Measure of distance between distributions or variables, such as Euclidean distance between points in n-space.

learn more… | top users | synonyms

0
votes
0answers
9 views

Multidimensional time series clustering

I have unemployment rates and interest rates per country over time. I want to cluster the countries that have similar dynamics and levels in both dimensions together. What could be a reasonable ...
1
vote
0answers
17 views

Measure how different are two groups in their answering on 25 ordinal variables

The research context: I'm interested in usage frequency of special interest websites and its predictors. I asked individuals (n=1000) for the usage of 25 different websites in 25 items in a survey ...
0
votes
0answers
10 views

Graph Edit Distance - strings versus matrix-->vector conversion?

I have two adjacency matrices and I want to find the graph edit distance between them. The only implementations I'm seeing (I need this fast) is edit distances in MATLAB (sigh...) for strings. I have ...
0
votes
0answers
6 views

Compare two simulations results of similar systems

I am simulating transcription regulation (a biological process) by four different mechanism using Ordinary Differential Equations. I am not sure about how to compare two different simulations (the ...
0
votes
0answers
10 views

Confidence interval for Jensen–Shannon divergence

I am just getting to grips with the concept of calculating (quasi) distances between probability distributions, and have recently encountered the Jensen–Shannon divergence, now I'm wondering ...
0
votes
0answers
7 views

Rank-sensitive distance estimator

So, for reasons that are a little complex to get into I find myself dealing with some improperly-normalized feature vectors. This means that when I try a traditional distance metric (euclidean, ...
1
vote
0answers
41 views

distances on a hypershere

I want to assess distances between pairs of high-dimensional vectors (~1500 features). My vectors have been normalized by their L2 norms, so they all have unit length and point to the surface of a ...
0
votes
0answers
11 views

Gower Distance, Ordinal Variable, R, Error?

I am trying to implement the CritCF function from http://www.sciencedirect.com/science/article/pii/S0031320310004905 for feature selection in clustering. I need to compute the distance from cluster ...
4
votes
2answers
82 views

Expected magnitude of a vector from a multivariate normal

What is the expected magnitude, i.e. euclidean distance from the origin, of a vector drawn from a p-dimensional spherical normal $\mathcal{N}_p(\mu,\Sigma)$ with $\mu=\vec{0}$ and $\Sigma=\sigma^2 I$, ...
0
votes
0answers
16 views

Clustering pairwise comparisons between samples of sparse binary data

I have 100 samples, like so: pos 1 1: 3 0 2: 4 1 3: 5 1 4: 7 1 5: 8 0 --- 196: 489 1 197: 490 1 198: 492 1 199: 495 0 200: 498 0 ...
5
votes
2answers
140 views

Is Mahalanobis distance equivalent to the Euclidean one on the PCA-rotated data?

I've been led to believe (see here and here) that Mahalanobis distance is the same as the Euclidean distance on the PCA-rotated data. In other words, taking multivariate normal data $X$, the ...
2
votes
3answers
36 views

Is there a distance metric that measures the ratio between the two rows of data?

I have about one hundred groups of chemical testing results data. Within each group there are between 1 and 200 chemical testing results. Each set of results contains testing data for 5 chemicals. ...
0
votes
1answer
59 views

Using correlation as distance metric (for hierarchical clustering)

I would like to hierarchically cluster my data, but rather than using Euclidean distance, I'd like to use correlation. Also, since the correlation coefficient ranges from -1 to 1, with both -1 and 1 ...
0
votes
1answer
29 views

How does the Proxy::dist package for r compute cross-distance matrix between two matrices?

I am trying to understand how a cross-distance matrix between two matrices is computed. Can anyone help? Maybe a simple example would help, two matrices having nrow observations of ncol variables ...
0
votes
0answers
3 views
1
vote
0answers
39 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 ...
0
votes
0answers
10 views

Is there any bibliography to cite the non-metric properties of the Gower distance?

