Comprehensive Guide on tSNE algorithm with implementation in R & Python
Introduction
Imagine you get a dataset with hundreds of features (variables) and have little understanding about the domain the data belongs to. You are expected to identify hidden patterns in the data, explore and analyze the dataset. And not just that, you have to find out if there is a pattern in the data – is it signal or is it just noise?
Does that thought make you uncomfortable? It made my hands sweat when I came across this situation for the first time. Do you wonder how to explore a multidimensional dataset? It is one of the frequently asked question by many data scientists. In this article, I will take you through a very powerful way to exactly do this.
What about PCA?
By now, some of you would be screaming “I’ll use PCA for dimensionality reduction and visualization”. Well, you are right! PCA is definitely a good choice for dimensionality reduction and visualization for datasets with a large number of features. But, what if you could use something more advanced than PCA? (If you don’t know PCA, I would strongly recommend to read this article first)
What if you could easily search for a pattern in nonlinear style? In this article, I will tell you about a new algorithm called tSNE (2008), which is much more effective than PCA (1933). I will take you through the basics of tSNE algorithm first and then will walk you through why tSNE is a good fit for dimensionality reduction algorithms.
You will also, get handson knowledge for using tSNE in both R and Python.
Read on!
Table of Content
 What is tSNE?
 What is dimensionality reduction?
 How does tSNE fit in the dimensionality reduction algorithm space
 Algorithmic details of tSNE
 Algorithm
 Time and Space Complexity
 What does tSNE actually do?
 Use cases
 tSNE compared to other dimensionality reduction algorithm
 Example Implementations
 In R
 Hyper parameter tuning
 Code
 Implementation Time
 Interpreting Results
 In Python
 Hyper parameter tuning
 Code
 Implementation Time
 In R
 Where and when to use
 Data Scientist
 Machine Learning Competition Enthusiast
 Student
 Common fallacies
1. What is tSNE?
(tSNE) tDistributed Stochastic Neighbor Embedding is a nonlinear dimensionality reduction algorithm used for exploring highdimensional data. It maps multidimensional data to two or more dimensions suitable for human observation. With help of the tSNE algorithms, you may have to plot fewer exploratory data analysis plots next time you work with high dimensional data.
2. What is dimensionality reduction?
In order to understand how tSNE works, let’s first understand what is dimensionality reduction?
Well, in simple terms, dimensionality reduction is the technique of representing multidimensional data (data with multiple features having a correlation with each other) in 2 or 3 dimensions.
Some of you might question why do we need Dimensionality Reduction when we can plot the data using scatter plots, histograms & boxplots and make sense of the pattern in data using descriptive statistics.
Well, even if you can understand the patterns in data and present it on simple charts, it is still difficult for anyone without statistics background to make sense of it. Also, if you have hundreds of features, you have to study thousands of charts before you can make sense of this data. (Read more about dimensionality reduction here)
With the help of dimensionality reduction algorithm, you will be able to present the data explicitly.
3. How does tSNE fit in the dimensionality reduction algorithm space?
Now that you have an understanding of what is dimensionality reduction, let’s look at how we can use tSNE algorithm for reducing dimensions.
Following are a few dimensionality reduction algorithms that you can check out:
 PCA (linear)
 tSNE (nonparametric/ nonlinear)
 Sammon mapping (nonlinear)
 Isomap (nonlinear)
 LLE (nonlinear)
 CCA (nonlinear)
 SNE (nonlinear)
 MVU (nonlinear)
 Laplacian Eigenmaps (nonlinear)
The good news is that you need to study only two of the algorithms mentioned above to effectively visualize data in lower dimensions – PCA and tSNE.
Limitations of PCA
PCA is a linear algorithm. It will not be able to interpret complex polynomial relationship between features. On the other hand, tSNE is based on probability distributions with random walk on neighborhood graphs to find the structure within the data.
