Questions tagged [ward]

Ward's method is one of "linkage rules" in hierarchical agglomerative cluster analysis. In Ward's method, those two clusters are chosen to merge at each step that would yield the lowest increase in error sum of squares.

Filter by
Sorted by
Tagged with
0 votes
0 answers
20 views

Does the distance matrix have to be symmetric for a cluster analysis using Ward's method?

Does a distance matrix used in a cluster analysis need to be symmetrical? My past experience with cluster analysis usually involved a lower triangular distance matrix but a recent method I came across ...
user avatar
1 vote
1 answer
35 views

Intuitive explanation of Ward's method

I got this explanation of the Ward's method of hierarchical clustering from Malhotra et. al (2017), and I don't really get what it means: Ward’s procedure is a variance method which attempts to ...
user avatar
0 votes
0 answers
28 views

Are height numbers meaningful when interpreting a cluster dendrogram? (Bray Curtis & ward.D2)

When interpreting a dendrogram produced with a Bray Curtis dissimilarity matrix, do the height numbers have more meany than just relative distance between clusters? Based on the dendrogram below and ...
user avatar
  • 213
0 votes
0 answers
11 views

Compare hierarchical clustering results with different imporance scaling

For an assignment at university, I am using hierarchical clustering of a dataset of 5 different parameters. The parameters all have different magnitudes, so I standardized the data using a z-score ...
user avatar
0 votes
0 answers
52 views

Breaking Tie with Ward's Method Hierarchical Clustering

Viewing the set of single-feature observations below, I think its obvious that the appropriate Euclidean distance-based (e.g., Ward's method) number of clusters is 3. ...
user avatar
  • 227
0 votes
0 answers
103 views

Objective for Ward's agglomerative clustering

As far as I understood the original article (Ward, J. H. (1963). Hierarchical grouping to optimize an objective function), Ward proposed the following criterion for agglomerative clustering. In each ...
user avatar
  • 801
0 votes
1 answer
17 views

How can I cluster plant biomass and grain weight for different plant varieties using Ward's method based clustering?

I have plant biomass and grain weight data for different plant varieties which I now need to cluster. Do I need to define the number of clusters if using Ward's method and Squared Euclidean distance ...
user avatar
1 vote
1 answer
1k views

How to validate clusters after calculating Gower distances and Ward's clustering in R

I am trying to apply Ward's clustering on a mixed types dataset, and wanna explain what I did (maybe helpful to others), and I have some questions regarding this analysis, mainly how to validate my ...
user avatar
  • 11
1 vote
1 answer
595 views

Does it make sense to cluster asymmetric binary data with Ward's method?

I'm working with 104x42 data set where all variables are (asymmetric) binary (0-1). I've read that Ward's linkage method doesn't work theoretically properly with binary data beaucause it requests ...
user avatar
  • 53
1 vote
1 answer
66 views

Hierarchical Cluster Analysis of 100 objects with 114 variables each

I'm intending to make a cluster analysis of 100 objects. I've read a couple of books and determined that a Hierarchical agglomerative procedure with Ward's linkage method should be used in my case. As ...
user avatar
1 vote
1 answer
5k views

Difference between Ward hierarchical clustering and K-Means for classification

I have a dataset where of socio-demographic features of a population (expressed as percentages over the total population of the municipality: e.g. 12% of freelancers, 5% of unemployed etc.), each ...
user avatar
  • 147
0 votes
0 answers
761 views

Why is only Euclidean distance allowed to be used for Ward's method? [duplicate]

Using scipy, I noticed that I am allowed to use only Euclidean distance for Ward's method. Is it because Ward's uses Error Sum of Squared? What if I use Ward's method with cosine similarity? Cosine ...
user avatar
  • 613
3 votes
1 answer
416 views

Hierarchical clustering Ward's method. The missing rationale in derivation

The Ward's method is taking distance as how much the sum of squares will increase when we merge them. $d(u,v) = \frac{|u||v|}{|u|+|v|}{|m_u-m_v|}^2$ Please refer to Page 3 of link below. https://...
user avatar
  • 613
1 vote
1 answer
2k views

Difference Between Cubic Clustering Criterion, Silhouette Score, and Calinski Harabasz

I am clustering a mixed geological data set containing numeric (pump pressure, bit speed, mud temperature), nominal (presence or absence of a specific stones), and ordinal data (relative concentration ...
user avatar
  • 141
1 vote
1 answer
251 views

Where does ward.d2 and cubic clustering start misclassifying for small sample sizes?

