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- Visualising high-dimensional datasets using PCA and t-SNE in Python
- sklearn.manifold.TSNE
- t-SNE Python Example
- An Introduction to t-SNE with Python Example
- Visualizing with t-SNE

## Visualising high-dimensional datasets using PCA and t-SNE in Python

It converts similarities between data points to joint probabilities and tries to minimize the Kullback-Leibler divergence between the joint probabilities of the low-dimensional embedding and the high-dimensional data. It is highly recommended to use another dimensionality reduction method e. This will suppress some noise and speed up the computation of pairwise distances between samples. Read more in the User Guide. The perplexity is related to the number of nearest neighbors that is used in other manifold learning algorithms. Larger datasets usually require a larger perplexity. Consider selcting a value between 5 and The choice is not extremely critical since t-SNE is quite insensitive to this parameter. Controls how tight natural clusters in the original space are in the embedded space and how much space will be between them. For larger values, the space between natural clusters will be larger in the embedded space. Again, the choice of this parameter is not very critical. If the cost function increases during initial optimization, the early exaggeration factor or the learning rate might be too high. The learning rate can be a critical parameter. It should be between and If the cost function gets stuck in a bad local minimum increasing the learning rate helps sometimes. The metric to use when calculating distance between instances in a feature array. If metric is a string, it must be one of the options allowed by scipy. Alternatively, if metric is a callable function, it is called on each pair of instances rows and the resulting value recorded. The callable should take two arrays from X as input and return a value indicating the distance between them. Initialization of embedding. PCA initialization cannot be used with precomputed distances and is usually more globally stable than random initialization. Pseudo Random Number generator seed control. If None, use the numpy. Note that different initializations might result in different local minima of the cost function. However, the exact method cannot scale to millions of examples. This method is not very sensitive to changes in this parameter in the range of 0. Angle less than 0. Otherwise it contains a sample per row. If True, will return the parameters for this estimator and contained subobjects that are estimators. The method works on simple estimators as well as on nested objects such as pipelines.## sklearn.manifold.TSNE

In contrast to other dimensionality reduction algorithms like PCA which simply maximizes the variance, t-SNE creates a reduced feature space where similar samples are modeled by nearby points and dissimilar samples are modeled by distant points with high probability. At a high level, t-SNE constructs a probability distribution for the high-dimensional samples in such a way that similar samples have a high likelihood of being picked while dissimilar points have an extremely small likelihood of being picked. Then, t-SNE defines a similar distribution for the points in the low-dimensional embedding. Finally, t-SNE minimizes the Kullback—Leibler divergence between the two distributions with respect to the locations of the points in the embedding. As mentioned previously, t-SNE takes a high dimensional dataset and reduces it to a low dimensional graph that retains a lot of the original information. Suppose we had a dataset composed of 3 distinct classes. We want to reduce the 2D plot into a 1D plot while maintaining clear boundaries between the clusters. Recall that simply projecting the data on to an axis is a poor approach to dimensionality reduction because we lose a substantial amount of information. Instead, we can use a dimensionality reduction technique hint: t-SNE to achieve what we want. The first step in the t-SNE algorithm involves measuring the distance from one point with respect to every other point. Instead of working with the distances directly, we map them to a probability distribution. In the distribution, the points with the smallest distance with respect to the current point have a high likelihood, whereas the points far away from the current point have very low likelihoods. Taking another look at the 2D plot, notice how the blue cluster is more spread out than the green one. To account for this fact, we divide by the sum of the likelihoods. Mathematically, we write the equation for a normal distribution as follows. If we drop everything before the exponent and use another point instead of the mean, all the while addressing the problem of scale discussed earlier, we get the equation from the paper. To accomplish this, we make use of something called the Kullback-Leiber divergence. The KL divergence is a measure of how different one probability distribution from a second. The lower the value of the KL divergence, the closer two distributions are to one another. A KL divergence of 0 implies that the two distributions in question are identical. This should hopefully bring about a flush of ideas. Recall how in the case of linear regression, we were able to determine the best fitting line by using gradient descent to minimize the cost function i. Well, in t-SNE, we use gradient descent to minimize the sum of the Kullback-Leiber divergences over data all the data points. We take the partial derivative of our cost function with respect to every point in order to give us the direction of each update. Often times we make use of some library without really understanding what goes on under the hood. In the proceeding section, I will attempt all be it unsuccessfully to implement the algorithm and associated mathematical equations as Python code. To help with the process, I took bits and pieces from the source code of the TSNE class in the scikit-learn library. The scikit-learn library provides a method for importing them into our program. On the other hand, perplexity is related to the number of nearest neighbors used in the algorithm. A different perplexity can cause drastic changes in the end results. In our case, we set it to the default value of the scitkit-learn implementation of t-SNE According to the numpy documentation, the machine epsilon is the smallest representable positive number such that 1. Next, we define the fit function.

