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31 views

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^...
1
vote
1answer
169 views

How to visualize proximity score in Random Forests

For a Random Forest, we can construct a N x N (where N is the number of data points) proximity matrix ...
1
vote
0answers
37 views

Multidimensional scaling with periodic boundaries

For a specific application at hand, I need to visualise samples from a high dimensional space into 2D, while respecting their distances as much as possible. Normally, I would simply use ...
0
votes
1answer
463 views

Multidimensional graph representation

I would like to know how to plot the following 30 observations on a graph, with 1 color for each country, using Kmeans or other methods on R. Each of the 40 independent variables can take value from 0 ...
4
votes
1answer
438 views

Alternative to MDS plot for random forest visualisation

I'm using R and 'randomForest' package for binary classification. I can MDS plot (from the same package) the initial (more or less) class separation based on training set. However, this doesn't allow ...
0
votes
1answer
48 views

Drawing a graph and grouping based on characteristics

Let's say that I have a list of my friends and each of them are tagged with some of their characteristics. That is, ...
21
votes
1answer
7k views

t-SNE versus MDS

Been reading some questions about t-SNE (t-Distributed Stochastic Neighbor Embedding) lately, and also visited some questions about MDS (Multidimensional Scaling). They are often used analogously, ...
3
votes
0answers
1k views

How could a hyperparameter grid search be visualised?

Consider a hyperparameter grid search that looks at the training and testing scores of an estimator with respect to multiple parameters like training epochs, number of nodes in layer 1, number of ...
19
votes
5answers
6k views

Are there any versions of t-SNE for streaming data?

My understanding of t-SNE and the Barnes-Hut approximation is that all data points are required so that all force interactions can be calculated at the same time and each point can be adjusted in the ...
2
votes
0answers
4k views

Multidimensional scaling using Python

I have 6,000 points for which I have all pairwise distances in a distance matrix. I want to get an idea whether these data were generated by a mixture of Gaussian distributions so I'm trying to get a ...
11
votes
3answers
4k views

How to project high dimensional space into a two-dimensional plane?

I have a set of data points in a N-dimensional space. In addition, I also have a centroid in this same N-dimensional space. Are there any approaches that can allow me to project these data points into ...
4
votes
2answers
5k views

How to best display crosstab data?

I have a 10x10 matrix composed of two variables with 10 brands each. One variable is the brand purchased, the other is the brand considered. My matrix shows a crosstabulation between the two. I need ...
1
vote
1answer
123 views

Is a Biplot suitable ? Domestic Violence VS Non-Violence data

I have a small data set that consists solely of counts. I have several variables. For example State, for each state (Mexican States), for example, Tamauplipas I have the counts of domestic violence ...
11
votes
2answers
4k views

Visualizing multi-dimensional data (LSI) in 2D

I'm using latent semantic indexing to find similarities between documents (thanks, JMS!) After dimension reduction, I've tried k-means clustering to group the documents into clusters, which works ...