def max_likelihood(self, data, weights=None, stats=None, lmbda=0.1):
"""
As an alternative to MCMC with Polya-gamma augmentation,
we also implement maximum likelihood learning via gradient
descent with autograd. This follows the pybasicbayes
convention.
:param data: list of tuples, (x,y), for each dataset.
:param weights: Not used in this implementation.
:param stats: Not used in this implementation.
"""
import autograd.numpy as anp
from autograd import value_and_grad, hessian_vector_product
from scipy.optimize import minimize
assert weights is None
assert stats is None
if not isinstance(data, list):
assert isinstance(data, tuple) and len(data) == 2
data = [data]
# Define a helper function for the log of the logistic fn
def loglogistic(psi):
return psi - anp.log(1+anp.exp(psi))
# optimize each row of A and b
for n in range(self.D_out):
# Define an objective function for the n-th row of hstack((A, b))
# This is the negative log likelihood of the n-th column of data.
def nll(abn):
an, bn = abn[:-1], abn[-1]
T = 0
ll = 0
for (x, y) in data:
T += x.shape[0]
yn = y[:, n]
psi = anp.dot(x, an) + bn
ll += anp.sum(yn * loglogistic(psi))
ll += anp.sum((1 - yn) * loglogistic(-1. * psi))
# Include a penalty on the weights
ll -= lmbda * T * anp.sum(an**2)
ll -= lmbda * T * bn**2
return -1 * ll / T
abn0 = np.concatenate((self.A[n], self.b[n]))
res = minimize(value_and_grad(nll), abn0,
tol=1e-3,
method="Newton-CG",
jac=True,
hessp=hessian_vector_product(nll))
assert res.success
self.A[n] = res.x[:-1]
self.b[n] = res.x[-1]
def test_hessian_tensor_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5, 4, 3)
V = npr.randn(5, 4, 3)
H = hessian(fun)(a)
check_equivalent(np.tensordot(H, V, axes=np.ndim(V)), hessian_vector_product(fun)(a, V))
def test_hessian_matrix_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5, 4)
V = npr.randn(5, 4)
H = hessian(fun)(a)
check_equivalent(np.tensordot(H, V), hessian_vector_product(fun)(a, V))
def test_hessian_vector_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5)
v = npr.randn(5)
H = hessian(fun)(a)
check_equivalent(np.dot(H, v), hessian_vector_product(fun)(a, v))
def test_hessian_vector_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5)
v = npr.randn(5)
H = hessian(fun)(a)
check_equivalent(np.dot(H, v), hessian_vector_product(fun)(a, v))
def test_hessian_tensor_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5, 4, 3)
V = npr.randn(5, 4, 3)
H = hessian(fun)(a)
check_equivalent(np.tensordot(H, V, axes=np.ndim(V)), hessian_vector_product(fun)(a, V))
def __init__(self, configurations, parameters, controls,
simulation_first_confirmed):
self.configurations = configurations
self.parameters = parameters
self.controls = controls
self.simulation_first_confirmed = simulation_first_confirmed
flat_args, self.unflatten = flatten(self.controls)
# self.obs = obs
# self.loc = loc
# if noise_covariance is not None:
# self.Gamma_noise_inv = np.linalg.inv(noise_covariance)
self.gx = grad(self.cost)
self.J = jacobian(self.forward)
self.hx = hessian_vector_product(self.cost)
self.hvp = hvp(self.hx)
y0, t_total, N_total, number_group, population_proportion, \
t_control, number_days_per_control_change, number_control_change_times, number_time_dependent_controls = configurations
self.N_total = N_total
self.number_group = number_group
self.t_control = t_control
self.dimension = len(self.t_control)
self.number_time_dependent_controls = number_time_dependent_controls
self.y0 = y0
self.t_total = t_total
self.interpolation = piecewiseLinear
if number_group > 1:
# contact matrix
school_closure = True
# calendar from February 15th
weekday = [2, 3, 4, 5, 6]
# calendar from April 1st
# weekday = [0, 1, 2, 5, 6]
# calendar from May 1st
# weekday = [0, 3, 4, 5, 6]
calendar = np.zeros(1000 + 1, dtype=int)
