In this note am going to recount “my favorite R bug.” It isn’t a bug in R. It is a bug in some code I wrote in R. I call it my favorite bug, as it is easy to commit and (thanks to R’s overly helpful nature) takes longer than it should to find.

# Category Archives: Expository Writing

# Does Balancing Classes Improve Classifier Performance?

It’s a folk theorem I sometimes hear from colleagues and clients: that you must balance the class prevalence before training a classifier. Certainly, I believe that classification tends to be *easier* when the classes are nearly balanced, especially when the class you are actually interested in is the rarer one. But I have always been skeptical of the claim that artificially balancing the classes (through resampling, for instance) always helps, when the model is to be run on a population with the native class prevalences.

On the other hand, there are situations where balancing the classes, or at least enriching the prevalence of the rarer class, might be necessary, if not desirable. Fraud detection, anomaly detection, or other situations where positive examples are hard to get, can fall into this case. In this situation, I’ve suspected (without proof) that SVM would perform well, since the formulation of hard-margin SVM is pretty much distribution-free. Intuitively speaking, if both classes are far away from the margin, then it shouldn’t matter whether the rare class is 10% or 49% of the population. In the soft-margin case, of course, distribution starts to matter again, but perhaps not as strongly as with other classifiers like logistic regression, which explicitly encodes the distribution of the training data.

So let’s run a small experiment to investigate this question.

Continue reading Does Balancing Classes Improve Classifier Performance?

# R bracket is a bit irregular

While skimming Professor Hadley Wickham’s Advanced R I got to thinking about nature of the square-bracket or extract operator in R. It turns out “`[,]`

” is a bit more irregular than I remembered.

The subsetting section of Advanced R has a very good discussion on the subsetting and selection operators found in R. In particular it raises the important distinction of two simultaneously valuable but incompatible desiderata: simplification of results versus preservation of results. Continue reading R bracket is a bit irregular

# Random Test/Train Split is not Always Enough

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

# Let’s try to motivate schemes

Recently there has been some controversy over David Mumford’s Nature magazine *invited* obituary of Alexander Grothendieck being initially rejected on submission (see here and here). At issue was the attempt to explain the mathematical idea of schemes (one of Alexander Grothendieck’s most important contributions) to a non-mathematician audience. Professor Mumford is a mathematician of great stature and his explanation is better than anything I could even attempt. However, in addition to the issues he raises I don’t think he was sensitive enough to what a non-mathematician considers motivation.

I’ll take a quick stab at explaining a very tiny bit of the motivation of schemes. I not sure the kind of chain of analogies argument I am attempting would work in an obituary (or in a short length), so I certainly don’t presume to advise professor Mumford on his obituary of a great mathematician (and person). Continue reading Let’s try to motivate schemes

# The Geometry of Classifiers

As John mentioned in his last post, we have been quite interested in the recent study by Fernandez-Delgado, et.al., “Do we Need Hundreds of Classifiers to Solve Real World Classification Problems?” (the “DWN study” for short), which evaluated 179 popular implementations of common classification algorithms over 120 or so data sets, mostly from the UCI Machine Learning Repository. For fun, we decided to do a follow-up study, using their data and several classifier implementations from `scikit-learn`

, the Python machine learning library. We were interested not just in classifier accuracy, but also in seeing if there is a “geometry” of classifiers: which classifiers produce predictions patterns that look similar to each other, and which classifiers produce predictions that are quite different? To examine these questions, we put together a Shiny app to interactively explore how the relative behavior of classifiers changes for different types of data sets.

# Great new post by Win-Vector’s Nina Zumel

Win-Vector LLC’s Nina Zumel has a great new article on the issue of taste in design and problem solving: Design, Problem Solving, and Good Taste. I think it is a *big* issue: how can you expect good work if you can’t even discuss how to tell good from bad?

# Estimating Generalization Error with the PRESS statistic

As we’ve mentioned on previous occasions, one of the defining characteristics of data science is the emphasis on the availability of “large” data sets, which we define as “enough data that statistical efficiency is not a concern” (note that a “large” data set need not be “big data,” however you choose to define it). In particular, we advocate the use of hold-out data to evaluate the performance of models.

There is one caveat: if you are evaluating a series of models to pick the best (and you usually are), then a single hold-out set is strictly speaking not enough. Hastie, et.al, say it best:

Ideally, the test set should be kept in a “vault,” and be brought out only at the end of the data analysis. Suppose instead that we use the test-set repeatedly, choosing the model with smallest test-set error. Then the test set error of the final chosen model will underestimate the true test error, sometimes substantially.

*The Elements of Statistical Learning*, 2nd edition.

The ideal way to select a model from a set of candidates (or set parameters for a model, for example the regularization constant) is to use a training set to train the model(s), a calibration set to select the model or choose parameters, and a test set to estimate the generalization error of the final model.

In many situations, breaking your data into three sets may not be practical: you may not have very much data, or the the phenomena you’re interested in are rare enough that you need a lot of data to detect them. In those cases, you will need more statistically efficient estimates for generalization error or goodness-of-fit. In this article, we look at the PRESS statistic, and how to use it to estimate generalization error and choose between models.

Continue reading Estimating Generalization Error with the PRESS statistic

# Automatic bias correction doesn’t fix omitted variable bias

Page 94 of Gelman, Carlin, Stern, Dunson, Vehtari, Rubin “Bayesian Data Analysis” 3rd Edition (which we will call BDA3) provides a great example of what happens when common broad frequentist bias criticisms are over-applied to predictions from ordinary linear regression: the predictions appear to fall apart. BDA3 goes on to exhibit what might be considered the kind of automatic/mechanical fix responding to such criticisms would entail (producing a bias corrected predictor), and rightly shows these adjusted predictions are far worse than the original ordinary linear regression predictions. BDA3 makes a number of interesting points and is worth studying closely. We work their example in a bit more detail for emphasis. Continue reading Automatic bias correction doesn’t fix omitted variable bias

# A bit of the agenda of Practical Data Science with R

The goal of Zumel/Mount: Practical Data Science with R is to teach, through guided practice, the skills of a data scientist. We define a data scientist as the person who organizes client input, data, infrastructure, statistics, mathematics and machine learning to deploy useful predictive models into production.

Our plan to teach is to:

- Order the material by what is expected from the data scientist.
- Emphasize the already available bread and butter machine learning algorithms that most often work.
- Provide a large set of worked examples.
- Expose the reader to a number of realistic data sets.

Some of these choices may put-off some potential readers. But it is our goal to try and spend out time on what a data scientist needs to do. Our point: the data scientist is responsible for end to end results, which is not always entirely fun. If you want to specialize in machine learning algorithms or only big data infrastructure, that is a fine goal. However, the job of the data scientist is to understand and orchestrate all of the steps (working with domain experts, curating data, using data tools, and applying machine learning and statistics).

Once you define what a data scientist does, you find fewer people want to work as one.

We expand a few of our points below. Continue reading A bit of the agenda of Practical Data Science with R