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Machine learning: How embeddings make circuitous data simple

Working with non-numerical data can be tough, even for accomplished data scientists. A archetypal apparatus acquirements model expects its appearance to be numbers, not words, emails, website pages, lists, graphs, or anticipation distributions. To be useful, data has to be adapted into a vector space first. But how?

One accepted access would be to . This could work well if the number of categories is small (for example, if data indicates a profession or a country). However, if we try to apply this method to emails, we will likely get as many categories as there are samples. No two emails are absolutely the same, hence this access would be of no use.

Another access would be to , a action that tells us how close any two samples are. Or we could define a , which would give us the same advice except that the ambit amid two close samples is small while affinity is large. Computing ambit (similarity) amid all data samples would give us a ambit (or similarity) matrix. This is after data we could use.

However, this data would have as many ambit as there are samples, which is usually not great if we want to use it as a affection (see curse of dimensionality) or to anticipate it (while one plot can handle even 6D, I have yet to see a 100D plot). Could we reduce the number of ambit to a reasonable amount?

The answer is yes! That’s what we have embeddings for.

What is an embedding and why should you use it?

An embedding is a low-dimensional representation of high-dimensional data. Typically, an embedding won’t abduction all advice independent in the aboriginal data. A good embedding, however, will abduction enough to solve the botheration at hand.

There exist many embeddings tailored for a accurate data structure. For example, you might have heard of word2vec for text data, or Fourier descriptors for shape image data. Instead, we will altercate how to apply embeddings to any data where we can define a ambit or a affinity measure. As long as we can compute a ambit matrix, the nature of data is absolutely irrelevant. It will work the same, be it emails, lists, trees, or web pages.

In this article, we will acquaint you to altered types of embedding and altercate how some accepted embeddings work and how we could use embeddings to solve real-world problems involving circuitous data. We will also go through the pros and cons of this method, as well as some alternatives. Yes, some problems can be solved better by other means, but unfortunately, there is no silver bullet in apparatus learning.

Let’s get started.

How embeddings work

All embeddings attack to reduce the ambit of data while attention “essential” advice in the data, but every embedding does it in its own way. Here, we will go through a few accepted embeddings that can be activated to a ambit or affinity matrix.

We won’t even attack to cover all the embeddings out there. There are at least a dozen acclaimed embeddings that can do that and many more lesser-known embeddings and their variations. Each of them has its own approach, advantages, and disadvantages.

If you’d like to see what other embeddings are out there, you could start here:

  • Scikit-learn User Guide
  • The Elements of Statistical Acquirements (Second Edition), Chapter 14

Distance matrix

Let’s briefly touch on ambit matrices. Award an adapted ambit for data requires a good compassionate of the problem, some ability of math, and . In the access declared in this article, that might be the most important factor accidental to the all-embracing success or abortion of your project.

You should also keep a few abstruse capacity in mind. Many embedding algorithms will assume that a ambit (or ) matrix

has zeros on its askew and is symmetric. If it’s not symmetric, we can use

instead. Algorithms using the kernel trick will also assume that a ambit is a metric, which means that the triangle asperity holds:

Also, if an algorithm requires a affinity matrix instead, we could apply any monotone-decreasing action to transform a ambit matrix to a affinity matrix: for example,

Principal Basic Assay (PCA)

Principal Basic Analysis, or PCA, is apparently the most widely used embedding to date. The idea is simple: .

Specifically, let appearance be a sample matrix

have appearance and dimensions. For simplicity, let’s assume that the data sample mean is zero. We can reduce the number of ambit from to by adding by an orthonormal matrix :

Then, will be the new set of features. To map the new appearance back to the aboriginal space (this operation is called ), we simply need to accumulate it again by .

Now, we are to find the matrix that minimizes the about-face error:

Columns of matrix are called arch basic directions, and columns of are called arch components. Numerically, we can find by applying SVD-decomposition to , although there are other appropriately valid ways to do it.

PCA can be activated anon to after features. Or, if our appearance are non-numerical, we can apply it to a ambit or affinity matrix.

