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Questions tagged [multidimensional-scaling]

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

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1answer
433 views

Scaling unknown time series for prediction with RNN

I'm trying to build a RNN model to predict arterial blood pressure (ABP) time series based on two other time series, namely, ECG and PPG. It is available to me a set of multivariate time series of ...
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1answer
299 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 it ...
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1answer
135 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 ...
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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^...
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265 views

NMDS anomaly - data does not support point placement

My data: Tracking forest communities (via species abundances) in various forest plots across time. My approach: Non-metric Multidimensional Scaling ordination I performed NMDS (using ...
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0answers
209 views

Temporal Multi Dimensional Scaling

Let's say I apply a multidimensional scaling(MDS) to a dynamic dataset of $n$ points (eg, time series). At each step I will obtain a projection (in 2/3D) of the $n$ points. If nothing meaningful ...
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1answer
138 views

Are NMDS Axis the same calculated for one or more dimensions?

I used NMDS axes of an ecological community as proxys for the community similarity in the different samples. I would like to "quantify" the importance of the different NMDS axis according to the ...
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1answer
38 views

Quantifying relationship between items, given many groups of items

I'm having trouble researching this, or even writing this question, because I'm not sure what this is called and I'm not familiar with a lot of the terminology. The best I can do is an example. Let's ...
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1answer
155 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 ...
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23 views

Explaining MDS space

I have a set of dummy variables (~300) indicating a particular feature, and rows which represent an individual. I plot this data after using nMDS to visualize which individuals are more similar to ...
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0answers
30 views

Is multidimensional scaling (PCoA) a linear dimensionality reduction technique?

Classic MDS (cMDS or PCoA) preserves global distances, characteristic of linear techniques. However, metric MDS seeks to minimize a cost function (stress), while non-metric MDS (nMDS) preserves only ...
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1answer
8k 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 ...
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2answers
1k 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 ...
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1answer
96 views

One-hot encoding for SOM

I have a question regarding how I should convert categorical data to numerical data. I'm using this kdd99cup intrusion detection dataset, which has a 41 attributes and class label is the type of ...
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27 views

Detrended Correspondence Analysis or Non-metric multidimensional scaling

For an ecology project I am analysing how and if the species composition of a habitat type (heathland for example) changes through time. This was done by measuring fixed plots within a habitat type ...
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23 views

Multidimensional scaling with censored and missing distances

I would like to apply MDS to a high-dimensional distance matrix but the difficulty is than the distance matrix contains many missing and censored values (i.e. distances like >8). Does anyone know of ...
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1answer
304 views

randomForest MDSplot help R [closed]

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 ...
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0answers
52 views

Non-metric multidimensional scaling, no convergence

I'm using MetaMDS from the VEGAN package to run a non-metric multidimensional scaling analysis. My stress level for 3 dimensions is in the excellent range (i.e., stress<.05), however, the model ...
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14 views

Parallel analysis for principle components analysis and Multi-dimensional scaling

Does the same method for conducting a parallel analysis for principal component analyses apply to find the cut-off point for multidimensional scaling? Under the pretense that PCA and linear MDS are ...
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26 views

Hierarchical clustering on principle components for multidimensional scaling

Essentially I have a data set of distant objects in which I've loaded onto factors using a multidimensional scaling technique. From my understanding, the factor loadings only differ between MDS and ...
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8 views

Setting the number of dimensions in an MDS

I have two distance matrixes. The distance matrixes are two topics of a Latent Dirichlet Allocation. The distance is computed based on the probability distribution of the 6 words with the highest ...
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1answer
35 views

k-means/k-nearest neighbours on multi-dimensional scaled data

I used the Python manifold library for multi-dimensional scaling on my distance matrix. Can I use k-means or k-nearest neighbours on ...
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1answer
90 views

Book about ordination in ecology

I am looking for a book that would cover a lot of different ordinations techniques (indirect gradient analysis e.g. PCA, CA, DCA, MDS, nMDS but also direct gradient analysis e.g. CCA, CCorA, RDA) with ...
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1answer
152 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 ...
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0answers
49 views

Does a PCoA (or MDS) assume normality of the variables behind distances?

More precisely, if I conduct a cmdscale (classical multidimensional scaling) on an Euclidean distance matrix by considering $n$ observations of $p$ variables i.e. $D_{ij}=\sqrt{ \sum_p (x_{ip} - x_{...
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55 views

Visualizing a Latent Dirichlet Allocation (LDA) by Multidimensional Scaling (MDS)

I did an LDA with four topics for four different Smartphones. This was done using customer Reviews of Amazon. ...
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27 views

Procrustes Analysis: Interpreting an Impulse Diagram of Residuals

I have applied 3 MDS techniques to a data set. They are; classical metric scaling, Kruskal's non-metric scaling and Sammon's metric least squares scaling. In order to compare the 3 configurations I am ...
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1answer
281 views

Is first dimension more informative in multidimensional scaling?

