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19 views

How to compare the distances or divergence between two groups of datasets

If I have two groups of data sets. Each group has two arrays of empirical data. In the first group each array has, say, 50,000 data points, and in the second group each array has 3,000 data points. ...
0
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0answers
9 views

How to test differences in multiple pairwise distances? With mixed model?

I want to compare two set of variables: X1 = All the pairwise distances between individuals from group A and group ref R X2 = ALL the pairwise distances between individuals from group B and group ...
1
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0answers
23 views

Occupancy octree metrics (Kullback-Leibler)

As I'm currently working on scan matching for outdoor environments I was wondering about the best metric to compare two occupancy octrees (one resulted from the scan matching and one ground truth ...
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0answers
18 views

Clustering using different distance measures [duplicate]

I do unsupervised clustering for a dataset using k-means algorithm. I want to know what is the difference between different distance measures (Euclidean, cityblock, cosine and correlation,...etc). I ...
1
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0answers
11 views

Partial correlations among three distance matrices

I am trying to test the hypothesis that related species should deviate more in niche space the more they overlap in geographic space. In other words, related species either forage similarly and don't ...
1
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1answer
23 views

Metric to compute structural similarity between two directed graphs

I'm working on a small project in which I try to compare directed a-cyclic graphs. Say I have (directed) three graphs: 1) ...
1
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1answer
18 views

Distribution of distances to an observation from the normal and the median of these distances

Given $x\sim \mathcal{N}(\mu=0, \sigma^2=1)$, the squared distances of the $x$ values to $\mu$ are distributed $\chi^2_1$. I am interested in the distribution of the squared distances to an arbitrary ...
0
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1answer
42 views

Mahalanobis distance in a hierarchical cluster analysis in SPSS

I am conducting a hierarchical cluster analysis in SPSS on my database with several neuropsychological and psychiatric variables. In my database, some of my variables (that is: two pairs of variables) ...
0
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1answer
21 views

Order of Matrix Operations in Mahalanobis Calculations

I'm teaching myself to translate equations to code after many years of letting my math skills atrophy, and am trying to do it on my own as much as possible. I've run into a couple of difficult ...
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2answers
59 views

Dynamic Time Warping for irregular time series

I have been reading a lot about Dynamic Time Warping (DTW) lately. I am very surprised that there is no literature at all on the application of DTW to irregular time series, or at least I could not ...
0
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0answers
40 views

R. function hclust, euclidean distances and cosines

My data is a table of cosines and I want to analyze it with hclust, which works on squared Euclidean distances. shall I do: d <- dist(mydata, method = "euclidean") fit <- hclust(d, ...
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0answers
17 views

Weighing a variable based on distance to a known date

In a bankruptcy model, you want to assign a higher weight to a variable as a big event date approaches (such as a company's quarterly earnings announcement date) and you reverse this weighing as you ...
2
votes
2answers
117 views

How to visualize the comparison of 3 different types of distances among objects

I need to calculate the difference between six time series in three ways: Time Series are: Kamel, Dumper, Graben, Traktor, Generator Methods are: Euclidean distance, Manhattan distance and maximum ...
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0answers
26 views

Representing a distance matrix in the plane [duplicate]

I've worked with observations as vectors with both continuous and categorical variables. In both cases one can use dimensionality reduction techniques such as PCA (in the latter case through ...
1
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1answer
41 views

Extract (ultrametric) distances from hclust or dendrogram

How can the matrix of (ultrametric) distances be extracted from the result of hclust (or a dendrogram in general) in R? The ...
0
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0answers
73 views

Computing a distance matrix between multiple multivariate time series

This question has also been asked on stackoverflow.com. Yet my aim is to ask for efficiency gains on the aforementioned platform. My aim here is the correctness of my approach. I am trying to cluster ...
0
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0answers
34 views

Dissimilar to multiple points

I have a few points in multiple dimensions. I am able to compute similarity between those items (using, say Cosine distance). For example, ...
1
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1answer
26 views

calculate Levenshtein Distance for web click stream data

I want to calculate Levenshtein Distance between to web click paths. I have a web page list around 500. ...
0
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0answers
36 views

How to test the significance of clusters?

