6 research outputs found
Enumeration of labelled chain graphs and labelled essential directed acyclic graphs
AbstractA chain graph is a digraph whose strong components are undirected graphs and a directed acyclic graph (ADG or DAG) G is essential if the Markov equivalence class of G consists of only one element. We provide recurrence relations for counting labelled chain graphs by the number of chain components and vertices; labelled essential DAGs by the number of vertices. The second one is a lower bound for the number of labelled essential graphs. The formula for labelled chain graphs can be extended in such a way, that allows us to count digraphs with two additional properties, which essential graphs have
Counting and Sampling from Markov Equivalent DAGs Using Clique Trees
A directed acyclic graph (DAG) is the most common graphical model for
representing causal relationships among a set of variables. When restricted to
using only observational data, the structure of the ground truth DAG is
identifiable only up to Markov equivalence, based on conditional independence
relations among the variables. Therefore, the number of DAGs equivalent to the
ground truth DAG is an indicator of the causal complexity of the underlying
structure--roughly speaking, it shows how many interventions or how much
additional information is further needed to recover the underlying DAG. In this
paper, we propose a new technique for counting the number of DAGs in a Markov
equivalence class. Our approach is based on the clique tree representation of
chordal graphs. We show that in the case of bounded degree graphs, the proposed
algorithm is polynomial time. We further demonstrate that this technique can be
utilized for uniform sampling from a Markov equivalence class, which provides a
stochastic way to enumerate DAGs in the equivalence class and may be needed for
finding the best DAG or for causal inference given the equivalence class as
input. We also extend our counting and sampling method to the case where prior
knowledge about the underlying DAG is available, and present applications of
this extension in causal experiment design and estimating the causal effect of
joint interventions
Uniform random generation of large acyclic digraphs
Directed acyclic graphs are the basic representation of the structure
underlying Bayesian networks, which represent multivariate probability
distributions. In many practical applications, such as the reverse engineering
of gene regulatory networks, not only the estimation of model parameters but
the reconstruction of the structure itself is of great interest. As well as for
the assessment of different structure learning algorithms in simulation
studies, a uniform sample from the space of directed acyclic graphs is required
to evaluate the prevalence of certain structural features. Here we analyse how
to sample acyclic digraphs uniformly at random through recursive enumeration,
an approach previously thought too computationally involved. Based on
complexity considerations, we discuss in particular how the enumeration
directly provides an exact method, which avoids the convergence issues of the
alternative Markov chain methods and is actually computationally much faster.
The limiting behaviour of the distribution of acyclic digraphs then allows us
to sample arbitrarily large graphs. Building on the ideas of recursive
enumeration based sampling we also introduce a novel hybrid Markov chain with
much faster convergence than current alternatives while still being easy to
adapt to various restrictions. Finally we discuss how to include such
restrictions in the combinatorial enumeration and the new hybrid Markov chain
method for efficient uniform sampling of the corresponding graphs.Comment: 15 pages, 2 figures. To appear in Statistics and Computin