This parameter belongs to the pathfinding step. Increasing the number of best paths allows for a more accurate estimation of the probability of a path but is computationally more expensive (takes longer).
Number of repeats
This refers to the number of times the stochastic optimization procedure is repeated. Increasing the number of repeats will contribute to the accuracy of the results (allows the algorithm to better approximate the true optimal) but comes at the expense of a higher computational cost.
The cost parameter affects the size of the inferred sub-network. Increasing the cost, decreases the size of the inferred sub-network. As it is hard to select the best cost parameter, IAMBEE performs a selection sweep over the cost parameters. The user can either use the default values or tune the range of the sweep manually. The sweep is defined by the minimal and maximal cost value and the step of the cost parameter used during the parameter sweep.
Decreasing the step size and increasing the minimum and maximum range of the sweep will increase the resolution of the results but is computationally more expensive. Therefore it is advised to first run the analysis with the default parameters and then tune based on those results a range of the sweep that is more appropriate for your own data. The optimal default parameters are determined automatically from the data. Information of what the default parameters are can be derived from the results folder ‘opt’.
To run the analysis for a single cost parameter, choose the minimal cost equal to the maximal cost.
This is a mere visualization parameter. It determines the maximal number of nodes that will be displayed in the network. Changing this parameter does not interfere with the search algorithm.