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/*-
*
* * Copyright 2015 Skymind,Inc.
* *
* * Licensed under the Apache License, Version 2.0 (the "License");
* * you may not use this file except in compliance with the License.
* * You may obtain a copy of the License at
* *
* * http://www.apache.org/licenses/LICENSE-2.0
* *
* * Unless required by applicable law or agreed to in writing, software
* * distributed under the License is distributed on an "AS IS" BASIS,
* * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* * See the License for the specific language governing permissions and
* * limitations under the License.
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*
*/
package org.nd4j.linalg.dimensionalityreduction;
import org.nd4j.linalg.api.ndarray.INDArray;
import org.nd4j.linalg.eigen.Eigen;
import org.nd4j.linalg.factory.Nd4j;
import org.nd4j.linalg.indexing.NDArrayIndex;
import org.nd4j.linalg.ops.transforms.Transforms;
/**
* PCA class for dimensionality reduction and general analysis
*
* @author Adam Gibson
* @author Luke Czapla - added methods used in non-static usage of PCA
*/
public class PCA {
private INDArray covarianceMatrix, mean, eigenvectors, eigenvalues;
private PCA() {}
/**
* Create a PCA instance with calculated data: covariance, mean, eigenvectors, and eigenvalues.
* @param dataset The set of data (records) of features, each row is a data record and each
* column is a feature, every data record has the same number of features.
*/
public PCA(INDArray dataset) {
INDArray[] covmean = covarianceMatrix(dataset);
this.covarianceMatrix = covmean[0];
this.mean = covmean[1];
INDArray[] pce = principalComponents(covmean[0]);
this.eigenvectors = pce[0];
this.eigenvalues = pce[1];
}
/**
* Return a reduced basis set that covers a certain fraction of the variance of the data
* @param variance The desired fractional variance (0 to 1), it will always be greater than the value.
* @return The basis vectors as columns, size N rows by ndims columns, where ndims is less than or equal to N
*/
public INDArray reducedBasis(double variance) {
INDArray vars = Transforms.pow(eigenvalues, -0.5, true);
double res = vars.sumNumber().doubleValue();
double total = 0.0;
int ndims = 0;
for (int i = 0; i < vars.columns(); i++) {
ndims++;
total += vars.getDouble(i);
if (total / res > variance)
break;
}
INDArray result = Nd4j.create(eigenvectors.rows(), ndims);
for (int i = 0; i < ndims; i++)
result.putColumn(i, eigenvectors.getColumn(i));
return result;
}
/**
* Takes a set of data on each row, with the same number of features as the constructing data
* and returns the data in the coordinates of the basis set about the mean.
* @param data Data of the same features used to construct the PCA object
* @return The record in terms of the principal component vectors, you can set unused ones to zero.
*/
public INDArray convertToComponents(INDArray data) {
INDArray dx = data.subRowVector(mean);
return Nd4j.tensorMmul(eigenvectors.transpose(), dx, new int[][] {{1}, {1}}).transposei();
}
/**
* Take the data that has been transformed to the principal components about the mean and
* transform it back into the original feature set. Make sure to fill in zeroes in columns
* where components were dropped!
* @param data Data of the same features used to construct the PCA object but as the components
* @return The records in terms of the original features
*/
public INDArray convertBackToFeatures(INDArray data) {
return Nd4j.tensorMmul(eigenvectors, data, new int[][] {{1}, {1}}).transposei().addiRowVector(mean);
}
/**
* Estimate the variance of a single record with reduced # of dimensions.
* @param data A single record with the same N features as the constructing data set
* @param ndims The number of dimensions to include in calculation
* @return The fraction (0 to 1) of the total variance covered by the ndims basis set.
*/
public double estimateVariance(INDArray data, int ndims) {
INDArray dx = data.sub(mean);
INDArray v = eigenvectors.transpose().mmul(dx.reshape(dx.columns(), 1));
INDArray t2 = Transforms.pow(v, 2);
double fraction = t2.get(NDArrayIndex.interval(0, ndims)).sumNumber().doubleValue();
double total = t2.sumNumber().doubleValue();
return fraction / total;
}
/**
* Generates a set of count random samples with the same variance and mean and eigenvector/values
* as the data set used to initialize the PCA object, with same number of features N.
* @param count The number of samples to generate
* @return A matrix of size count rows by N columns
*/
public INDArray generateGaussianSamples(int count) {
INDArray samples = Nd4j.randn(count, eigenvalues.columns());
INDArray factors = Transforms.pow(eigenvalues, -0.5, true);
samples.muliRowVector(factors);
return Nd4j.tensorMmul(eigenvectors, samples, new int[][] {{1}, {1}}).transposei().addiRowVector(mean);
}
/**
* Calculates pca vectors of a matrix, for a flags number of reduced features
* returns the reduced feature set
* The return is a projection of A onto principal nDims components
*
* To use the PCA: assume A is the original feature set
* then project A onto a reduced set of features. It is possible to
* reconstruct the original data ( losing information, but having the same
* dimensionality )
*
*
*
* @param A the array of features, rows are results, columns are features - will be changed
* @param nDims the number of components on which to project the features
* @param normalize whether to normalize (adjust each feature to have zero mean)
* @return the reduced parameters of A
*/
public static INDArray pca(INDArray A, int nDims, boolean normalize) {
INDArray factor = pca_factor(A, nDims, normalize);
return A.mmul(factor);
}
/**
* Calculates pca factors of a matrix, for a flags number of reduced features
* returns the factors to scale observations
*
* The return is a factor matrix to reduce (normalized) feature sets
*
* @see pca(INDArray, int, boolean)
*
* @param A the array of features, rows are results, columns are features - will be changed
* @param nDims the number of components on which to project the features
* @param normalize whether to normalize (adjust each feature to have zero mean)
* @return the reduced feature set
*/
public static INDArray pca_factor(INDArray A, int nDims, boolean normalize) {
if (normalize) {
// Normalize to mean 0 for each feature ( each column has 0 mean )
INDArray mean = A.mean(0);
A.subiRowVector(mean);
}
int m = A.rows();
int n = A.columns();
// The prepare SVD results, we'll decomp A to UxSxV'
INDArray s = Nd4j.create(m < n ? m : n);
INDArray VT = Nd4j.create(n, n, 'f');
// Note - we don't care about U
Nd4j.getBlasWrapper().lapack().gesvd(A, s, null, VT);
// for comparison k & nDims are the equivalent values in both methods implementing PCA
// So now let's rip out the appropriate number of left singular vectors from
// the V output (note we pulls rows since VT is a transpose of V)
INDArray V = VT.transpose();
INDArray factor = Nd4j.create(n, nDims, 'f');
for (int i = 0; i < nDims; i++) {
factor.putColumn(i, V.getColumn(i));
}
return factor;
}
/**
* Calculates pca reduced value of a matrix, for a given variance. A larger variance (99%)
* will result in a higher order feature set.
*
* The returned matrix is a projection of A onto principal components
*
* @see pca(INDArray, int, boolean)
*
* @param A the array of features, rows are results, columns are features - will be changed
* @param variance the amount of variance to preserve as a float 0 - 1
* @param normalize whether to normalize (set features to have zero mean)
* @return the matrix representing a reduced feature set
*/
public static INDArray pca(INDArray A, double variance, boolean normalize) {
INDArray factor = pca_factor(A, variance, normalize);
return A.mmul(factor);
}
/**
* Calculates pca vectors of a matrix, for a given variance. A larger variance (99%)
* will result in a higher order feature set.
*
* To use the returned factor: multiply feature(s) by the factor to get a reduced dimension
*
* INDArray Areduced = A.mmul( factor ) ;
*
* The array Areduced is a projection of A onto principal components
*
* @see pca(INDArray, double, boolean)
*
* @param A the array of features, rows are results, columns are features - will be changed
* @param variance the amount of variance to preserve as a float 0 - 1
* @param normalize whether to normalize (set features to have zero mean)
* @return the matrix to mulitiply a feature by to get a reduced feature set
*/
public static INDArray pca_factor(INDArray A, double variance, boolean normalize) {
if (normalize) {
// Normalize to mean 0 for each feature ( each column has 0 mean )
INDArray mean = A.mean(0);
A.subiRowVector(mean);
}
int m = A.rows();
int n = A.columns();
// The prepare SVD results, we'll decomp A to UxSxV'
INDArray s = Nd4j.create(m < n ? m : n);
INDArray VT = Nd4j.create(n, n, 'f');
// Note - we don't care about U
Nd4j.getBlasWrapper().lapack().gesvd(A, s, null, VT);
// Now convert the eigs of X into the eigs of the covariance matrix
for (int i = 0; i < s.length(); i++) {
s.putScalar(i, Math.sqrt(s.getDouble(i)) / (m - 1));
}
// Now find how many features we need to preserve the required variance
// Which is the same percentage as a cumulative sum of the eigenvalues' percentages
double totalEigSum = s.sumNumber().doubleValue() * variance;
int k = -1; // we will reduce to k dimensions
double runningTotal = 0;
for (int i = 0; i < s.length(); i++) {
runningTotal += s.getDouble(i);
if (runningTotal >= totalEigSum) { // OK I know it's a float, but what else can we do ?
