ACTG320 exploratory analysis

[bcjaeger]

aorsf works very well on ACTG320 mortality prediction and it would be great to figure out why it works well

Plan:

• Fit several models
• Use different node sizes
• Death outcome
• use Out of bag error estimate from aorsf to compare the different model's prediction accuracy

Here is a little synopsis of what I would like to check with the actg320 data:

The data have two main endpoints, death and aids diagnosis. For both endpoints, I want to see how well aorsf performs with a number of different hyper-parameter values. In other words, I am guessing that the performance of aorsf on this dataset is going to depend on how well we tune it. The main tuning parameters for aorsf are below (copied from ?aorsf::orsf). I think we could set up a simple experiment where we make a dataset with one column for each tuning parameter, with each row having a specific set of inputs for orsf(), and then we assess the performance of each set of parameter inputs using cross-validation, probably with just 3 folds b/c the count of events is low. This would be a great exercise and should also provide some useful info for us, i.e., we may change the default values of orsf() for datasets with smaller event counts.

@kristinlenoir, would you like to help me with this?

[kristinlenoir]

I would love to help with this!

[kristinlenoir]

FIrst analysis - observe how performance varies across leaf_min events. I used a 3 fold cross-validation with 10 repeats and a prediction horizon of 350 days.

This is the c-statistic for AIDS - this trend has been consistent Death - fewer events. The performance has been rather inconsistent prior to when I set a seed. A line is fit, but there is really little trend (possible that leaf_min_events=4 is an outlier). The c-statistic, however, is not bad across the board.

Future plans: Amend code to make it more efficient with better output format Add Brier score vary split_num_obs Perhaps try Monte Carlo in addition to CV (increase number of repeats?) Maybe try varying the mtry down the line (probably not the n_retry) Adding curved line to performance graphs may be preferable in anticipation of some point of optimal performance