# set work days as 1 and school days as 2
for i in range(1001):
if np.remainder(i, 7) in weekday:
calendar[i] = 1
if not school_closure: # and i < 45
calendar[i] = 2
self.calendar = calendar
contact = np.load("utils/contact_matrix.npz")
self.c_home = contact["home"]
self.c_school = contact["school"]
self.c_work = contact["work"]
self.c_other = contact["other"]
self.contact_full = self.c_home + 5. / 7 * (
(1 - school_closure) * self.c_school +
self.c_work) + self.c_other
self.load_data(fips)
def test_optimization_objective(self):
def objective_fun(x):
return np.sum(x ** 4)
x0 = np.random.random(5)
obj = paragami.OptimizationObjective(
objective_fun, print_every=0)
assert_array_almost_equal(objective_fun(x0), obj.f(x0))
assert_array_almost_equal(
autograd.grad(objective_fun)(x0), obj.grad(x0))
assert_array_almost_equal(
autograd.hessian(objective_fun)(x0), obj.hessian(x0))
assert_array_almost_equal(
autograd.hessian_vector_product(objective_fun)(
x0, x0),
obj.hessian_vector_product(x0, x0))
def test_print_and_log(num_evals, expected_prints, expected_logs):
with captured_output() as (out, err):
init_num_iterations = obj.num_iterations()
for iter in range(num_evals):
# Funtion evaluations should be printed and logged.
obj.f(x0)
# Derivatives should not count towards printing or logging.
obj.grad(x0)
obj.hessian(x0)
obj.hessian_vector_product(x0, x0)
lines = out.getvalue().splitlines()
self.assertEqual(init_num_iterations + num_evals,
obj.num_iterations())
self.assertEqual(len(lines), expected_prints)
self.assertEqual(len(obj.optimization_log), expected_logs)
# Test reset.
obj.set_print_every(1)
obj.set_log_every(1)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
# Test that the first iteration prints and logs no matter what.
obj.set_print_every(2)
obj.set_log_every(2)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
test_print_and_log(num_evals=1, expected_prints=0, expected_logs=1)
# Test combinations of print and log.
for print_every, log_every in itertools.product([0, 1], [0, 1]):
obj.set_print_every(print_every)
obj.set_log_every(log_every)
obj.reset()
test_print_and_log(
num_evals=3,
expected_prints=3 * print_every,
expected_logs=3 * log_every)
for print_every, log_every in itertools.product([0, 3], [0, 3]):
obj.set_print_every(print_every)
obj.set_log_every(log_every)
obj.reset()
test_print_and_log(
num_evals=6,
expected_prints=(print_every != 0) * 2,
expected_logs=(log_every != 0) * 2)
# Test reset only printing or logging.
obj.set_print_every(2)
obj.set_log_every(1)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
test_print_and_log(num_evals=1, expected_prints=0, expected_logs=2)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
obj.reset_iteration_count()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=2)
obj.reset()
test_print_and_log(num_evals=1, expected_prints=1, expected_logs=1)
obj.reset_log()
test_print_and_log(num_evals=1, expected_prints=0, expected_logs=1)
def set_hvp(self, gamma):
self.hvp = lambda theta, v: \
autograd.hessian_vector_product(self.f)(theta, v) + np.sum(gamma * theta)
def hvp(x, vec):
result = hessian_vector_product(loss)(x, vec)
print('hessian-vector product evaluated at: ({}, {})'.format(x, vec))
hvp_traj.append((x, vec, result))
return result
num_per_class=100,
rate=0.4)
def objective(params):
return -gmm_log_likelihood(params, data)
flattened_obj, unflatten, flattened_init_params =\
flatten_func(objective, init_params)
fig = plt.figure(figsize=(12, 8), facecolor='white')
ax = fig.add_subplot(111, frameon=False)
plt.show(block=False)
def callback(flattened_params):
params = unflatten(flattened_params)
print("Log likelihood {}".format(-objective(params)))
ax.cla()
ax.plot(data[:, 0], data[:, 1], 'k.')
