# Questions tagged [tsne]

T-distributed stochastic neighbor embedding (t-SNE) is a nonlinear dimensionality reduction algorithm introduced by van der Maaten and Hinton in 2008.

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### How to evaluate performance and optimize hyperparameters for clustering algorithms on a dataset with continuous labels?

I'm working on a clustering problem where my dataset's labels are continuous numerical values, not discrete categories. I'm using t-SNE and UMAP to reduce the dimensionality of my dataset's features ...
1 vote
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### Dimensionality reduction and precomputed distance matrix

I have a question about dimensionality reduction. I want to understand how methods like MDS and t-SNE work. In particular, I'd like to understand the difference when I precompute the distance matrix ...
43 views

### Applying clustering algorithms after t-SNE in R

So I'm doing my bachelor`s work and I'm applying different clustering algorithms on certain data. Before all the clustering of course I'm using a dimensionality reduction algorithm such as t-SNE for ...
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### Finding parameters which reveal clustering in t-SNE

These data are from SAMHSA, Mental Health Client-Level Data. I am trying to find the right parameters to obtain clustering as in this paper. Code here. For now, I'm dropping columns which aren't ...
1 vote
54 views

### Examples of UMAP performing poorly

Can anyone suggest some datasets or examples that would be useful for showing situations where UMAP performs poorly, say in the sense of producing spurious clusters, or missing clusters? For t-SNE, ...
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### Why does the t-SNE paper claim that "large clusters of points that are far apart interact in just the same way as individual points"?

In the original t-SNE paper, the authors explain the use of the t-distribution with one degree of freedom (i.e. Cauchy distribution) for the map points, $(1 + |y_i - y_j|^2)^{-1}$, as follows: ...[it]...
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### interpreting t-sne scatter plot

I attempted to perform t-sne on some variables: Probability (%) of dying between age 30 and exact age 70 from illness (all)', 'Suicides per 100000 (all)', 'social_support', 'birth_health', 'freedom', '...
1 vote
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### When is it appropriate to use t-SNE and how can I trust its output to faithfully represent higher dimensional separation?

Given the discussion on this answer what appropriate assumptions and contingencies would allow tSNE to have an informative interpretation? It's hard to come away from that answer feeling like I can ...
126 views

### Normalization/standardization impact on T-SNE and K-means

I have a dataset of 20K samples on 27 features that I am trying to cluster with k-means. The dataset is in its majority rather sparse, i.e. 98% of samples have a single nonzero value in one of its ...
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### Should I separate my data into different batches and then perform tsne on each batch?

I have a very huge dataset and required to reduce the embedding of 768 dimension to 128dimension with TSNE. Since I have more than 1million rows, it takes more than weeks to complete dimension ...
1 vote
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### tSNE visualize 2D CNN output features

I want to visualize the 2D CNN output features with tSNE, but most methods use FCN output, this is 1-D feature, for exmaple in https://cs.stanford.edu/people/karpathy/cnnembed/, but my problem is that ...
36 views

### Alternative to PCA that maintains densities/distances

The question is the same as posed in the title; is there an alternative to PCA that doesn't rely on the linear assumption but maintains distances (i.e. the main issue with UMAP/tSNE)? Thanks!
1 vote
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### Which tool is more suitable for visualizing the distribution of multiple real and synthetic image datasets, t-SNE or PCA?

I am doing a thesis on the generation of synthetic data for training a deep learning model and evaluating it on real data. I have a few different real datasets, and I generated multiple synthetic ...
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### t-SNE of a 99% sparse data set

I have a sparse matrix of representing 12 cancer types. It's a very sparse with about 99% of elements are zeros. I have a t-SNE looks like: What can I interpret from this t-SNE?
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1 vote
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### Any reason for choosing t-SNE over UMAP when visualizing?

