def test_2():
# test that random state is used correctly
dim = 2
x0 = np.zeros(dim)
cov = np.array([[1, 1.98], [1.98, 4]])
icov = np.linalg.inv(cov)
samples1 = hmc(lnprob_gaussian,
x0,
args=(icov, ),
n_samples=10,
n_burn=0,
n_steps=10,
epsilon=0.25,
return_diagnostics=False,
random_state=0)
samples2 = hmc(lnprob_gaussian,
x0,
args=(icov, ),
n_samples=10,
n_burn=0,
n_steps=10,
epsilon=0.25,
return_diagnostics=False,
random_state=0)
np.testing.assert_array_almost_equal(samples1, samples2)
def sample_with_progress(repeats, n_samps, n_steps, epsilon, path=None):
if path is not None:
dirname = os.path.dirname(path)
if not os.path.exists(dirname):
os.makedirs(dirname)
last = np.random.randn(num_dimensions)
timestamps = []
all_samples = []
nfevals = []
start = time()
for i in range(repeats):
samples = hmc(lnpdf,
x0=last,
n_samples=int(n_samps),
n_steps=n_steps,
epsilon=epsilon)
last = samples[-1]
nfevals.append(lnpdf.counter)
all_samples.append(samples)
if path is not None:
np.savez(path + '_iter' + str(i),
true_means=true_means,
true_covs=true_covs,
samples=last,
timestamps=timestamps,
nfevals=nfevals)
timestamps.append(time() - start)
if path is not None:
np.savez(path,
samples=np.array(all_samples),
true_means=true_means,
true_covs=true_covs,
timestamps=np.array(timestamps),
fevals=np.array(nfevals))
def sample_with_progress(repeats, n_samps, n_steps, epsilon, path=None):
if path is not None:
dirname = os.path.dirname(path)
if not os.path.exists(dirname):
os.makedirs(dirname)
last = np.random.randn(D)
timestamps = []
all_samples = []
nfevals = []
for i in range(repeats):
timestamps.append(time())
samples = hmc(lnpdf,
x0=last,
n_samples=int(n_samps),
n_steps=n_steps,
epsilon=epsilon)
last = samples[-1]
nfevals.append(lnpdf.counter)
all_samples.append(samples)
if path is not None:
np.savez(path + '_iter' + str(i),
samples=last,
timestamps=timestamps,
nfevals=nfevals)
timestamps.append(time())
if path is not None:
np.savez(path,
samples=all_samples,
timestamps=timestamps,
nfevals=nfevals)
def sample(self):
assert pyhmc_imported, 'the ``pyhmc`` package is required.'
alpha = self.prior_alpha
beta = self.prior_beta
if np.isscalar(self.prior_alpha):
# symmetric dirichlet
alpha = self.prior_alpha * np.ones(self.n_states_)
if np.isscalar(self.prior_beta):
beta = self.prior_beta * np.ones(
len(self.theta0_) - self.n_states_)
def func(theta):
logp, grad = _log_posterior(theta,
self.countsmat_,
alpha=alpha,
beta=beta,
n=self.n_states_)
return logp, grad
epsilon = self.epsilon / len(self.theta0_)
start = time.time()
all_theta, diag = hmc(func,
x0=self.theta0_,
n_samples=self.n_samples,
epsilon=epsilon,
n_steps=self.n_steps,
display=self.verbose,
return_diagnostics=True)
self._is_dirty = True
return all_theta, diag, time.time() - start
def test_1():
try:
from matplotlib import pyplot as pp
except ImportError:
raise SkipTest('Not making QQ plot')
# check that ldirichlet_softmax_pdf is actually giving a dirichlet
# distribution, by comparing a QQ plot with np.random.dirichlet
alpha = np.array([1, 2, 3], dtype=float)
def logprob(x, alpha):
grad = np.zeros_like(x)
logp = ldirichlet_softmax(x, alpha, grad=grad)
return logp, grad
samples, diag = hmc(logprob,
x0=np.random.normal(size=(3, )),
n_samples=1000,
args=(alpha, ),
n_steps=10,
return_diagnostics=True)
expx = np.exp(samples)
pi1 = expx / np.sum(expx, 1, keepdims=True)
pi2 = np.random.dirichlet(alpha=alpha, size=1000)
sm.qqplot_2samples(pi1[:, 0], pi2[:, 0], line='45')
pp.savefig('bayes_ratematrix-test-1.png')
def test_2():
# test that random state is used correctly
dim = 2
x0 = np.zeros(dim)
cov = np.array([[1, 1.98], [1.98, 4]])
