# Tagged Questions

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

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### FindClusters and friends run out of memory

I have a 50k lists, each has 1024 real numbers and I wanted to cluster them, but this happened: Are there any ways around these issues and to be able to cluster high dimensional vectors?
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### Do you know the options of RandomSeed in ClusteringComponents? [on hold]

ClusteringComponents[data, 4, 1, Method -> "KMeans", DistanceFunction-> EuclideanDistance, "RandomSeed" -> 10] As above, 4 means cluster number, ...
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### Clustering using Mathematica

I've got a two column table (Fields, Methods) and I'd like to find which Methods relates to many Fields. Can I accomplish this task using Mathematica? This are the sample data. https://jpst.it/L6I5
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### Clustering using PAM method

Why Clustering using PAM method often attributes one point in the middle of one cluster to another cluster? (for example here K-means clustering ) I have the similar results with my set of data.
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### Revealing correlation between one parameter and set of parameters.

Probably it is duplicate (but I could not fine it) or it is a question for MathOverflow. Still I would like to use Mathematica to analyze my data. In experiment I measure the parameter "P" of the set ...
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### Where can I find documentation on the methods/algorithm used in FindGraphPartition in Mathematica 10?

I am working on a graph theoretical project where it would be helpful to know the name of the algorithm used in FindGraphPartition. Question: Where can I find ...
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### Specifying number of clusters and members in CommunityGraphPlot

The Issue I am trying to specify the number of clusters and the number of members in each cluster that the CommunityGraphPlot function forms as part of a larger project. The Code This code ...
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### How to customize the order of leaf labels in a dendrogram plot?

Take the following simple case as an example: Needs["HierarchicalClustering"] SeedRandom[99]; Sort@RandomInteger[99, {10}] gives {2, 7, 22, 34, 42, 58, 60, ...
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### 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 ...
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### What is the default SignificanceTest setting for FindClusters with Optimize method?

According to the documentation, the default value of FindCluster's Method option is Optimize....
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### Can parallelization speed up FindClusters?

I have a clustering task that would take FindClusters 2-3 months1 to complete. Can this calculation be sped up with parallelization? (FWIW, the data to be ...
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### 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: ...
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### How can I access the Criterion function of KI method in FindThreshold for a dataset?

I want to find a threshold for some data set, using Kittler-Illingworth minimum error thresholding method (KI method). To do so, I use the Mathematica built-in function ...
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### 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?
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### 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 ...
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### Number of clusters varies rapidly

I'm having some trouble with FindClusters. I've got a list of 7,598 vectors, each with 10 real numbers generally between 0 and 1. The number of clusters for the ...
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### 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 ...
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### 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 ...
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### How to get the SIFT features of an image?

According to the documentation, the function KeyPoints[] computes features only using SURF, but what about SIFT or FAST features?
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### 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 ...
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### Cluto functionality in Mathematica

Hi is there a function or library that is available in Mathematica that will enable Cluto-like cluster analysis
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### 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 ...
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### 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 ...
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### User-defined distance functions in FindClusters

I am trying to use FindClusters to segment data points into two special parts data ...
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### 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 <...
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### 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 ...
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### 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 ...
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### Question on ClusteringComponents [duplicate]

I am fairly new to Mathematica. I've been playing around with ClusteringComponents. Assume we are clustering points in the plane using k-means clustering and ...
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### Statistical significance test of FindCluster

I have a list of vectors which could be roughly divided into two clusters. The list is huge so I have to use RandomChoice[list, 20000] to speed up the calculation. ...
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### How can I cluster a continuous percentage? [closed]

I've got a table with 3 columns. 1 is descriptive A 1 is a percentage B 1 is a decimal number C I would like to investigate for the clusters (ie. B is high ad C is low, or viceversa). How can I ...
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### 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 ...
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### Cluster entities by a combination of values

I can plot the population of zip codes in NY with something like ...
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### Partitioning a list in n sublists with constrains in their sums

Is there a way to put cluster level limits on clusters? For example, if I run: FindClusters[{1, 2, 3, 4, 4, 6, 7, 10}] I get back two lists, ...
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### 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 ...
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### 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 ...
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### 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 ...
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### 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 ?
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### Cluster a time series by labels

I have a time series, tab delimited dataset with the following format ...
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### 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 ...
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### How to get the centroids of the ClusterComponents function

I use the ClusterComponent function to get the k-means clustering: ...
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### 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: <...
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### 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 ...
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### 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 ...
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### 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?
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### 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 ...
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### 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): ...
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### 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 ...