k = i + 1; // we will keep this many features to preserve the reqd. variance
break;
}
}
if (k == -1) { // if we need everything
throw new RuntimeException("No reduction possible for reqd. variance - use smaller variance");
}
// So now let's rip out the appropriate number of left singular vectors from
// the V output (note we pulls rows since VT is a transpose of V)
INDArray V = VT.transpose();
INDArray factor = Nd4j.create(n, k, 'f');
for (int i = 0; i < k; i++) {
factor.putColumn(i, V.getColumn(i));
}
return factor;
}
/**
* This method performs a dimensionality reduction, including principal components
* that cover a fraction of the total variance of the system. It does all calculations
* about the mean.
* @param in A matrix of datapoints as rows, where column are features with fixed number N
* @param variance The desired fraction of the total variance required
* @return The reduced basis set
*/
public static INDArray pca2(INDArray in, double variance) {
// let's calculate the covariance and the mean
INDArray[] covmean = covarianceMatrix(in);
// use the covariance matrix (inverse) to find "force constants" and then break into orthonormal
// unit vector components
INDArray[] pce = principalComponents(covmean[0]);
// calculate the variance of each component
INDArray vars = Transforms.pow(pce[1], -0.5, true);
double res = vars.sumNumber().doubleValue();
double total = 0.0;
int ndims = 0;
for (int i = 0; i < vars.columns(); i++) {
ndims++;
total += vars.getDouble(i);
if (total / res > variance)
break;
}
INDArray result = Nd4j.create(in.columns(), ndims);
for (int i = 0; i < ndims; i++)
result.putColumn(i, pce[0].getColumn(i));
return result;
}
/**
* Returns the covariance matrix of a data set of many records, each with N features.
* It also returns the average values, which are usually going to be important since in this
* version, all modes are centered around the mean. It's a matrix that has elements that are
* expressed as average dx_i * dx_j (used in procedure) or average x_i * x_j - average x_i * average x_j
*
* @param in A matrix of vectors of fixed length N (N features) on each row
* @return INDArray[2], an N x N covariance matrix is element 0, and the average values is element 1.
*/
public static INDArray[] covarianceMatrix(INDArray in) {
int dlength = in.rows();
int vlength = in.columns();
INDArray sum = Nd4j.create(vlength);
INDArray product = Nd4j.create(vlength, vlength);
for (int i = 0; i < vlength; i++)
sum.getColumn(i).assign(in.getColumn(i).sumNumber().doubleValue() / dlength);
for (int i = 0; i < dlength; i++) {
INDArray dx1 = in.getRow(i).sub(sum);
product.addi(dx1.reshape(vlength, 1).mmul(dx1.reshape(1, vlength)));
}
product.divi(dlength);
return new INDArray[] {product, sum};
}
/**
* Calculates the principal component vectors and their eigenvalues (lambda) for the covariance matrix.
* The result includes two things: the eigenvectors (modes) as result[0] and the eigenvalues (lambda)
* as result[1].
*
* @param cov The covariance matrix (calculated with the covarianceMatrix(in) method)
* @return Array INDArray[2] "result". The principal component vectors in decreasing flexibility are
* the columns of element 0 and the eigenvalues are element 1.
*/
public static INDArray[] principalComponents(INDArray cov) {
assert cov.rows() == cov.columns();
INDArray[] result = new INDArray[2];
result[0] = Nd4j.eye(cov.rows());
result[1] = Eigen.symmetricGeneralizedEigenvalues(result[0], cov, true);
return result;
}
public INDArray getCovarianceMatrix() {
return covarianceMatrix;
}
public INDArray getMean() {
return mean;
}
public INDArray getEigenvectors() {
return eigenvectors;
}
public INDArray getEigenvalues() {
return eigenvalues;
}
}
