The Win-Vector LLC vtreat library is a library we supply (under a GPL license) for automating the simple domain independent part of variable cleaning an preparation.
The idea is you supply (in R) an example general
data.frame to vtreat’s
designTreatmentsC method (for single-class categorical targets) or
designTreatmentsN method (for numeric targets) and vtreat returns a data structure that can be used to
prepare data frames for training and scoring. A vtreat-prepared data frame is nice in the sense:
- All result columns are numeric.
- No odd type columns (dates, lists, matrices, and so on) are present.
- No columns have
- Categorical variables are expanded into multiple indicator columns with all levels present which is a good encoding if you are using any sort of regularization in your modeling technique.
- No rare indicators are encoded (limiting the number of indicators on the translated
- Categorical variables are also impact coded, so even categorical variables with very many levels (like zip-codes) can be safely used in models.
- Novel levels (levels not seen during design/train phase) do not cause
NA or errors.
The idea is vtreat automates a number of standard inspection and preparation steps that are common to all predictive analytic projects. This leaves the data scientist more time to work on important domain specific steps. vtreat also leaves as much of variable selection to the down-stream modeling software. The goal of vtreat is to reliably (and repeatably) generate a
data.frame that is safe to work with.
This note explains a few things that are new in the vtreat library. Continue reading What is new in the vtreat library?
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?
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
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.
Continue reading The Geometry of Classifiers
Continuing our series of reading out loud from a single page of a statistics book we look at page 224 of the 1972 Dover edition of Leonard J. Savage’s “The Foundations of Statistics.” On this page we are treated to an example attributed to Leo A. Goodman in 1953 that illustrates how for normally distributed data the maximum likelihood, unbiased, and minimum variance estimators of variance are in fact typically three different values. So in the spirit of gamesmanship you always have at least two reasons to call anybody else’s estimator incorrect. Continue reading Bias/variance tradeoff as gamesmanship
What is the Gauss-Markov theorem?
From “The Cambridge Dictionary of Statistics” B. S. Everitt, 2nd Edition:
A theorem that proves that if the error terms in a multiple regression have the same variance and are uncorrelated, then the estimators of the parameters in the model produced by least squares estimation are better (in the sense of having lower dispersion about the mean) than any other unbiased linear estimator.
This is pretty much considered the “big boy” reason least squares fitting can be considered a good implementation of linear regression.
Suppose you are building a model of the form:
y(i) = B . x(i) + e(i)
B is a vector (to be inferred),
i is an index that runs over the available data (say
x(i) is a per-example vector of features, and
y(i) is the scalar quantity to be modeled. Only
y(i) are observed. The
e(i) term is the un-modeled component of
y(i) and you typically hope that the
e(i) can be thought of unknowable effects, individual variation, ignorable errors, residuals, or noise. How weak/strong assumptions you put on the
e(i) (and other quantities) depends on what you know, what you are trying to do, and which theorems you need to meet the pre-conditions of. The Gauss-Markov theorem assures a good estimate of
B under weak assumptions.
How to interpret the theorem
The point of the Gauss-Markov theorem is that we can find conditions ensuring a good fit without requiring detailed distributional assumptions about the
e(i) and without distributional assumptions about the
x(i). However, if you are using Bayesian methods or generative models for predictions you may want to use additional stronger conditions (perhaps even normality of errors and even distributional assumptions on the
We are going to read through the Wikipedia statement of the Gauss-Markov theorem in detail.
Continue reading Reading the Gauss-Markov theorem
When you apply machine learning algorithms on a regular basis, on a wide variety of data sets, you find that certain data issues come up again and again:
- Missing values (
NA or blanks)
- Problematic numerical values (
NaN, sentinel values like 999999999 or -1)
- Valid categorical levels that don’t appear in the training data (especially when there are rare levels, or a large number of levels)
- Invalid values
Of course, you should examine the data to understand the nature of the data issues: are the missing values missing at random, or are they systematic? What are the valid ranges for the numerical data? Are there sentinel values, what are they, and what do they mean? What are the valid values for text fields? Do we know all the valid values for a categorical variable, and are there any missing? Is there any principled way to roll up category levels? In the end though, the steps you take to deal with these issues will often be the same from data set to data set, so having a package of ready-to-go functions for data treatment is useful. In this article, we will discuss some of our usual data treatment procedures, and describe a prototype R package that implements them.
Continue reading Vtreat: designing a package for variable treatment
A quick R mini-tip: don’t use
data.matrix when you mean
model.matrix. If you do so you may lose (without noticing) a lot of your model’s explanatory power (due to poor encoding). Continue reading R minitip: don’t use data.matrix when you mean model.matrix
Been reading a lot of Gelman, Carlin, Stern, Dunson, Vehtari, Rubin “Bayesian Data Analysis” 3rd edition lately. Overall in the Bayesian framework some ideas (such as regularization, and imputation) are way easier to justify (though calculating some seemingly basic quantities becomes tedious). A big advantage (and weakness) of this formulation is statistics has a much less “shrink wrapped” feeling than the classic frequentist presentations. You feel like the material is being written to peers instead of written to calculators (of the human or mechanical variety). In the Bayesian formulation you don’t feel like you will be yelled at for using 1 tablespoon of sugar when the recipe calls for 3 teaspoons (at least if you live in the United States).
Some other stuff reads differently after this though. Continue reading Skimming statistics papers for the ideas (instead of the complete procedures)