iii
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@ -203,7 +203,7 @@ class LplsXCorrelationPlot(BlmScatterPlot):
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facecolor='gray',
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alpha=.1,
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zorder=1)
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c50 = patches.Circle(center, radius=radius/2.0,
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c50 = patches.Circle(center, radius= sqrt(radius/2.0),
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facecolor='gray',
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alpha=.1,
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zorder=2)
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@ -228,7 +228,7 @@ class LplsZCorrelationPlot(BlmScatterPlot):
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facecolor='gray',
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alpha=.1,
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zorder=1)
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c50 = patches.Circle(center, radius=radius/2.0,
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c50 = patches.Circle(center, radius=sqrt(radius/2.0),
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facecolor='gray',
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alpha=.1,
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zorder=2)
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@ -14,6 +14,7 @@ try:
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except:
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has_sym = False
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def pca(a, aopt,scale='scores',mode='normal',center_axis=0):
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""" Principal Component Analysis.
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@ -187,7 +188,7 @@ def pcr(a, b, aopt, scale='scores',mode='normal',center_axis=0):
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dat.update({'Q':Q, 'F':F, 'expvary':expvary})
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return dat
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def pls(a, b, aopt=2, scale='scores', mode='normal', ax_center=0, ab=None):
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def pls(a, b, aopt=2, scale='scores', mode='normal', center_axis=0, ab=None):
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"""Partial Least Squares Regression.
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Performs PLS on given matrix and returns results in a dictionary.
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@ -244,6 +245,10 @@ def pls(a, b, aopt=2, scale='scores', mode='normal', ax_center=0, ab=None):
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assert(m==mm)
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else:
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k, l = m_shape(b)
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if center_axis>=0:
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a = a - expand_dims(a.mean(center_axis), center_axis)
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b = b - expand_dims(b.mean(center_axis), center_axis)
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W = empty((n, aopt))
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P = empty((n, aopt))
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@ -255,25 +260,28 @@ def pls(a, b, aopt=2, scale='scores', mode='normal', ax_center=0, ab=None):
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if ab==None:
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ab = dot(a.T, b)
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for i in range(aopt):
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if ab.shape[1]==1:
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if ab.shape[1]==1: #pls 1
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w = ab.reshape(n, l)
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w = w/vnorm(w)
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elif n<l:
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elif n<l: # more yvars than xvars
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if has_sym:
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s, u = symeig(dot(ab.T, ab),range=[l,l],overwrite=True)
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s, u = symeig(dot(ab, ab.T),range=[l,l],overwrite=True)
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else:
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u, s, vh = svd(dot(ab, ab.T))
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w = u[:,0]
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else:
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else: # standard wide xdata
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if has_sym:
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s, u = symeig(dot(ab.T, ab),range=[l,l],overwrite=True)
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s, q = symeig(dot(ab.T, ab),range=[l,l],overwrite=True)
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else:
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u, s, vh = svd(dot(ab.T, ab))
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w = dot(ab, u)
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q, s, vh = svd(dot(ab.T, ab))
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q = q[:,:1]
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w = dot(ab, q)
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w = w/vnorm(w)
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r = w.copy()
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if i>0:
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for j in range(0, i, 1):
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r = r - dot(P[:,j].T, w)*R[:,j][:,newaxis]
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print vnorm(r)
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t = dot(a, r)
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tt = vnorm(t)**2
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p = dot(a.T, t)/tt
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@ -345,9 +353,13 @@ def w_pls(aat, b, aopt):
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""" Pls for wide matrices.
