# Tagged Questions

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

2k 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. ...
6k 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 ...
1k 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 ...
1k 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 ...
502 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 ...
877 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 ...
177 views

### User-defined distance functions in FindClusters

I am trying to use FindClusters to segment data points into two special parts data ...
242 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 ...
1k 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 ...
483 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 ...
280 views

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

Consider the data set corresponding to recorded trajectories for a particle: ...
445 views

### Creating Identification/Classification trees

I have data given in following format; from which I need to create identification/classification trees (three different trees from three different criterion, that is average disorder, gain ratio and ...
283 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: ...
428 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: ...
172 views

### Cluster numbers into n partitions so that each partitions sum is closest to total/n

For example having data data = {16, 4, 17, 10, 15, 4, 4, 6, 7, 14, 9, 17, 27, 6, 1, 9, 0, 12, 20, 8, 0, 3, 4, 0, 3, 4} I want to cluster them int 4 partitions <...
362 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: ...
396 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: ...
202 views

### Clustered heatmaps with dendrograms

In biology it's common to cluster both dimensions of a matrix, display it as a heatmap (MatrixPlot, ArrayPlot) and show ...
539 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 ...
233 views

### How to speed up computation of medoids?

I need to compute medoids (based on SquaredEuclideanDistance for large lists of k-vectors (k = 14). My implementations so far are impractically slow. Here is a ...
539 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 ...
285 views

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

I use the ClusterComponent function to get the k-means clustering: ...
232 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 ...
561 views

### Identifying subsets with minimal standard deviation

Consider the following: ...
423 views

### Code elegance and compactness. Help needed with Map, Apply

I need some help with code optimization and compactness. I have a set of two-dimensional points and I can use the Mathematica function FindClusters to find 4 clusters. I'd like to plot the points ...
367 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 ...
171 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): ...
102 views

### How to get FindCurvePath to return only one list

As you can see below, FindCurvePath returns only a part of the list, resulting in a partial interpolation. I would like to interpolate all the points. Complete ...
962 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 ...
509 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 ...
55 views

### How many clusters does DominantColors return?

Is there any documentation on how it automatically chooses the number of colors - does it use X-means or some other heuristic to determine the number of clusters it automatically returns?
680 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 ...
291 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: ...
185 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., <...
157 views

### Agglomerate output to Graph

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

### How to automatically label the cluster distances in a DendrogramPlot?

I have a distance matrix data, and want to visualize it as below: The current codes I am using is: ...
136 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++. ...
433 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 ...
241 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 ...
296 views

### Spectral Clustering

I am attempting to implement a spectral clustering routine using Mathematica, but I am encountering difficulties. Using the standard Gaussian similarity function found in section 2.2 of this paper ...
170 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 ...
361 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 cluster)....
226 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 ...
228 views

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

I have experimental 2D-spectroscopy data, in a format similar to this: ...
420 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: ...
49 views

### Clustering with restrictions

I have this dataset of a ranking of roughly 32.5k players in increasing order. The third column contains the number of players which have the corresponding score, whilst the second is the number ...
85 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?
466 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 ...