From: Semantic similarity in the biomedical domain: an evaluation across knowledge sources
Benchmark | Concept graph | Knowledge based | Distributional | |||||||
---|---|---|---|---|---|---|---|---|---|---|
 |  | Path | Intrinsic IC | PPR |  |  | ||||
 |  | Wu & Palmer | Path LCH | Lin | Path | LCH | Taxonomy | All | Lin | Vector |
Pedersen Coders N=29 | Pedersen 2006 [13] | Â | 0.51 | Â | Â | Â | Â | Â | 0.75 | 0.75 |
sct | 0.66 | 0.66 | 0.61 | 0.60 | 0.61 | 0.61 | 0.66 | Â | Â | |
sct-umls | 0.56 | 0.54 | 0.49 | 0.45 | 0.45 | 0.70 | +0.26 | Â | Â | |
sct-msh | 0.64 | 0.76 | 0.59 | 0.58 | 0.61 | 0.75 | 0.46 | Â | Â | |
 | umls | 0.74 | 0.65 | 0.70 | 0.69 | 0.69 | 0.76 | 0.73 |  |  |
Pedersen Physicians N=29 | Pedersen 2006 | Â | 0.36 | Â | Â | Â | Â | Â | 0.60 | 0.84 |
sct | 0.54 | 0.50 | 0.52 | 0.49 | 0.49 | 0.49 | 0.62 | Â | Â | |
sct-umls | 0.44 | 0.38 | 0.41 | +0.35 | +0.35 | 0.56 | +0.19 | Â | Â | |
sct-msh | 0.57 | 0.62 | 0.53 | 0.52 | 0.53 | 0.60 | 0.43 | Â | Â | |
 | umls | 0.66 | 0.60 | 0.72 | 0.69 | 0.69 | 0.67 | 0.63 |  |  |
Pedersen Combined N=29 | Pedersen 2006 | Â | 0.48 | Â | Â | Â | Â | Â | 0.69 | 0.76 |
sct | 0.59 | 0.56 | 0.56 | 0.53 | 0.54 | 0.55 | 0.67 | Â | Â | |
sct-umls | 0.49 | 0.44 | 0.45 | 0.38 | 0.38 | 0.63 | +0.20 | Â | Â | |
sct-msh | 0.62 | 0.69 | 0.57 | 0.56 | 0.57 | 0.66 | 0.45 | Â | Â | |
 | umls | 0.70 | 0.61 | 0.72 | 0.70 | 0.70 | 0.69 | 0.68 |  |  |
Mayo N=101 | Pakhomov 2011 [41] | 0.30 | 0.29 | Â | Â | Â | Â | Â | Â | Â |
sct-umls | +0.05 | +0.03 | +0.09 | +0.12 | *0.30 | +0.17 | +0.00 | Â | Â | |
sct-msh | 0.28 | 0.22 | 0.32 | 0.33 | 0.35 | 0.44 | +0.13 | Â | Â | |
 | umls | 0.38 | 0.30 | 0.39 | 0.41 | 0.44 | 0.46 | 0.21 |  |  |
UMN similarity N=566 | Pakhomov 2010 [19] | Â | 0.14 | Â | Â | Â | Â | Â | Â | 0.02 |
sct-umls | 0.21 | 0.23 | 0.22 | 0.23 | **0.36 | 0.23 | +0.00 | Â | Â | |
sct-msh | 0.30 | 0.30 | 0.32 | 0.32 | **0.37 | 0.33 | 0.07 | Â | Â | |
 | umls | 0.39 | 0.40 | 0.43 | 0.43 | 0.46 | 0.41 | 0.25 |  |  |
UMN relatedness N=587 | Pakhomov 2010 |  | 0.10 |  |  |  |  |  |  | −0.13 |
sct-umls | 0.14 | 0.17 | 0.16 | 0.16 | **0.30 | 0.17 | −0.01 |  |  | |
sct-msh | 0.21 | 0.20 | 0.22 | 0.23 | **0.31 | 0.23 | +0.04 | Â | Â | |
 | umls | 0.32 | 0.34 | 0.35 | 0.35 | 0.39 | 0.33 | 0.18 |  |  |
UMN relatedness subset N=430 | Liu 2010 [32] | Â | Â | Â | Â | Â | Â | Â | Â | 0.46 |
sct-umls | 0.13 | 0.17 | 0.16 | 0.16 | **0.30 | 0.17 | +0.03 | Â | Â | |
sct-msh | 0.20 | 0.20 | 0.22 | 0.23 | *0.32 | 0.23 | +0.05 | Â | Â | |
 | umls | 0.33 | 0.36 | 0.36 | 0.36 | 0.40 | 0.35 | 0.22 |  |  |