# Tagged Questions

Technique that renders observed or computed (dis)similarities among objects into distances in a low-dimensional space (usually Euclidean). It thus constructs dimensions for the data; the objects can be plotted and conceptualized in those dimensions

7 views

### How to perform multidimensional scaling where a subset of points are already fixed?

I have two sets of psychological variables. For simplicity, there is set A (10 variables) and Set B (10 variables). When you map Set A using two-dimensional multidimensional scaling (e.g., using <...
22 views

### Learning vector embeddings from distances

So... I have a set of entities $\mathcal{E} = \{e_i \mid i \in [1,n]\}$, and I have a proper distance metric defined over $\mathcal{E}\times\mathcal{E}$, call it $d$, so the distance between $e_i$ ...
24 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, ...
34 views

### Is it legit to run clustering on MDS result of a distance matrix?

I am new to the topic of clustering and face the following problem: I have multiple binary datasets with 10k to 40k entries and 135 features each:  \begin{matrix} \newcommand{\feat}{\text{feat}} \...
26 views

### Analyse the data of two responses while having two different scales

I am working on data analysis these days and stuck on analysis when I have to compare and analyse two kinds of responses. Responses are of similar nature. First, I have gathered the data on the self ...
48 views

### What is the most effective way to get a baseline rating prediction from netflix rating data?

I am doing an assignment where I am working with some of the Netflix Challenge data. I have a database that maps movie ids to customer ratings of that movie and a database of customers mapped to ...
33 views

### MDS: Are there measures of stress that are not affected by the number of objects?

This question flows naturally out of a previous question, in which it was explained that Stress-1 is somewhat impacted by the number of objects. You can assume that the number of objects in the ...
100 views

### MDS: Is Kruskal's Stress-1 affected by scale of the data, or the number of points?

In Multidimensional Scaling, Kruskal's Stress-1 is a commonly used measure of fit. It is defined as: $\sqrt{\frac{\sum (d_{ij}-\delta_{ij})^{2}}{\sum d_{ij}^{2}}}$ where $d_{ij}$ represents the ...
10 views

### Is normalization required in Sammon mapping

I have a data set of 480 samples with 7-dimensions and I want to implement a Sammon mapping into 3-dimensions. In Principal Component Analysis to my understanding we need to normalize the data in ...
70 views

### Using metric MDS with non-metric distances and assessing the fit quality

I'm going to perform MDS by means of cmdscale function of standard R library. I spent several hours googling it and finally have ...
68 views

### Do we have to scale new unseen feature data for prediction

In machine learning most algorithms require some kind of scaling to decrease error. This is my code: ...
62 views

### Finding optimal correspondences between objects given two square distance matrices

I would like to find the optimal correspondences between two systems of objects based on the distances between objects WITHIN the two systems. So, the input to the algorithm would be two square ...
23 views

### ordination of non gaussian data

I'm trying to ordinate a quite big dataset (44 variables with scaled values between 0 and 1, with 800 observations), with evident correlations between them (both spearman and pearson pairwise r ...
33 views

### Detect outliers in multi dimenstions

I tried to implement outlier detection for one dimension using inter quartile. for instance , a given variable cost or revenue or profit. but I'm missing outliers in other dimensions when running for ...
29 views

### How can I scale the $k$-th moment of a time series to a different time frequency?

I have a time series, let's say N daily log-returns. I want to study the moments (possibly the distribution) of the weekly returns. I have two ways: 1) Using the time-additivity property of ...
28 views

### Does it makes sense to perform MDS when $n<p$?

According to the reference quoted below, when performing a classical MDS on a dataset, I have to compute a centered matrix $B$ based on the dissimilarity matrix and then to compute the eigen-...
46 views

### randomForest MDSplot help R

I am new to R and randomForests so bear with me. I am trying to visualise my randomForest a little better using the MDSplot() function in Random Forest. There are two things i would like to do, and i ...
49 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 ...
428 views

### Input Normalisation for ReLU neurons

According to LeCun (1998) it is good practice to normalise all inputs so that they are centred around 0 and lie within the range of the maximum second derivative. So for example we would use [-0.5,0.5]...
36 views

### how to calculate the variance contribution of individual coordinates for multidimensional scaling analysis

I have searched the CrossValidated and stak Overflow and found the following related threads, Standard method for calculating contribution of individual variable to outcome Non-metric Stress in 3 ...
43 views

### How to recursively normalize my histogram count

I need to scale my histogram as I cannot store them with large numbers. Hence, I need to normalize it. I have taken normalization factor as sum of total population. But this need to happen recursively....
41 views

### Multidimensional Unfolding permutation test with smacof package - What does p.value mean here?

I have a dissimilarity data matrix with 7 rows and 7 columns (two ways). Having done unfolding on it, I wanted to evaluate the observed stress value. Using permutation test with 1000 replication, the ...
29 views

### How to determine the number of random initializations to use in non-metric multidimensional scaling?

I'm trying to determine how many random initializations (restarts) I should use when performing an nMDS ordination. I understand I want to choose the solution that minimizes the stress, but how many ...
130 views

