Cophenetic correlation

Last updated

In statistics, and especially in biostatistics, cophenetic correlation [1] (more precisely, the cophenetic correlation coefficient) is a measure of how faithfully a dendrogram preserves the pairwise distances between the original unmodeled data points. Although it has been most widely applied in the field of biostatistics (typically to assess cluster-based models of DNA sequences, or other taxonomic models), it can also be used in other fields of inquiry where raw data tend to occur in clumps, or clusters. [2] This coefficient has also been proposed for use as a test for nested clusters. [3]

Contents

Calculating the cophenetic correlation coefficient

Suppose that the original data {Xi} have been modeled using a cluster method to produce a dendrogram {Ti}; that is, a simplified model in which data that are "close" have been grouped into a hierarchical tree. Define the following distance measures.

Then, letting be the average of the x(i, j), and letting be the average of the t(i, j), the cophenetic correlation coefficient c is given by [4]

Software implementation

It is possible to calculate the cophenetic correlation in R using the dendextend R package. [5]

In Python, the SciPy package also has an implementation. [6]

In MATLAB, the Statistic and Machine Learning toolbox contains an implementation. [7]

See also

Related Research Articles

<span class="mw-page-title-main">Correlation</span> Statistical concept

In statistics, correlation or dependence is any statistical relationship, whether causal or not, between two random variables or bivariate data. Although in the broadest sense, "correlation" may indicate any type of association, in statistics it usually refers to the degree to which a pair of variables are linearly related. Familiar examples of dependent phenomena include the correlation between the height of parents and their offspring, and the correlation between the price of a good and the quantity the consumers are willing to purchase, as it is depicted in the so-called demand curve.

<span class="mw-page-title-main">Pearson correlation coefficient</span> Measure of linear correlation

In statistics, the Pearson correlation coefficient (PCC) is a correlation coefficient that measures linear correlation between two sets of data. It is the ratio between the covariance of two variables and the product of their standard deviations; thus, it is essentially a normalized measurement of the covariance, such that the result always has a value between −1 and 1. As with covariance itself, the measure can only reflect a linear correlation of variables, and ignores many other types of relationships or correlations. As a simple example, one would expect the age and height of a sample of teenagers from a high school to have a Pearson correlation coefficient significantly greater than 0, but less than 1.

<span class="mw-page-title-main">Spearman's rank correlation coefficient</span> Nonparametric measure of rank correlation

In statistics, Spearman's rank correlation coefficient or Spearman's ρ, named after Charles Spearman and often denoted by the Greek letter (rho) or as , is a nonparametric measure of rank correlation. It assesses how well the relationship between two variables can be described using a monotonic function.

In data mining and statistics, hierarchical clustering is a method of cluster analysis that seeks to build a hierarchy of clusters. Strategies for hierarchical clustering generally fall into two categories:

<span class="mw-page-title-main">Cluster analysis</span> Grouping a set of objects by similarity

Cluster analysis or clustering is the task of grouping a set of objects in such a way that objects in the same group are more similar to each other than to those in other groups (clusters). It is a main task of exploratory data analysis, and a common technique for statistical data analysis, used in many fields, including pattern recognition, image analysis, information retrieval, bioinformatics, data compression, computer graphics and machine learning.

<span class="mw-page-title-main">Coefficient of determination</span> Indicator for how well data points fit a line or curve

In statistics, the coefficient of determination, denoted R2 or r2 and pronounced "R squared", is the proportion of the variation in the dependent variable that is predictable from the independent variable(s).

In statistics, ordinary least squares (OLS) is a type of linear least squares method for choosing the unknown parameters in a linear regression model by the principle of least squares: minimizing the sum of the squares of the differences between the observed dependent variable in the input dataset and the output of the (linear) function of the independent variable.

<span class="mw-page-title-main">Kernel density estimation</span> Estimator

In statistics, kernel density estimation (KDE) is the application of kernel smoothing for probability density estimation, i.e., a non-parametric method to estimate the probability density function of a random variable based on kernels as weights. KDE answers a fundamental data smoothing problem where inferences about the population are made, based on a finite data sample. In some fields such as signal processing and econometrics it is also termed the Parzen–Rosenblatt window method, after Emanuel Parzen and Murray Rosenblatt, who are usually credited with independently creating it in its current form. One of the famous applications of kernel density estimation is in estimating the class-conditional marginal densities of data when using a naive Bayes classifier, which can improve its prediction accuracy.

Fuzzy clustering is a form of clustering in which each data point can belong to more than one cluster.

<span class="mw-page-title-main">Simple linear regression</span> Linear regression model with a single explanatory variable

In statistics, simple linear regression (SLR) is a linear regression model with a single explanatory variable. That is, it concerns two-dimensional sample points with one independent variable and one dependent variable and finds a linear function that, as accurately as possible, predicts the dependent variable values as a function of the independent variable. The adjective simple refers to the fact that the outcome variable is related to a single predictor.