icov = np.linalg.inv(cov)
samples1 = hmc(lnprob_gaussian, x0, args=(icov,),
n_samples=10, n_burn=0,
n_steps=10, epsilon=0.25, return_diagnostics=False,
random_state=0)
samples2 = hmc(lnprob_gaussian, x0, args=(icov,),
n_samples=10, n_burn=0,
n_steps=10, epsilon=0.25, return_diagnostics=False,
random_state=0)
np.testing.assert_array_almost_equal(samples1, samples2)
def sample(n_samps, n_steps, epsilon, path):
if path is not None:
dirname = os.path.dirname(path)
if not os.path.exists(dirname):
os.makedirs(dirname)
start = time()
samples = hmc(lnpdf, x0=np.random.randn(num_dimensions), n_samples=int(n_samps), n_steps=n_steps, epsilon=epsilon)
end = time()
np.savez(path, samples=samples, wallclocktime=end-start)
#samples = np.vstack([c[0] for c in chain])
print("done")
def test_3():
rv = scipy.stats.loggamma(c=1)
eps = np.sqrt(np.finfo(float).resolution)
def logprob(x):
return rv.logpdf(x), approx_fprime(x, rv.logpdf, eps)
samples = hmc(logprob, [0], epsilon=1, n_steps=10, window=3, persistence=True)
# import matplotlib.pyplot as pp
(osm, osr), (slope, intercept, r) = scipy.stats.probplot(
samples[:,0], dist=rv, fit=True)
assert r > 0.99
def func_thread(proposal, queue, **kwargs):
"""
Sample from log probability density function proposal with pyhmc,
see https://github.com/rmcgibbo/pyhmc for tutorials.
"""
res = hmc(proposal,
args=(*kwargs['pr_args'], ),
x0=np.random.randn(kwargs['dim']) + 1.5 * np.ones(kwargs['dim']),
n_samples=kwargs['n_samples'],
display=False,
n_steps=40,
n_burn=kwargs['n_burn'],
epsilon=kwargs['epsilon'],
return_diagnostics=True)
queue.put(res[0])
def test_ldirchlet_softmax_pdf_qq():
# check that ldirichlet_softmax_pdf is actually giving a dirichlet
# distribution, by comparing a QQ plot with np.random.dirichlet
alpha = np.array([1, 2, 3], dtype=float)
def logprob(x, alpha):
grad = np.zeros_like(x)
logp = ldirichlet_softmax(x, alpha, grad=grad)
return logp, grad
samples, diag = hmc(logprob, x0=np.random.normal(size=(3,)), n_samples=1000,
args=(alpha,), n_steps=10, return_diagnostics=True)
expx = np.exp(samples)
pi1 = expx / np.sum(expx, 1, keepdims=True)
pi2 = np.random.dirichlet(alpha=alpha, size=1000)
def test_ldirchlet_softmax_pdf_qq():
# check that ldirichlet_softmax_pdf is actually giving a dirichlet
# distribution, by comparing a QQ plot with np.random.dirichlet
alpha = np.array([1, 2, 3], dtype=float)
def logprob(x, alpha):
grad = np.zeros_like(x)
logp = ldirichlet_softmax(x, alpha, grad=grad)
return logp, grad
samples, diag = hmc(logprob, x0=np.random.normal(size=(3,)), n_samples=1000,
args=(alpha,), n_steps=10, return_diagnostics=True)
expx = np.exp(samples)
pi1 = expx / np.sum(expx, 1, keepdims=True)
pi2 = np.random.dirichlet(alpha=alpha, size=1000)
def generate(self, func):
def logprob(pos, func):
def f_logp(x):
return np.log(func(x))
logp = f_logp(pos)
grad = egrad(f_logp)(pos)
return logp, grad
return hmc(logprob,
x0=np.random.randn(self.nelec * self.ndim),
args=(func, ),
n_samples=self.nwalkers,
epsilon=1,
n_burn=int(self.nstep / 10))
def Ex1_hmc():
def U(theta):
return (-2 * theta**2 + theta**4)
# True gradient
gradU = jacobian(U, argnum=0)
# Noisy gradient, based on what they do in the paper for Fig 1
def noisy_gradU(theta, x, n, batch_size):
'''Noisy gradient \Delta\tilde{U}(\theta)=\Delta U(\theta)+N(0,4)
Extra args (x, n, batch_size) for compatibility with sghmc()'''
return -4 * theta + 4 * theta**3 + np.random.normal(0, 2)
# define your probability distribution
def logprob(theta):
logp = -2 * theta**2 + theta**4
grad = -4 * theta + 4 * theta**3
return logp, grad
# run the HMC sampler (use same theta_0 and niter as SGHMC)
np.random.seed(1234)
