Sim_AIC_2014

Sim_AIC_2014

Sim_AIC_2014(
  dag,
  terms,
  IC_method = "IC_annotation",
  verbose = simona_opt$verbose
)

Methods

Sim_AIC_2014

It uses the aggregate information content from ancestors. First define the semantic weight (Sw) of a term t in the DAG:

Sw = 1/(1 + exp(-1/IC(t)))

Then calculate the aggregation only in the common ancestors and the aggregationn in the ancestors of the two terms a and b separatedly:

SV_{common ancestors} = sum_{t in common ancestors}(Sw(t))
SV_a = sum{a' in a's ancestors}(Sw(a'))
SV_b = sum{b' in b's ancestors}(Sw(b'))

The similarity is calculated as the ratio between the aggregation on the common ancestors and the average on a's ancestors and b's ancestors separatedly.

sim = 2*SV_{common_ancestors}/(SV_a + SV_b)

Paper link: doi:10.1109/tcbb.2013.176 .