# Interpretation of partial dependence plots for multinomial GBM

I've been a big fan of the gbm package for some time, but am having difficulty understanding the output from the partial dependence plots in the case for multinomial classification problems.

Below is the partial dependence plot for 3 of the many variables I'm considering:

My problem is that the probability for ‘Good’ is always much higher than the others (including on variables not pictured here), but it's not overly prevalent in the data OR in the predictions from the model. Here is some further output to clarify that point:

Confusion Matrix and Statistics

Reference
MIDDLE  150   1016  231
GOOD    396    209 1651

Overall Statistics

Accuracy : 0.7382
95% CI : (0.7255, 0.7506)
No Information Rate : 0.4262
P-Value [Acc > NIR] : < 2.2e-16

Kappa : 0.5961
Mcnemar's Test P-Value : < 2.2e-16

Statistics by Class:

Class: BAD Class: MIDDLE Class: GOOD
Sensitivity              0.6158        0.7628      0.8073
Specificity              0.9200        0.8901      0.7802
Pos Pred Value           0.7642        0.7273      0.7318
Neg Pred Value           0.8505        0.9071      0.8450
Prevalence               0.2962        0.2776      0.4262
Detection Rate           0.1824        0.2118      0.3441
Detection Prevalence     0.2386        0.2912      0.4702
Balanced Accuracy        0.7679        0.8264      0.7938


So while the model is able to correctly classify many of the targets as 'Neutral/Middle' (forgive my labelling), the partial dependence plots would suggest this hardly ever happens...

I'm guessing there is something obvious I have missed.. Any insight or thoughts would be hugely appreciated!

I would like more clarity on your data, but have this to work with.

Assumptions:

• the clusters for "good", "neutral", and "bad" are the target disposition for the classifier
• the variables "a", "b", and "c" are the independent variables trying to predict the class