Besides consulting and training, Jeroen is currently a Lead Data Scientist at Elsevier in Amsterdam. Previously, he worked in New York City at YPlan and Visual Revenue (which was acquired by Outbrain). Jeroen has an MSc in Artificial Intelligence and a PhD in Machine Learning. Recently, he wrote a book titled Data Science at the Command Line. He blogs at http://jeroenjanssens.com.

Dimensionality reduction at the command line

Introducing Tapkee, an efficient command-line tool and C++ library for linear and nonlinear dimensionality reduction.

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Editor’s Note: This post is a slightly adapted excerpt from Jeroen Janssens’ recent book, “Data Science at the Command Line.” To follow along with the code, and learn more about the various tools, you can install the Data Science Toolbox, a free virtual machine that runs on Microsoft Windows, Mac OS X, and Linux, and has all the command-line tools pre-installed.

The goal of dimensionality reduction is to map high-dimensional data points onto a lower dimensional space. The challenge is to keep similar data points close together on the lower-dimensional mapping. As we’ll see in the next section, our data set contains 13 features. We’ll stick with two dimensions because that’s straightforward to visualize.

Dimensionality reduction is often regarded as being part of the exploring step. It’s useful for when there are too many features for plotting. You could do a scatter plot matrix, but that only shows you two features at a time. It’s also useful as a preprocessing step for other machine-learning algorithms. Most dimensionality reduction algorithms are unsupervised, which means that they don’t employ the labels of the data points in order to construct the lower-dimensional mapping.

In this post, we’ll use Tapkee, a new command-line tool to perform dimensionality reduction. More specifically, we’ll demonstrate two techniques: PCA, which stands for Principal Components Analysis (Pearson, 1901) and t-SNE, which stands for t-distributed Stochastic Neighbor Embedding (van der Maaten & Hinton, 2008). Coincidentally, t-SNE was discussed in detail in a recent O’Reilly blog post. But first, let’s obtain, scrub, and explore the data set we’ll be using. Read more…