Reusable modeling pipelines are a practical idea that gets re-developed many times in many contexts.
wrapr supplies a particularly powerful pipeline notation, and a pipe-stage re-use system (notes here). We will demonstrate this with the
vtreat data preparation system.
Continue reading Sharing Modeling Pipelines in R
[Reader’s Note. Some of our articles are applied and some of our articles are more theoretical. The following article is more theoretical, and requires fairly formal notation to even work through. However, it should be of interest as it touches on some of the fine points of cross-validation that are quite hard to perceive or discuss without the notational framework. We thought about including some “simplifying explanatory diagrams” but so many entities are being introduced and manipulated by the processes we are describing we found equation notation to be in fact cleaner than the diagrams we attempted and rejected.]
Please consider either of the following common predictive modeling tasks:
- Picking hyper-parameters, fitting a model, and then evaluating the model.
- Variable preparation/pruning, fitting a model, and then evaluating the model.
In each case you are building a pipeline where “y-aware” (or outcome aware) choices and transformations made at each stage affect later stages. This can introduce undesirable nested model bias and over-fitting.
Our current standard advice to avoid nested model bias is either:
- Split your data into 3 or more disjoint pieces, such as separate variable preparation/pruning, model fitting, and model evaluation.
- Reserve a test-set for evaluation and use “simulated out of sample data” or “cross-frame”/“cross simulation” techniques to simulate dividing data among the first two model construction stages.
The first practice is simple and computationally efficient, but statistically inefficient. This may not matter if you have a lot of data, as in “big data”. The second procedure is more statistically efficient, but is also more complicated and has some computational cost. For convenience the cross simulation method is supplied as a ready to go procedure in our
R data cleaning and preparation package
What would it look like if we insisted on using cross simulation or simulated out of sample techniques for all three (or more) stages? Please read on to find out.
Hyperbole and a Half copyright Allie Brosh (use allowed in some situations with attribution)
Edit: we are going to be writing on a situation of some biases that do leak into the cross-frame “new data simulation.” So think of cross-frames as bias (some small amount is introduced) / variance (reduced be appearing to have a full sized data set at all stages) trade-off.
Nina Zumel recently mentioned the use of Laplace noise in “count codes” by Misha Bilenko (see here and here) as a known method to break the overfit bias that comes from using the same data to design impact codes and fit a next level model. It is a fascinating method inspired by differential privacy methods, that Nina and I respect but don’t actually use in production.
Nested dolls, Wikimedia Commons
Please read on for my discussion of some of the limitations of the technique, and how we solve the problem for impact coding (also called “effects codes”), and a worked example in R. Continue reading Laplace noising versus simulated out of sample methods (cross frames)
vtreat cross frames
John Mount, Nina Zumel
As a follow on to “On Nested Models” we work R examples demonstrating “cross validated training frames” (or “cross frames”) in vtreat.
Continue reading vtreat cross frames
We have been recently working on and presenting on nested modeling issues. These are situations where the output of one trained machine learning model is part of the input of a later model or procedure. I am now of the opinion that correct treatment of nested models is one of the biggest opportunities for improvement in data science practice. Nested models can be more powerful than non-nested, but are easy to get wrong.
Continue reading On Nested Models
Most data science projects are well served by a random test/train split. In our book Practical Data Science with R we strongly advise preparing data and including enough variables so that data is exchangeable, and scoring classifiers using a random test/train split.
With enough data and a big enough arsenal of methods, it’s relatively easy to find a classifier that looks good; the trick is finding one that is good. What many data science practitioners (and consumers) don’t seem to remember is that when evaluating a model, a random test/train split may not always be enough.
Continue reading Random Test/Train Split is not Always Enough
We demonstrate a dataset that causes many good machine learning algorithms to horribly overfit.
The example is designed to imitate a common situation found in predictive analytic natural language processing. In this type of application you are often building a model using many rare text features. The rare text features are often nearly unique k-grams and the model can be anything from Naive Bayes to conditional random fields. This sort of modeling situation exposes the modeler to a lot of training bias. You can get models that look good on training data even though they have no actual value on new data (very poor generalization performance). In this sort of situation you are very vulnerable to having fit mere noise.
Often there is a feeling if a model is doing really well on training data then must be some way to bound generalization error and at least get useful performance on new test and production data. This is, of course, false as we will demonstrate by building deliberately useless features that allow various models to perform well on training data. What is actually happening is you are working through variations of worthless models that only appear to be good on training data due to overfitting. And the more “tweaking, tuning, and fixing” you try only appears to improve things because as you peek at your test-data (which you really should have held some out until the entire end of project for final acceptance) your test data is becoming less exchangeable with future new data and more exchangeable with your training data (and thus less helpful in detecting overfit).
Any researcher that does not have proper per-feature significance checks or hold-out testing procedures will be fooled into promoting faulty models. Continue reading Bad Bayes: an example of why you need hold-out testing