Conditional independence tests in Weka are slightly different from the standard tests described in the literature. To test whether variables and are conditionally independent given a set of variables , a network structure with arrows is compared with one with arrows . A test is performed by using any of the score metrics described in Section 2.1.
At the moment, only the ICS and CI algorithm are implemented.
The ICS algorithm makes two steps, first find a skeleton (the undirected graph with edges there is an arrow in network structure) and second direct all the edges in the skeleton to get a DAG.
Starting with a complete undirected graph, we try to find conditional independencies in the data. For each pair of nodes , , we consider sets starting with cardinality , then up to a user defined maximum. Furthermore, the set is a subset of nodes that are neighbors of both and . If an independency is identified, the edge between and is removed from the skeleton.
The first step in directing arrows is to check for every configuration where and not connected in the skeleton whether is in the set of variables that justified removing the link between and (cached in the first step). If is not in , we can assign direction .
Finally, a set of graphical rules is applied  to direct the remaining arrows.
Rule 1: i->j--k & i-/-k => j->k Rule 2: i->j->k & i--k => i->k Rule 3 m /|\ i | k => m->j i->j<-k \|/ j Rule 4 m / \ i---k => i->m & k->m i->j \ / j Rule 5: if no edges are directed then take a random one (first we can find)
The ICS algorithm comes with the following options.
Since the ICS algorithm is focused on recovering causal structure, instead of
finding the optimal classifier, the Markov blanket correction can be made
The maxCardinality option determines the largest subset of to be considered in conditional independence tests .
The scoreType option is used to select the scoring metric.