Adding to Luis answer: OpenML currently contains many results at least for Weka.
For R we have 99% percent of the structure in place to do the same. This would then allow a comparison of many ML algorithms, across tools. The algorithms are evaluated with a wide range of performance measures, we are also interested in timing comparisons.
We are optimistic that the result database will grow a lot this year and we can also offer summarizing reports / analysis.
You might also want to look into the no-free-lunch theorems. You cannot have a universal machine learning algorithm that will perform well on every data set, so any comparison can only be restricted on some domain-specific application.
I know you asked for a research paper, but it may be interesting for you to explore OpenML (http://www.openml.org/) that is a collaborative and open effort to build a huge repository of experiments with different algorithms in different tasks. It allows you to obtain interesting comparative results on a very large set of algorithms on a equally large set of tasks, and moreover you may freely download and re-use the workflows. More on this project in the paper at the link I include.
Cheers
Article OpenML: Networked science in machine learning
Adding to Luis answer: OpenML currently contains many results at least for Weka.
For R we have 99% percent of the structure in place to do the same. This would then allow a comparison of many ML algorithms, across tools. The algorithms are evaluated with a wide range of performance measures, we are also interested in timing comparisons.
We are optimistic that the result database will grow a lot this year and we can also offer summarizing reports / analysis.
We have tried to touch upon this from the perspective of feature selection It can be read @ Feature Selection: A Practitioner View http://www.mecs-press.org/ijitcs/ijitcs-v6-n11/v6n11-10.html
Outside the research domain there is a study done by Dr, Karl Rexer , which I found to be useful, http://www.rexeranalytics.com/. You may take a look.