# Don't actually need 'data' in this example, just use
# it as a place-holder to fit into our function.
n = 100
x = np.array([np.random.normal(0, 1, (n, 1))]).reshape(-1, 1)
# Set up start values and tuning params
theta_0 = np.array([0.0]) # Initialize theta
batch_size = n # since we're not actually using the data, don't need to batch it
niter = 500000 # Lots of iterations
samps_hmc = hmc(logprob, x0=theta_0, n_samples=niter)
# plot the samples from the HMC algorithm
sns.kdeplot(samps_hmc.reshape(-1))
# The hmc() function with that many iterations goes kind of insane...
# How about less samples? Also redefine logprob(theta) to use funs from above
#def logprob(theta):
#return U(theta, x, n, batch_size), gradU(theta, x, n, batch_size).reshape(1)
# run the HMC sampler (use same theta_0 as above but fewer samples)
#samps_hmc = hmc(logprob, x0=theta_0, n_samples=500) # NOPE! Still looks bad.
# plot the samples from the HMC algorithm
# plot the samples from the algorithm and save to a file
kdeplt = sns.kdeplot(samps_hmc.reshape(-1)) # Plot the joint density
fig = kdeplt.get_figure()
fig.savefig('Example1_b.png')
return (samps_hmc)
def test_3():
rv = scipy.stats.loggamma(c=1)
eps = np.sqrt(np.finfo(float).resolution)
def logprob(x):
return rv.logpdf(x), approx_fprime(x, rv.logpdf, eps)
samples = hmc(logprob, [0],
epsilon=1,
n_steps=10,
window=3,
persistence=True)
# import matplotlib.pyplot as pp
(osm, osr), (slope, intercept, r) = scipy.stats.probplot(samples[:, 0],
dist=rv,
fit=True)
assert r > 0.99
def test_1():
# test sampling from a highly-correlated gaussian
dim = 2
x0 = np.zeros(dim)
cov = np.array([[1, 1.98], [1.98, 4]])
icov = np.linalg.inv(cov)
samples, logp, diag = hmc(lnprob_gaussian, x0, args=(icov,),
n_samples=10**4, n_burn=10**3,
n_steps=10, epsilon=0.20, return_diagnostics=True,
return_logp=True, random_state=2)
C = np.cov(samples, rowvar=0, bias=1)
np.testing.assert_array_almost_equal(cov, C, 1)
for i in range(100):
np.testing.assert_almost_equal(
lnprob_gaussian(samples[i], icov)[0],
logp[i])
def run_pyHMC(self):
samples = hmc(self.numeric_posterior,
x0=self.prm_init,
n_samples=self.nsamples,
epsilon=self.epsilon,
return_diagnostics=True,
return_logp=True,
n_burn=1e3)
self.rejection_rate = samples[2]["rej"]
if self.plotsamples:
counts = np.linspace(1,
len(self.prm_init),
len(self.prm_init),
dtype=int)
figure = corner.corner(samples[0],
show_titles=True,
labels=counts,
truths=self.actual_rhos)
figure.savefig('{}.png'.format(self.corner_plot))
def MoN_hmc():
# define your probability distribution
# note some fiddling to get dimensions to be compatible
def logprob(theta):
logp = np.sum(U(theta, x=x, n=n, batch_size=n))
gradu = gradU(theta, x=x, n=n, batch_size=n).reshape((-1, ))
return logp, gradu
# run the HMC sampler
# ideally would use same theta_0 and niter as SGHMC,
# but computing the full gradient is prohibtively slow!!
samps_hmc = hmc(logprob, x0=theta_0.reshape((-1)), n_samples=100)
# plot the samples from the algorithm and save to a file
kdeplt = sns.kdeplot(samps[0, :], samps[1, :]) # FIGURE 2b FOR PAPER
fig = kdeplt.get_figure()
fig.savefig('MixNorm_b.png')
return (samps_hmc)
def sample(self):
assert pyhmc_imported, 'the ``pyhmc`` package is required.'
