# Tagged Questions

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

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### Do you know the options of RandomSeed in ClusteringComponents?

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 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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### 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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### 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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### 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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### 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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### 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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### 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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### 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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### 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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### 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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### 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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### 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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### Cluster entities by a combination of values

I can plot the population of zip codes in NY with something like ...
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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 ...
242 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 ?
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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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### 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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### 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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### How to get the centroids of the ClusterComponents function

I use the ClusterComponent function to get the k-means clustering: ...
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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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### 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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### 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 ...
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### Agglomerate output to Graph

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