This course will introduce the learner to applied machine learning, focusing more on the techniques and methods than on the statistics behind these methods. The course will start with a discussion of how machine learning is different than descriptive statistics, and introduce the scikit learn toolkit through a tutorial. The issue of dimensionality of data will be discussed, and the task of clustering data, as well as evaluating those clusters, will be tackled. Supervised approaches for creating predictive models will be described, and learners will be able to apply the scikit learn predictive modelling methods while understanding process issues related to data generalizability (e.g. cross validation, overfitting). The course will end with a look at more advanced techniques, such as building ensembles, and practical limitations of predictive models. By the end of this course, students will be able to identify the difference between a supervised (classification) and unsupervised (clustering) technique, identify which technique they need to apply for a particular dataset and need, engineer features to meet that need, and write python code to carry out an analysis. This course should be taken after Introduction to Data Science in Python and Applied Plotting, Charting & Data Representation in Python and before Applied Text Mining in Python and Applied Social Analysis in Python.
Dimensionality Reduction and Manifold Learning
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From the course by University of Michigan
Applied Machine Learning in Python
2106 ratings
University of Michigan
2106 ratings
Course 3 of 5 in the Specialization Applied Data Science with Python
From the lesson
Module 4: Supervised Machine Learning - Part 2
This module covers more advanced supervised learning methods that include ensembles of trees (random forests, gradient boosted trees), and neural networks (with an optional summary on deep learning). You will also learn about the critical problem of data leakage in machine learning and how to detect and avoid it.
Meet the Instructors
Kevyn Collins-ThompsonAssociate Professor
School of Information
Another very important family of unsupervised learning methods that fall into
the transformation category are known as dimensionality reduction algorithms.
As the name suggests, this kind of transform
takes your original dataset that might contain say,
200 features and finds an approximate version of dataset that uses,
say, only 10 dimensions.
One very common need for dimensionality reduction arises when first exploring a dataset,
to understand how the samples may be grouped or related to each
other by visualizing it using a two-dimensional scatterplot.
One very important form of dimensionality reduction is called
principal component analysis, or PCA.
Intuitively, what PCA does is take
your cloud of original data points and finds a rotation of it.
So the dimensions are statistically uncorrelated.
PCA then typically drops all but
the most informative initial dimensions that
capture most of the variation in the original dataset.
Here's a simple example of what I mean with a synthetic two-dimensional dataset.
Here, if we have two original features that are highly
correlated represented by this cloud of points,
PCA will rotate the data so
the direction of highest variance - called the first principal component,
which is along the long direction of the cloud,
becomes the first dimension.
It will then find the direction at right angles
that maximally captures the remaining variance.
This is the second principle component.
In two dimensions, there's
only one possible such direction at right angles of the first principal component,
but for higher dimensions,
there would be infinitely many.
With more than two dimensions,
the process of finding successive principal components at right angles to
the previous ones would continue until
the desired number of principal components is reached.
One result of applying PCA is that we now know
the best one-dimensional approximation to the original two-dimensional data.
In other words, we can take any data point that used two features
before - x and y - and approximate it using just one feature,
namely its location when projected onto the first principal component.
Here's an example of using scikit learn to apply PCA to a higher dimensional dataset;
the breast cancer dataset.
To perform PCA, we import the PCA class from sklearn.decomposition.
It's important to first transform the dataset so that
each features range of values has zero mean and unit variance.
And we can do this using the fit and transform
methods of the standard scalar class, as shown here.
We then create the PCA object,
specify that we want to retain just the first two principal components to reduce
the dimensionality to just two columns and call the fit method using our normalized data.
This will set up PCA so that it learns the right rotation of the dataset.
We can then apply this properly prepared PCA object to project
all the points in our original input dataset to this new two-dimensional space.
Notice here since we're not doing
supervised learning in evaluating a model against a test set,
we don't have to split our dataset into training and test sets.
You see that if we take the shape of the array that's returned from PCA,
it's transformed our original dataset with
30 features into a new array that has just two columns,
essentially expressing each original data point in terms of
two new features representing the position of
the data point in this new two-dimensional PCA space.