alpha = self.prior_alpha
beta = self.prior_beta
if np.isscalar(self.prior_alpha):
# symmetric dirichlet
alpha = self.prior_alpha * np.ones(self.n_states_)
if np.isscalar(self.prior_beta):
beta = self.prior_beta * np.ones(len(self.theta0_) - self.n_states_)
def func(theta):
logp, grad = _log_posterior(theta, self.countsmat_,
alpha=alpha, beta=beta, n=self.n_states_)
return logp, grad
epsilon = self.epsilon / len(self.theta0_)
start = time.time()
all_theta, diag = hmc(func, x0=self.theta0_, n_samples=self.n_samples,
epsilon=epsilon, n_steps=self.n_steps,
display=self.verbose, return_diagnostics=True)
self._is_dirty = True
return all_theta, diag, time.time() - start
def test_1():
# test sampling from a highly-correlated gaussian
dim = 2
x0 = np.zeros(dim)
cov = np.array([[1, 1.98], [1.98, 4]])
icov = np.linalg.inv(cov)
samples, logp, diag = hmc(lnprob_gaussian,
x0,
args=(icov, ),
n_samples=10**4,
n_burn=10**3,
n_steps=10,
epsilon=0.20,
return_diagnostics=True,
return_logp=True,
random_state=2)
C = np.cov(samples, rowvar=0, bias=1)
np.testing.assert_array_almost_equal(cov, C, 1)
for i in range(100):
np.testing.assert_almost_equal(
lnprob_gaussian(samples[i], icov)[0], logp[i])
def test_1():
try:
from matplotlib import pyplot as pp
except ImportError:
raise SkipTest('Not making QQ plot')
# check that ldirichlet_softmax_pdf is actually giving a dirichlet
# distribution, by comparing a QQ plot with np.random.dirichlet
alpha = np.array([1, 2, 3], dtype=float)
def logprob(x, alpha):
grad = np.zeros_like(x)
logp = ldirichlet_softmax(x, alpha, grad=grad)
return logp, grad
samples, diag = hmc(logprob, x0=np.random.normal(size=(3,)), n_samples=1000,
args=(alpha,), n_steps=10, return_diagnostics=True)
expx = np.exp(samples)
pi1 = expx / np.sum(expx, 1, keepdims=True)
pi2 = np.random.dirichlet(alpha=alpha, size=1000)
sm.qqplot_2samples(pi1[:, 0], pi2[:, 0], line='45')
pp.savefig('bayes_ratematrix-test-1.png')
grad = -((27 * density + 27 - T_obs) * 27) / sigma_T**2
c = np.linalg.det(cov)
prefactor_likelihood = 1 / (np.sqrt(2 * np.pi) * c)**len(T_obs)
prefactor = (prefactor_likelihood + prefactor_prior)
logp = prefactor + (prior_rhos + trans_X_C_X)
return logp, grad
def withCov_logprob(density):
c = np.linalg.det(cov)
prefactor_likelihood = np.log(1 / (np.sqrt(2 * np.pi) * c)**len(T_obs))
trans_X = (-0.5) * (27 * density + 27 - T_obs).T
trans_X_C = np.dot(trans_X, np.linalg.inv(cov))
trans_X_C_X = np.dot(trans_X_C, (27 * density + 27 - T_obs))
logp = trans_X_C_X * prefactor_likelihood
grad = -((27 * density + 27 - T_obs) * 27) / sigma_T**2
return logp, grad
og = logprob(one_rho)
og_new = withCov_logprob(one_rho)
for eps in [0.0001]:
# for eps in [0.0001]:
samples = hmc(logprob, x0=one_rho, n_samples=int(1e5), epsilon=eps)
figure = corner.corner(samples,
show_titles=True,
labels=["d1", "d2", "d3", "d4"])
figure.savefig('../STAT_IMAGES/all_pngs/testing_{}.png'.format(eps))
# samples *= sigma_D
# The PyHMC package requires a function returning both the logprob and its gradient
def logposterior_and_grad(model_amplitudes):
return pm.get_log_posterior(model_amplitudes), pm.get_grad_log_posterior(
model_amplitudes)
# Draw samples from the log posterior using hamiltonian monte carlo
print("A sensible sample would be..." + str(nz))
initial_position = np.random.rand(10)
nb_samples = 10
print("The initial position is..." + str(initial_position))
samples = hmc(logposterior_and_grad,
x0=initial_position,
n_samples=100000,
