PCA用SVD來實現
SVD(奇異值分解)是線性代數中一個常見的decomposition；PCA也是dimension reduction領域中的經典之作。初學者在學習PCA的時候可能會對PCA的演算法步驟有那麼一些“繁瑣”的感覺。結合svd分解，會讓你在編寫PCA演算法的時候達到一種什麼樣的得心應手的程度呢？且聽說慢慢道來 先簡單描述一下PCA的演算法步驟（當然，你要對PCA有所理解啦，不甚理解也行，僅從程式設計師的角度一步一步地編程式碼也能實現）。步驟如下：
在compute eigvector這一步後，選擇eigvectors中的前k個作為主成分。如果用SVD來做，又怎麼樣呢？
step1: X = [X1; X2; ..... Xi], each Xj is a row data point;
step2: Substract the mean from X
step3: Solve SVD decomposition: X = U*S*V'(V'是V的轉置)
step4: 選擇要降的維數k, 取V的前k個column作為主成分。
看到沒有，一個SVD分解就把主成分取出來了，很方便吧。現在在回過頭來想想，為什麼可以這麼做呢？
記憶一下線性代數中的特徵值和特徵向量的定義：
Ax = bx, b是特徵值，x是特徵向量..........(1)
若在A中每一個data point是一個row的話，那麼要求A的主要成分，根據PCA演算法，就是要求出A'A這個矩陣的特徵向量的前 k個column(注意這些特徵向量是按對應的特徵值的從大到小排列的)。又根據svd分解有：
A = U*S*V'; 而 (A'*A)*V = (U*S*V')' * (U*S*V') * V = V*S'*U' * (U*S*V')*V = V*S'*(U'*U)*S* (V'*V) = V*(S'*S)*E*E (E是單位矩陣) = （S的平方）*V (S在對角線上才有值，其餘全為0)....(2)
對照(1)(2)式我們可以看到，A的SVD分解出來的V就是(A'*A)這個矩陣的特徵向量！所以PCA演算法中我們不需要計算擴散矩陣(A'*A)，對A進行SVD分解，得到V，取V的前k個columns即可。
/*
PCA program (using SVD)
Written by Y. Bin Mao
Video and Image Processing and Analysis Group (VIPAG)
School of Automation, NJUST
Jan. 8, 2008
All rights reserved. (c)
Here is a matlab description of the algorithm
% PCA2: Perform PCA using SVD.
% data --- MxN matrix of input data ( M dimensions, N trials )
% signals --- MxN matrix of projected data
% PC --- each column is a PC
% V --- Mx1 matrix of variances
%
function [signals, PC, V] = pca2( data )
[M, N] = size( data );
% subtract off the mean for each dimension
mn = mean( data, 2 );
data = data - repmat( mn, 1, N );
% construct the matrix Y
Y = data' / sqrt(N-1);
% SVD does it all
[u, S, PC] = svd( Y );
% calculate the variances
S = diag( S );
V = S .* S;
% project the original data
signals = PC' * data;
*/
# include <stdio.h>
# include <stdlib.h>
# include <math.h>
void ppp( double a[], double e[], double s[],
double v[], int m, int n )
{
int i,j,p,q;
double d;
if ( m >= n ) i = n;
else i = m;
for ( j = 1; j <= i-1; j++ )
{
a[(j-1)*n+j-1] = s[j-1];
a[(j-1)*n+j] = e[j-1];
}
a[(i-1)*n+i-1] = s[i-1];
if ( m < n ) a[(i-1)*n+i] = e[i-1];
for ( i = 1; i <= n-1; i++ )
for ( j = i+1; j <= n; j++ )
{
p = (i-1)*n+j-1; q = (j-1)*n+i-1;
d = v[p]; v[p] = v[q]; v[q] = d;
}
return;
}
void sss( double fg[2], double cs[2] )
{
double r, d;
if ( ( fabs(fg[0]) + fabs(fg[1] ) ) == 0.0 )
{
cs[0] = 1.0; cs[1] = 0.0; d = 0.0;
}
else
{
d = sqrt( fg[0]*fg[0]+fg[1]*fg[1] );
if ( fabs( fg[0] ) > fabs( fg[1] ) )
