Section: Research Program

Algorithms and estimation for graph data

A graph data structure consists of a set of nodes, together with a set of (either unordered or ordered) pairs of these nodes called edges. This type of data is frequently used in various domains of application (in particular in biology) because they provide a mathematical representation of many concepts such as physical or biological structures and networks of relationship in a population. Some attention has recently been focused in the group on modeling and inference for graph data.

Suppose that we know the value of $p$ variables on $n$ subjects (in many applications, we have $n\ll p$). Inference network consists in evaluating the link between two variables knowing the others. [106] gives a very good introduction and many references about network inference and mining. Gaussian Graphical model is a convenient framework to infer network between quantitative variables: there is a edge between two variables if the partial correlation between them is non zero. So the problem is to compute the partial correlations trough the concentration matrix. Many methods are available to infer and test partial correlations in the context $n\ll p$ [106], [82], [60], [62]. However, when dealing with abundance data, because inflated zero data, data are far from gaussian assumption. Some authors work only with the binary "presence-absence" indicator via log-linear [65]. Models for inflated zero variables are not used for network inference and we want to develop them.

Among graphs, trees play a special role because they offer a good model for many biological concepts, from RNA to phylogenetic trees through plant structures. Our research deals with several aspects of tree data. In particular, we work on statistical inference for this type of data under a given stochastic model (critical Galton-Watson trees for example): in this context, the structure of the tree depends on an integer-valued distribution that we estimate from the observation of either only one tree, or a forest. We also work on lossy compression of trees via linear directed acyclic graphs. These methods make us able to compute distances between tree data faster than from the original structures and with a high accuracy. These results are valuable in the context of very large trees arising for instance in biology of plants.