A major problem with, linear dimensionality reduction algorithms is that they concentrate on placing dissimilar data points far apart in a lower dimension representation. But in order to represent high dimension data on low dimension, nonlinear manifold, it is important that similar datapoints must be represented close together, which is not what linear dimensionality reduction algorithms do.
Now, you have a brief understanding of what PCA endeavors to do.
Local approaches seek to map nearby points on the manifold to nearby points in the lowdimensional representation. Global approaches on the other hand attempt to preserve geometry at all scales, i.e mapping nearby points to nearby points and far away points to far away points
It is important to know that most of the nonlinear techniques other than tSNE are not capable of retaining both the local and global structure of the data at the same time.
4. Algorithmic details of tSNE (optional read)
This section is for the people interested in understanding the algorithm in depth. You can safely skip this section if you do not want to go through the math in detail.
Let’s understand why you should know about tSNE and the algorithmic details of tSNE. tSNE is an improvement on the Stochastic Neighbor Embedding (SNE) algorithm.
4.1 Algorithm
Step 1
Stochastic Neighbor Embedding (SNE) starts by converting the highdimensional Euclidean distances between data points into conditional probabilities that represent similarities. The similarity of datapoint to datapoint is the conditional probability, , would pick as its neighbor if neighbors were picked in proportion to their probability density under a Gaussian centered at .
For nearby datapoints, is relatively high, whereas for widely separated datapoints, will be almost infinitesimal (for reasonable values of the variance of the Gaussian, ). Mathematically, the conditional probability is given by
where is the variance of the Gaussian that is centered on datapoint
If you are not interested in the math, think about it in this way, the algorithm starts by converting the shortest distance (a straight line) between the points into probability of similarity of points. Where, the similarity between points is: the conditional probability that would pick as its neighbor if neighbors were picked in proportion to their probability density under a Gaussian (normal distribution) centered at .
Step 2
For the lowdimensional counterparts and of the highdimensional datapoints and it is possible to compute a similar conditional probability, which we denote by .
Note that, pii and pjj are set to zero as we only want to model pair wise similarity.
In simple terms step 1 and step2 calculate the conditional probability of similarity between a pair of points in
 High dimensional space
 In low dimensional space
For the sake of simplicity, try to understand this in detail.
Let us map 3D space to 2D space. What step1 and step2 are doing is calculating the probability of similarity of points in 3D space and calculating the probability of similarity of points in the corresponding 2D space.
Logically, the conditional probabilities and must be equal for a perfect representation of the similarity of the datapoints in the different dimensional spaces, i.e the difference between and must be zero for the perfect replication of the plot in high and low dimensions.
By this logic SNE attempts to minimize this difference of conditional probability.
Step 3
Now here is the difference between the SNE and tSNE algorithms.
To measure the minimization of sum of difference of conditional probability SNE minimizes the sum of KullbackLeibler divergences overall data points using a gradient descent method. We must know that KL divergences are asymmetric in nature.
In other words, the SNE cost function focuses on retaining the local structure of the data in the map (for reasonable values of the variance of the Gaussian in the highdimensional space,).
Additionally, it is very difficult (computationally inefficient) to optimize this cost function.
So tSNE also tries to minimize the sum of the difference in conditional probabilities. But it does that by using the symmetric version of the SNE cost function, with simple gradients. Also, tSNE employs a heavytailed distribution in the lowdimensional space to alleviate both the crowding problem (the area of the twodimensional map that is available to accommodate moderately distant data points will not be nearly large enough compared with the area available to accommodate nearby data points) and the optimization problems of SNE.
