Advanced Parameters

These advanced parameters directly influence the size of the search space used by IAMBEE to infer the sub-network. This allows for potentially more optimal selected sub-networks in expense for higher computational load.

We suggest to run a default job with your data, IAMBEE will select an appropiate cost taking into account this set of parameters, the complete results will tell you the cost values used in order to have stringent output.

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.

N-best Paths

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.