n_steps=10,
epsilon=0.0001)
print("Samples drawn: \n" + str(samples))
# Plot the estimated amplitude distribution
log_prob_samples = []
for sample in samples:
log_prob_samples.append(pm.get_log_posterior(sample))
print(log_prob_samples)
plt.hist(log_prob_samples[70000:], bins=30)
plt.xlabel("Log-Posterior value")
plt.ylabel("Number of samples")
plt.show()
print("A sensible log-posterior value would be..." +
str(pm.get_log_posterior(nz)))
import numpy as np
from pyhmc import hmc
import corner
# define your probability distribution
def logprob(x, ivar):
logp = -0.5 * np.sum(ivar * x**2)
grad = -ivar * x
return logp, grad
# run the sampler
ivar = 1. / np.random.rand(5)
samples = hmc(logprob, x0=np.random.randn(5), args=(ivar, ), n_samples=1e4)
# Optionally, plot the results
figure = corner.corner(samples)
figure.savefig('triangle.pdf')
def optimize_snp_new(self, snp_id, path_chain):
"""
Optimisation of parameters for a SNPs by Hamiltonian Monte Carlo
:param snp_id: Id of SNP
:param path_chain: path to save MCMC chain
"""
# snp_id = 6
# print(snp_id)
k1 = self.q[:, snp_id]
n1 = self.n[:, snp_id]
# In the number of alternative alleles in all locations is zero - return
if sum(k1) == 0:
return
if sum(k1) == sum(n1):
return
if (self.n_loc - sum(k1 == 0)) <= 2:
# print('Skip zero', path_chain, snp_id)
return
if (self.n_loc - sum(k1 == n1)) <= 2:
# print('Skip non-zero', path_chain, snp_id)
return
# niter = 50000
# samples = hmc(self.logprob, x0=[0] + list(np.random.uniform(-1, 1, self.n_loc)) + [0.1] + [1] * 2,
# args=(snp_id,), n_samples=2000, epsilon=0.1)
# print(samples[-1])
# samples = hmc(self.logprob, x0=samples[-1],
# args=(snp_id,), n_samples=niter, epsilon=0.2)
# print(list(zip(k1, n1)))
# Burn-in
niter = 5000
samples = [[k1.sum() / n1.sum()] +
list(np.random.uniform(-1, 1, self.n_loc)) + [0.1] + [1] * 2
]
params = np.array(samples[-1])
print(self.logprob(np.array(samples[-1]), snp_id))
eps = 0.11
while len(samples) < (niter / 4):
eps = eps - 0.01
samples = hmc(self.logprob,
x0=samples[-1],
args=(snp_id, ),
n_samples=niter,
epsilon=eps)
_, idx = np.unique(samples, axis=0, return_index=True)
samples = samples[np.sort(idx)]
print(len(samples), eps)
# Find epsilon after burn-in
niter = 5000
eps = 0.18
x0 = samples[-1]
samples = []
while len(samples) < (niter / 4) and eps > 0:
if eps > 0.019:
eps -= 0.01
else:
eps = eps * 0.7
samples = hmc(self.logprob,
x0=x0,
args=(snp_id, ),
n_samples=niter,
epsilon=eps)
_, idx = np.unique(samples, axis=0, return_index=True)
samples = samples[np.sort(idx)]
print(len(samples), eps)
niter = 100000
if eps > 0:
samples = hmc(self.logprob,
x0=samples[-1],
args=(snp_id, ),
n_samples=niter,
epsilon=eps)
_, idx = np.unique(samples, axis=0, return_index=True)
samples = samples[np.sort(idx)]
else:
print('Bad epsilon')
print('Len', path_chain, snp_id, len(samples), eps)
if len(samples) < niter / 4:
print('Low number of samples', path_chain, snp_id)
np.savetxt(fname=path_chain + 'snp' + str(snp_id) + '.txt',
X=samples,
fmt='%.10f')
np.savetxt(fname=path_chain + 'eps' + str(snp_id) + '.txt',
X=eps,
fmt='%.10f')
n_thin = 10
samples = samples[::n_thin]
np.savetxt(fname=path_chain + 'mean' + str(snp_id) + '.txt',
X=samples.mean(0),
fmt='%.10f')
if 0 in samples.var(0):
print('Bad News', snp_id)
np.savetxt(fname=path_chain + 'var' + str(snp_id) + '.txt',
X=samples.var(0),
fmt='%.10f')
c = np.linalg.det(cov)
exp_1 = (-0.5) * (T_vec - (alpha * rho_vec**2)).T