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Fast pls for crossval, used in calc rmsep for wide X
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There is no P or W. T is normalised
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aat = centered kernel matrix
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b = centered y
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"""
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bb = b.copy()
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m, m = aat.shape
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k, l = m_shape(b)
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m, m = m_shape(aat)
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U = empty((m, aopt)) # W
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T = empty((m, aopt))
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R = empty((m, aopt)) # R
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@ -355,23 +367,28 @@ def w_pls(aat, b, aopt):
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for i in range(aopt):
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if has_sym:
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pass
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s, q = symeig(dot(dot(b.T, aat), b), range=(l,l),overwrite=True)
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else:
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q, s, vh = svd(dot(dot(b.T, aat), b), full_matrices=0)
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q = q[:,:1]
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u = dot(b , q) #y-factor scores
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U[:,i] = u.ravel()
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t = dot(aat, u)
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print "Norm of t: %s" %vnorm(t)
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print "s: %s" %s
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t = t/vnorm(t)
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T[:,i] = t.ravel()
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r = dot(aat, t) #score-weights
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r = dot(aat, t)#score-weights
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#r = r/vnorm(r)
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print "Norm R: %s" %vnorm(r)
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R[:,i] = r.ravel()
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PROJ[:,: i+1] = dot(T[:,:i+1], inv(dot(T[:,:i+1].T, R[:,:i+1])) )
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if i<aopt:
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b = b - dot(PROJ[:,:i+1], dot(R[:,:i+1].T,b) )
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b = b - dot(PROJ[:,:i+1], dot(R[:,:i+1].T, b) )
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C = dot(bb.T, T)
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return {'T':T, 'U':U, 'Q':C, 'H':H}
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return {'T':T, 'U':U, 'Q':C, 'R':R}
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def bridge(a, b, aopt, scale='scores', mode='normal', r=0):
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"""Undeflated Ridged svd(X'Y)
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@ -476,6 +493,8 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], mode='normal', sca
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P = empty((n, a_max))
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K = empty((o, a_max))
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L = empty((u, a_max))
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B = empty((a_max, n, l))
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b0 = empty((a_max, m, l))
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var_x = empty((a_max,))
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var_y = empty((a_max,))
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var_z = empty((a_max,))
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@ -485,8 +504,8 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], mode='normal', sca
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print "\n Working on comp. %s" %a
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u = Y[:,:1]
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diff = 1
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MAX_ITER = 100
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lim = 1e-5
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MAX_ITER = 200
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lim = 1e-16
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niter = 0
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while (diff>lim and niter<MAX_ITER):
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niter += 1
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@ -526,8 +545,8 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], mode='normal', sca
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var_y[a] = pow(Y, 2).sum()
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var_z[a] = pow(Z, 2).sum()
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B = dot(dot(W, inv(dot(P.T, W))), Q.T)
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b0 = mnY - dot(mnX, B)
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B[a] = dot(dot(W[:,:a+1], inv(dot(P[:,:a+1].T, W[:,:a+1]))), Q[:,:a+1].T)
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b0[a] = mnY - dot(mnX, B[a])
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# variance explained
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evx = 100.0*(1 - var_x/varX)
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@ -546,6 +565,116 @@ def nipals_lpls(X, Y, Z, a_max, alpha=.7, mean_ctr=[2, 0, 1], mode='normal', sca
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def nipals_pls(X, Y, a_max, alpha=.7, ax_center=0, mode='normal', scale='scores', verbose=False):
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"""Partial Least Sqaures Regression by the nipals algorithm.
