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