{
d = fabs(d);
if ( fg[0] < 0.0 ) d = -d;
}
if ( fabs( fg[1] ) >= fabs( fg[0] ) )
{
d = fabs(d);
if ( fg[1] < 0.0 ) d = -d;
}
cs[0] = fg[0]/d; cs[1] = fg[1]/d;
}
r = 1.0;
if ( fabs( fg[0] ) > fabs( fg[1] ) )
r = cs[1];
else
if ( cs[0] != 0.0 ) r = 1.0/cs[0];
fg[0] = d; fg[1] = r;
return;
}
/*
一般實矩陣奇異值分解
徐士良. 常用演算法程式集（C語言描述），第版. 清華大學出版社. 2004
double a[m][n] --- 存放mxn維實矩陣A。返回時其對角線給出奇異值（以非遞增次序排列）
其餘元素均為
int m, int n --- 實矩陣A的行數和列數
double u[m][m] --- 返回左奇異向量U
double v[n][n] --- 返回右奇異向量V'
double eps --- 給定的精度要求
int ka --- 其值為max(m, n) + 1
返回值：
若返回標誌值小於，則表示程式工作失敗；
若返回標誌值大於，則表示正常返回
*/
int svd( double a[], int m, int n, double u[], double v[],
double eps, int ka )
{
int i, j, k, l, it, ll, kk, ix, iy, mm, nn, iz, m1, ks;
double d, dd, t, sm, sm1, em1, sk, ek, b, c, shh, fg[2], cs[2];
double * s, * e, * w;
s = ( double * )malloc( ka * sizeof(double) );
e = ( double * )malloc( ka * sizeof(double) );
w = ( double * )malloc( ka * sizeof(double) );
it = 60; k = n;
if ( m-1 < n ) k = m-1;
l = m;
if ( n-2 < m ) l = n-2;
if ( l < 0 ) l = 0;
ll = k;
if ( l > k ) ll = l;
if ( ll >= 1 )
{
for ( kk = 1; kk <= ll; kk++ )
{
if ( kk <= k )
{
d = 0.0;
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*n+kk-1; d = d+a[ix]*a[ix];
}
s[kk-1] = sqrt(d);
if ( s[kk-1] != 0.0 )
{
ix = (kk-1)*n+kk-1;
if ( a[ix] != 0.0 )
{
s[kk-1] = fabs( s[kk-1] );
if ( a[ix] < 0.0 ) s[kk-1] = -s[kk-1];
}
for ( i = kk; i <= m; i++ )
{
iy = (i-1)*n+kk-1;
a[iy] = a[iy]/s[kk-1];
}
a[ix] = 1.0+a[ix];
}
s[kk-1] = -s[kk-1];
}
if ( n >= kk+1 )
{
for ( j = kk+1; j <= n; j++ )
{
if (( kk <= k ) && ( s[kk-1] != 0.0 ) )
{
d = 0.0;
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*n+kk-1;
iy = (i-1)*n+j-1;
d = d+a[ix]*a[iy];
}
d = -d/a[(kk-1)*n+kk-1];
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*n+j-1;
iy = (i-1)*n+kk-1;
a[ix] = a[ix]+d*a[iy];
}
}
e[j-1] = a[(kk-1)*n+j-1];
}
}
if ( kk <= k )
{
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*m+kk-1;
iy = (i-1)*n+kk-1;
u[ix] = a[iy];
}
}
if ( kk <= l )
{
d = 0.0;
for ( i = kk+1; i <= n; i++ )
d = d + e[i-1]*e[i-1];
e[kk-1] = sqrt(d);
if ( e[kk-1] != 0.0 )
{
if ( e[kk] != 0.0 )
{
e[kk-1] = fabs(e[kk-1]);
if ( e[kk] < 0.0 ) e[kk-1] = -e[kk-1];
}
for ( i = kk+1; i <= n; i++ )
e[i-1] = e[i-1]/e[kk-1];
e[kk] = 1.0+e[kk];
}
e[kk-1] = -e[kk-1];
if (( kk+1 <= m ) && ( e[kk-1] != 0.0 ) )
{
for ( i = kk+1; i <= m; i++ ) w[i-1] = 0.0;
for ( j = kk+1; j <= n; j++)
