def sarkar_embedding_3D(tree, root, **kwargs):
eps = kwargs.get("eps",0.1)
weighted = kwargs.get("weighted", True)
tau = kwargs.get("tau")
max_deg = max(tree.degree)[1]
if tau is None:
tau = (1+eps)/eps * mpm.log(2*max_deg/ mpm.pi)
prc = kwargs.get("precision")
if prc is None:
prc = _embedding_precision(tree,root,eps)
mpm.mp.dps = prc
n = tree.order()
emb = mpm.zeros(n,3)
place = []
# place the children of root
fib = fib_2D_code(tree.degree[root])
for i, v in enumerate(tree[root]):
r = mpm.tanh(tau*tree[root][v].get("weight",1.))
v_emb = r * mpm.matrix([[fib[i,0],fib[i,1],fib[i,2]]])
emb[v,:]=v_emb
place.append((root,v))
while place:
u, v = place.pop() # u is the parent of v
u_emb, v_emb = emb[u,:], emb[v,:]
# reflect and rotate so that embedding(v) is at (0,0,0)
# and embedding(u) is in the direction of (0,0,1)
u_emb = poincare_reflect0(v_emb, u_emb, precision=prc)
R = rotate_3D_mp(mpm.matrix([[0.,0.,1.]]), u_emb)
#u_emb = (R.T * u_emb).T
# place children of v
fib = fib_2D_code(tree.degree[v])
i=0
for w in tree[v]:
if w == u: # i=0 is for u (parent of v)
continue
i+=1
r = mpm.tanh(tau*tree[w][v].get("weight",1.))
w_emb = r * mpm.matrix([[fib[i,0],fib[i,1],fib[i,2]]])
#undo reflection and rotation
w_emb = (R * w_emb.T).T
w_emb = poincare_reflect0(v_emb, w_emb, precision=prc)
emb[w,:] = w_emb
place.append((v,w))
return emb
def tanh_warp_arb(X, l1, l2, lw, x0):
r"""Warps the `X` coordinate with the tanh model
.. math::
l = \frac{l_1 + l_2}{2} - \frac{l_1 - l_2}{2}\tanh\frac{x-x_0}{l_w}
Parameters
----------
X : :py:class:`Array`, (`M`,) or scalar float
`M` locations to evaluate length scale at.
l1 : positive float
Small-`X` saturation value of the length scale.
l2 : positive float
Large-`X` saturation value of the length scale.
lw : positive float
Length scale of the transition between the two length scales.
x0 : float
Location of the center of the transition between the two length scales.
Returns
-------
l : :py:class:`Array`, (`M`,) or scalar float
The value of the length scale at the specified point.
"""
if isinstance(X, scipy.ndarray):
if isinstance(X, scipy.matrix):
X = scipy.asarray(X, dtype=float)
return 0.5 * ((l1 + l2) - (l1 - l2) * scipy.tanh((X - x0) / lw))
else:
return 0.5 * ((l1 + l2) - (l1 - l2) * mpmath.tanh((X - x0) / lw))
def tanh_warp_arb(X, l1, l2, lw, x0):
r"""Warps the `X` coordinate with the tanh model
.. math::
l = \frac{l_1 + l_2}{2} - \frac{l_1 - l_2}{2}\tanh\frac{x-x_0}{l_w}
Parameters
----------
X : :py:class:`Array`, (`M`,) or scalar float
`M` locations to evaluate length scale at.
l1 : positive float
Small-`X` saturation value of the length scale.
l2 : positive float
Large-`X` saturation value of the length scale.
lw : positive float
Length scale of the transition between the two length scales.
x0 : float
Location of the center of the transition between the two length scales.
Returns
-------
l : :py:class:`Array`, (`M`,) or scalar float
The value of the length scale at the specified point.
