Cost Values


The cost affects the size of the inferred sub-network. Increasing the cost, decreases the size of the inferred sub-network but as the algorithm tends to find the most ‘explanatory edges’ first, irrespective of the cost parameter smaller networks are mostly contained within the larger ones.

IMPORTANT: By default, the default cost option is selected. This will allow IAMBEE to automatically select a cost. By emailing the complete results folder you can observe in detail the values selected and re-run and analysis with a more stringent costs values.
Using the Cost Values

The edge cost sweep is an optimization value. In case of fewer solutions or sub-optimal ranking (e.g High number of genes sharing the same rank) it will require additional tuning by yourself. Sometimes several runs with different parameters and settings will be needed.

The Step Size is sensitive, when using a small value generally generate more interesting rankings. However, the the runtime will increase drastically.

Similarly, lower cost values will generate larger networks and vice versa when using high cost values. Important, the use of very low cost values, as they will generate very large networks with an excessive runtime.