How can one test the significance of the clusters obtained after a clustering procedure? Are there separate tests for the distance/similarity/dissimilarity measure used to get the distance matrix and ...
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3answers
544 views

Calculate the Kullback-Leibler Divergence in practice?

I am using KL Divergence as a measure of dissimilarity between 2 $p.m.f.$ $P$ and $Q$. $$D_{KL}(P||Q) = \sum_{i=1}^N \ln \left( \frac{P_i}{Q_i} \right) P_i$$ $$=-\sum P(X_i)ln\left(Q(X_i)\right) + ...
3
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0answers
40 views

Using similarity matrix to measure diversity of a group

I wish to measure the "diversity" of a group of objects. Right now I'm using Euclidean distance to compute the similarity matrix between all the objects in the group. I'm searching for a measure of ...
1
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0answers
62 views

PDF for net displacement of bivariate normal X and Y

this is my first post on StackExchange so I hope I'm posting in the right place. I'm trying to derive the correct probability density function for the net displacement of random variables X and Y ...
2
votes
1answer
77 views

Distribution of distance from center of sample group

We have a bivariate normal process where $X, Y \sim N(0, \sigma)$, with no covariance. (For convenience we can assert that $\sigma = 1$, or that we have a good estimate for its value.) What is the ...
1
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1answer
72 views

Problem with estimating probability using the multivariate Gaussian

I'm working on a problem where I need to find the probability of a given data sample belonging to a give class using the Bayes Theorem for classification. From everything I've been able to find so ...
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1answer
63 views

Cluster with distance threshold in R

I'd like to get clusters with a maximum inner distance threshold. Now I use hc <- hclust(d) and cutree(hc, numofclasses). ...
1
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0answers
43 views

Average minimum distance between two random vectors

Let $\mathbf{y_1} =\begin{bmatrix}g_1x_1 & g_2x_1 & \dots & g_Nx_1 \end{bmatrix}$ and $\mathbf{y_2} = \begin{bmatrix} f_1x_2 & f_2x_2 & \dots & f_Nx_2\end{bmatrix}$. All the ...
2
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1answer
106 views

Multidimensional Scaling “eurodist”

I have a question regarding Multidimensional Scaling. I used the dataset eurodist from the package datasets to generate a 2 ...
0
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0answers
9 views

Too Large Values with Assembled Distance Transform

I am trying to apply ADT as a distance between two images or their DCT coefficents. The ADT is given as (image taken from "Bidirectional PCA with assembled matrix distance metric for image recognition ...
0
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0answers
44 views

How genetic beta-diversity reflects traditional beta-diversity?

Im trying to figure out how betadisper {vegan, R}, and more specifically how the 'average distance to median' relates to betadiversity in a more traditional sense. betadisper calculates the variance ...
1
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0answers
161 views

Normalized cross correlation vs Euclidean distance in template matching

What is the difference between normalized cross-correlation and Euclidean distance in pattern recognition? -- especially if we want to do recognition with template matching. I understand about ...
0
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1answer
26 views

Distance Transform In Image?

I understand how to compute Distance Transform for BW image In BW image we can calculate the distance of the pixel with non zero pixel value using Eucledian Distance. But I dont undertand how to ...
0
votes
1answer
35 views

string clustering: similarity criterion

I have a set of strings of dimension $10,000$. I want to group similar strings together in one group, perform clustering. As string metric, I am using the ...
3
votes
1answer
164 views

Is there an intuitive characterization of distance correlation?