### Does Dimensionality curse effect some models more than others?

The places I have been reading about dimensionality curse explain it in conjunction to kNN primarily, and linear models in general. I regularly see top rankers in Kaggle using thousands of features on ...
45 views

### scale and rescale the data predicted from neuralnetwork

i am trying to use neuralnet or mlp function on my data and then iuse to predict on my test data output [B], at the beginning i am using this code to rescale my data : maxs <- apply(data, 2, max) ...
371 views

### Multiple regression - how to calculate the predicted value after feature normalization?

I'm currently doing the Andrew Ng machine learning course on coursera, and in Week2 he discusses feature scaling. I have seen the lecture and read many posts; I understand the reasoning behind ...
69 views

### Proper way to do multivariate analysis of relative abundance data table

I have a data table, which is a result of running software MetaPhlAn. The values are relative abundances of each microbe taxon in samples. Samples are independent of each other. I want to know how ...
147 views

### In multidimensional scaling, how can one determine dimensionality of a solution given a stress value?

In multidimensional scaling, how can one determine dimensionality of a solution given a stress value? From what I understand, stress value is inversely related to the number of dimensions of a MDS ...
15 views

### Manual multidimensional scaling in R

Given a matrix A, I want to complete Multidimensional Scaling by hand, instead of using any given R functions. As such, I have calculated the centered matrix ...
49 views

### Support Vector Regression and Data Rescaling

I am currently working on Support Vector Regression and I've read that it is recommended to implement data rescaling, e.g. to interval $[-1;1]$, to obtain better results. My first question is: should ...
85 views

### Interpret multidimensional scaling plot

I have data with 4 observations and 24 variables. To understand the underlying relationship I performed Multi-Dimensional Scaling (MDS), and got a plot like this: Now the issue is with the correct ...
65 views

### Unsupervised Learning on Multilevel/Multidimensional Data

I am working on a case-control study, where I for each individual have high dimensional data (like illustrated in the image). I would like to do both PCA analysis and Clustering on this data, but ...
26 views

### NMDS on data with different measure units

Is it correct to apply non-metric multidimensional scaling(NMDS) on data with different measure units and so, different ranges? Is there the possibility that the variable with higher values (due to ...
30 views

### What's right/wrong with using multi-dimensional scaling to analyze voting patterns of for members of an 11-member city council?

I'm trying to analyze voting patterns of an 11-member city council over a period of five years. Description of data file: each row (vector) is labeled as a councilmember; each column records ...
261 views

### The Shepard function in R package MASS

The function Shepard is listed in the help file for MASS::isoMDS, but nothing is said about it. What does this function do?
292 views

### Using similarity measures as distances

I have a matrix where each row corresponds to an observation with binary attributes, and I am interested in performing multidimensional scaling using cmdscale on ...
182 views

### Representing experimental data by unconstrained ordination: PCA, PCoA, or NMDS?

I have a dataset composed by presence of different bacterial families in function at different pesticide treatment. I need to find a good representation of my data but I don't know which method (...
308 views

### Fitting various environmental variables to an NMDS

I have two sets of environmental variables (e.g. river flow and river temperature statistics). I would like to assess which of these explains the highest amount of variance of a community community (e....
90 views

### Using a distance matrix *with errors* to find the coordinates of points

(I asked this same question in stackoverflow, without getting any answer, but maybe this is a more appropriate forum.) I would like to find the coordinates of a set of points in 3D from a distance ...
37 views

### Clustering before or after ordination

Can someone explain the implications of performing clustering either before or after performing NMDS? I have some ecological data and I am performing a clustering analysis to identify communities of ...
70 views

### What does “ideal points” mean in multidimensional unfolding?

I am reading some materials about multidimensional unfolding and this concept "ideal points" are mentioned several times. I check these readings several times and could not find definition of this ...
195 views

### Similarities and dissimilarities in classical multidimensional scaling

I am having trouble reconciling between several terms in MDS. According to [1], Section 14.8, Classical MDS takes similarities as inputs. In [2], also cited in Wikipedia, Classical MDS takes ...
1k views

### interpreting NMDS ordinations that show both samples and species

I am using the vegan package in R to plot non-metric multidimensional scaling (NMDS) ordinations. I am using this package because of its compatibility with common ...
118 views

### Apply trained MDS model to new data

I have both a distance matrix and the original vectors, and am using MDS (Multidimensional Scaling) with R to generate vectors in more dimensions for the data. With dimensionality reduction (for ...
697 views

### non-metric multi-dimensional scaling in R: help with plotting and understanding Stress for isoMDS vs. metaMDS

I have a dataframe with 900 observations. There are 11 columns: 9 measured variables and 1 representing region. ...
186 views

### Using Non-Euclidean Distance Matrix in Multi-Dimensional Scaling

I'm trying to use a non-euclidean distance matrix in MDS. Specifically, I'm using cmdscale in R. The resulting eigen vector appears to have huge negative values. From what I've read it appears that ...
174 views

### Goodness of fit for multi dimensional scaling

What is considered to be an acceptable value for goodness-of-fit in multi-dimensional scaling (MDS). I tried to run an MDS analysis on my data with four dimensions in R. The goodness of fit comes ...
188 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 ...