Questions on the cluster analysis functions of Mathematica, including the Hierarchical Clustering Package.

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23
votes
4answers
1k views

Clustering of space-time data

Below is an example of a gaze sequence I recorded during a 3 seconds display. That is, where the eye was at every millisecond. While we should have 3000 points, we are missing some due to blinking. ...
16
votes
3answers
3k views

K-means clustering

In MATLAB, there is a command kmeans() that divides an array into $k$ clusters and calculates the centroid of each cluster. Is there any command in Mathematica to ...
16
votes
4answers
766 views

Generating an “average curve” from a dense set of “semicontinuous curves” which clear trends

This question is related to a previous one of mine: Partitioning a superset of coordinates into subsets that generate continuous curves, where the challenge was to partition a data set into two ...
16
votes
4answers
540 views

Clustering a set of points

I have a set of 2D points in the square defined by {-1, -1} and {1, 1}. These points typically form compact groups. I need to ...
10
votes
1answer
502 views

Visualize cluster distances in DendrogramPlot

I want to perform a cluster analysis using the HierarchicalClustering package. Is there a way to display the inter-cluster distances in a dendrogram plot? An ...
10
votes
1answer
388 views

Cluster analysis returns questionable results

A few weeks ago I ran a cluster analysis on some economic data and (unfortunately only) now I found out that some results do not make sense. For instance I analyzed the development of unemployment ...
9
votes
4answers
678 views

data clustering

I have some data set which i would like to partition into 3 groups a:set 1 b: set 2 c: background. I use FindClusters[] function but as you can see (after ...
9
votes
2answers
213 views

Partitioning a superset of coordinates into subsets that generate continuous curves

Consider the data set corresponding to recorded trajectories for a particle: ...
8
votes
1answer
223 views

FindClusters for 3D Pancake/Platelet Shapes

I'm looking to properly cluster a dataset of roughly 3 million data points in 3-space. The shapes form closely spaced "clusters" that resemble pancakes. Here is a downsampled dataset: ...
8
votes
2answers
304 views

Why doesn't FindClusters find any clusters in this case?

I am trying to use FindClusters to segment data points into similar numbers but so far I couldn't get it work for this example: ...
8
votes
0answers
133 views

Strategies to find curves on messy data using FindCurvePath

I have a set of data points that correspond to roots of a transcendental equation with respect to a parameter (the abscissa) which, by the properties of the system, define continuous curves (might be ...
7
votes
3answers
206 views

Morphological Components with periodic boundary conditions

I would like to find the connected(with periodic boundary conditions) components in a large binary matrix. What I've tried, and it does a fair job is: ...
7
votes
0answers
283 views

Cluster a signal into areas of equal intensity

Introduction I have a greyscale photograph that I want to partition into areas of equal intensity. This means, that the integral over each partition should be (roughly) equal. There is no unique ...
6
votes
1answer
383 views

Clustering adjacent points in 2D

I need to find all clusters of adjacent white points in a binary image. By term "adjacent" I mean that coordinates of two points differ by no more than 1 (i.e. the points ...
6
votes
2answers
271 views

Different highlight for each cluster in DendrogramPlot

Is there any way to have each cluster in the DendrogramPlot highlight in a different color? I've tried the obvious way but it doesn't work: ...
5
votes
4answers
443 views

Identifying subsets with minimal standard deviation

Consider the following: ...
5
votes
1answer
419 views

Clustering 3D Data Points on a Periodic Cubic Grid

I have a set of 3D data points on a cubic grid. The data can be downloaded from here https://skydrive.live.com/redir?resid=F96524B72DCD75FB!14240 and read into a variable ...
5
votes
2answers
359 views

Custom distance metric for agglomerative clustering in Mathematica

Is it possible to have a custom distance metric defined to determine the distance between two clusters in Agglomerative clustering in Mathematica? I have a 3 dimension data with string values along ...
5
votes
1answer
166 views

Stopping Agglomerative clustering under a condition in Mathematica

How do I instruct Agglomerative clustering to stop/NOT merging two particular clusters if the distance between the two clusters is larger than a threshold value? I know that we can implement a custom ...
4
votes
2answers
499 views

Clustering a bivariate data set with Mathematica

I need to partition a bivariate data set into predetermined "n" clusters and, at the same time, to fix the centroid position of each cluster. Is the ...
4
votes
3answers
253 views

make specific cluster

I have set of coordinates. I want to make clusters in which every point is within 1.5 distance unit of it's neighbor. ex of point coordinates: ...
4
votes
1answer
115 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
3
votes
2answers
220 views

Which group of points connects more strongly?