I can't find a paper confirming that Gower distance does not cover all four properties of a metric distance. Any suggestion?
0
votes
0answers
12 views

Analysis of pairwise differences in species composition between sampling dates

I have six timepoints (months) with 60 samples each. I want to assess the species composition changes over time. For single taxa i used glht() (multcomp) with the ...
0
votes
0answers
58 views

Normalization or standardization for distances in a Q-mode cluster and principal components analyses

I want to run a cluster analysis and a PCA between some sites to classify them in terms of their multivariate dissimilarity. This is a Q-mode analysis. I am working on a data matrix made of sites in ...
1
vote
1answer
20 views

Distance between Vectors with Confidence Intervals

I have a machine learning application where I extract numerical features $a_{i1}, a_{i2}, \dots, a_{ik}$ for each object $a_i$ to study. Objects are then compared using standard euclidean distance. ...
0
votes
0answers
19 views

Robust Sparse K Means clusters and valid index

I used the robust sparse k-means for clustering my dataset and I would like to calculate some distance-based statistics for evaluating my results. Should I compute them on the dissimilarity matrix ...
0
votes
0answers
20 views

How to compare closeness of points with 4 variables

I have data for the percentage of people of different races and ethnicities for each state the US as of 2013. I also have this same data on a national level from 1900-2060, using Census predictions. ...
3
votes
1answer
40 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 ...
1
vote
0answers
24 views

show the distance between two groups with same variables using mahalanobis distance

There are two groups in my database, the first group is called unhealthy group and the other group is healthy group. each group has 4 variables (Same variables) but different values for similar ...
0
votes
0answers
15 views

Statistical distance in R with samples of different lengths

I have it really hard to find R functions that estimate various statistical distances (e.g. the Hellinger distance between two samples that have different lengths. I have gone through the R package ...
5
votes
4answers
338 views

How I can convert distance (Euclidean) to similarity score

I am using $k$ means clustering to cluster speaker voices. When I compare an utterance with clustered speaker data I get (Euclidean distance-based) average distortion. This distance can be in range of ...
2
votes
2answers
146 views

K-means: Why minimizing WCSS is maximizing Distance between clusters?

From a conceptual and algorithmic standpoint, I understand how K-means works. However, from a mathematical standpoint, I don't understand why minimizing the WCSS (within-cluster sums of squares) will ...
0
votes
0answers
26 views

Distance between blocks in a file

I am working on my research and it's computer related. I need to calculate how blocks in a file are close to each other (the distance between the blocks). For example, if we have the following three ...
0
votes
1answer
19 views

learning ranked instance similarity by machine learning

Here there are many vectors with rank. a = c(1, 2, 3, 5, 10,...) b = c(4,2,3,2,8,...) ... please note, here it's the rank of value but not the value itself in these vectors. There are a few ...
0
votes
0answers
15 views

What is the best practice to deal with NA values when calculating a dissimilarity matrix?

I need to calculate a matrix of distances between sites where different variables were measured. I will use it in a cluster analysis. The following is a sample of the matrix I am dealing with: ...
0
votes
1answer
55 views

Comparing Euclidean distances

I have 3 sets of values for X, Y & Z eg X = 7,8,7,8,6,9,8 Y = 8,7,7,6,7,8,8 Z = 8,8,8,7,8,9,9 I want compare the euclidean distance between these sets (X ...
0
votes
0answers
13 views

distances for partial rankings

I would like to know how I can compute the "Kendall distance" and the "Footrule distance" for partial rankings. I know only the general definitions for these distance that are exploitable only on full ...
1
vote
0answers
37 views

assumptions to compute mahalanobis distance

Which are the assumptions to compute the Mahalanobis distance between two groups? Do all the variables of the two groups be normal distributed?
0
votes
1answer
77 views

Doubt with a distance based Redundancy analysis

I conducted a distance based redundancy analysis (dbRDA) to explore the relevance of some environmental variables in explaining the patterns of the distribution (i.e., spatial and temporal) of two ...
0
votes
1answer
54 views