Step 4
If we see the equation to calculate the conditional probability, we have left out the variance from the discussion as of now. The remaining parameter to be selected is the variance of the student’s tdistribution that is centered over each highdimensional datapoint . It is not likely that there is a single value of that is optimal for all data points in the data set because the density of the data is likely to vary. In dense regions, a smaller value of is usually more appropriate than in sparser regions. Any particular value of induces a probability distribution, , over all of the other data points. This distribution has an
This distribution has an entropy which increases as increases. tSNE performs a binary search for the value of that produces a with a fixed perplexity that is specified by the user. The perplexity is defined as
where H() is the Shannon entropy of measured in bits
The perplexity can be interpreted as a smooth measure of the effective number of neighbors. The performance of SNE is fairly robust to changes in the perplexity, and typical values are between 5 and 50.
The minimization of the cost function is performed using gradient decent. And physically, the gradient may be interpreted as the resultant force created by a set of springs between the map point and all other map points . All springs exert a force along the direction ( – ). The spring between and repels or attracts the map points depending on whether the distance between the two in the map is too small or too large to represent the similarities between the two highdimensional datapoints. The force exerted by the spring between and is proportional to its length, and also proportional to its stiffness, which is the mismatch (pji – qji + p i j − q i j ) between the pairwise similarities of the data points and the map points[1].
4.2 Time and Space Complexity
Now that we have understood the algorithm, it is time to analyze its performance. As you might have observed, that the algorithm computes pairwise conditional probabilities and tries to minimize the sum of the difference of the probabilities in higher and lower dimensions. This involves a lot of calculations and computations. So the algorithm is quite heavy on the system resources.
tSNE has a quadratic time and space complexity in the number of data points. This makes it particularly slow and resource draining while applying it to data sets comprising of more than 10,000 observations.
5. What does tSNE actually do?
After we have looked into the mathematical description of how does the algorithms works, to sum up, what we have learned above. Here is a brief explanation of how tSNE works.
It’s quite simple actually, tSNE a nonlinear dimensionality reduction algorithm finds patterns in the data by identifying observed clusters based on similarity of data points with multiple features. But it is not a clustering algorithm it is a dimensionality reduction algorithm. This is because it maps the multidimensional data to a lower dimensional space, the input features are no longer identifiable. Thus you cannot make any inference based only on the output of tSNE. So essentially it is mainly a data exploration and visualization technique.
But tSNE can be used in the process of classification and clustering by using its output as the input feature for other classification algorithms.
6. Use cases
You may ask, what are the use cases of such an algorithm. tSNE can be used on almost all high dimensional data sets. But it is extensively applied in Image processing, NLP, genomic data and speech processing. It has been utilized for improving the analysis of brain and heart scans. Below are a few examples:
6.1 Facial Expression Recognition
A lot of progress has been made on FER and many algorithms like PCA have been studied for FER. But, FER still remains a challenge due to the difficulties of dimension reduction and classification. tStochastic Neighbor Embedding (tSNE) is used for reducing the highdimensional data into a relatively lowdimensional subspace and then using other algorithms like AdaBoostM2, Random Forests, Logistic Regression, NNs and others as multiclassifier for the expression classification.
In one such attempt for facial recognition based on the Japanese Female Facial Expression (JAFFE) database with tSNE and AdaBoostM2. Experimental results showed that the proposed new algorithm applied to FER gained the better performance compared with those traditional algorithms, such as PCA, LDA, LLE and SNE.[2]
The flowchart for implementing such a combination on the data could be as follows:
Preprocessing → normalization → tSNE→ classification algorithm
PCA LDA LLE SNE tSNE
SVM 73.5% 74.3% 84.7% 89.6% 90.3%
AdaboostM2 75.4% 75.9% 87.7% 90.6% 94.5%
6.2 Identifying Tumor subpopulations (Medical Imaging)
Mass spectrometry imaging (MSI) is a technology that simultaneously provides the spatial distribution for hundreds of biomolecules directly from tissue. Spatially mapped tdistributed stochastic neighbor embedding (tSNE), a nonlinear visualization of the data that is able to better resolve the biomolecular intratumor heterogeneity.
