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A distribution factorizes according to a Directed acyclic graph when its joint density is the product of the conditional density of each variable given its graphical parents. This factorization implies the graph's global Markov property of a directed acyclic graph.

A distribution is faithful to a Directed acyclic graph when, for all disjoint vertex sets $A,B,S$, $Z_A\perp Z_B\mid Z_S$ holds if and only if $A$ and $B$ are D-separated by $S$. This includes the graph's global Markov property of a directed acyclic graph and excludes additional independences caused by parameter cancellations. If faithfulness is used to name only the reverse implication, the Markov property must be assumed separately.

The moral graph of a Directed acyclic graph is formed by joining any two parents of a common child and then removing the directions from all edges. For D-separation, a path in the underlying undirected graph is active given $S$ when every noncollider on it is outside $S$, and every collider has itself or a descendant in $S$. Disjoint vertex sets $A$ and $B$ are D-separated by $S$ if no such active path connects them.

The adjacency characterization isA one-edge path cannot be blocked by conditioning on other vertices. For a nonadjacent pair, choose the later vertex $v$ in a topological ordering. The earlier vertex $u$ is a nondescendant and is not a parent of $v$, so the parents of $v$ separate the pair by the local Markov property of a directed acyclic graph.

Use faithfulness of a directed acyclic graph to mean that graphical and probabilistic independences agree, for all disjoint sets:This includes the global Markov property of a directed acyclic graph as well as the absence of extra independences. The conditional independence graph of $P$ is the undirected graph in which $u-v$ is absent exactly when $Z_u\perp Z_v\mid Z_{V\setminus \{u,v\}}$.

To identify this graph, condition on every vertex other than $u,v$. Any noncollider in the interior of a path is then conditioned on, so an active path must have only colliders internally. Two adjacent interior vertices cannot both be colliders: the arrow joining them has an arrowhead at only one of its ends. Thus an active path can have no interior vertex, giving a direct edge, or just one, giving $u\to w\leftarrow v$. In the latter case the conditioned common child $w$ activates the path. These possibilities are exactly the edges added or retained by moralization. Faithfulness therefore provesThis is why the moral graph equals the conditional independence graph under faithfulness.

For Gaussian graph estimation, collect the data into an $n\times p$ matrix $D$ and let $S_n=n^{-1}{\sum }_i{x}_i{x}_i^T$. The precision matrix $\Theta ={\Sigma }^{-1}$ has ${\Theta }_{jk}=0$ precisely for absent graph edges, by Gaussian conditional independence. In neighbourhood selection, fit a Lasso regression of each column on the others:Select the nonzero coefficients as neighbours of $j$, then make the graph undirected using either the OR rule, retaining an edge selected in at least one regression, or the AND rule, requiring both. These are instances of Nodewise Lasso.

The Graphical Lasso estimates the whole precision matrix jointly, for example byRead off its nonzero off-diagonal entries as graph edges. This expression uses an off-diagonal penalty; an all-entry penalty is another convention.

To reduce computation in the PC algorithm, start its skeleton search from an estimate of the conditional independence graph rather than the complete graph. The exact graph contains the true DAG skeleton, so oracle tests can remove its extra edges while retaining the true adjacencies. Fewer initial edges and smaller neighbourhoods reduce both candidate pairs and candidate conditioning sets.

For correctness of the orientation stage, preserve valid separating-set records. With an exact conditional independence graph, an initially absent pair $u,v$ has the full complement $V\setminus \{u,v\}$ as a separating set. Record that set, and record the usual discovered sets for edges removed later. Leaving an initially absent pair with an empty default could falsely mark an unshielded noncollider as a collider. This describes PC initialization from a conditional independence graph; with an estimated initial graph, screening errors can propagate into the output.

A path in a causal directed acyclic graph is active given a conditioning set $K$ when every noncollider on the path is outside $K$ and every collider has itself or a descendant in $K$. Two vertex sets are d-separated by $K$ when no path between them is active given $K$. The global Markov property of a directed acyclic graph then turns d-separation into conditional independence.

In the displayed graph, the edges areEvery observed pair except $(X_1,X_4)$ and $(X_2,X_4)$ is joined by a direct edge, which remains active under conditioning on any other observed variables. The pair $(X_2,X_4)$ is always joined by the fork $X_2\leftarrow U\to X_4$, because the unobserved noncollider $U$ cannot be conditioned on.

For $(X_1,X_4)$, if $X_3$ is not conditioned on, $X_1\to X_3\to X_4$ is active. If $X_3$ is conditioned on, the pathbecomes active because its collider $X_2$ has conditioned descendant $X_3$; conditioning on $X_2$ itself also opens it. Thus every observed pair is d-connected given every subset of the other observed variables. Any conditional independence between two nonempty observed subvectors would imply one between each selected pair, so the graph entails none.