Distances in PCA space

I'm working on a project involving PCA, and my knowledge up till now with this method is quite good. My work involves finding nearest neighbors (having the least Euclidean distance) to a particular ...
6
votes
1answer
219 views

Efficient way to compute distances between centroids from distance matrix

Let us have square symmetric matrix of squared euclidean distances $\bf D$ between $n$ points and vector lengthed $n$ indicating cluster or group membership ($k$ clusters) of the points; a cluster may ...
4
votes
3answers
146 views

Is it feasible to use k-Nearest Neighbours to identify text language?

I have seen various language identification libraries that claim to use naive Bayes classifier for text language identification, like CLD2 and language detector, but not any library that uses other ...
1
vote
1answer
110 views

k means with binary variables

Is it OK to use kmeans with binary variables? I mean Euclidean distance? I guess the binary variables will be the ones that get the most power to determine the ...
4
votes
1answer
66 views

Cholesky factorization and forward substitution less accurate than inversion?

I recently asked this question asking for an efficient way to compute the Mahalanobis distance (without calculating the inverse). The accepted solution was to use the Cholesky factorization and ...
5
votes
1answer
279 views

Efficient/fast Mahalanobis distance computation

Suppose I have $n$ data points $x_1,\dots,x_n$, each of which is $p$-dimensional. Let $\Sigma$ be the (non-singular) population covariance of these samples. With respect to $\Sigma$, what is the most ...
0
votes
0answers
18 views

calculating distance among unordered set partitions for k-mean clustering?

I have a dataset for which I construct unordered set partitions for each data point, e.g. {{1,2,3}{4,6}{5}} for one and {{1,3}{2,4,5}{6}} for the next. I would like to perform k-means clustering on ...
0
votes
1answer
32 views

FAMES in case of Dynamic Time Warping

I found this paper Using Pivots to Speed-Up k-Medoids Clustering in which authors explain how to use triangular geometry and cosine law to speed up search of new medoids in case of K-medoids. My ...
1
vote
0answers
57 views

Appropriate distance measure between two finite state Markov chain models?

I am empirically creating Markov chains similar to this question. I end up with several finite state Markov chain models with the same nodes but varying transition probabilities. I want to calculate a ...
0
votes
1answer
28 views

Asymmetric distance measure in k-NN classifier?

What is the problem with an asymmetric distance measure in k-NN classifier? I think it will not cause problem, so long as I compute the distance consistently, say always from ...
4
votes
1answer
100 views

Get k most diverse objects from dendrogram (hierarchical clustering)

I have a dendrogram which groups similar object in a hierarchical order. The problem I try to solve is based on a dendrogram how to get k most diverse objects. E.g. We start with some random (?) ...
0
votes
0answers
89 views

Correlation of Distance Matrix

I have a matrix with 15 samples and ~10,000 data points (all z-scores). I calculated a distance matrix with euclidean distances using R. Is it valid to calculate and present a correlation on this ...
2
votes
0answers
35 views

Distance between independent observations of a categorical variable

I have a random variable $T: \{ \text{blue}, \text{green}, \text{red} \} \rightarrow [0,1]$ and a number of observations of $T$: ...
0
votes
0answers
21 views

Weights in computing mahalanobis distance

I need to compute distance among 200 observations and 17 variables. Variables are on different scales and not equally important. I computed Mahalanobis distance as Euclidean distance for the principal ...
0
votes
0answers
52 views

Can I compare Mahalanobis distances from different distributions?

I have a multivariate dataset representing multiple locations, each of which has a set of reference observations and a single test observation. For each location, I would like to measure how anomalous ...
0
votes
0answers
17 views

Online clustering with distances

I'm pretty new to this field so please excuse me if my question sounds naive. I have a stream of distance tuples in the form of (A, B, d) where ...