for ( i = kk+1; i <= m; i++ )
w[i-1] = w[i-1]+e[j-1]*a[(i-1)*n+j-1];
for ( j = kk+1; j <= n; j++ )
for ( i = kk+1; i <= m; i++ )
{
ix = (i-1)*n+j-1;
a[ix] = a[ix]-w[i-1]*e[j-1]/e[kk];
}
}
for ( i = kk+1; i <= n; i++ )
v[(i-1)*n+kk-1] = e[i-1];
}
}
}
mm = n;
if ( m+1 < n ) mm = m+1;
if ( k < n ) s[k] = a[k*n+k];
if ( m < mm ) s[mm-1] = 0.0;
if ( l+1 < mm) e[l] = a[l*n+mm-1];
e[mm-1] = 0.0;
nn = m;
if ( m > n ) nn = n;
if ( nn >= k+1 )
{
for ( j = k+1; j <= nn; j++ )
{
for ( i = 1; i <= m; i++ )
u[(i-1)*m+j-1] = 0.0;
u[(j-1)*m+j-1] = 1.0;
}
}
if ( k >= 1)
{
for (ll = 1; ll <= k; ll++ )
{
kk = k-ll+1; iz = (kk-1)*m+kk-1;
if ( s[kk-1] != 0.0 )
{
if ( nn >= kk+1 )
for ( j = kk+1; j <= nn; j++ )
{
d = 0.0;
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*m+kk-1;
iy = (i-1)*m+j-1;
d = d+u[ix]*u[iy]/u[iz];
}
d = -d;
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*m+j-1;
iy = (i-1)*m+kk-1;
u[ix] = u[ix]+d*u[iy];
}
}
for ( i = kk; i <= m; i++ )
{
ix = (i-1)*m+kk-1; u[ix] = -u[ix];
}
u[iz] = 1.0+u[iz];
if ( kk-1 >= 1 )
for ( i = 1; i <= kk-1; i++ )
u[(i-1)*m+kk-1] = 0.0;
}
else
{
for ( i = 1; i <= m; i++ )
u[(i-1)*m+kk-1] = 0.0;
u[(kk-1)*m+kk-1] = 1.0;
}
}
}
for ( ll = 1; ll <= n; ll++ )
{
kk = n-ll+1; iz = kk*n+kk-1;
if ( (kk<=l) && (e[kk-1] != 0.0) )
{
for ( j = kk+1; j <= n; j++ )
{
d = 0.0;
for ( i = kk+1; i <= n; i++ )
{
ix = (i-1)*n+kk-1; iy = (i-1)*n+j-1;
d = d+v[ix]*v[iy]/v[iz];
}
d = -d;
for ( i = kk+1; i <= n; i++ )
{
ix = (i-1)*n+j-1; iy = (i-1)*n+kk-1;
v[ix] = v[ix]+d*v[iy];
}
}
}
for ( i = 1; i <= n; i++ )
v[(i-1)*n+kk-1] = 0.0;
v[iz-n] = 1.0;
}
for ( i = 1; i <= m; i++ )
for ( j = 1; j <= n; j++ )
a[(i-1)*n+j-1] = 0.0;
m1 = mm; it = 60;
while ( 1==1 )
{
if ( mm == 0 )
{
ppp( a, e, s, v, m, n );
free( s );
free( e );
free( w );
return( 1 );
}
if ( it == 0 )
{
ppp( a, e, s, v, m, n );
free( s );
free( e );
free( w );
return( -1 );
}
kk = mm-1;
while ( (kk != 0) && (fabs(e[kk-1]) != 0.0) )
{
d = fabs(s[kk-1])+fabs(s[kk]);
dd = fabs(e[kk-1]);
if ( dd > eps*d )
kk = kk-1;
else
e[kk-1] = 0.0;
}
if ( kk == mm-1 )
{
kk = kk+1;
if ( s[kk-1] < 0.0 )
{
s[kk-1] = -s[kk-1];
for ( i = 1; i <= n; i++ )
{
ix = (i-1)*n+kk-1;
v[ix] = -v[ix];
}
}
while ( (kk!=m1) && (s[kk-1] < s[kk]) )
{
d = s[kk-1];
s[kk-1] = s[kk];
s[kk] = d;
if ( kk < n )
for (i=1; i<=n; i++)
{
ix = (i-1)*n+kk-1; iy = (i-1)*n+kk;
d = v[ix]; v[ix] = v[iy]; v[iy] = d;
}
if ( kk < m )
for ( i = 1; i <= m; i++ )