According to the UMAP paper: Our algorithm is competitive with t-SNE for visualization quality and arguably preserves more of the global structure with superior run time performance. paper It seems ...
68 views

### tSNE on OCTMNIST dataset (part of MedMNIST) not working

I have been trying to generate the tSNE plot for the OCTMNIST dataset which is a part of MedMNIST v2(https://medmnist.com/). The code that I have been using is- ...
965 views

### What is wrong with using t-SNE for predictions?

If I have a dataset with hundreds of samples and thousands of features, and t-SNE does a good job of separating classes compared to others classifiers, I don't understand why I can't rerun the ...
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1 vote
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### sklearn vs RtSNE : Number of PCA components to retain in tSNE [closed]

In the R implementation you can pass the number of components to keep in PCA step. I cannot figure out if this is possible in sklearn implementation. Is it possible or I am missing it? Thank you! R: ...
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### How do interpret this result for t-SNE plot results?

I am trying to interpret this plot I created for a malware dataset. The dataset contains Benign and Malware data. I am having a hard time understanding what it means. Any advice or help would be ...
1 vote
790 views

### Variance used in t-SNE

While the original paper of t-SNE is based on the SNE and SNE uses $\sigma_i^2$ (note the subscript $i$) while calculating the similarity of point $x_i$ WRT other points $j$. i.e., for each data point ...
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### How to reveal specific relationship using tSNE?

I’ve been using tSNE in attempts of finding and visualising some relationships in my data. I came to a following problem. If my data is say 1000 points, and I want to know about some relations between ...
1 vote
2k views

### t-SNE number of output components

Why do most tSNE implementations suggest using 2 or 3 output dimensions? For PCA, the number of output components is typically choosen based on the number of components needed to explain 80% of ...
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### Are t-SNE and UMAP for dimensionality reduction compatible with cross-validation in machine learning applications?

t-SNE: Based on how I understand the original t-SNE algorithm, it requires a whole dataset for doing the transformation. That is, there are no distinct "fitting" and "transformation&...
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### How to interpret axis of UMAP?

Hi in PCA one can interpret the level of variance with x vs y, with x often times explaining much of the variance. As one plot higher dimensions the variance percent would go down. My question is, ...
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1 vote
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### How does t-SNE preserves embedding orders?

According to the triplet loss Wikipedia page: t-SNE (t-distributed Stochastic Neighbor Embedding) preserves embedding orders via probability distributions, whereas triplet loss works directly on ...
243 views

### t-SNE perplexity for groups of different sizes

I have a data set of about 1200 samples that I expect to be divided in to about 40 groups but the group sizes vary from about 5 to 150 samples. About half of the groups have 10-40 samples, 10 have ...
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### What happens if I increased the number of principal components used in t-SNE?

I see that most of the tutorials in t-SNE use mostly the top 10 PCs to run t-SNE, I tried to run top 100 PCs and top 500 PCs, the results are different but I don't really get the changes Thank you
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### Can I use t-SNE for checking the goodness of a clustering based on Gower distance matrix?

I am currently working in Python with a dataset with both categorical and continuous variables. The main objective is to do clustering and find how different features help to create the clusters. This ...
316 views

### What dimensionality reduction methods allow a lower dimensional reconstruction of the original data besides PCA via invertible transformations?

In eigenfaces, one used the inverse transformation PCA is capable of doing to reconstruct the low dimensional face image. In tsne one may not reconstruct the original dataset to produce something akin ...
957 views

### Data nicely separated by UMAP but less by T-SNE

If some data are nicely separated into clusters using UMAP but not as nicely using T-SNE, what could be the interpretation ?
1 vote
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### How to interpret data not separated by PCA but by T-sne/UMAP

I have a classification problem, to have a first look at my data I do a PCA followed by TSNE and UMAP. My clusters are nicely separated by TSNE and UMAP but not by PCA. Does it have implication for ...
1 vote
171 views

### Interpret t-SNE plot groups

I am trying to interpret some t-SNE results (using the Rtsne package in R). I used t-SNE on class probabilities from a multiclass model with 6 levels to try and visualize the relationships between the ...
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1 vote
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### t-SNE and normalization / standardization

