ukSlide 24 The input names in order Maximum age (years) N(200,625) Water potential (M Pa) N(3,0.25) Leaf life span (days) N(190,1600) Leaf mortality index N(0.005,6.25e-6) Bud burst limit (degree days) N(135,6.25) Seeding density (m 2 ) N(0.1,0.0001) Soil sand (%) N(43.27,222.12) Soil clay (%) N(22.36,49.21) log(stem growth rate) N(-5.116, ) Bulk density N(1.214,0.0325)

mucm.group.shef.ac.ukSlide 25 Main effects plots The plug-in estimate of the NBP is far away from our mean for NBP as the main effect plot for bulk density is concave around it’s expected value of

mucm.group.shef.ac.ukSlide 26 Producing main/joint effects plots for publication In the files section of the edit project window, there are two fields that allow the user to specify where the main/joint effects data should be written. These files can be used to produce graphs like the one I showed earlier. The main effects file is structured as follows: There are a number of blocks of function realisations – one for each input. These are controlled by

mucm.group.shef.ac.ukSlide 27 Limitations of GEM-SA In theory, the methods used by GEM-SA are limitless; however, the program itself isn’t. It can handle up to 30 inputs and 400 training data. Also, the distributions that are used to express our uncertainty about the inputs are limited to uniform or normal.

mucm.group.shef.ac.ukSlide 28 When it all goes wrong… How do we know when the emulator is not working? Large roughness parameters Especially ones hitting the limit of 99 Large emulation variance on UA mean Poor CV standardised prediction error Especially when some are extremely large In such cases, see if a larger training set helps Other ideas like transforming output scale

mucm.group.shef.ac.ukSlide 29 Where to find the program GEM-SA is available on the web along with tutorial slides from a longer course and further example data sets. Links to it can be found on my website where there is also a technical report explaining the perils of using the “plug-in” approach: j-p-gosling.staff.shef.ac.uk