Posted on Categories Practical Data Science, Pragmatic Data Science, Programming, Statistics, TutorialsTags , 3 Comments on R style tip: prefer functions that return data frames

R style tip: prefer functions that return data frames

While following up on Nina Zumel’s excellent Trimming the Fat from glm() Models in R I got to thinking about code style in R. And I realized: you can make your code much prettier by designing more of your functions to return data.frames. That may seem needlessly heavy-weight, but it has a lot of down-stream advantages. Continue reading R style tip: prefer functions that return data frames

Posted on Categories Coding, data science, Practical Data Science, Programming, Statistics, TutorialsTags , , 10 Comments on Trimming the Fat from glm() Models in R

Trimming the Fat from glm() Models in R

One of the attractive aspects of logistic regression models (and linear models in general) is their compactness: the size of the model grows in the number of coefficients, not in the size of the training data. With R, though, glm models are not so concise; we noticed this to our dismay when we tried to automate fitting a moderate number of models (about 500 models, with on the order of 50 coefficients) to data sets of moderate size (several tens of thousands of rows). A workspace save of the models alone was in the tens of gigabytes! How is this possible? We decided to find out.

As many R users know (but often forget), a glm model object carries a copy of its training data by default. You can use the settings y=FALSE and model=FALSE to turn this off.

set.seed(2325235)


# Set up a synthetic classification problem of a given size
# and two variables: one numeric, one categorical
# (two levels).
synthFrame = function(nrows) {
   d = data.frame(xN=rnorm(nrows),
      xC=sample(c('a','b'),size=nrows,replace=TRUE))
   d$y = (d$xN + ifelse(d$xC=='a',0.2,-0.2) + rnorm(nrows))>0.5
   d
}


# first show that model=F and y=F help reduce model size

dTrain = synthFrame(1000)
model1 = glm(y~xN+xC,data=dTrain,family=binomial(link='logit'))
model2 = glm(y~xN+xC,data=dTrain,family=binomial(link='logit'),
             y=FALSE)
model3 = glm(y~xN+xC,data=dTrain,family=binomial(link='logit'),
              y=FALSE, model=FALSE)

#
# Estimate the object's size as the size of its serialization
#
length(serialize(model1, NULL))
# [1] 225251
length(serialize(model2, NULL))
# [1] 206341
length(serialize(model3, NULL))
# [1] 189562

dTest = synthFrame(100)
p1 = predict(model1, newdata=dTest, type='response')
p2 = predict(model2, newdata=dTest, type='response')
p3 = predict(model3, newdata=dTest, type='response')
sum(abs(p1-p2))
# [1] 0
sum(abs(p1-p3))
# [1] 0

Continue reading Trimming the Fat from glm() Models in R

Posted on Categories data science, Statistics, TutorialsTags , , , , , , 2 Comments on A clear picture of power and significance in A/B tests

A clear picture of power and significance in A/B tests

A/B tests are one of the simplest reliable experimental designs.

Controlled experiments embody the best scientific design for establishing a causal relationship between changes and their influence on user-observable behavior.

“Practical guide to controlled experiments on the web: listen to your customers not to the HIPPO” Ron Kohavi, Randal M Henne, and Dan Sommerfield, Proceedings of the 13th ACM SIGKDD international conference on Knowledge discovery and data mining, 2007 pp. 959-967.

The ideas is to test a variation (called “treatment” or “B”) in parallel with continuing to test a baseline (called “control” or “A”) to see if the variation drives a desired effect (increase in revenue, cure of disease, and so on). By running both tests at the same time it is hoped that any confounding or omitted factors are nearly evenly distributed between the two groups and therefore not spoiling results. This is a much safer system of testing than retrospective studies (where we look for features from data already collected).

Interestingly enough the multi-armed bandit alternative to A/B testing (a procedure that introduces online control) is one of the simplest non-trivial Markov decision processes. However, we will limit ourselves to traditional A/B testing for the remainder of this note. Continue reading A clear picture of power and significance in A/B tests

Posted on Categories Coding, Expository Writing, Programming, TutorialsTags , , , 9 Comments on You don’t need to understand pointers to program using R

You don’t need to understand pointers to program using R

R is a statistical analysis package based on writing short scripts or programs (versus being based on GUIs like spreadsheets or directed workflow editors). I say “writing short scripts” because R’s programming language (itself called S) is a bit of an oddity that you really wouldn’t be using except it gives you access to superior analytics data structures (R’s data.frame and treatment of missing values) and deep ready to go statistical libraries. For longer pure programming tasks you are better off using something else (be it Python, Ruby, Java, C++, Javascript, Go, ML, Julia, or something else). However, the S language has one feature that makes it pleasant to learn (despite any warts): it can be initially used and taught without having the worry about the semantics of references or pointers. Continue reading You don’t need to understand pointers to program using R

Posted on Categories data science, Opinion, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , , 2 Comments on Can a classifier that never says “yes” be useful?