I have 7 parameters with different scales. If I understand correctly, before applying t-SNE or other dimension reduction methods I should apply a standardization or normalization method on my ...
427 views

### Randomness of t-SNE

The stochastic part of t-SNE is presumably from the randomness of the initial placement of the points in the low-dimensional space. Does this mean that t-SNE should be re-run on re-seeded randomness ...
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### Circles in tSNE output

Does anybody know when tSNE produces circles as embeddings (as a property of the input features)? I've ran tSNE with the default params in R Rtsne function.
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### Linear and nonlinear feature extraction methods

I far what i understand, the assumptions for PCA is that data should be linear. What does that imply? let say if i have a data of 1000*100. So all independent variables should be linearly separable ...
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### Multivariate Jensen-Shannon divergence

This paper says multivariate Jensen-Shannon divergence is $$JS(\mathbf{p}_1,\dots,\mathbf{p}_K) = \frac{1}{m} \sum KL(\mathbf{p}_i || \bar{\mathbf{p}})$$ with $KL$ being the KL-divergence of the ...
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### Why doesn't t-SNE need the labels before visualization?

In the original Maaten and Hinton paper, they explicitly say that the class membership is not used by the t-SNE calculations, only for picking colors in the plot. For all of the data sets, there is ...
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1 vote
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### multiple tsne (and pca) transforms on one plot

I'm reviewing a paper, in which the researcher fitted different t-sne transforms and plotted them on one plot, showing clusters in 2-d after dimensionality reduction (t-sne). Each cluster was fitted ...
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### Can t-SNE be directly used as a clustering algorithm?

I've been working on a dataset about a few millions commuters and their travel patterns with around 50 dimensions. And I'm applying t-SNE to the dataset. My initial goal of applying t-SNE was to ...
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### t-sne embedding to medium-dimensions (e.g. 100 dimensions)?

I am using t-sne on 252 dimensional data to embed to lower-dimensions. I am curious to know if it is academically justifiable to embed it into medium dimensions such as 100 dimensions, or 80 ...
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### Understand important features in UMAP

I am using a dimensionality reduction algorithm (UMAP) to cluster high-dimensional data. Particularly, I have ~50000 vectors of dimension ~20000 to visualise. These vectors are highly structured: ...
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### PCA provides principal directions, what does tSNE provide?

One of my main frustrations with the current state of single cell transcriptome analysis is representations of cells within $tSNE$ plots. These $tSNE$ plots provide amazing separation of the data and ...
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1 vote
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### What is the connection between fat tailedness of student t distribution and sparsity inducement in lower dimensions in context of t-sne

I have read that the t distribution is a heavy tailed distribution in comparison to Normal distribution. Also some say that heavy tailed distributions help in creating more sparsity. My question is ...
1 vote
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### Connection between Stochastic Neighbor Embedding and MDS

In the original SNE paper the authors mention a connection between the SNE objective function and an MDS-like stress function in the regime $\sigma_i \rightarrow \infty$, as follows. When \$\sigma_i^...
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### Can the sum of two conditional probability distributions give a joint probability distribution?

A paper describing symmetric SNE for the conditional probability distribution $$p_{j|i}=\frac{e^{-\left|x_i-x_j\right|^2/2\sigma_i}}{\displaystyle\sum_{k\neq i}e^{-\left|x_k-x_i\right|^2/2\sigma_i}}$$...
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### SVD -> PCA -> t-SNE; Does it make sense?

I have a data set of size (4600, 10000). I did L2 normalization at first, then I did the following two steps to visualize it in a lower dimension: ...
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### Perform normalization before using t-SNE components in any ML algorithms and while appending new features to these components?

I have a large data set (around 4600 rows and 10000 columns). First, I performed L2 normalization and did PCA to obtained 50 components. Then I performed t-SNE and obtained 2 components. I did the ...
1 vote
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### Interpreting snake-like structures in the UMAP visualization of a FASTA data set

I'm looking for some guidance to interpret a UMAP plot. I started with two FASTA files for two different genes. I concatenated everything into a single string of only ACGT. Then I split that ...
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