In an unbiased manner, tSNE can uncover tumor subpopulations that are statistically linked to patient survival in gastric cancer and metastasis status in primary tumors of breast cancer. Survival analysis performed on each tSNE clusters will provide significantly useful results.[3]
6.3 Text comparison using wordvec
Word vector representations capture many linguistic properties such as gender, tense, plurality and even semantic concepts like “capital city of”. Using dimensionality reduction, a 2D map can be computed where semantically similar words are close to each other. This combination of techniques can be used to provide a bird’seye view of different text sources, including text summaries and their source material. This enables users to explore a text source like a geographical map.[4]
7. tSNE compared to other dimensionality reduction algorithms
While comparing the performance of tSNE with other algorithms, we will compare tSNE with other algorithms based on the achieved accuracy rather than the time and resource requirements with relation to accuracy.
tSNE outputs provide better results than PCA and other linear dimensionality reduction models. This is because a linear method such as classical scaling is not good at modeling curved manifolds. It focuses on preserving the distances between widely separated data points rather than on preserving the distances between nearby data points.
The Gaussian kernel employed in the highdimensional space by tSNE defines a soft border between the local and global structure of the data. And for pairs of data points that are close together relative to the standard deviation of the Gaussian, the importance of modeling their separations is almost independent of the magnitudes of those separations. Moreover, tSNE determines the local neighborhood size for each datapoint separately based on the local density of the data (by forcing each conditional probability distribution to have the same perplexity)[1]. This is because the algorithm defines a soft border between the local and global structure of the data. And unlike other nonlinear dimensionality reduction algorithms, it performs better than any of them.
8. Example Implementations
Let’s implement the tSNE algorithm on MNIST handwritten digit database. This is one of the most explored dataset for image processing.
1. In R
The “Rtsne” package has an implementation of tSNE in R. The “Rtsne” package can be installed in R using the following command typed in the R console:
install.packages(“Rtsne”)

Hyper parameter tuning

Code
MNIST data can be downloaded from the MNIST website and can be converted into a csv file with small amount of code.For this example, please download the following preprocessed MNIST data. link
## calling the installed package train< read.csv(file.choose()) ## Choose the train.csv file downloaded from the link above library(Rtsne) ## Curating the database for analysis with both tSNE and PCA Labels<train$label train$label<as.factor(train$label) ## for plotting colors = rainbow(length(unique(train$label))) names(colors) = unique(train$label) ## Executing the algorithm on curated data tsne < Rtsne(train[,1], dims = 2, perplexity=30, verbose=TRUE, max_iter = 500) exeTimeTsne< system.time(Rtsne(train[,1], dims = 2, perplexity=30, verbose=TRUE, max_iter = 500)) ## Plotting plot(tsne$Y, t='n', main="tsne") text(tsne$Y, labels=train$label, col=colors[train$label])

Implementation Time
exeTimeTsne user system elapsed 118.037 0.000 118.006 exectutiontimePCA user system elapsed 11.259 0.012 11.360
As can be seen tSNE takes considerably longer time to execute on the same sample size of data than PCA.

Interpreting Results
The plots can be used for exploratory analysis. The output x & y coordinates and as well as cost can be used as features in classification algorithms.
2. In Python
An important thing to note is that the “pip install tsne” produces an error. Installing “tsne” package is not recommended. tSNE algorithm can be accessed from sklearn package.

Hyper parameter tuning

Code
The following code is taken from the sklearn examples on the sklearn website.
Python Code:

Implementation Time
Tsne: 13.40 s PCA: 0.01 s
9. Where and When to use tSNE?
9.1 Data Scientist
Well for the data scientist the main problem while using tSNE is the black box type nature of the algorithm. This impedes the process of providing inferences and insights based on the results. Also, another problem with the algorithm is that it doesn’t always provide a similar output on successive runs.
So then how could you use the algorithm? The best way to used the algorithm is to use it for exploratory data analysis. It will give you a very good sense of patterns hidden inside the data. It can also be used as an input parameter for other classification & clustering algorithms.