Given Two univariate Gaussian distributions with unit variance and means and separated by distance 'dx', from which samples of size N are drawn from each distribution. Find the minimum value of dx ...
user avatar
  • 8,290
0 votes
0 answers
44 views

How do I identify the object most 'typical' of a hierarchical clustering analysis?

I have used Matlab to carry out hierarchical clustering on habitat types. Each habitat has a set of physical characteristics that are quantifiable. Using a set of 50 habitats with 5 variables per ...
user avatar
2 votes
0 answers
1k views

Step-by-step: Ward's method for calculating linkage

I'm trying to use Ward's method to calculate linkage for hierarchical agglomerative clustering with the data points below: $$a=(0,0)$$ $$b=(1,2)$$ $$c=(3,4)$$ $$d=(4,1)$...
user avatar
  • 61
4 votes
2 answers
2k views

Applying Ward's method for calculating linkage

For an assignment, I have used iPython to create the dendrogram below, using Ward's method and Euclidean distance, from the following data: $$a=(0,0)$$ $$b=(1,2)$$ $$c=(3,4)$$ $$d=(4,1)$$ $$e=(2,2)$$ ...
user avatar
  • 61
0 votes
0 answers
149 views

cluster centers very similar while dendogram shows high merge cost

I'm running a hierarchical cluster analysis (ward method, euclidean distance in the standardized variable space using scale function) and by looking at the ...
user avatar
2 votes
1 answer
95 views

Why does the row order of the sequences in TraMineR influence clustering results (Wards method)?

We have a large sample (44,933 sequences each of potential length 35) with 9 states. We create a standard dissimilarity matrix: ...
user avatar
  • 21
4 votes
0 answers
5k views

A high cophenetic correlation coefficient but dendrogram seems bad

I have 2 results for the same dataset. One is hierarchical clustering using Ward's method and I got 0.75 cophenetic correlation coefficient. The second is average method and I got 0.91 cophenetic ...
user avatar
0 votes
1 answer
1k views

Using Ward's method for clustering and Dice's similarity coefficient for binary data

I am trying to isolate the most similar groups from a set of binary variables while minimizing variation within the clusters. Is it valid to use Ward's method for clustering and measure similarly by ...
user avatar
3 votes
1 answer
4k views

How to interpret the numeric values for "height" in a dendrogram using Ward's clustering method

I am a biology student investigating a new method of creating a dichotomous identification key. I have created a dendrogram using data I have collected from a survey on how people rate how similar ...
user avatar
3 votes
0 answers
4k views

Gower's dissimilarity measure and Ward's clustering method

I have read some threads on this website saying that it is not OK to use Gower's dissimilarity matrix for Ward's clustering algorithm. I have mixed type variables, first I had a dissimilarity matrix ...
user avatar
19 votes
3 answers
44k views

What algorithm does ward.D in hclust() implement if it is not Ward's criterion?

The one used by option "ward.D" (equivalent to the only Ward option "ward" in R versions <= 3.0.3) does not implement Ward's (1963) clustering criterion, whereas option "ward.D2" implements ...
user avatar
  • 1,424
7 votes
2 answers
5k views

Is there an advantage to squaring dissimilarities when using Ward clustering?

Is there a reason to prefer squaring or not squaring the dissimilarities when clustering with Ward's method? The question is motivated by the following statement in the documentation for R's ...
user avatar
  • 899
3 votes
1 answer
489 views

Which similarity coefficient should I use with Ward linkage?

I just attempted implementations of Ward linkage and UPGMA linkage, as well as Pearson and Euclid similarity coefficients. To my surprise, both similarity coefficients gave the same clustering with ...
user avatar
0 votes
1 answer
352 views

Is there any way to know if my clusters are meaningful or meaningless? [duplicate]

Possible Duplicate: How to tell if data is “clustered” enough for clustering algorithms to produce meaningful results? I have used hierarchical clustering, e.g, Ward's method, single,...
user avatar
  • 21
7 votes
2 answers
17k views

Gower's (dis)similarity index

I would like to ask a question about Gower similarity/dissimilarity index. Is it ok to use the Gower dissimilarity measure with Ward linkage clustering? I was reading that the Gower similarity index ...
user avatar
6 votes
2 answers
9k views

How does "ward" clustering (in R's hclust function) work?

A simple example: plot(hclust(dist(c(1:3)),method = "ward")) I would like to know which calculations (in R) can reproduce the distance of 3 from {1,2} to be 1.67 ...
user avatar
  • 20.1k
19 votes
4 answers
8k views

Is it ok to use Manhattan distance with Ward's inter-cluster linkage in hierarchical clustering?

I am using hierarchical clustering to analyze time series data. My code is implemented using the Mathematica function DirectAgglomerate[...], which generates ...
user avatar
  • 191