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

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How to correctly UPDATE the Centroids in the Fuzzy C Means (FCM) algorithm? [migrated]

ATTENTION TO THE MODERATORS: In a previous time, my question was arbitrarily moved to stackoverflow forum, despite my inquiring to not do it, then it later was deleted from that forum by another ...
2
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1answer
43 views

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.
1
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1answer
53 views

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 ...
1
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0answers
34 views

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 ...
0
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1answer
50 views

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 ...
1
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0answers
25 views

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, ...
6
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3answers
231 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 ...
2
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1answer
32 views

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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0answers
49 views

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 ...
4
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1answer
107 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: ...
2
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0answers
78 views

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 ...
5
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0answers
53 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?
7
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1answer
196 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 ...
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0answers
45 views

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 ...
16
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2answers
501 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
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0answers
48 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 ...
2
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0answers
138 views

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?
23
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4answers
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 ...
0
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0answers
28 views

Cluto functionality in Mathematica

Hi is there a function or library that is available in Mathematica that will enable Cluto-like cluster analysis
5
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1answer
98 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 ...
8
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2answers
423 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 ...
12
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1answer
172 views

User-defined distance functions in FindClusters

I am trying to use FindClusters to segment data points into two special parts data ...
8
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4answers
165 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 <...
3
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1answer
292 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 ...
26
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4answers
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 ...
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0answers
47 views

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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0answers
73 views

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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1answer
89 views

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 ...
5
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2answers
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 ...
2
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1answer
319 views

Cluster entities by a combination of values

I can plot the population of zip codes in NY with something like ...
2
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1answer
77 views

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, ...
3
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1answer
222 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 ...
6
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3answers
534 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 ...
2
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0answers
236 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
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1answer
124 views

Cluster a time series by labels

I have a time series, tab delimited dataset with the following format ...
2
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0answers
111 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 ...
6
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2answers
280 views

How to get the centroids of the ClusterComponents function

I use the ClusterComponent function to get the k-means clustering: ...
1
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1answer
80 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: <...
0
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1answer
343 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 ...
1
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1answer
81 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 ...
3
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0answers
84 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
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0answers
74 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
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1answer
167 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): ...
1
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1answer
123 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
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1answer
157 views

Agglomerate output to Graph

I'm using the HierarchicalClustering package to cluster some data. So let's say I have this: ...
2
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3answers
455 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
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1answer
263 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
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1answer
88 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 ...