Section: Scientific Foundations
Analysis of structures resulting from meristem activity
To analyse plant growth and structure, we focus mainly on methods for analysing sequences and treestructured data. Theses methods range from algorithms for computing distance between sequences or treestructured data to statistical models.

Combinatorial approaches : plant structures exhibit complex branching organizations of their organs like internodes, leaves, shoots, axes, branches, etc. These structures can be analysed with combinatorial methods in order to compare them or to reveal particular types of organisation. We investigate a family of techniques to quantify distances between branching systems based on nonlinear structural alignment (similar to editoperation methods used for sequence comparison). Based on these techniques, we study the notion of (topologybased) selfsimilarity of branching structures in order to define a notion of degree of redundancy for any tree structure and to quantify in this way botanical notions, such as the physiological states of a meristem, fundamental to the description of plant morphogenesis.

Statistical modeling : We investigate different categories of statistical models corresponding to different types of structures.

Longitudinal data corresponding to plant growth follow up: the statistical models of interest are equilibrium renewal processes and generalized linear mixed models for longitudinal count data.

Repeated patterns within sequences or trees: the statistical models of interest are (hidden) variableorder Markov chains and lumped processes constructed from Markov chains. Variableorder Markov chains are in particular applied to identify complex branching patterns resulting from local inhibition phenomena.

Homogeneous zones (or change points) within sequences or trees: most of the statistical models of interest are hidden Markovian models (hidden semiMarkov chains, semiMarkov switching linear mixed models and semiMarkov switching generalized linear models for sequences and different families of hidden Markov tree models). A complementary approach consists in applying multiple changepoint models. The branching structure of a parent shoot is often organized as a succession of branching zones while the succession of shoot at the more macroscopic scale exhibit roughly stationary phases separated by marked change points.
We investigate both estimation methods and diagnostic tools for these different categories of models. In particular we focus on diagnostic tools for Markovian and hidden Markovian models (in this latter case to explore the hidden state sequence or tree space).


A new generation of morphogenesis models : Designing morphogenesis models of the plant development at the macroscopic scales is a challenging problem. As opposed to modeling approaches that attempt to describe plant development on the basis of the integration of purely mechanistic models of various plant functions, we intend to design models that tightly couple mechanistic and empirical submodels that are elaborated in our plant architecture analysis approach. Empirical models are used as a powerful complementary source of knowledge in places where knowledge about mechanistic processes is lacking or weak. We chose to implement such integrated models in a programming language dedicated to dynamical systems with dynamical structure (DS)^{2} , such as Lsystems or MGS. This type of language plays the role of an integration framework for submodels of heterogeneous nature.