Genetic programming needs better baselines


We’ve been talking about deficiencies in genetic programming experimental practice, benchmarking, and so on for a while. Our first paper on this topic was Genetic programming needs better benchmarks. Now I want to focus on a more specific issue in experimental practice, which is the use of appropriate baselines in experiments.

Gratuitous metaphor

Imagine we’re managing a football team, and we’re trying to decide who will take penalty kicks for us. We already have a guy who takes them. He’s a bit old, and maybe the goalkeeper stops his shots too often, but at least he always hits the target.

But we’ve spent a huge amount of money on three new players, all have great reputations, and we’re confident that they’ll be much better. We test the new guys out:

How should we respond?

I propose that if we spend our time discussing which of the new players was the best, then the opposing team are probably going to laugh at us.

That is the situation we could find ourselves in when we spend a lot of time developing new and exciting methods for genetic programming symbolic regression, if we are not careful. The opposing team – remember, they are laughing at us – are people who use non-evolutionary methods for regression. They know when their methods are failing to beat the old, reliable, linear regression.


I’ve seen some papers which fail this test recently. One example is Vanneschi et al, A new implementation of geometric semantic GP and its application to problems in pharmacokinetics, available here (best paper award EuroGP 2013). Another is Spector and Helmuth, Uniform linear transformation with repair and alternation in genetic programming (GPTP 2013). I can’t find it available online yet.

To reproduce my results, download this script as well as the data linked above. The script requires Python, Numpy and Scikit-learn. It reads a single data file, taking the last column as the dependent variable, and it has parameters for shuffling the data and setting the train/test split. (Shuffling the data makes a small but noticeable difference to the result, even though both linear regression and prediction of a constant are deterministic.)

I think it would be interesting to try the same test – predicting a constant or using linear regression – on a large selection of published symbolic regression papers which don’t state baseline results. I suspect we’d find a few more which fail to beat linear regression. If someone has the time, please go ahead!

Now, the interpretation of these facts is not obvious. I am not saying that failing to beat linear regression makes a symbolic regression paper worthless, or anything like that. A new technique might be very useful on some problems, even if it performs worse than standard GP or linear regression. Even if it’s not better on any problem, a well-motivated study is still worth publishing. We should not be playing the “up-the-wall” game. But in order to say “our result may be negative, but it is still worth publishing”, we have to first know and state that the result actually is negative.

I also think that the bioavailability problem, and the protein plasma binding one, and the toxicity one often associated with them, are not necessarily damaged as benchmarks by this result. We want our benchmark problems to be difficult, and these clearly are. Previously our benchmark result on these problems was as stated by previous work using standard GP and variations. Now we know that the benchmark result – the one we should be aiming to beat – is actually set by linear regression or even by predicting a constant. So, have at it!


I have focussed here on symbolic regression, but similar comments apply to any GP problem. In symbolic regression an obvious choice of baseline is linear regression, or prediction of a constant. In other cases it might be an ARIMA-style time-series prediction, or a 1-nearest neighbours classification, or something else. It depends on the problem. I think the best approach is to identify an appropriate baseline for the task, and carry it out before doing a single GP run.

One obvious lesson for symbolic regression researchers is that standard GP symbolic regression sometimes does really, really badly – not only worse than linear regression, but far far worse on test data.

The authors of the papers I point to above are senior researchers, big names in the field, with excellent reputations for doing excellent work. I am not trying to attack them or single them out. I know they are interested in improving GP experimental standards. And I am not pointing fingers: it is a lesson I have only really learned recently, and I might well have written papers which have similar flaws. I think we all benefit from discussion of higher standards in experiments and benchmarking.

Authors, reviewers and editors all have a responsibility in this: