Principal component analysis
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Principal component analysis (PCA) is a linear dimensionality reduction technique with applications in exploratory data analysis, visualization and data preprocessing.
The data is linearly transformed onto a new coordinate system such that the directions (principal components) capturing the largest variation in the data can be easily identified.
The principal components of a collection of points in a real coordinate space are a sequence of unit vectors, where the -th vector is the direction of a line that best fits the data while being orthogonal to the first vectors. Here, a best-fitting line is defined as one that minimizes the average squared perpendicular distance from the points to the line. These directions (i.e., principal components) constitute an orthonormal basis in which different individual dimensions of the data are linearly uncorrelated. Many studies use the first two principal components in order to plot the data in two dimensions and to visually identify clusters of closely related data points.[1]
Principal component analysis has applications in many fields such as population genetics, microbiome studies, and atmospheric science.
When performing PCA, the first principal component of a set of variables, presumed to be jointly normally distributed, is the derived variable formed as a linear combination of the original variables that explains the most variance. The second principal component explains the most variance in what is left once the effect of the first component is removed, and we may proceed through iterations until all the variance is explained. PCA is most commonly used when many of the variables are highly correlated with each other and it is desirable to reduce their number to an independent set.
The first principal component can equivalently be defined as a direction that maximizes the variance of the projected data. The -th principal component can be taken as a direction orthogonal to the first principal components that maximizes the variance of the projected data.
For either objective, it can be shown that the principal components are eigenvectors of the data's covariance matrix. Thus, the principal components are often computed by eigendecomposition of the data covariance matrix or singular value decomposition of the data matrix. PCA is the simplest of the true eigenvector-based multivariate analyses and is closely related to factor analysis. Factor analysis typically incorporates more domain-specific assumptions about the underlying structure and solves eigenvectors of a slightly different matrix. PCA is also related to canonical correlation analysis (CCA). CCA defines coordinate systems that optimally describe the cross-covariance between two datasets while PCA defines a new orthogonal coordinate system that optimally describes variance in a single dataset.[2][3][4][5] Robust and L1-norm-based variants of standard PCA have also been proposed.[6][7][8][5]
PCA was invented in 1901 by Karl Pearson,[9] as an analogue of the principal axis theorem in mechanics; it was later independently developed and named by Harold Hotelling in the 1930s.[10] Depending on the field of application, it is also named the discrete Karhunen–Loève transform (KLT) in signal processing, the Hotelling transform in multivariate quality control, proper orthogonal decomposition (POD) in mechanical engineering, singular value decomposition (SVD) of X (invented in the last quarter of the 19th century[11]), eigenvalue decomposition (EVD) of XTX in linear algebra, factor analysis (for a discussion of the differences between PCA and factor analysis see Ch. 7 of Jolliffe's Principal Component Analysis),[12] Eckart–Young theorem (Harman, 1960), or empirical orthogonal functions (EOF) in meteorological science (Lorenz, 1956), empirical eigenfunction decomposition (Sirovich, 1987), quasiharmonic modes (Brooks et al., 1988), spectral decomposition in noise and vibration, and empirical modal analysis in structural dynamics.
PCA can be thought of as fitting a p-dimensional ellipsoid to the data, where each axis of the ellipsoid represents a principal component. If some axis of the ellipsoid is small, then the variance along that axis is also small.
To find the axes of the ellipsoid, we must first center the values of each variable in the dataset on 0 by subtracting the mean of the variable's observed values from each of those values. These transformed values are used instead of the original observed values for each of the variables. Then, we compute the covariance matrix of the data and calculate the eigenvalues and corresponding eigenvectors of this covariance matrix. Then we must normalize each of the orthogonal eigenvectors to turn them into unit vectors. Once this is done, each of the mutually-orthogonal unit eigenvectors can be interpreted as an axis of the ellipsoid fitted to the data. This choice of basis will transform the covariance matrix into a diagonalized form, in which the diagonal elements represent the variance of each axis. The proportion of the variance that each eigenvector represents can be calculated by dividing the eigenvalue corresponding to that eigenvector by the sum of all eigenvalues.
Biplots and scree plots (degree of explained variance) are used to interpret findings of the PCA.
PCA is defined as an orthogonal linear transformation on a real inner product space that transforms the data to a new coordinate system such that the greatest variance by some scalar projection of the data comes to lie on the first coordinate (called the first principal component), the second greatest variance on the second coordinate, and so on.[12]
Consider an data matrix, X, with column-wise zero empirical mean (the sample mean of each column has been shifted to zero), where each of the n rows represents a different repetition of the experiment, and each of the p columns gives a particular kind of feature (say, the results from a particular sensor).
Mathematically, the transformation is defined by a set of size of p-dimensional vectors of weights or coefficients that map each row vector of X to a new vector of principal component scores , given by
in such a way that the individual variables of t considered over the data set successively inherit the maximum possible variance from X, with each coefficient vector w constrained to be a unit vector (where is usually selected to be strictly less than to reduce dimensionality).
First component
In order to maximize variance, the first weight vector w(1) thus has to satisfy
Equivalently, writing this in matrix form gives
Since w(1) has been defined to be a unit vector, it equivalently also satisfies
The quantity to be maximised can be recognised as a Rayleigh quotient. A standard result for a positive semidefinite matrix such as XTX is that the quotient's maximum possible value is the largest eigenvalue of the matrix, which occurs when w is the corresponding eigenvector.
With w(1) found, the first principal component of a data vector x(i) can then be given as a score t1(i) = x(i) ⋅ w(1) in the transformed co-ordinates, or as the corresponding vector in the original variables, {x(i) ⋅ w(1)} w(1).
Further components
The k-th component can be found by subtracting the first k − 1 principal components from X:
and then finding the weight vector which extracts the maximum variance from this new data matrix
It turns out that this gives the remaining eigenvectors of XTX, with the maximum values for the quantity in brackets given by their corresponding eigenvalues. Thus the weight vectors are eigenvectors of XTX.
The k-th principal component of a data vector x(i) can therefore be given as a score tk(i) = x(i) ⋅ w(k) in the transformed coordinates, or as the corresponding vector in the space of the original variables, {x(i) ⋅ w(k)} w(k), where w(k) is the kth eigenvector of XTX.
The full principal components decomposition of X can therefore be given as
where W is a p-by-p matrix of weights whose columns are the eigenvectors of XTX. The transpose of W is sometimes called the whitening or sphering transformation. Columns of W multiplied by the square root of corresponding eigenvalues, that is, eigenvectors scaled up by the variances, are called loadings in PCA or in Factor analysis.
Covariances
XTX itself can be recognized as proportional to the empirical sample covariance matrix of the dataset XT.[12]: 30–31
The sample covariance Q between two of the different principal components over the dataset is given by:
where the eigenvalue property of w(k) has been used to move from line 2 to line 3. However eigenvectors w(j) and w(k) corresponding to eigenvalues of a symmetric matrix are orthogonal (if the eigenvalues are different), or can be orthogonalised (if the vectors happen to share an equal repeated value). The product in the final line is therefore zero; there is no sample covariance between different principal components over the dataset.
Another way to characterise the principal components transformation is therefore as the transformation to coordinates which diagonalise the empirical sample covariance matrix.
In matrix form, the empirical covariance matrix for the original variables can be written
The empirical covariance matrix between the principal components becomes
where Λ is the diagonal matrix of eigenvalues λ(k) of XTX. λ(k) is equal to the sum of the squares over the dataset associated with each component k, that is, λ(k) = Σi tk2(i) = Σi (x(i) ⋅ w(k))2.
Dimensionality reduction
The transformation T = X W maps a data vector x(i) from an original space of p variables to a new space of p variables which are uncorrelated over the dataset. However, not all the principal components need to be kept. Keeping only the first L principal components, produced by using only the first L eigenvectors, gives the truncated transformation
where the matrix TL now has n rows but only L columns. In other words, PCA learns a linear transformation where the columns of p × L matrix form an orthogonal basis for the L features (the components of representation t) that are decorrelated.[13] By construction, of all the transformed data matrices with only L columns, this score matrix maximises the variance in the original data that has been preserved, while minimising the total squared reconstruction error or .
Such dimensionality reduction can be a very useful step for visualising and processing high-dimensional datasets, while still retaining as much of the variance in the dataset as possible. For example, selecting L = 2 and keeping only the first two principal components finds the two-dimensional plane through the high-dimensional dataset in which the data is most spread out, so if the data contains clusters these too may be most spread out, and therefore most visible to be plotted out in a two-dimensional diagram; whereas if two directions through the data (or two of the original variables) are chosen at random, the clusters may be much less spread apart from each other, and may in fact be much more likely to substantially overlay each other, making them indistinguishable.
Similarly, in regression analysis, the larger the number of explanatory variables allowed, the greater is the chance of overfitting the model, producing conclusions that fail to generalise to other datasets. One approach, especially when there are strong correlations between different possible explanatory variables, is to reduce them to a few principal components and then run the regression against them, a method called principal component regression.
Dimensionality reduction may also be appropriate when the variables in a dataset are noisy. If each column of the dataset contains independent identically distributed Gaussian noise, then the columns of T will also contain similarly identically distributed Gaussian noise (such a distribution is invariant under the effects of the matrix W, which can be thought of as a high-dimensional rotation of the co-ordinate axes). However, with more of the total variance concentrated in the first few principal components compared to the same noise variance, the proportionate effect of the noise is less—the first few components achieve a higher signal-to-noise ratio. PCA thus can have the effect of concentrating much of the signal into the first few principal components, which can usefully be captured by dimensionality reduction; while the later principal components may be dominated by noise, and so disposed of without great loss. If the dataset is not too large, the significance of the principal components can be tested using parametric bootstrap, as an aid in determining how many principal components to retain.[14]
Singular value decomposition
The principal components transformation can also be associated with another matrix factorization, the singular value decomposition (SVD) of X,
Here Σ is an n-by-p rectangular diagonal matrix of positive numbers σ(k), called the singular values of X; U is an n-by-n matrix, the columns of which are orthogonal unit vectors of length n called the left singular vectors of X; and W is a p-by-p matrix whose columns are orthogonal unit vectors of length p and called the right singular vectors of X.
In terms of this factorization, the matrix XTX can be written
where is the square diagonal matrix with the singular values of X and the excess zeros chopped off that satisfies . Comparison with the eigenvector factorization of XTX establishes that the right singular vectors W of X are equivalent to the eigenvectors of XTX, while the singular values σ(k) of are equal to the square-root of the eigenvalues λ(k) of XTX.
Using the singular value decomposition the score matrix T can be written
so each column of T is given by one of the left singular vectors of X multiplied by the corresponding singular value. This form is also the polar decomposition of T.
Efficient algorithms exist to calculate the SVD of X without having to form the matrix XTX, so computing the SVD is now the standard way to calculate a principal components analysis from a data matrix,[15] unless only a handful of components are required.
As with the eigen-decomposition, a truncated n × L score matrix TL can be obtained by considering only the first L largest singular values and their singular vectors:
The truncation of a matrix M or T using a truncated singular value decomposition in this way produces a truncated matrix that is the nearest possible matrix of rank L to the original matrix, in the sense of the difference between the two having the smallest possible Frobenius norm, a result known as the Eckart–Young theorem [1936].
The singular values (in Σ) are the square roots of the eigenvalues of the matrix XTX. Each eigenvalue is proportional to the portion of the "variance" (more correctly of the sum of the squared distances of the points from their multidimensional mean) that is associated with each eigenvector. The sum of all the eigenvalues is equal to the sum of the squared distances of the points from their multidimensional mean. PCA essentially rotates the set of points around their mean in order to align with the principal components. This moves as much of the variance as possible (using an orthogonal transformation) into the first few dimensions. The values in the remaining dimensions, therefore, tend to be small and may be dropped with minimal loss of information (see below). PCA is often used in this manner for dimensionality reduction. PCA has the distinction of being the optimal orthogonal transformation for keeping the subspace that has largest "variance" (as defined above). This advantage, however, comes at the price of greater computational requirements if compared, for example, and when applicable, to the discrete cosine transform, and in particular to the DCT-II which is simply known as the "DCT". Nonlinear dimensionality reduction techniques tend to be more computationally demanding than PCA.
PCA is sensitive to the scaling of the variables. If we have just two variables and they have the same sample variance and are completely correlated, then the PCA will entail a rotation by 45° and the "weights" (they are the cosines of rotation) for the two variables with respect to the principal component will be equal. But if we multiply all values of the first variable by 100, then the first principal component will be almost the same as that variable, with a small contribution from the other variable, whereas the second component will be almost aligned with the second original variable. This means that whenever the different variables have different units (like temperature and mass), PCA is a somewhat arbitrary method of analysis. (Different results would be obtained if one used Fahrenheit rather than Celsius for example.) Pearson's original paper was entitled "On Lines and Planes of Closest Fit to Systems of Points in Space" – "in space" implies physical Euclidean space where such concerns do not arise. One way of making the PCA less arbitrary is to use variables scaled so as to have unit variance, by standardizing the data and hence use the autocorrelation matrix instead of the autocovariance matrix as a basis for PCA. However, this compresses (or expands) the fluctuations in all dimensions of the signal space to unit variance.
Mean subtraction (a.k.a. "mean centering") is necessary for performing classical PCA to ensure that the first principal component describes the direction of maximum variance. If mean subtraction is not performed, the first principal component might instead correspond more or less to the mean of the data. A mean of zero is needed for finding a basis that minimizes the mean square error of the approximation of the data.[16]
Mean-centering is unnecessary if performing a principal components analysis on a correlation matrix, as the data are already centered after calculating correlations. Correlations are derived from the cross-product of two standard scores (Z-scores) or statistical moments (hence the name: Pearson Product-Moment Correlation). Also see the article by Kromrey & Foster-Johnson (1998) on "Mean-centering in Moderated Regression: Much Ado About Nothing". Since covariances are correlations of normalized variables (Z- or standard-scores) a PCA based on the correlation matrix of X is equal to a PCA based on the covariance matrix of Z, the standardized version of X.
PCA is a popular primary technique in pattern recognition. It is not, however, optimized for class separability.[17] However, it has been used to quantify the distance between two or more classes by calculating center of mass for each class in principal component space and reporting Euclidean distance between center of mass of two or more classes.[18] The linear discriminant analysis is an alternative which is optimized for class separability.