Parameter	Type	Effect of tuning parameters
d	Vector of positive integers	Default: 5, 20, 40 The vector of potential delays, for which the corresponding RDI values are calculated. Setting this argument too small may limit the ability of Scribe to detect causal relationships, while setting it too large can result in the discovery of incorrect or indirect causal relationships, resulting in false delays and conditioning.
L	Non-negative Integer	Default: 0 The number of the top incoming node(s) to the target, excluding the source, over which RDI is conditioned. L = 0 corresponds to no conditioning (Plain pair-wise RDI). Any L > 0 corresponds to conditional RDI (cRDI). Conditioning over more nodes approaches the theoretical prerequisite of conditioning over all genes, excluding the source and target, needed for inferring the true causal network, however it imposes more computational burden and undesirably reduces the accuracy of the RDI estimator with fixed number of samples N, as it exponentially increases the dimension of the state space used to calculate the k-nearest neighbors.
k	Positive Integer	Default: 5 Number of the nearest neighbors in the kNN estimator for the conditional mutual information. The parameter should be set in such a way so the neighborhood captures an adequate number of samples for a good estimate of the probability corresponding to each sample.
Uniformization	Boolean	Default: False If True, uRDI instead of RDI will be used. While imposing higher computational burden over the same data than RDI, uRDI is expected to improve the causal inference in the cases with highly-biased sampling distributions.