If you use Python, PCA is implemented in scikit-learn.

The advantage of this method is that it is fast to compute and quite robust to noise in data.

The disadvantage would be that it can only abduction linear structures, so non-linear advice independent in the aboriginal data is likely to be lost.

Kernel PCA

Kernel PCA is a non-linear adaptation of PCA. The idea is to use , which you have apparently heard of if you are accustomed with Abutment Vector Machines SVM.

Specifically, there exist a few altered ways to compute PCA. One of them is to compute eigendecomposition of the double-centered adaptation of gram matrix . Now, if we compute a for our data, Kernel PCA will treat it as a gram matrix in order to find arch components.

Let , be the affection samples. Kernel matrix is authentic by a kernel action .

A accepted choice is a radial kernel:

where is a ambit function.

Kernel PCA adapted us to specify a distance. For example, for after features, we could use Euclidean distance: .

For non-numerical features, we may need to get creative. One thing to bethink is that this algorithm assumes our ambit to be a metric.

If you use Python, Kernel PCA is implemented in scikit-learn.

The advantage of the Kernel PCA method is that it can abduction non-linear data structures.

The disadvantage is that it is acute to noise in data and that the choice of ambit and kernel functions will abundantly affect the results.

Multidimensional ascent (MDS)

Multidimensional ascent (MDS) tries to bottle distances amid samples globally. The idea is quite automatic and works well with ambit matrices.

Specifically, given affection samples , and a ambit action , we compute new affection samples , by aspersing a :

If you use Python, MDS is implemented in scikit-learn. However, scikit-learn does not abutment transformation of out-of-sample points, which could be annoying if we want to use an embedding in affiliation with a corruption or allocation model. In principle, however, it is possible.

The advantage of MDS is that its idea accords altogether with our framework and that it is not much afflicted by noise in data.

The disadvantage is that its accomplishing in scikit-learn is quite slow and does not abutment out-of-sample transformation.

Use case: addition tracking

The dataset contains advice on 200 tracked shipments. For every tracked shipment, there is a list of (x,y)-coordinates of all locations where the amalgamation was spotted, which is about about amid 20 and 50 observations. The plot below shows how this data looks.

Use Case: Addition Tracking

This data looks like trouble—two altered flavors of trouble, actually.

The first botheration is that the data we’re ambidextrous with is high-dimensional. For example, if every amalgamation was spotted at 50 locations, our data would have 100 dimensions—sounds like a lot, compared to the 200 samples at your disposition.

The second problem: Altered addition routes absolutely have a altered number of observations, so we cannot simply stack the lists with coordinates to represent the data in a collapsed form (and even if they had, that still wouldn’t really make sense).

This is where ambit matrices and embeddings will come in handy. We just need to find a way to assay two addition routes. Fréchet ambit seems to be a reasonable choice. With a distance, we can compute a ambit matrix.

Note: This step might take a while. We need to compute

distances with each ambit having iterations, where is the number of samples and

is the number of observations in one sample. Writing a ambit action calmly is key. For example, in Python, you could use numba to advance this ciphering manyfold.

Visualizing embeddings

Now, we can use an embedding to reduce the number of ambit from 200 to just a few. We can acutely see that there are only a few trade routes, so we may hope to find a good representation of the data even in two or three dimensions. We will use embeddings we discussed earlier: PCA, Kernel PCA, and MDS.

On the plots below, you can see the labeled route data (given for the sake of demonstration) and its representation by an embedding in 2D and 3D (from left to right). The labeled data marks four trade posts affiliated by six trade routes. Two of the six trade routes are bidirectional, which makes eight addition groups in total (6 2). As you can see, we got a pretty clear break of all the eight addition groups with 3D embeddings.

Visualizing Embeddings

This is a good start.

Embeddings in a model pipeline

Now, we are ready to train an embedding. Although MDS showed the best results, it is rather slow; also, scikit-learn’s accomplishing does not abutment out-of-sample transformation. It’s not a botheration for assay but it can be for production, so we will use Kernel PCA instead. For Kernel PCA, we should not forget to apply a radial kernel to the ambit matrix beforehand.

