Tagged Questions

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

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3
votes
1answer
46 views

Clustering image data by intensity and position

I'd like to apply FindClusters or ClusteringComponents to image data of an indistinct edge, with the goal of segmenting the ...
2
votes
0answers
27 views

Max iterations in K-means clustering algorithm

I want to use k-means for clustering. I have used the ClusteringComponents function but I said how can I control the max-iteration for k-means ?
1
vote
1answer
53 views

Cluster a time series by labels

I have a time series, tab delimited dataset with the following format ...
1
vote
0answers
36 views

Matrix clustering in Mathematica?

Suppose I have a square matrix $M$, which you can think of as the weighted adjacency matrix of a graph $G$. I want to order the vertices of $G$ in such a way that the entries of the matrix $M$ are ...
1
vote
1answer
41 views

ClusteringComponents returning only ones

I am trying to use ClusteringComponents without having to specify the number of clusters initially... so the algorithm can find itself the optimal number of clusters... My data is of the form: ...
1
vote
1answer
47 views

Bug in ClusteringComponents yielding different results on practically same input?

I am using the image below. I want to run a simple ClusteringComponents, using the KMeans method and ...
6
votes
2answers
102 views

How to get the centroids of the ClusterComponents function

I use the ClusterComponent function to get the k-means clustering: ...
1
vote
0answers
43 views

k-means clustering in parallel

How can the k-means algorithm for some given distance function be implemented using ParallelMap or other parallel processing program constructs in Mathematica?
2
votes
0answers
46 views

k-means clustering using squared correlation in Mathematica

I am trying to cluster data using the squared correlation coefficient since in the case of my data, -1 correlation is equivalent to 1 correlation (polarities do not matter). How can this be done in ...
5
votes
1answer
126 views

FindClusters giving wrong groupings

I am having trouble getting FindClusters to find the right clustering for this set of data (and many other sets of data similar to it): ...
0
votes
0answers
94 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 ...
1
vote
1answer
51 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 ...
4
votes
1answer
122 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
2
votes
3answers
185 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
161 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 ...
1
vote
1answer
63 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 ...
9
votes
0answers
141 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 ...
0
votes
1answer
87 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 ...
7
votes
3answers
216 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: ...
3
votes
1answer
141 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
103 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 ...
0
votes
1answer
211 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 ...
5
votes
1answer
498 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 ...
2
votes
1answer
117 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 ...
4
votes
3answers
257 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: ...
17
votes
4answers
800 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 ...
9
votes
2answers
221 views

Partitioning a superset of coordinates into subsets that generate continuous curves

Consider the data set corresponding to recorded trajectories for a particle: ...
3
votes
1answer
205 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
207 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: ...
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 ...
8
votes
1answer
229 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: ...
16
votes
4answers
630 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 ...
6
votes
2answers
281 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: ...
4
votes
1answer
168 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., ...
3
votes
1answer
289 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 ...
8
votes
2answers
311 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: ...
3
votes
2answers
224 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 ...
7
votes
0answers
286 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 ...
3
votes
1answer
110 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++. ...
10
votes
4answers
718 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 ...
4
votes
2answers
514 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 ...
10
votes
1answer
533 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 ...
17
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 ...
6
votes
1answer
397 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 ...
5
votes
1answer
169 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 ...
5
votes
2answers
371 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
4answers
455 views

Identifying subsets with minimal standard deviation

Consider the following: ...
10
votes
1answer
405 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 ...
26
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. ...