9.2 Machine Learning Hacker
Reduce the dataset to 2 or 3 dimensions and stack this with a nonlinear stacker. Using a holdout set for stacking / blending. Then you can boost the tSNE vectors using XGboost to get better results.
9.3 Data Science Enthusiasts
For data science enthusiasts who are beginning to work with data science, this algorithm presents the best opportunities in terms of research and performance enhancements. There have been a few research papers attempting to improve the time complexity of the algorithm by utilizing linear functions. But an optimal solution is still required. Research papers on implementing tSNE for a variety of NLP problems and image processing applications is an unexplored territory and has enough scope.
10. Common Fallacies
Following are a few common fallacies to avoid while interpreting the results of tSNE:
 For the algorithm to execute properly, the perplexity should be smaller than the number of points. Also, the suggested perplexity is in the range of (5 to 50)
 Sometimes, different runs with same hyper parameters may produce different results.
 Cluster sizes in any tSNE plot must not be evaluated for standard deviation, dispersion or any other similar measures. This is because tSNE expands denser clusters and contracts sparser clusters to even out cluster sizes. This is one of the reasons for the crisp and clear plots it produces.
 Distances between clusters may change because global geometry is closely related to optimal perplexity. And in a dataset with many clusters with different number of elements one perplexity cannot optimize distances for all clusters.
 Patterns may be found in random noise as well, so multiple runs of the algorithm with different sets of hyperparameter must be checked before deciding if a pattern exists in the data.
 Different cluster shapes may be observed at different perplexity levels.
 Topology cannot be analyzed based on a single tSNE plot, multiple plots must be observed before making any assessment.
Reference
[1] L.J.P. van der Maaten and G.E. Hinton. Visualizing HighDimensional Data Using tSNE. Journal of Machine Learning Research 9(Nov):25792605, 2008
[2] Jizheng Yi et.al. Facial expression recognition Based on tSNE and AdaBoostM2.
IEEE International Conference on Green Computing and Communications and IEEE Internet of Things and IEEE Cyber,Physical and Social Computing (2013)
[3] Walid M. Abdelmoulaa et.al. Datadriven identification of prognostic tumor subpopulations using spatially mapped tSNE of mass spectrometry imaging data.
12244–12249  PNAS  October 25, 2016  vol. 113  no. 43
[4] Hendrik Heuer. Text comparison using word vector representations and dimensionality reduction. 8th EUR. CONF. ON PYTHON IN SCIENCE (EUROSCIPY 2015)
End Notes
I hope you enjoyed reading this article. In this article, I have tried to explore all the aspects to help you get started with tSNE. I’m sure you must be excited to explore more on tSNE algorithm and use it at your end.
Share your experience of working with tSNE algorithm and if you think its better than PCA. If you have any doubts or questions, feel free to post it in the comments section.
