Section: Research Program

Algorithms and estimation for graph data

A graph data structure consists of a set of nodes, together with a set of pairs of these nodes called edges. This type of data is frequently used in biology because they provide a mathematical representation of many concepts such as biological structures and networks of relationships in a population. Some attention has recently been focused in the group on modeling and inference for graph data.

Network inference is the process of making inference about the link between two variables taking into account the information about other variables. [81] gives a very good introduction and many references about network inference and mining. Many methods are available to infer and test edges in Gaussian graphical models [81], [64], [52], [53]. However, when dealing with abundance data, because inflated zero data, we are far from gaussian assumption and we want to develop inference in this case.

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. We also work on lossy compression of trees via directed acyclic graphs. These methods enable us to compute distances between tree data faster than from the original structures and with a high accuracy.