Implement the approach from Hand & Till for generalization the AUC to the multi-class setting

[matdoering]

I've implement the approach from Hand & Till for generalizing the AUC to the multi-class setting by adjusting the multiclass.roc function. For individual decision values, it still works as before since I'm simply calling the original version of the function. For multivariate decision values, I added a new implementation according to the paper from 2001. Note that for matrix input, the function does not support the additional arguments. I've adjusted the raw R documentation accordingly since I couldn't find any roxygen comments.

[codecov]

Codecov Report

Merging #37 into master will decrease coverage by 0.94%.
The diff coverage is 0%.

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##           master      #37      +/-   ##
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- Coverage   46.41%   45.47%   -0.94%     
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  Files          33       33              
  Lines        3342     3411      +69     
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  Hits         1551     1551              
- Misses       1791     1860      +69

Impacted Files	Coverage Δ
R/multiclass.R	0% <0%> (ø)	⬆️

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[codecov]

Codecov Report

Merging #37 into master will decrease coverage by 0.71%.
The diff coverage is 0%.

@@            Coverage Diff            @@
##           master     #37      +/-   ##
=========================================
- Coverage   46.41%   45.7%   -0.71%     
=========================================
  Files          33      33              
  Lines        3342    3394      +52     
=========================================
  Hits         1551    1551              
- Misses       1791    1843      +52

Impacted Files	Coverage Δ
R/multiclass.R	0% <0%> (ø)	⬆️

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[xrobin]

Thank you Matthias.
You are correct there is no roxygen comments, the documentation is directly in the Rd files.
Can I please ask you to:

• Add an example of how to use it in the \example section in man/multiclass.Rd
• Remove the reference to Roxygen you added to the DESCRIPTION file

In addition I was wondering: the compute.A.conditional seems to be calculating an AUC, is that correct?
If so, wouldn't it be possible to use the built-in roc and auc functions of pROC instead? This would allow the additional arguments such as percent, partial.auc; and avoid duplicating the AUC calculation.
Otherwise it would be nice if passing those extra arguments would raise an error, to avoid unnecessary confusion, as this would be quite different from the usual behavior of pROC.

[matdoering]

Thanks for the review 👍

Indeed, I think that A(i|j) is an AUC value. Thus, I replaced the conditional calculation from before with the call to pROC::roc. I've also included examples for typical scenarios with artificial data. The results seem reasonable for all of them.

There are two problems remaining:

1. It's not possible to output a bona fide multiclass.roc object because we need to calculate A(i|j) and A(j|i) individually. When you lump the values together in a single roc object, the auc function would not be well-defined anymore. Thus, I manually calculate the mean from A(i|j) and A(j|i) and then place it into the auc slot of the multiclass.roc list. I guess this is a bit ugly because the resulting object won't work as expected (e.g. calling auc on the object will fail) since rocs is not as expected (list of 2-member lists rather than list of roc objects). Unfortunately, I think this cannot be circumvented, except by customizing some other code such as the auc function.

2. I have retained my previous code (multiclass.roc.multivariate.custom) because the results between my original code (custom calculations according to the paper) and the new code (using auc) are slightly different (run examples with multiclass.roc.multivariate.custom and multiclass.rocto compare). I guess that the auc function normalizes AUCs to be in [0.5,1] and that's causing the difference. The docs say that this can be done (not the default) for partial curves only. Still, I haven't seen an AUC < 0.5 by pROC yet, so I'm a bit puzzled about the interpretation of the AUC here (particularly for the worst-case classifier example where the new function outputs 1 and the old function outputs 0; I guess both interpretations make sense where the first assumes that the output can be flipped and the second one doesn't). Could you investigate this?

[matdoering]

I've just fixed the second problem. In the multiclass setting using direction = "auto" (the default) leads to inconsistent decision rules. Now, I am enforcing direction = ">" if direction = "auto" was set to ensure that the results are consistent for multiple calls of roc across pairs of classes. Now the AUC for the worst-case classifier is also at 0, as expected.

[xrobin]

Due to some tight deadlines here I haven't had time to really look into this, and probably won't for the next two weeks I'm afraid. But I will be able to do that after Christmas.

The Travis builds are failing due to some small issues in the help file. If you have a chance to look into it that would be great, otherwise I'll do it once the branch is merged.

[matdoering]

Right, I just saw that I forgot to document the direction parameter, which I added. Fixed that.

No problem, I know those kind of deadlines. I wish you a lot of success and a nice christmas!

[xrobin]

I merged into a new branch multiclass-hand-till so that I can have a better look at it before merging into master.

You are correct with point 1), this is not a mutliclass.roc any longer. I am thinking the best thing to do is to create a new class of object, for instance ht.multiclass.roc or something like that.
Also as you said the object returned won't be an auc. Currently the auc(multiclass.roc) method returns a multiclass.auc object, not an auc. We should have something similar here.

I checked and the multiclass.auc is already not really an auc. For instance it doesn't support stuff like ci or var. I will use the opportunity to do some cleanup on that one too. The best thing to do would be to implement those with bootstrap but it's beyond the scope here.

The only other method I could find that consumes amulticlass.roc is the print function. Again it will probably easiest to create a new method for ht.multiclass.roc.

Re point 2) indeed you need to fix the direction. In the bootstrap operations I fix it with the direction obtained on the main ROC curve. I'm not sure if that would make sense here, or if it would even make a difference as you calculate both A(i|j) and A(j|i) anyway.

[xrobin]

Quick update. I have started to implement the new class for the new multivariate ROC and AUC (see multiclass-hand-till branch). I called it mv.multiclass.roc and mv.multiclass.auc.

Re. the direction: I changed a few things so the default behavior for univariate multiclass.roc doesn't change ("auto" makes a lot of sense there). Basically using match.arg in the parent function and checking if the argument is missing(). It is now an error to pass "auto" to the new multivariate case. I regret not having been strict enough with invalid argument combinations in the past, so let's not do the mistake again.

I still need to implement:

• print.mv.multiclass.auc
• auc.mv.multiclass.roc
  -> Some of the functionality of multiclass.roc.multivariate should be moved there. I think the mv.multivariate.roc can contain the list 'rocs' calculated there as 'pair_rocs' list element. Then the auc function can do the rest (from mean.AUCs on) and the mv.multivariate.auc can store 'pair_aucs'.
• It would be nice to have the multivariate case hooked up with the multiclass.roc.formula method. The multivariate option would make a lot of sense with a formula. That's a 'would be nice' thing.

We need to specify/document:

• behavior if some response levels/predictors levels are missing or mismatching

Finally I'd like to add a few testthat unit tests:

• Basic static test set, test AUC (these can be taken straight from the examples, the only difference being checking the value of the AUC)
• Behavior with various 'direction' arguments (including error with 'auto')
• Behavior if data is missing for a response level, according to spec above

Once all that is done I can merge into master and prepare a release.

[xrobin]

I've been implementing and testing the functions above. Pretty happy so far.
There are a few changes:

• I don't store pair_AUCs any longer
• The auc is calculated in the auc function

The CI is broken, and has been so for a while for univariate multiclass.roc for a while a believe. See issue #38. I'll have a look at it later and see if I can implement CI for the new mv.multiclass.roc at the same time.

[xrobin]

Formulas worked pretty easily. I found a few other issues along the way which were fixed.

I'd still want to look at the behavior upon invalid/incomplete data and make sure it is consistent with the other functions of the package, and then I'll be able to merge into the master branch and prepare for the release.

[xrobin]

The code is now available in the main master branch. Thanks for it!
I added you as a contributor in the package description. Please let me know if you'd like to be credited differently.