16 thoughts on "Comprehensive Guide on tSNE algorithm with implementation in R & Python"
Dr.D.K.Samuel says: January 23, 2017 at 5:28 am
Nice keep them coming but it says Error: object 'train' not found > Labels train$label<as.factor(train$label) Error in is.factor(x) : object 'train' not founddataslee says: January 23, 2017 at 6:30 am
the train data you must have yourselfSaurabh jugalkishor Jaju says: January 23, 2017 at 7:32 am
Dear Dr Samuel, The data to execute the R code must be loaded in the R environment. I will provide the link to the dataset. Please download the data, read it in the R environment and then run the code. Please download the data curated for the R code from this link: https://drive.google.com/file/d/0B6E7D59TV2zWYlJLZHdGeUYydlk/view?usp=sharing Then load the data in R using : read.csv(file.choose()) command in R. Thankyou for reading the article and please feel free to contact me with anything else relating to the article. Regards, SaurabhPete says: January 23, 2017 at 4:33 pm
Hi, This is a great article covering the topic comprehensively. Would appreciate if you can you share the complete R code. Looking forward to more articles from you on Advanced topics. Thanks PeteMantej Singh Dhanjal says: January 24, 2017 at 3:14 pm
Nicely explained. Another great article from Analytics Vidhya. Thank you very much for such a useful information! I’ll look into that example.padhma says: January 31, 2017 at 1:21 pm
I simply want to tell you that I’m all new to blogs and truly liked you’re blog site. Very likely I’m likely to bookmark your site .You surely come with remarkable articles. Cheers for sharing your website page.Kern Paillard says: February 02, 2017 at 12:15 pm
Great article! I'm curious to know of your thoughts on Kernel PCA...compated to tSNE. Essentially, kernel PCA also maps the high dimensions using nonlinear methods... There is a scikit implementation of it here, http://scikitlearn.org/stable/auto_examples/decomposition/plot_kernel_pca.html I've found performance issues when using Kernel PCA on even relatively medium sized data sets for e.g. ~= 100k rows and had to resort to carrying out kernel pca on chunks of data..Donald E. Foss says: February 10, 2017 at 10:30 pm
Can you explain the large time delta in the execution in R versus Python? I assume the data set was the same. PCA R: 11.360 seconds Python: 0.01 seconds tSNE R: 118.006 seconds Python: 13.40 seconds The delta with tSNE is nearly a magnitude, and the delta with PCA is incredible.saurabh.jaju2 says: February 11, 2017 at 3:56 am
Actually the datasets are not the same.The point of the code was to show the implementations of tSNE and PCA and compare them in each language. Comparison of performance of python code to R code was not intended .The dataset for R is provided as a link in the article and the dataset for python is loaded sklearn package.考察数据科学家数据降维知识的40道题，快来测测吧(附答案)  36大数据 says: April 27, 2017 at 1:00 am
[…] RPython实现的tSNE算法综合指南 […]samira mzn says: April 27, 2017 at 2:29 pm
Hello, I tested the R code for the tSNE method and it worked very well, I would also like to know if you have informations on the two dimensionality reduction methods : NeRV and JSE, with the codes R ? Thanks,考察数据科学家数据降维知识的40道题，快来测测吧(附答案)  大数据多客 says: June 07, 2017 at 9:28 pm
[…] RPython实现的tSNE算法综合指南 […]Cynthia says: October 12, 2017 at 11:22 am
Great guide  thanks for this! If you want to check out an interesting use of tSNE, Displayr recently used it to analyze Middle Eastern politics. Fascinating read: https://www.displayr.com/usingmachinelearningtsnetounderstandmiddleeasternpolitics/ Thanks, CynthiaShane says: December 01, 2017 at 8:49 pm
in order to use this technique for machine learning, the tSNE model would need to convert future observations (e.g. from a test set), based on the results from the training set so is it possible for example, to do something like test_set_transformed < predict(tsne, newdata = test_set) where tsne is the model/output from Rtsne() and the training set in your codeQueen Ohandjo says: December 20, 2017 at 1:24 pm
Excellent post. Code worked well Now i have to prepare my dataset in this format for a successful run. Thanks alot. *crossing fingers* code works on my dataQueen Ohandjo says: January 10, 2018 at 1:02 am
Hi, I was able to successfully run the train.csv file. But when i run my dataset i get the error below Any help will be much appreciated > ## calling the installed package > prostate library(Rtsne) > > ## Curating the database for analysis with both tSNE and PCA > Labels prostate$label<as.factor(prostate$label) Error in `$ > ## for plotting > colors = rainbow(length(unique(prostate$label))) > names(colors) = unique(prostate$label) > > ## Executing the algorithm on curated data > tsne exeTimeTsne > ## Plotting > plot(tsne$Y, t='n', main="tsne") > text(tsne$Y, labels=prostate$label, col=colors[prostate$label])