Resulting Network Size
Default Value: 80
This parameter specifies the final number of nodes of the resulting network.
By default parameter a network of 80 nodes is created. However, this value can be tuned by the user in taking into account the data used as input.
Number of Repeats
Default Value: 3
This parameter determines how many times IAMBEE will calculate an optimal sub-network for a specified cost.
Due to the stochastic behavior of IAMBEE some repeats are needed. This will simulate the run with the same parameters, which in theory can generate different results. IAMBEE will select the the best result among each repeat as final output.
A higher number of repeat can be selected for difficult datasets. Consequently, more runtime will be needed to complete the analysis.
Default Value: 25
This parameter determines how many possible paths exist between two entities (e.g. From a specific mutated gene to any other gene of interest).
The selection of this parameter defines the size of the search space from which the most optimal sub-network will be inferred. Larger values for N will sample a larger search space and a potential more optimal selected sub-network, but might come at the expense of longer running times. The parameter can be set between 5 and 50, with a default of 25.