A property of Principal Components Analysis (PCA) is that the first dimension is the most informative, next the second and so on. Is this property true also for multidimensional scaling (MDS)?
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1answer
216 views

K means clustering of MDS data

I've recently run a very large data set through a multidimensional scaling analysis and am attempting to cluster the results into groups. I've read a few papers that utilize hierarchical clustering to ...
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0answers
24 views

Principle coordinates analysis - visualization and assigning text to graph in r [closed]

I've recently run a principle coordinates analysis in r with ~ 200 subjects and 17 binary variables. I've plotted my points successfully, the challenge I'm facing is that when I plot the text with the ...
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1answer
120 views

Confusion about multidimensional scaling

I was given just a distance matrix (I'm talking about distance between cities), and I have to perform a classical multidimensional scaling. But mapping my results, I've noticed that my map is upside ...
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1answer
24 views

When is the result of multidimensional-scaling unique up to isometry?

What conditions on the ambient space and/or the given matrix of dissimilarities guarantee that all point configurations that minimise the error function of multidimensional scaling (MDS) are congruent,...
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1answer
728 views

Feature scaling/normalization and prediction

I have a dataset which I have split into a training and a test set. I have thereafter applied normalization on the training set and saved the mean (U) and standard deviation (SD) estimated based on ...
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2answers
1k views

R - Multidimensional Scaling and Missing Values

I include MDS analysis in a customer survey and have about 10 brands I want to include in the perceptual map at the end. Meaning the customers would have to rate 45 comparisons and give a similarity ...
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0answers
885 views

Statistically correct to apply Multi-dimensional scaling or PCA to cosine similarity matrix?

Supposing I have a document-term matrix as scripted below: ...
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0answers
101 views

How to localize points from an incomplete distance matrix in R?

Suppose you have 3 shops and 2 supply units, and you only know the 6 pairwise (Euclidean, assuming 2D) distances between each shop and each supply unit, but not the pairwise distances between the ...
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0answers
42 views

Interpretation of a Multidimensional Scaling graph

I used the variables "number of children in the family", "Wife's age", "Religious wife", and "Midia exposure". The "number of children" and "Wife' age" are both numerical variables. "Religious wife" ...
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4answers
12k views

Performing PCA with only a distance matrix

I want to cluster a massive dataset for which I have only the pairwise distances. I implemented a k-medoids algorithm, but it's taking too long to run so I would like to start by reducing the ...
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0answers
56 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 ...
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2answers
112 views

Can the distances of two MDS plots be quantitatively compared?

Let's say that I have one population that can be divided by a 2-level factor. I run MDS twice (using prcomp() {stats} in R), using the 2-level factor to separate my subjects. If I reduce to two ...
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1answer
287 views

Project new point into MDS space

I am trying to project a new point A(x, y, z) into a predefined MDS space in R. This is what I have so far: ...
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1answer
272 views

Is it necessary to deal with the outliers if we perform Normalisation on the data?

I am wondering, if it is necessary to remove outliers from the dataset if we perform Normalisation on the data as after Normalisation, all the values will shrink to value between 0 and 1. So, is it ...
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0answers
2k views

Gower distance and MDS: How to determine which variables count?

I have morphological data from two different determined groups (It and Nd), where the variables are heterogeneous (continuous, ...
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1answer
2k views

Multidimensional scaling in R with Spearman's rank correlation

I'm new to MDS, but I found some good starter code here (http://mhermans.net/static/postdata/r-examples/neighbours-mds/neighbours-mds-example.html) and which I borrowed for below. The code works fine, ...
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1answer
328 views

Negative eigenvalues when computing MultiDimensional Scaling given nonnegative distance matrix

I am using the Smile MDS https://github.com/haifengl/smile/blob/master/core/src/main/java/smile/mds/MDS.java and occasionally running into: ...
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0answers
302 views

Non-metric multidimensional scaling with dichotomous independent variables?

I have a set of t-rflp fragment-length profiles from an investigation into microbial degradation of hydrocarbons as part of my undergrad dissertation. I want to study the effect of various variables ...
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2answers
501 views

How to embed in Euclidean space

I have what I think might be a standard machine learning problem but I can't find a clear solution. I have lots vectors of different dimensions. For each pair of vectors I can compute their ...
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1answer
2k views

Multidimensional scaling on distance or similarity matrix

Why doesn't the scatter plot change when I perform multidimensional scaling on distance or similarity matrix? This figure uses similarity matrix And this figure use distance matrix (sqrt(1-...
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0answers
632 views

Convert distance matrix to coordinate(s)

I have a (SNP) distance matrix that I would like to convert to coordinates (ideally just one linear scale) in R. I am planning to use the transformed coordinates in principle component analysis along ...
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1answer
626 views

Detect outliers in multi dimensions [duplicate]

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 ...