{
ix = (i-1)*m+kk-1; iy = (i-1)*m+kk;
d = u[ix]; u[ix] = u[iy]; u[iy] = d;
}
kk = kk+1;
}
it = 60;
mm = mm-1;
}
else
{
ks = mm;
while ( (ks>kk) && (fabs(s[ks-1]) != 0.0 ) )
{
d = 0.0;
if ( ks != mm ) d = d+fabs(e[ks-1]);
if ( ks != kk+1 ) d = d+fabs(e[ks-2]);
dd = fabs(s[ks-1]);
if ( dd > eps*d ) ks = ks-1;
else s[ks-1] = 0.0;
}
if ( ks == kk )
{
kk = kk+1;
d = fabs(s[mm-1]);
t = fabs(s[mm-2]);
if ( t > d ) d = t;
t = fabs( e[mm-2] );
if ( t > d ) d = t;
t = fabs( s[kk-1] );
if ( t > d ) d = t;
t = fabs( e[kk-1] );
if ( t > d ) d = t;
sm = s[mm-1]/d; sm1 = s[mm-2]/d;
em1 = e[mm-2]/d;
sk = s[kk-1]/d; ek = e[kk-1]/d;
b = ((sm1+sm)*(sm1-sm)+em1*em1)/2.0;
c = sm*em1; c = c*c; shh = 0.0;
if ( (b!=0.0) || (c!=0.0) )
{
shh = sqrt( b*b+c );
if ( b < 0.0 ) shh = -shh;
shh = c/(b+shh);
}
fg[0] = (sk+sm)*(sk-sm)-shh;
fg[1] = sk*ek;
for ( i = kk; i <= mm-1; i++ )
{
sss( fg, cs );
if ( i != kk ) e[i-2] = fg[0];
fg[0] = cs[0]*s[i-1]+cs[1]*e[i-1];
e[i-1] = cs[0]*e[i-1]-cs[1]*s[i-1];
fg[1] = cs[1]*s[i];
s[i] = cs[0]*s[i];
if ( (cs[0] != 1.0) || (cs[1] != 0.0) )
for ( j = 1; j <= n; j++ )
{
ix = (j-1)*n+i-1;
iy = (j-1)*n+i;
d = cs[0]*v[ix]+cs[1]*v[iy];
v[iy] = -cs[1]*v[ix]+cs[0]*v[iy];
v[ix] = d;
}
sss( fg, cs );
s[i-1] = fg[0];
fg[0] = cs[0]*e[i-1]+cs[1]*s[i];
s[i] = -cs[1]*e[i-1]+cs[0]*s[i];
fg[1] = cs[1]*e[i];
e[i] = cs[0]*e[i];
if ( i < m )
if ( ( cs[0] != 1.0 ) || ( cs[1] != 0.0 ) )
for ( j = 1; j <= m; j++ )
{
ix = (j-1)*m+i-1;
iy = (j-1)*m+i;
d = cs[0]*u[ix]+cs[1]*u[iy];
u[iy] = -cs[1]*u[ix]+cs[0]*u[iy];
u[ix] = d;
}
}
e[mm-2] = fg[0];
it = it-1;
}
else
{
if ( ks == mm )
{
kk = kk+1;
fg[1] = e[mm-2]; e[mm-2] = 0.0;
for ( ll = kk; ll <= mm-1; ll++ )
{
i = mm+kk-ll-1;
fg[0] = s[i-1];
sss( fg, cs );
s[i-1] = fg[0];
if ( i != kk )
{
fg[1] = -cs[1]*e[i-2];
e[i-2] = cs[0]*e[i-2];
}
if ( (cs[0]!=1.0)||(cs[1]!=0.0) )
for ( j = 1; j <= n; j++ )
{
ix = (j-1)*n+i-1;
iy = (j-1)*n+mm-1;
d = cs[0]*v[ix]+cs[1]*v[iy];
v[iy] = -cs[1]*v[ix]+cs[0]*v[iy];
v[ix] = d;
}
}
}
else
{
kk = ks+1;
fg[1] = e[kk-2];
e[kk-2] = 0.0;
for ( i = kk; i <= mm; i++ )
{
fg[0] = s[i-1];
sss( fg, cs );
s[i-1] = fg[0];
fg[1] = -cs[1]*e[i-1];
e[i-1] = cs[0]*e[i-1];
if ( (cs[0]!=1.0)||(cs[1]!=0.0) )
for (j=1; j<=m; j++)
{
ix = (j-1)*m+i-1;
iy = (j-1)*m+kk-2;
d = cs[0]*u[ix]+cs[1]*u[iy];
u[iy] = -cs[1]*u[ix]+cs[0]*u[iy];
u[ix] = d;
}
}
}
}
}
}
return( 1 );
}
# define EPS 0.000001
/*
PCA2: Perform PCA using SVD.