"""
if isinstance(X, scipy.ndarray):
if isinstance(X, scipy.matrix):
X = scipy.asarray(X, dtype=float)
return 0.5 * ((l1 + l2) - (l1 - l2) * scipy.tanh((X - x0) / lw))
else:
return 0.5 * ((l1 + l2) - (l1 - l2) * mpmath.tanh((X - x0) / lw))
def logistic_gaussian(m, v):
if m == oo:
if v == oo:
return oo
return Float('1.0')
if v == oo:
return Float('0.5')
mpmath.mp.dps = 500
mmpf = m._to_mpmath(500)
vmpf = v._to_mpmath(500)
# The integration routine below is obtained by substituting x = atanh(t)
# into the definition of logistic_gaussian
#
# f = lambda x: mpmath.exp(-(x - mmpf) * (x - mmpf) / (2 * vmpf)) / (1 + mpmath.exp(-x))
# result = 1 / mpmath.sqrt(2 * mpmath.pi * vmpf) * mpmath.quad(f, [-mpmath.inf, mpmath.inf])
#
# Such substitution makes mpmath.quad call much faster.
tanhm = mpmath.tanh(mmpf)
# Not really a precise threshold, but fine for our data
if tanhm == mpmath.mpf('1.0'):
return Float('1.0')
f = lambda t: mpmath.exp(-(mpmath.atanh(t) - mmpf) ** 2 / (2 * vmpf)) / ((1 - t) * (1 + t + mpmath.sqrt(1 - t * t)))
coef = 1 / mpmath.sqrt(2 * mpmath.pi * vmpf)
int, err = mpmath.quad(f, [-1, 1], error=True)
result = coef * int
if mpmath.mpf('1e50') * abs(err) > abs(int):
print(f"Suspiciously big error when evaluating an integral for logistic_gaussian({m}, {v}).")
print(f"Integral: {int}")
print(f"integral error estimate: {err}")
print(f"Coefficient: {coef}")
print(f"Result (Coefficient * Integral): {result}")
return Float(result)
def sf(x, loc=0, scale=1):
"""
Survival function of the logistic distribution.
"""
with mpmath.extradps(5):
x = mpmath.mpf(x)
loc = mpmath.mpf(loc)
scale = mpmath.mpf(scale)
z = (x - loc) / scale
p = (1 - mpmath.tanh(z / 2)) / 2
return p
def cdf(x, loc=0, scale=1):
"""
CDF of the logistic distribution.
"""
with mpmath.extradps(5):
x = mpmath.mpf(x)
loc = mpmath.mpf(loc)
scale = mpmath.mpf(scale)
z = (x - loc) / scale
p = (1 + mpmath.tanh(z / 2)) / 2
return p
def v(x, t, s, b):
# c is atrificial parameter for findroot.
c = 10**(-10)
if x > b:
return j * mp.findroot(lambda y: re(w(j * y, s, b) - (x - t)),
[-s / 2 + c, 0 - c], "bisect")
elif x < -b:
return j * mp.findroot(lambda y: re(w(j * y, s, b) - (x - t)),
[0 + c, s / 2 - c], "bisect")
else:
tolerant = 10**(-20)
normparam = 10**11
return 1 / 2 + j * mp.findroot(
lambda y: tanh(re(w(1 / 2 + j * y, s, b) - (x - t)) / normparam),
0,
tol=tolerant)
def sigmoid(x):
return mpmath.tanh(x)
def pearsonr_ci(r, n, alpha, alternative='two-sided'):
"""
Confidence interval of Pearson's correlation coefficient.
This function uses Fisher's transformation to compute the confidence
interval of Pearson's correlation coefficient.
Examples
--------
Imports:
>>> import mpmath
>>> mpmath.mp.dps = 20
>>> from mpsci.stats import pearsonr, pearsonr_ci
Sample data:
>>> a = [2, 4, 5, 7, 10, 11, 12, 15, 16, 20]
>>> b = [2.53, 2.41, 3.60, 2.69, 3.19, 4.05, 3.71, 4.65, 4.33, 4.70]
Compute the correlation coefficient:
>>> r, p = pearsonr(a, b)
>>> r
mpf('0.893060379514729854846')
>>> p
mpf('0.00050197523992669206603645')
Compute the 95% confidence interval for r:
>>> rlo, rhi = pearsonr_ci(r, n=len(a), alpha=0.05)
>>> rlo
mpf('0.60185206817708369265664')
>>> rhi
mpf('0.97464778383702233502275')
"""
if alternative not in ['two-sided', 'less', 'greater']:
raise ValueError("alternative must be 'two-sided', 'less', or "
"'greater'.")