## t-SNE Python Example

Unlike, PCA, one of the commonly used dimensionality reduction techniques, tSNE is non-linear and probabilistic technique. What this means tSNE can capture non-linaer pattern in the data. Since it is probabilistic, you may not get the same result for the same data. The objective function is minimized using a gradient descent optimization that is initiated randomly. As a result, it is possible that different runs give you different solutions. Notice that it is perfectly fine to run t-SNE a number of times with the same data and parametersand to select the visualization with the lowest value of the objective function as your final visualization. Let us load the packages needed for performing tSNE. We will first use digits dataset available in sklearn. Let us first load the dataset needed for dimensionality reduction with tSNE. In addition to the images, sklearn also has the numerical data ready to use for any dimensionality reduction techniques. We can see that digits. Let us subset the data so that we can do the tSNE faster. Her we subset both the data set and the actual digit it correspond to. We can call tSNE from sklearn. Let us first initialize tSNE and get two components. We get a low dimensional representation of our original data in just two dimension. Here it is simply a two dimesional numpy array. We have actually done the tSNE. Let us make a scatter plot to visualize the low-dimensional representation of the data. Let us store results from tSNE as a Pandas dataframe with the target integer for each data point. Let us first make a scatter plot with using the two arrays we got from tSNE. We see that the data clusters nicely. We can clearly see that tSNE nicely captured the patterns in our data. Same digits are mostly in the same cluster. Labeled tSNE plot: Visualizing high dimensional data. Email Address. Share this: Twitter Facebook. Return to top of page.

## An Introduction to t-SNE with Python Example

Update: April 29, Updated some of the code to not use ggplot but instead use seaborn and matplotlib. I also added an example for a 3d-plot. I also changed the syntax to work with Python3. The first step around any data related challenge is to start by exploring the data itself. This could be by looking at, for example, the distributions of certain variables or looking at potential correlations between variables. The problem nowadays is that most datasets have a large number of variables. In other words, they have a high number of dimensions along which the data is distributed. Visually exploring the data can then become challenging and most of the time even practically impossible to do manually. However, such visual exploration is incredibly important in any data-related problem. Therefore it is key to understand how to visualise high-dimensional datasets. This can be achieved using techniques known as dimensionality reduction. More about that later. Lets first get some high-dimensional data to work with. There is no need to download the dataset manually as we can grab it through using Scikit Learn. We are going to convert the matrix and vector to a Pandas DataFrame. This is very similar to the DataFrames used in R and will make it easier for us to plot it later on. The randomisation is important as the dataset is sorted by its label i. We now have our dataframe and our randomisation vector. Lets first check what these numbers actually look like. If you were, for example, a post office such an algorithm could help you read and sort the handwritten envelopes using a machine instead of having humans do that. Obviously nowadays we have very advanced methods to do this, but this dataset still provides a very good testing ground for seeing how specific methods for dimensionality reduction work and how well they work. This is where we get to dimensionality reduction. Lets first take a look at something known as Principal Component Analysis. PCA is a technique for reducing the number of dimensions in a dataset whilst retaining most information. It is using the correlation between some dimensions and tries to provide a minimum number of variables that keeps the maximum amount of variation or information about how the original data is distributed. It does not do this using guesswork but using hard mathematics and it uses something known as the eigenvalues and eigenvectors of the data-matrix.

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