# Tagged Questions

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

89 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 ...
40 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 ?
60 views

### Cluster a time series by labels

I have a time series, tab delimited dataset with the following format ...
43 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 ...
44 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: ...
53 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 ...
111 views

### How to get the centroids of the ClusterComponents function

I use the ClusterComponent function to get the k-means clustering: ...
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?
49 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 ...
129 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): ...
99 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 ...
53 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 ...
123 views

### Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
199 views

### Clustering data sets with multiple variables

I am learning how to cluster large datasets and this maybe a newbie question, but I havenâ€™t found a suitable answer in the Documentation or on this board. My question is best illustrated by an ...
167 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 ...
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 ...
142 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 ...
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### 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 ...
220 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: ...
146 views

### Clustering of 2D map, based on similarity in spectra

I have experimental 2D-spectroscopy data, in a format similar to this: ...
328 views

### Finding connected components in an array

I have an $w\times h$ array with non-negative integers. I wish to partition the set of coordinates $(c,r)$ with $1\leq c \leq w$ and $1\leq r \leq h$, in subsets, so that each subset corresponds to a ...
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 ...
223 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 ...
255 views

### Provided an array of 2D point clouds, can we quickly replace distance- and index-based cliques of points with their median or mean values?

Imagine I have $N \approx 10^5$ clouds of points in an array of the form: UPDATED ...
520 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 ...
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 ...
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: ...
815 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 ...
221 views

### Partitioning a superset of coordinates into subsets that generate continuous curves

Consider the data set corresponding to recorded trajectories for a particle: ...
210 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 ...
213 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: ...
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### 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 ...
231 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: ...
679 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 ...
284 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: ...
170 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., ...
293 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 ...
313 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: ...
225 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 ...
290 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 ...
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++. ...
739 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 ...
520 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 ...
550 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 ...
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 ...
403 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 ...
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 ...
381 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 ...