Can a classifier that never says “yes” be useful?

Many data science projects and presentations are needlessly derailed by not having set shared business relevant quantitative expectations early on (for some advice see Setting expectations in data science projects). One of the most common issues is the common layman expectation of “perfect prediction” from classification projects. It is important to set expectations correctly so your partners know what you are actually working towards and do not consider late choices of criteria disappointments or “venue shopping.” Continue reading Can a classifier that never says “yes” be useful?

Posted on Categories data science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , , , , , 3 Comments on Bad Bayes: an example of why you need hold-out testing

Bad Bayes: an example of why you need hold-out testing

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

Posted on Categories Mathematics, Rants, Statistics, TutorialsTags , , , 14 Comments on Use standard deviation (not mad about MAD)

Use standard deviation (not mad about MAD)

Nassim Nicholas Taleb recently wrote an article advocating the abandonment of the use of standard deviation and advocating the use of mean absolute deviation. Mean absolute deviation is indeed an interesting and useful measure- but there is a reason that standard deviation is important even if you do not like it: it prefers models that get totals and averages correct. Absolute deviation measures do not prefer such models. So while MAD may be great for reporting, it can be a problem when used to optimize models. Continue reading Use standard deviation (not mad about MAD)

Posted on Categories Coding, math programming, Statistics, TutorialsTags , , , , , , , 4 Comments on The Extra Step: Graphs for Communication versus Exploration

The Extra Step: Graphs for Communication versus Exploration

Visualization is a useful tool for data exploration and statistical analysis, and it’s an important method for communicating your discoveries to others. While those two uses of visualization are related, they aren’t identical.

One of the reasons that I like ggplot so much is that it excels at layering together multiple views and summaries of data in ways that improve both data exploration and communication. Of course, getting at the right graph can be a bit of work, and often I will stop when I get to a visualization that tells me what I need to know — even if no one can read that graph but me. In this post I’ll look at a couple of ggplot graphs that take the extra step: communicating effectively to others.

For my examples I’ll use a pre-treated sample from the 2011 U.S. Census American Community Survey. The dataset is available as an R object in the file phsample.RData; the data dictionary and additional information can be found here. Information about getting the original source data from the U.S. Census site is at the bottom of this post.

The file phsample.RData contains two data frames: dhus (household information), and dpus (information about individuals; they are joined to households using the column SERIALNO). We will only use the dhus data frame.

library(ggplot2)
load("phsample.RData")

# Restrict to non-institutional households
# (No jails, schools, convalescent homes, vacant residences)
hhonly = subset(dhus, (dhus$TYPE==1) &(dhus$NP > 0))

Continue reading The Extra Step: Graphs for Communication versus Exploration

Posted on Categories Expository Writing, math programming, Mathematics, TutorialsTags , , , ,

Unspeakable bets: take small steps

I was watching my cousins play Unspeakable Words over Christmas break and got interested in the end game. The game starts out as a spell a word from cards and then bet some points game, but in the end (when you are down to one marker) it becomes a pure betting game. In this article we analyze an idealized form of the pure betting end game. Continue reading Unspeakable bets: take small steps

Posted on Categories data science, Practical Data Science, Pragmatic Data Science, Pragmatic Machine Learning, Statistics, TutorialsTags , , , , 1 Comment on Generalized linear models for predicting rates

Generalized linear models for predicting rates

I often need to build a predictive model that estimates rates. The example of our age is: ad click through rates (how often a viewer clicks on an ad estimated as a function of the features of the ad and the viewer). Another timely example is estimating default rates of mortgages or credit cards. You could try linear regression, but specialized tools often do much better. For rate problems involving estimating probabilities and frequencies we recommend logistic regression. For non-frequency (and non-categorical) rate problems (such as forecasting yield or purity) we suggest beta regression.

In this note we will work a toy problem and suggest some relevant R analysis libraries. Continue reading Generalized linear models for predicting rates