I have two groups of points, and the lenth of them may be different.I want to know which group of points connects more strongly, are there any existing algorithms for this? Here are two groups of ...
3
votes
1answer
180 views

What's the main difference between FindClusters and ClusteringComponents? [closed]

In many cases, FindClusters and ClusteringComponents provide similar results. Options for hierarchical and agglomerative ...
3
votes
1answer
97 views

Setting label in DendrogramPlot

I want to create a dendrogram with the labels being a visual representation of the data. Something like this: How can I do that in Mathematica? My attempt so far hasn't been very successful. The ...
3
votes
1answer
283 views

Plotting reordered clusters with different colors and joined lines

I would like to show how typical days of energy load (found through clustering of a years worth of data) are spread throughout a year in a single graph with a color for each 'typical day' (or ...
3
votes
1answer
130 views

Clustering of 2D map, based on similarity in spectra

I have experimental 2D-spectroscopy data, in a format similar to this: ...
3
votes
1answer
191 views

How to determine cluster membership using FindClusters?

I have a 1000 by 3 data matrix in which for each person we have 3 scores. I want to cluster those persons into 8 cluster using Agglomerative method. I did the clusetring by: ...
3
votes
1answer
108 views

How to give ClusteringComponents initial values?

I came across a variant of k-means that adds a algorithm to select good starting values called k-means++. ...
2
votes
3answers
147 views

Clustering data sets with multiple variables

I am learning how to cluster large datasets and this maybe a newbie question, but I haven’t found a suitable answer in the Documentation or on this board. My question is best illustrated by an ...
2
votes
1answer
160 views

How does DistanceFunction work with images in ClusteringComponents?

Does anyone know the syntax to DistanceFunction? I am trying to define my own function to use with ClusteringComponents; e.g., ...
2
votes
1answer
148 views

Hierarchical clustering: convert Mathematica cluster hierarchy to NEWICK format

Can anyone tell me a clever way to convert the hierarchical clustering object, created, say, by Agglomerate or DirectAgglomerate ...
2
votes
1answer
110 views

DirectAgglomerate not working for Large Matrices

I am trying to graphically display a distance matrix with similar elements visually clustered into groups. My original matrix has the elements in a random order so the first thing I do is to change ...
1
vote
1answer
40 views

Using FindGraphCommunities, write community membership for each vertex to CSV

I have a network that I've loaded into Mathematica, and I've used FindGraphCommunitites[network,Method->"Hierarchical"] to identify the communities in the ...
1
vote
1answer
60 views

What does the VertexMoving method for FindGraphCommunities do?

I've been applying the VertexMoving method to some graph data, and it's producing very useful results. However, I've got no clue as to what this method actually is, and the documentation is ...
0
votes
1answer
184 views

Mean path length of randomly generated graphs

I am looking to find the the average path length of 1000 random graphs with the following degree distribution, a few of the vertex degrees are included below ...
0
votes
1answer
76 views

How to efficiently distinguish the rewired edges in WattsStrogatzGraphDistribution?

The WattsStrogatzGraphDistribution function is a way to construct random graphs based on Watts and Strogatz small world model. The ...
0
votes
0answers
90 views

Spectral Clustering

I am interested in the following question: How is it possible to check whether an algorithm is working properly? However, this question is too general for the post and I'd like to restrict attention ...
0
votes
0answers
35 views

Import/Export Cluster Object [duplicate]

I want to export and then import back in a cluster object from Agglomerate. After the import, the imported object does not behave as a cluster - for example, ClusterSplit does not recognize it as a ...