ax.set_xticks([])
ax.set_yticks([])
plot_gaussian_mixture(params, ax)
plt.draw()
plt.pause(1.0 / 60.0)
minimize(flattened_obj,
flattened_init_params,
jac=grad(flattened_obj),
hessp=hessian_vector_product(flattened_obj),
method='Newton-CG',
callback=callback)
def test_hessian_matrix_product():
fun = lambda a: np.sum(np.sin(a))
a = npr.randn(5, 4)
V = npr.randn(5, 4)
H = hessian(fun)(a)
check_equivalent(np.tensordot(H, V), hessian_vector_product(fun)(a, V))
data = make_pinwheel(radial_std=0.3, tangential_std=0.05, num_classes=3,
num_per_class=100, rate=0.4)
def objective(params):
return -gmm_log_likelihood(params, data)
flattened_obj, unflatten, flattened_init_params =\
flatten_func(objective, init_params)
fig = plt.figure(figsize=(12,8), facecolor='white')
ax = fig.add_subplot(111, frameon=False)
plt.show(block=False)
def callback(flattened_params):
params = unflatten(flattened_params)
print("Log likelihood {}".format(-objective(params)))
ax.cla()
ax.plot(data[:, 0], data[:, 1], 'k.')
ax.set_xticks([])
ax.set_yticks([])
plot_gaussian_mixture(params, ax)
plt.draw()
plt.pause(1.0/60.0)
minimize(flattened_obj, flattened_init_params,
jac=grad(flattened_obj),
hessp=hessian_vector_product(flattened_obj),
method='Newton-CG', callback=callback)
def test_objective(self):
model = Model(dim=3)
objective = obj_lib.Objective(par=model.x, fun=model.f)
model.set_inits()
x_free = model.x.get_free()
x_vec = model.x.get_vector()
model.set_opt()
self.assertTrue(objective.fun_free(x_free) > 0.0)
np_test.assert_array_almost_equal(objective.fun_free(x_free),
objective.fun_vector(x_vec))
grad = objective.fun_free_grad(x_free)
hess = objective.fun_free_hessian(x_free)
np_test.assert_array_almost_equal(np.matmul(hess, grad),
objective.fun_free_hvp(x_free, grad))
self.assertTrue(objective.fun_vector(x_vec) > 0.0)
grad = objective.fun_vector_grad(x_vec)
hess = objective.fun_vector_hessian(x_vec)
np_test.assert_array_almost_equal(
np.matmul(hess, grad), objective.fun_vector_hvp(x_free, grad))
# Test Jacobians.
vec_objective = obj_lib.Objective(par=model.x, fun=model.get_x_vec)
vec_jac = vec_objective.fun_vector_jacobian(x_vec)
np_test.assert_array_almost_equal(model.b_mat, vec_jac)
free_jac = vec_objective.fun_free_jacobian(x_free)
x_free_to_vec_jac = \
model.x.free_to_vector_jac(x_free).todense()
np_test.assert_array_almost_equal(
np.matmul(model.b_mat, np.transpose(x_free_to_vec_jac)), free_jac)
# Test the preconditioning
preconditioner = 2.0 * np.eye(model.dim)
preconditioner[model.dim - 1, 0] = 0.1 # Add asymmetry for testing!
objective.preconditioner = preconditioner
np_test.assert_array_almost_equal(
objective.fun_free_cond(x_free),
objective.fun_free(np.matmul(preconditioner, x_free)),
err_msg='Conditioned function values')
fun_free_cond_grad = autograd.grad(objective.fun_free_cond)
grad_cond = objective.fun_free_grad_cond(x_free)
np_test.assert_array_almost_equal(
fun_free_cond_grad(x_free),
grad_cond,
err_msg='Conditioned gradient values')
fun_free_cond_hessian = autograd.hessian(objective.fun_free_cond)
hess_cond = objective.fun_free_hessian_cond(x_free)
np_test.assert_array_almost_equal(fun_free_cond_hessian(x_free),
hess_cond,
err_msg='Conditioned Hessian values')
fun_free_cond_hvp = autograd.hessian_vector_product(
objective.fun_free_cond)
np_test.assert_array_almost_equal(
fun_free_cond_hvp(x_free, grad_cond),
objective.fun_free_hvp_cond(x_free, grad_cond),
err_msg='Conditioned Hessian vector product values')