We can then create a scatterplot that uses
these two new features to see how the data forms clusters.
In this example, we've used the dataset that has labels for supervised learning;
namely, the malignant and benign labels on cancer cells.
So we can see how well PCA serves to find clusters in the data.
Here's the result of plotting
all the 30 feature data samples using the two new features computed with PCA.
We can see that the malignant and benign cells do
indeed tend to cluster into two groups in the space.
In fact, we could now apply a linear classifier to
this two-dimensional representation of
the original dataset and we can see that it would likely do fairly well.
This illustrates another use of dimensionality reduction methods like PCA to find
informative features that could then be used in a later supervised learning stage.
We can create a heat map that visualizes the first two principal components of
the breast cancer dataset to get an idea of
what feature groupings each component is associated with.
Note that we can get the arrays representing
the two principal component axes that define the PCA space using the
PCA.components_attribute that's filled in after the PCA fit method is used on the data.
We can see that the first principle component is all positive,
showing a general correlation between all 30 features.
In other words, they tend to vary up and down together.
The second principle component has a mixture of
positive and negative signs; but in particular,
we can see a cluster of negatively signed features that co-vary
together and in the opposite direction of the remaining features.
Looking at the names, it makes sense the subset wold co-vary together.
We see the pair mean texture and worst texture and
the pair mean radius and worst radius varying together and so on.
PCA gives a good initial tool for exploring a dataset,
but may not be able to find more subtle groupings that
produce better visualizations for more complex datasets.
There is a family of unsupervised algorithms called Manifold Learning Algorithms that are
very good at finding low dimensional structure in
high dimensional data and are very useful for visualizations.
One classic example of
a low dimensional subset in
a high dimensional space is this data set in three dimensions,
where the points all lie on a two-dimensional sheet with an interesting shape.
This lower dimensional sheet within a higher dimensional space is called the manifold.
PCA is not sophisticated enough to find this interesting structure.
One widely used manifold learning method is called multi-dimensional scaling, or MDS.
There are many flavors of MDS,
but they all have the same general goal;
to visualize a high dimensional dataset and project
it onto a lower dimensional space - in most cases,
a two-dimensional page - in a way that preserves
information about how the points in the original data space are close to each other.
In this way, you can find and visualize
clustering behavior in your high dimensional data.
Using a technique like MDS and scikit learn is quite similar to using PCA.
Like with PCA, each feature should be normalized
so its feature values have zero mean and unit variants.
After importing the MDS class from sklearn.manifold and transforming the input data,
you create the MDS object,
specifying the number of components - typically set to two dimensions for visualization.
You then fit the object using the transform data,
which will learn the mapping and then you can apply
the MDS mapping to the transformed data.
Here's an example of applying MDS to the fruit dataset.
And you can see it does a pretty good job of
visualizing the fact that the different fruit types
do indeed tend to cluster into groups.
An especially powerful manifold learning algorithm
for visualizing your data is called t-SNE.
t-SNE finds a two-dimensional representation of your data,
such that the distances between points in the 2D scatterplot match as closely
as possible the distances between
the same points in the original high dimensional dataset.
In particular, t-SNE gives much more weight to preserving
information about distances between points that are neighbors.
Here's an example of t-SNE applied to the images in the handwritten digits dataset.
You can see that this two-dimensional plot preserves
the neighbor relationships between images that are similar in terms of their pixels.
For example, the cluster for most of the digit
eight samples is closer to the cluster for the digits three and five,
in which handwriting can appear more similar than to say the digit one,
whose cluster is much farther away.
And here's an example of applying t-SNE on the fruit dataset.
The code is very similar to applying MDS and essentially just replaces MDS with t-SNE.
The interesting thing here is that t-SNE does a poor job of
finding structure in this rather small and simple fruit dataset,
which reminds us that we should try at least a few different approaches when
visualizing data using manifold learning to
see which works best for a particular dataset.
t-SNE tends to work better on datasets that have more well-defined local structure;
in other words, more clearly defined patterns of neighbors.
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