exp_1 = np.dot(exp_1, np.linalg.inv(cov))
exp_1 = np.dot(exp_1, (T_vec - (alpha * rho_vec**2))).flatten()
prefactor_prior = np.log(1 / (2 * np.pi *
(sigma_a * sigma_d**(len(rho_vec)))))
prefactor_likelihood = np.log(1 / (2 * np.pi * c))
num_post = prefactor_likelihood * prefactor_prior * (exp_1 + prior_alpha +
prior_rhos)
global i
i = i + 1
if i % 1000:
print("{} samples".format(i))
return num_post, gradients(prm, cov, Tarr)
cov = np.asarray([[0.01, 0, 0], [0, 0.01, 0], [0, 0, 0.01]])
Tarr = np.asarray([1, 1, 1])
PRIOR_sigma = [2, 2]
# print(numeric_posterior(np.asarray([1, 1, 1]), alpha, cov, Tarr)
samples = hmc(numeric_posterior,
x0=[1, 1, 1, 1],
args=(cov, Tarr, PRIOR_sigma),
n_samples=int(1e6))
figure = corner.corner(samples,
labels=["alpha", "d_1", "d_2", "d_3"],
show_titles=True,
title_kwargs={"fontsize": 12})
figure.savefig('adrian_sigma_2_3.png')
def hmc(self,X,T,Z,n_samples=100,n_steps=10,epsilon=0.2,seed=None):
'''
Draws n_samples samples from the posterior distribution using hamiltonian monte
carlo (implemented in pyhmc).
Arguments:
X (list): List of feature sequences (structure will vary with prior model)
T (list): List of (L_i,) numpy arrays containing instance timestamps
Z (list): List of observation sequence (structure will vary with prior model)
n_samples: number of samples returned
n_steps: number of hamiltonian steps taken between samples
epsilon: step size
seed: random seed for initialization
Returns:
self
'''
# get seed
if seed is None:
np.random.seed(int(time.time()))
else:
np.random.seed(seed)
# Initialize the base classifier
self.initialize_base_classifier(X,Y)
# Initialize self
self.initialize()
# Preprocess the data
# e.g. perform prefiltering
X_aug = self.preprocess_data(X,Y,True)
# Set gradient functions for regularizers
self.set_grads()
# Get the objective and gradient functions
obj = self.get_obj(X_aug,Y)
g_fun = self.get_grad(X_aug,Y)
# get any parameter bounds
# keyboard()
bounds = self.get_bounds(X_aug,Y)
# get start tiem
start_time = time.time()
def logp_and_grad(w):
return -obj(w),-g_fun(w)
# Samples
if self.warm_start:
w0 = self.init_params(X,Y)
res = minimize(obj,w0,jac=g_fun,method='L-BFGS-B',tol=self.tol,options={"disp":self.verbose,"maxiter":25},bounds=bounds)
w0 = res.x
else:
w0 = np.random.randn(self.n_params)
self.param_samples,self.sampling_logps,self.sampling_diagnostics = hmc(logp_and_grad,x0=w0,n_samples=n_samples,n_steps=n_steps,epsilon=epsilon,display=True,return_logp=True,return_diagnostics=True)
# Store total training time
self.train_time = time.time() - start_time
if self.verbose > 0: print "Train time:", self.train_time
# Clear gradient functions
# TODO: move this to pickle helper functions
self.ig_grad = None
self.n_grad = None
self.beta_grad = None
self.base_reg_grad = None
return self
# def logprob(x, ivar):
# logp = -0.5 * np.sum(ivar * x**2)
# grad = -ivar * x
# return logp, grad
def gradients(prm, alpha, cov, Tarr):
# placeholder
densities = prm # what we're sampling
sigma_2 = cov[0][0] # sigma^2, one element of cov matrix
grads = (1 / sigma_2**2) * (
-alpha * densities**2 + Tarr
) # calculated gradients for each density value
return grads
def numeric_posterior(m, x, b):
return num_post, gradients(prm, alpha, cov, Tarr)
samples = hmc(numeric_posterior,
x0=[.5, 1.5, 1],
args=(alpha, cov, Tarr),
n_samples=int(1e6))
# print(samples)
# # pip install triangle_plot
figure = corner.corner(samples)
figure.savefig('testing_more_samples.png')
