Section: Research Program
Parameter estimation
The Stochastic Approximation Expectation Maximization (SAEM) algorithm has shown to be extremely efficient for maximum likelihood estimation in incomplete data models, and particularly in mixed effects models for estimating the population parameters. However, there are several practical situations for which extensions of SAEM are still needed:
High dimensional model: a complex physiological model may have a large number of parameters (in the order of 100). Then several problems arise:

when most of these parameters are associated with random effects, the MCMC algorithm should be able to sample, for each of the $N$ individuals, parameters from a high dimensional distribution. Efficient MCMC methods for high dimensions are then required.

Practical identifiability of the model is not ensured with a limited amount of data. In other words, we cannot expect to be able to properly estimate all the parameters of the model, including the fixed effects and the variancecovariance matrix of the random effects. Then, some random effects should be removed, assuming that some parameters do not vary in the population. It may also be necessary to fix the value of some parameters (using values from the literature for instance). The strategy to decide which parameters should be fixed and which random effects should be removed remains totally empirical. Xpop aims to develop a procedure that will help the modeller to take such decisions.
Large number of covariates: the covariate model aims to explain part of the interpatient variability of some parameters. Classical methods for covariate model building are based on comparisons with respect to some criteria, usually derived from the likelihood (AIC, BIC), or some statistical test (Wald test, LRT, etc.). In other words, the modelling procedure requires two steps: first, all possible models are fitted using some estimation procedure (e.g. the SAEM algorithm) and the likelihood of each model is computed using a numerical integration procedure (e.g. Monte Carlo Importance Sampling); then, a model selection procedure chooses the "best" covariate model. Such a strategy is only possible with a reduced number of covariates, i.e., with a "small" number of models to fit and compare.
As an alternative, we are thinking about a Bayesian approach which consists of estimating simultaneously the covariate model and the parameters of the model in a single run. An (informative or uninformative) prior is defined for each model by defining a prior probability for each covariate to be included in the model. In other words, we extend the probabilistic model by introducing binary variables that indicate the presence or absence of each covariate in the model. Then, the model selection procedure consists of estimating and maximizing the conditional distribution of this sequence of binary variables. Furthermore, a probability can be associated to any of the possible covariate models.
This conditional distribution can be estimated using an MCMC procedure combined with the SAEM algorithm for estimating the population parameters of the model. In practice, such an approach can only deal with a limited number of covariates since the dimension of the probability space to explore increases exponentially with the number of covariates. Consequently, we would like to have methods able to find a small number of variables (from a large starting set) that influence certain parameters in populations of individuals. That means that, instead of estimating the conditional distribution of all the covariate models as described above, the algorithm should focus on the most likely ones.
Fixed parameters: it is quite frequent that some individual parameters of the model have no random component and are purely fixed effects. Then, the model may not belong to the exponential family anymore and the original version of SAEM cannot be used as it is. Several extensions exist:

introduce random effects with decreasing variances for these parameters,

apply the stochastic approximation directly on the sequence of estimated parameters, instead of the sufficient statistics of the model.
None of these methods always work correctly. Furthermore, what are the pros and cons of these methods is not clear at all. Then, developing a robust methodology for such model is necessary.
Convergence toward the global maximum of the likelihood: convergence of SAEM can strongly depend on thie initial guess when the observed likelihood has several local maxima. A kind of simulated annealing version of SAEM was previously developed and implemented in Monolix . The method works quite well in most situations but there is no theoretical justification and choosing the settings of this algorithm (i.e. how the temperature decreases during the iterations) remains empirical. A precise analysis of the algorithm could be very useful to better understand why it "works" in practice and how to optimize it.
Convergence diagnostic: Convergence of SAEM was theoretically demonstrated under very general hypothesis. Such result is important but of little interest in practice at the time to use SAEM in a finite amount of time, i.e. in a finite number of iterations. Some qualitative and quantitative criteria should be defined in order to both optimize the settings of the algorithm, detect a poor convergence of SAEM and evaluate the quality of the results in order to avoid using them unwisely.