Does the C++ implementation support sparse data? How to read them in?

imbs-hl / ranger

A Fast Implementation of Random Forests

http://imbs-hl.github.io/ranger/

772 stars 193 forks source link

Does the C++ implementation support sparse data? How to read them in? #352

Open UnixJunkie opened 6 years ago

UnixJunkie commented 6 years ago

Hello,

Very nice software. I will give it a try and may write a thin OCaml wrapper if it works well (I will cite it also).

Hence, I have several questions:

do you support sparse data?
what is the format they should be read from?
do you have an example data file to run ranger on (both for regression and classification). If you support sparse and dense data, I would appreciate seeing an example data file for both, along with the required command line to train a model, save it, then run it on new data.

So, this is more a request for some more documentation than a real issue/bug report. Hope you don't mind.

Best regards, Francois.

UnixJunkie commented 6 years ago

Currently, I am interested by classification and regression, not survival.

UnixJunkie commented 6 years ago

related to https://github.com/imbs-hl/ranger/issues/305 for a simple usage example with related example input file

UnixJunkie commented 6 years ago

If you plan to support a sparse file format, I recommend the CSR file format. For example: https://github.com/UnixJunkie/orrandomForest/blob/master/data/Boston_test_features.csr each entry in a line is a column index ':' the value for that feature index for the current line. All other entries are assumed to be 0.

mnwright commented 6 years ago

We have support for sparse data - but only in the R version. It's very easy to use, see https://github.com/imbs-hl/ranger/issues/135#issuecomment-293284786 for an example.

It's probably not that hard to include sparse data in the pure C++ version. We already have a DataSparse class using Eigen, see https://github.com/imbs-hl/ranger/blob/master/src/DataSparse.h and https://github.com/imbs-hl/ranger/blob/master/src/DataSparse.cpp. We just have to fill that with some data. Unfortunately I don't have the time for this at the moment. Feel free to create a pull request. ;)

Btw., these to files are under GPL license because they are currently used only in the R version. If required I can change them to MIT, I don't see any GPL dependencies there.

Regarding the example file, you already found #305. I have renamed that issue.

UnixJunkie commented 6 years ago

Can you point me to the code that does the data file reading for the C++ version? I guess that's where I should make changes to support a new format. I might have a look at it, but I'm doubtful I can contribute such a big feature. My C++ is all rotten also.

mnwright commented 6 years ago

That's here: https://github.com/imbs-hl/ranger/blob/9490a26e1d11ec57949db033c992ebf3a631a2a9/src/Data.cpp#L43