The k-medoids problem is a clustering problem similar to k-means. The name was coined by Leonard Kaufman and Peter J. Rousseeuw with their PAM algorithm. Both the k-means and k-medoids algorithms are partitional and attempt to minimize the distance between points labeled to be in a cluster and a point designated as the center of that cluster. In contrast to the k-means algorithm, k-medoids chooses actual data points as centers, and thereby allows for greater interpretability of the cluster centers than in k-means, where the center of a cluster is not necessarily one of the input data points. Furthermore, k-medoids can be used with arbitrary dissimilarity measures, whereas k-means generally requires Euclidean distance for efficient solutions. Because k-medoids minimizes a sum of pairwise dissimilarities instead of a sum of squared Euclidean distances, it is more robust to noise and outliers than k-means.

In statistics, the Kendall rank correlation coefficient, commonly referred to as Kendall's τ coefficient, is a statistic used to measure the ordinal association between two measured quantities. A τ test is a non-parametric hypothesis test for statistical dependence based on the τ coefficient. It is a measure of rank correlation: the similarity of the orderings of the data when ranked by each of the quantities. It is named after Maurice Kendall, who developed it in 1938, though Gustav Fechner had proposed a similar measure in the context of time series in 1897.

In statistics, the concordance correlation coefficient measures the agreement between two variables, e.g., to evaluate reproducibility or for inter-rater reliability.

In statistics, single-linkage clustering is one of several methods of hierarchical clustering. It is based on grouping clusters in bottom-up fashion, at each step combining two clusters that contain the closest pair of elements not yet belonging to the same cluster as each other.

In statistics, a generalized estimating equation (GEE) is used to estimate the parameters of a generalized linear model with a possible unmeasured correlation between observations from different timepoints. Although some believe that Generalized estimating equations are robust in everything even with the wrong choice of working-correlation matrix, Generalized estimating equations are only robust to loss of consistency with the wrong choice.

BIRCH is an unsupervised data mining algorithm used to perform hierarchical clustering over particularly large data-sets. With modifications it can also be used to accelerate k-means clustering and Gaussian mixture modeling with the expectation–maximization algorithm. An advantage of BIRCH is its ability to incrementally and dynamically cluster incoming, multi-dimensional metric data points in an attempt to produce the best quality clustering for a given set of resources. In most cases, BIRCH only requires a single scan of the database.

Ordering points to identify the clustering structure (OPTICS) is an algorithm for finding density-based clusters in spatial data. It was presented by Mihael Ankerst, Markus M. Breunig, Hans-Peter Kriegel and Jörg Sander. Its basic idea is similar to DBSCAN, but it addresses one of DBSCAN's major weaknesses: the problem of detecting meaningful clusters in data of varying density. To do so, the points of the database are (linearly) ordered such that spatially closest points become neighbors in the ordering. Additionally, a special distance is stored for each point that represents the density that must be accepted for a cluster so that both points belong to the same cluster. This is represented as a dendrogram.

The Fowlkes–Mallows index is an external evaluation method that is used to determine the similarity between two clusterings, and also a metric to measure confusion matrices. This measure of similarity could be either between two hierarchical clusterings or a clustering and a benchmark classification. A higher value for the Fowlkes–Mallows index indicates a greater similarity between the clusters and the benchmark classifications. It was invented by Bell Labs statisticians Edward Fowlkes and Collin Mallows in 1983.

In statistics and, in particular, in the fitting of linear or logistic regression models, the elastic net is a regularized regression method that linearly combines the L1 and L2 penalties of the lasso and ridge methods.

Taylor diagrams are mathematical diagrams designed to graphically indicate which of several approximate representations of a system, process, or phenomenon is most realistic. This diagram, invented by Karl E. Taylor in 1994 facilitates the comparative assessment of different models. It is used to quantify the degree of correspondence between the modeled and observed behavior in terms of three statistics: the Pearson correlation coefficient, the root-mean-square error (RMSE) error, and the standard deviation.

References

  1. Sokal, R. R. and F. J. Rohlf. 1962. The comparison of dendrograms by objective methods. Taxon, 11:33-40
  2. Dorthe B. Carr, Chris J. Young, Richard C. Aster, and Xioabing Zhang, Cluster Analysis for CTBT Seismic Event Monitoring (a study prepared for the U.S. Department of Energy)
  3. Rohlf, F. J. and David L. Fisher. 1968. Test for hierarchical structure in random data sets. Systematic Zool., 17:407-412 (link)
  4. Mathworks statistics toolbox
  5. "Introduction to dendextend".
  6. "scipy.cluster.hierarchy.cophenet — SciPy v0.14.0 Reference Guide". docs.scipy.org. Retrieved 2019-07-11.
  7. "Cophenetic correlation coefficient - MATLAB cophenet".