How do you select the number of output dimensions? The assay showed that even 3D works okay. Just to be on the safe side and not leave out any important information, let’s set the embedding output to 10D. For the best performance, the number of output ambit can be set as a model hyper-parameter and then tuned by cross-validation.

So, we will have 10 after appearance that we can use as an input for pretty much any allocation model. How about one linear and one non-linear model: say, Logistic Corruption and Gradient Boosting? For comparison, let’s also use these two models with a full ambit matrix as the input. On top of it, let’s test SVM too (SVM is advised to work with a ambit matrix directly, so no embedding would be required).

The model accurateness on the test set is shown below (10 train and test datasets were generated so we could appraisal the about-face of the model):

  • Gradient Boosting paired with an embedding (KernelPCA GB) gets the first place. It outperformed Gradient Boosting with no embedding (GB). Here, Kernel PCA proved to be useful.
  • Logistic Regression did okay. What’s absorbing is that Logistic Corruption with no embedding (LR) did better than with an embedding (KernelPCA LR). This is not absolutely unexpected. Linear models are not very adjustable but almost difficult to overfit. Here, the loss of advice caused by an embedding seems to outweigh the account of abate input dimensionality.
  • Last but not least, SVM performed well too, although the about-face of this model is quite significant.

Model accuracy

Model accuracy

The Python code for this use case is accessible at GitHub.

We’ve explained what embeddings are and approved how they can be used in affiliation with ambit matrices to solve real-world problems. Time for the verdict:

Are embeddings commodity that a data scientist should use? Let’s take a look at both sides of the story.

Pros & cons of using embeddings


  • This access allows us to work with abnormal or circuitous data structures as long as you can define a distance, which—with a assertive degree of knowledge, imagination, and luck—you usually can.
  • The output is low-dimensional after data, which you can easily analyze, cluster, or use as model appearance for pretty much any apparatus acquirements model out there.


  • Using this approach, we will necessarily lose some information:
    • During the first step, when we alter aboriginal data with affinity matrix
    • During the second step, when we reduce ambit using an embedding
  • Depending on data and ambit function, ciphering of a ambit matrix may be time-consuming. This may be mitigated by an calmly accounting ambit function.
  • Some embeddings are very acute to noise in data. This may be mitigated by added data cleaning.
  • Some embeddings are acute to the choice of its hyper-parameters. This may be mitigated by accurate assay or hyper-parameter tuning.

Alternatives: why not use…?

  • Why not just use an embedding anon on data, rather than a ambit matrix?
    If you know an embedding that can calmly encode your data directly, by all means, use it. The botheration is that it does not always exist.
  • Why not just use clusterization on a ambit matrix?
    If your only goal is to articulation your dataset, it would be absolutely okay to do so. Some clusterization methods advantage embeddings too (for example, Spectral Clustering). If you’d like to learn more, here is a tutorial on clusterization.
  • Why not just use a ambit matrix as features?
    The size of a ambit matrix is
  • Not all models can deal with it efficiently—some may overfit, some may be slow to fit, some may fail to fit all together. Models with low about-face would be a good choice here, such as linear and/or affiliated models.
  • Why not just use SVM with a ambit matrix?
    SVM is a great model, which performed well in our use case. However, there are some caveats. First, if we want to add other appearance (could be just simple after numbers), we won’t be able to do it directly. We’d have to absorb them into our affinity matrix and potentially lose some admired information. Second, as good as SVM is, addition model may work better for your accurate problem.
  • Why not just use deep learning?
    It is true, for any problem, you can find a acceptable neural arrangement if you search long enough. Keep in mind, though, that the action of finding, training, validating, and deploying this neural arrangement will not necessarily be a simple one. So, as always, use your best judgment.

Embeddings in affiliation with ambit matrices are an abundantly useful tool if you happen to work with circuitous non-numerical data, abnormally when you cannot transform your data into a vector space anon and would prefer to have a low-dimensional input for your model.

Published July 24, 2020 — 06:30 UTC

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