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The hyper-parameters and the hyper-posterior distribution involved in Magma can be learned thanks to an EM algorithm implemented in train_magma. By providing a dataset, the model hypotheses (hyper-prior mean parameter and covariance kernels) and initialisation values for the hyper-parameters, the function computes maximum likelihood estimates of the HPs as well as the mean and covariance parameters of the Gaussian hyper-posterior distribution of the mean process.


  prior_mean = NULL,
  ini_hp_0 = NULL,
  ini_hp_i = NULL,
  kern_0 = "SE",
  kern_i = "SE",
  common_hp = TRUE,
  grid_inputs = NULL,
  pen_diag = 1e-10,
  n_iter_max = 25,
  cv_threshold = 0.001,
  fast_approx = FALSE



A tibble or data frame. Required columns: ID, Input , Output. Additional columns for covariates can be specified. The ID column contains the unique names/codes used to identify each individual/task (or batch of data). The Input column should define the variable that is used as reference for the observations (e.g. time for longitudinal data). The Output column specifies the observed values (the response variable). The data frame can also provide as many covariates as desired, with no constraints on the column names. These covariates are additional inputs (explanatory variables) of the models that are also observed at each reference Input.


Hyper-prior mean parameter (m_0) of the mean GP. This argument can be specified under various formats, such as:

  • NULL (default). The hyper-prior mean would be set to 0 everywhere.

  • A number. The hyper-prior mean would be a constant function.

  • A vector of the same length as all the distinct Input values in the data argument. This vector would be considered as the evaluation of the hyper-prior mean function at the training Inputs.

  • A function. This function is defined as the hyper_prior mean.

  • A tibble or data frame. Required columns: Input, Output. The Input values should include at least the same values as in the data argument.


A named vector, tibble or data frame of hyper-parameters associated with kern_0, the mean process' kernel. The columns/elements should be named according to the hyper-parameters that are used in kern_0. If NULL (default), random values are used as initialisation.


A tibble or data frame of hyper-parameters associated with kern_i, the individual processes' kernel. Required column : ID. The ID column contains the unique names/codes used to identify each individual/task. The other columns should be named according to the hyper-parameters that are used in kern_i. Compared to ini_hp_0 should contain an additional 'noise' column to initialise the noise hyper-parameter of the model. If NULL (default), random values are used as initialisation.


A kernel function, associated with the mean GP. Several popular kernels (see The Kernel Cookbook) are already implemented and can be selected within the following list:

  • "SE": (default value) the Squared Exponential Kernel (also called Radial Basis Function or Gaussian kernel),

  • "LIN": the Linear kernel,

  • "PERIO": the Periodic kernel,

  • "RQ": the Rational Quadratic kernel. Compound kernels can be created as sums or products of the above kernels. For combining kernels, simply provide a formula as a character string where elements are separated by whitespaces (e.g. "SE + PERIO"). As the elements are treated sequentially from the left to the right, the product operator '*' shall always be used before the '+' operators (e.g. 'SE * LIN + RQ' is valid whereas 'RQ + SE * LIN' is not).


A kernel function, associated with the individual GPs. ("SE", "PERIO" and "RQ" are also available here).


A logical value, indicating whether the set of hyper-parameters is assumed to be common to all individuals.


A vector, indicating the grid of additional reference inputs on which the mean process' hyper-posterior should be evaluated.


A number. A jitter term, added on the diagonal to prevent numerical issues when inverting nearly singular matrices.


A number, indicating the maximum number of iterations of the EM algorithm to proceed while not reaching convergence.


A number, indicating the threshold of the likelihood gain under which the EM algorithm will stop. The convergence condition is defined as the difference of likelihoods between two consecutive steps, divided by the absolute value of the last one ( \((LL_n - LL_n-1) / |LL_n|\) ).


A boolean, indicating whether the EM algorithm should stop after only one iteration of the E-step. This advanced feature is mainly used to provide a faster approximation of the model selection procedure, by preventing any optimisation over the hyper-parameters.


A list, gathering the results of the EM algorithm used for training in Magma. The elements of the list are:

  • hp_0: A tibble of the trained hyper-parameters for the mean process' kernel.

  • hp_i: A tibble of all the trained hyper-parameters for the individual processes' kernels.

  • hyperpost: A sub-list gathering the parameters of the mean processes' hyper-posterior distributions, namely:

    • mean: A tibble, the hyper-posterior mean parameter (Output) evaluated at each training reference Input.

    • cov: A matrix, the covariance parameter for the hyper-posterior distribution of the mean process.

    • pred: A tibble, the predicted mean and variance at Input for the mean process' hyper-posterior distribution under a format that allows the direct visualisation as a GP prediction.

  • ini_args: A list containing the initial function arguments and values for the hyper-prior mean, the hyper-parameters. In particular, if those arguments were set to NULL, ini_args allows us to retrieve the (randomly chosen) initialisations used during training.

  • seq_loglikelihood: A vector, containing the sequence of log-likelihood values associated with each iteration.

  • converged: A logical value indicated whether the EM algorithm converged or not.

  • training_time: Total running time of the complete training.


The user can specify custom kernel functions for the argument kern_0 and kern_i. The hyper-parameters used in the kernel should have explicit names, and be contained within the hp argument. hp should typically be defined as a named vector or a data frame. Although it is not mandatory for the train_magma function to run, gradients can be provided within kernel function definition. See for example se_kernel to create a custom kernel function displaying an adequate format to be used in Magma.


#> [1] TRUE