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(X!Z)->Y
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:input:
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X : data matrix (m, n)
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Y : data matrix (m, l)
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:output:
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T : X-scores
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W : X-weights/Z-weights
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P : X-loadings
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Q : Y-loadings
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U : X-Y relation
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B : Regression coefficients X->Y
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b0: Regression coefficient intercept
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evx : X-explained variance
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evy : Y-explained variance
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evz : Z-explained variance
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:Notes:
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"""
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if ax_center>=0:
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mn_x = expand_dims(X.mean(ax_center), ax_center)
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mn_y = expand_dims(Y.mean(ax_center), ax_center)
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X = X - mn_x
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Y = Y - mn_y
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varX = pow(X, 2).sum()
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varY = pow(Y, 2).sum()
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m, n = X.shape
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k, l = Y.shape
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# initialize
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U = empty((k, a_max))
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Q = empty((l, a_max))
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T = empty((m, a_max))
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W = empty((n, a_max))
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P = empty((n, a_max))
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B = empty((a_max, n, l))
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b0 = empty((a_max, m, l))
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var_x = empty((a_max,))
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var_y = empty((a_max,))
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t1 = X[:,:1]
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for a in range(a_max):
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if verbose:
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print "\n Working on comp. %s" %a
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u = Y[:,:1]
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diff = 1
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MAX_ITER = 100
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lim = 1e-16
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niter = 0
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while (diff>lim and niter<MAX_ITER):
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niter += 1
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#u1 = u.copy()
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w = dot(X.T, u)
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w = w/sqrt(dot(w.T, w))
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#l = dot(Z, w)
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#k = dot(Z.T, l)
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#k = k/sqrt(dot(k.T, k))
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#w = alpha*k + (1-alpha)*w
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#w = w/sqrt(dot(w.T, w))
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t = dot(X, w)
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q = dot(Y.T, t)
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q = q/sqrt(dot(q.T, q))
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u = dot(Y, q)
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diff = vnorm(t1 - t)
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t1 = t.copy()
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if verbose:
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print "Converged after %s iterations" %niter
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#tt = dot(t.T, t)
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#p = dot(X.T, t)/tt
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#q = dot(Y.T, t)/tt
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#l = dot(Z, w)
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p = dot(X.T, t)/dot(t.T, t)
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p_norm = vnorm(p)
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t = t*p_norm
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w = w*p_norm
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p = p/p_norm
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U[:,a] = u.ravel()
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W[:,a] = w.ravel()
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P[:,a] = p.ravel()
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T[:,a] = t.ravel()
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Q[:,a] = q.ravel()
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X = X - dot(t, p.T)
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Y = Y - dot(t, q.T)
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var_x[a] = pow(X, 2).sum()
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var_y[a] = pow(Y, 2).sum()
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B[a] = dot(dot(W[:,:a+1], inv(dot(P[:,:a+1].T, W[:,:a+1]))), Q[:,:a+1].T)
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b0[a] = mn_y - dot(mn_x, B[a])
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# variance explained
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evx = 100.0*(1 - var_x/varX)
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evy = 100.0*(1 - var_y/varY)
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if scale=='loads':
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tnorm = apply_along_axis(vnorm, 0, T)
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T = T/tnorm
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W = W*tnorm
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Q = Q*tnorm
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return {'T':T, 'W':W, 'P':P, 'Q':Q, 'U':U, 'B':B, 'b0':b0, 'evx':evx, 'evy':evy}
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########### Helper routines #########
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@ -1,7 +1,7 @@
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"""This module implements some common validation schemes from pca and pls.
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"""
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from scipy import ones,mean,sqrt,dot,newaxis,zeros,sum,empty,\
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apply_along_axis,eye,kron,array,sort
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apply_along_axis,eye,kron,array,sort,zeros_like,argmax
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from scipy.stats import median
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from scipy.linalg import triu,inv,svd,norm
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@ -122,7 +122,7 @@ def lpls_val(X, Y, Z, a_max=2, nsets=None,alpha=.5):
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B = dat['B']
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b0 = dat['b0']
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for a in range(a_max):
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Yhat[a,ind,:] = b0[a][0][0] + dot(xi, B[a])
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Yhat[a,ind,:] = b0[a][0][0] + dot(xi-xcal.mean(0), B[a])
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Yhat_class = zeros_like(Yhat)
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for a in range(a_max):
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for i in range(k):
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@ -132,7 +132,7 @@ text.dvipnghack : False # some versions of dvipng don't handle
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# default fontsizes for ticklabels, and so on. See
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# http://matplotlib.sourceforge.net/matplotlib.axes.html#Axes
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axes.hold : True # whether to clear the axes by default on
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axes.facecolor : white # axes background color
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axes.facecolor : 0.6 # axes background color
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axes.edgecolor : black # axes edge color
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axes.linewidth : 1.0 # edge linewidth
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axes.grid : True # display grid or not
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