I've been staring at the wikipedia page for distance correlation where it seems to be characterized by how it can be calculated. While I could do the calculations I struggle to get what distance ...
3
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2answers
137 views

Confidence interval for distance from center

We have a bivariate normal process where $X \sim N(\mu_x, \sigma), \, Y \sim N(\mu_y, \sigma)$, with no covariance. $(\mu_x, \mu_y)$ are unknown. (For convenience we can assert that $\sigma = 1$, or ...
0
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0answers
42 views

Learning from distance matrices

I have a task to build multi-task classification model based on distance (similarity) matrix only. They are already precalculated and no changes here can be applied. Can you, please, recommend me ...
1
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0answers
35 views

Why it is better to use the cumulative distribution to compute distances?

In the comments of this question, it was pointed out that, when comparing two distributions, it is more natural and more general use the cumulative distribution (CDF) instead of the distribution ...
0
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0answers
46 views

Distance between nominal vectors: a review

I have a seemingly easy question which however is troubling me a bit. I have couples of vectors made up of nominal attributes. They can be of different length and sometimes some of the attributes in ...
1
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0answers
23 views

Computing a “concentration of event occurrence” index

I'm looking at the concentration of an event occurrences in a given interval of time. For example, we suppose that an event occurred 4 times in an interval of length 10. I can represent this as a ...
2
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0answers
79 views

Genetic distance over spatial scales

I have matrices of genetic distances for x number of individuals within a population and their corresponding point coordinates -one genetic distance matrix per point coordinates. I was imagining ...
1
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1answer
118 views

Jensen-Shannon divergence for finite samples

I have two finite samples $s_1$ and $s_2$ and two distributions $p_1(s_1)$ and $p_2(s_2)$ that are associated to these samples. I'm essentially interested to measure the distance or similarity between ...
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0answers
24 views

Distance from bivariate Gaussian mean in terms of variance

Not sure if my question is a valid one but I will just put it out here. Consider a bivariate data set $(x_i, y_i)$ $[i=1,...,n]$ to which a bivariate Gaussian Distribution is fitted. Now, consider ...
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1answer
84 views

Earth Mover's Distance (EMD) between two Gaussians

Is there a close formula (or some kind of bound) on the EMD between $x_1\sim N(\mu_1, \Sigma_1)$ and $x_2 \sim N(\mu_2, \Sigma_2)$?
1
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0answers
108 views

Summing up two matrices of distances among centroids

I am ecologist, using mainly the 'vegan' R package. I want to combine ('cbind') 2 matrices (sample x species) but samples (row) are different. I sampled within 24 sites, by using 2 distinct methods, ...
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0answers
80 views

Finding the best path through the matrix in DTW

I have two time series q and c and I want to calculate dynamic time wrapping (DTW) distance between these two time series: ...
3
votes
1answer
76 views

Multi-variate normal distribution distance from vector sub-space

let X $\sim {\cal N}(\mu,C)$ be a random variable obeying multi-variate normal distribution in $\mathbb{R}^n$ and $U \subset \mathbb{R}^n$ be a vector space with $\dim(U)=n-1$. What is the probability ...
1
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1answer
93 views

Cook's distance and $R^2$

I am currently running a linear regression and calculating its $R^2$ After that. I calculate the Cook's distance of all points and throw away from the analysis all of the points with a distance ...
1
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1answer
93 views

Support Vector Machine for Longitude-Latitude data

I am wondering if someone could point me to the direction of support vector machines being used for longitude latitude. It seems logical that the possible complexity in SVM would be great for ...
2
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2answers
1k views

Which distance to use? e.g., manhattan, euclidean, Bray-Curtis, etc

I am not community ecologists but working these days on community ecology data. What I couldnt understand, apart from the mathematics of these distances, is the criteria to which distance to be used ...
0
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1answer
206 views

Use of a Poisson distribution from a distance matrix to determine dbscan parameters

I´ve been researching about automatic determination of parameters for DBSCAN (a density-based clustering algorithm -- http://en.wikipedia.org/wiki/DBSCAN), especially eps, and have found the following ...
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1answer
55 views

How to make similarity matrix from two distributions?

My domain expertise is not in statistics, therefore my question might sound stupid to you. I have two different distributions, first has studentIDs as columns and features in row. First Distribution ...