Table 1.  Results of evaluation.
Performance of approximately 2100 disease-gene pairs.
Assoc score↓  Cohen’s d (+)  Mann-W U norm. (-)  Logistic log loss (-)  Logistic Brier score (-)
Cosine (w2v)  1.31  0.197  0.51  0.168
Raw PMI  2.07  0.0953  0.374  0.116
Raw PMI -log(pctile)  2.15  0.0947  0.355  0.111
Exp PMI  2.17  0.0897  0.356  0.109
Exp PMI -log(pctile)  2.21  0.0903  0.341  0.105
Raw Local Score  2.35  0.0828  0.312  0.0947
Raw Local Score -log(pctile)  2.28  0.0832  0.317  0.0963
Exp Local Score  2.34  0.0812   *0.301   *0.0915
Exp Local Score -log(pctile)   *2.36   *0.0811  0.308  0.093
log(coocc)  2.24  0.097  0.348  0.105
Interpretation of the above table.
Each row corresponds to an association score whereas each column corresponds to one of the evaluation metrics. A (+) in the column means a higher evaluation metric value, the better the association score in that row separates the positive and random pairs. A (-) means a lower evaluation metric is better. Note all the metrics are immune to linear rescalings; also the Mann-Whitney U score is nonparametric.