I've generated a gradient boosting model using r-caret on data which I expect to have little to no predictive value. Class distribution is heavily skewed with ~15000 negative and ~1000 positive. Caret's confusionMatrix function reports a sensitivity of ~0.02 and a specificity of >0.99. How should I interpret this?
Sensitivity (SEN) is defined as TP/(TP+FN). It represents the ratio of positive samples labeled correctly out of all the positive samples. Similarly, Specificity (SPC) is defined as TN/(TN+FP), which is the ratio of negative samples labeled correctly out of all negative samples.
Now, you have a 15:1 negative:positive samples ratio. A very naive algorithm, which always returns "False" regardless of the sample given, would naturally produce SPC=1 and SEN=0. A random algorithm, which returns "True" 1% of the time (regardless of the sample given) and "False" 99% of the time, would produce on average SEN=0.01 and SPC=0.99. This means that your model is pretty much in the range of a random model, and not very useful for classification.
Try oversampling (or better, get more positive data) to improve the model.