Sim_Shen_2010

Sim_Shen_2010

Sim_Shen_2010(
  dag,
  terms,
  IC_method = "IC_annotation",
  distance = "shortest_distances_via_NCA",
  verbose = simona_opt$verbose
)

Methods

Sim_Shen_2010

It is based on the information content of terms on the path connecting term a and b via their MICA term c.

Denote a list of terms a, ..., c, ..., b which are composed by the shortest path from a to c and from b to c, the difference between a and b is the sum of 1/IC of the terms on the path:

sum_{x in the path}(1/IC(x))

Then the distance is scaled into [0, 1] by an arctangent tarnsformation:

atan(sum_{x in the path}(1/IC(x)))/(pi/2)

And finally the similarity is:

sim = 1 - atan(sum_{x in the path}(1/IC(x)))/(pi/2)

Paper link: doi:10.1109/BIBM.2010.5706623 .