data --- MxN matrix of input data ( M dimensions, N trials )
signals --- MxN matrix of projected data
PC --- each column is a PC
V --- Mx1 matrix of variances
row = M dimensions, col = N trials
*/
int pca2( double * data, int row, int col,
double * signals, double * PC, double * V )
{
int x, y, i, ka, rvalue;
double * mean;
double * u;
double * d;
double * v;
double * sd;
double * data1;
double sqrt_col_1;
int col1, row1;
if ( row <= 1 || col <= 1 ) return( -1 );
/* subtract off the mean for each dimension */
mean = ( double * )malloc( sizeof( double )*row );
data1 = ( double * ) malloc( sizeof( double )*row*col );
for ( y = 0; y < row; y++ ) /* calculate mean */
{
mean[y] = 0;
for ( x = 0; x < col; x++ )
mean[y] += data[y*col+x];
}
for ( y = 0; y < row; y++ ) mean[y] = mean[y]/col;
for ( y = 0; y < row; y++ ) /* subtract mean */
for ( x = 0; x < col; x++ )
{
data1[y*col+x] = data[y*col+x]-mean[y];
}
free( mean );
/* construct the matrix Y: Y = data' / sqrt(col-1); */
/* construct the matrix Y: Y = data' / sqrt(col-1); */
sqrt_col_1 = sqrt(col-1.0);
row1 = col;
col1 = row;
sd = (double *)malloc( sizeof(double)*col1*row1 );
u = (double *)malloc( sizeof(double)*row1*row1 );
v = (double *)malloc( sizeof(double)*col1*col1 );
for ( y = 0; y < row1; y++ )
for ( x = 0; x < col1; x++ )
{
sd[y*col1+x] = data1[x*row1+y]/sqrt_col_1;
}
/* SVD does it all: [u, S, PC] = svd( Y ); */
if ( row1 >= col1 )
ka = row1+1;
else
ka = col1+1;
rvalue = svd( sd, row1, col1, u, v, EPS, ka ); /* svd decomposition */
d = (double *)malloc( sizeof(double) * col1 );
for ( i = 0; i < col1; i++ ) d[i] = 0;
if ( row1 <= col1 )
{
for ( i = 0; i < row1; i++ )
d[i] = sd[i*col1+i];
}
else
{
for ( i = 0; i < col1; i++ )
d[i] = sd[i*col1+i];
}
/* calculate the variances: S = diag( S ); V = S .* S; */
for ( x = 0; x < col1; x++ )
V[x] = d[x] * d[x];
/* get PC */
for ( y = 0; y < col1; y++ )
for ( x = 0; x < col1; x++ )
{
PC[y*col1+x] = v[x*col1+y];
}
/* project the original data: signals = PC' * data; */
for ( y = 0; y < row; y++ )
for ( x = 0; x < col; x++ )
{
signals[y*col+x] = 0;
for ( i = 0; i < row; i++ )
signals[y*col+x] += PC[i*row+y] * data1[i*col+x];
}
free( u );
free( v );
free( sd );
free( d );
free( data1 );
return( 1 );
}
/*
main function
*/
int main()
{
double data[20] = { 2, 3, 8, 2, 3,
7, 9, 29, 3, 5,
3, 8, 22, 12, 1,
3, 12, 12, 33, 2};
int row = 4, col = 5;
double signals[20], PC[16], V[4];
int x, y;
pca2( data, row, col, signals, PC, V );
printf( "Project to Principal Component: \n" );
for ( y = 0; y < row; y++ )
{
for ( x = 0; x < col; x++ )
{
printf( "%7.4f ", signals[y*col+x] );
}
printf( "\n" );
}
printf( "Eigen Values (in deceasing order): \n" );
for ( y = 0; y < row; y++ )
printf( "%7.4f ", V[y] );
printf( "\n" );
printf( "Eigen Vectors: \n" );
for ( y = 0; y < row; y++ )
{
for ( x = 0; x < row; x++ )
{
printf( "%7.4f ", PC[y*row+x] );
}
printf( "\n" );
}
return( 1 );
}
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