with mpmath.mp.extradps(5):
zr = mpmath.atanh(r)
n = mpmath.mp.mpf(n)
alpha = mpmath.mp.mpf(alpha)
s = mpmath.sqrt(1 / (n - 3))
if alternative == 'two-sided':
h = normal.invcdf(1 - alpha / 2)
zlo = zr - h * s
zhi = zr + h * s
rlo = mpmath.tanh(zlo)
rhi = mpmath.tanh(zhi)
elif alternative == 'less':
h = normal.invcdf(1 - alpha)
zhi = zr + h * s
rhi = mpmath.tanh(zhi)
rlo = -mpmath.mp.one
else:
# alternative == 'greater'
h = normal.invcdf(1 - alpha)
zlo = zr - h * s
rlo = mpmath.tanh(zlo)
rhi = mpmath.mp.one
return rlo, rhi
def DDs(self, x):
return -2 * pow(mpmath.sech(x), 2) * mpmath.tanh(x)
def s(self, x):
return mpmath.tanh(x)
def disp_rel_mp(self, W, K, M_A):
return self.m0_mp(W, M_A)**2 * W**4 + 1/self.R1 * 1/self.R2 * self.m1_mp(W) * self.m2_mp(W) * (1 - (W - M_A)**2)**2 - \
0.5 * W**2 * self.m0_mp(W, M_A) * (1 - (W - M_A)**2) * (1/self.R1 * self.m1_mp(W) + 1/self.R2 * self.m2_mp(W)) * \
(mp.tanh(self.m0_mp(W, M_A) * K) + mp.tanh(self.m0_mp(W, M_A) * K)**(-1))
def sarkar_embedding(tree, root, **kwargs):
'''
Embed a tree in the Poincare disc using Sarkar's algorithm
from "Low Distortion Delaunay Embedding of Trees in Hyperbolic Plane.
Args:
tree (networkx.Graph) : The tree represented with int node labels.
Weighted trees should have the edge attribute "weight"
root (int): The node to use as the root of the embedding
Keyword Args:
weighted (bool): True if the tree is weighted (default True)
tau (float): the scaling factor for distances.
By default it is calculated based on statistics of the tree.
epsilon (float): parameter >0 controlling distortion bound (default 0.1).
precision (int): number of bits of precision to use.
By default it is calculated based on tau and epsilon.
Returns:
size N x 2 mpmath.matrix containing the coordinates of embedded nodes
'''
eps = kwargs.get("epsilon",0.1)
weighted = kwargs.get("weighted", True)
tau = kwargs.get("tau")
max_deg = max(tree.degree)[1]
if tau is None:
tau = (1+eps)/eps * mpm.log(2*max_deg/ mpm.pi)
prc = kwargs.get("precision")
if prc is None:
prc = _embedding_precision(tree,root,eps)
mpm.mp.dps = prc
n = tree.order()
emb = mpm.zeros(n,2)
place = []
# place the children of root
for i, v in enumerate(tree[root]):
if weighted:
r = mpm.tanh( tau*tree[root][v]["weight"])
else:
r = mpm.tanh(tau)
theta = 2*i*mpm.pi / tree.degree[root]
emb[v,0] = r*mpm.cos(theta)
emb[v,1] = r*mpm.sin(theta)
place.append((root,v))
# TODO parallelize this
while place:
u, v = place.pop() # u is the parent of v
p, x = emb[u,:], emb[v,:]
rp = poincare_reflect0(x, p, precision=prc)
arg = mpm.acos(rp[0]/mpm.norm(rp))
if rp[1] < 0:
arg = 2*mpm.pi - arg
theta = 2*mpm.pi / tree.degree[v]
i=0
for w in tree[v]:
if w == u: continue
i+=1
if weighted:
r = mpm.tanh(tau*tree[v][w]["weight"])
else:
r = mpm.tanh(tau)
w_emb = r * mpm.matrix([mpm.cos(arg+theta*i),mpm.sin(arg+theta*i)]).T
w_emb = poincare_reflect0(x, w_emb, precision=prc)
emb[w,:] = w_emb
place.append((v,w))
return emb
def eval(self, z):
return mpmath.tanh(z)
def eval(self, z):
return mpmath.tanh(z)
def Activation(x, xm, eta):
return 0.5 * (mpmath.tanh(eta * (x - xm)) + 1.0)