Winnow algorithm in C++ for multiclass classification
In a recent paper (How To Winnow Actives from Inactives: Introducing Molecular Orthogonal Sparse Bigrams (MOSBs) and Multiclass Winnow) I applied the Winnow algorithm to the prediction of biological activities of molecules.
I thought that it would certainly be of much use to provide the code to anybody who may want to use this methodology as well. So here we go: the source code of the inplementation can be downloaded here: multiclass winnow in C++, with MySQL support (covered by the GNU General Public Licence; for what that means either read the copy enclosed or read it online).
This program is provided as is without any guarantees that it will work or anything else. For the structure of the underlying MySQL tables, should you wish to use that feature, there is no documentation yet. You can easily find the required information by reading through the source code in the file Winnow.h. If I get round to doing it, I will provide some more documentation in a while here on this page. If you have any questions, please feel free to contact me and I will try to help you out.
The program is capable of either reading the training and test data from text files, or otherwise from MySQL tables. It also includes the possibilities of bagging multiple classifiers, to use a thick threshold, as well as orthogonal sparse bigrams or an exhaustive enumeration of all features provided. Invoking the program without any arguments will display a list of all available options.
There are still a couple of very useful things that can be done with this algorithm in the area of cheminformatics. I won’t spend an excessive amount of time pushing that project any further, therefore I would be happy to share some ideas with people who may want to collaborate on a project.
I would be more than happy to receive any comments or suggestions. In particular, if there is anybody out there who would be willing to write a graphical interface, then I would be very happy to help out as much as I can. But I do not have the time to focus on that for the time being.
Tags: C++, Cheminformatics, chemistry, source, winnow
April 25th, 2008 at 1:15 pm
Should you use the newest release of mysqlpp then you may have to change every occurence of the result sets (can’t remember exactly what they renamed it too). But these are the only changes that have to be applied to make it work.
If I get round to doing it I may provide a patch, or otherwise remove the MySQL part conditionally in function of a compilation flag.