def body_fn(i, val):
idx = idxs[i]
support_size = support_sizes_flat[idx]
rng_key, z, pe = val
rng_key, z_new, pe_new, log_accept_ratio = proposal_fn(
rng_key,
z,
pe,
potential_fn=potential_fn,
idx=idx,
support_size=support_size)
rng_key, rng_accept = random.split(rng_key)
# u ~ Uniform(0, 1), u < accept_ratio => -log(u) > -log_accept_ratio
# and -log(u) ~ exponential(1)
z, pe = cond(
random.exponential(rng_accept) > -log_accept_ratio,
(z_new, pe_new), identity, (z, pe), identity)
return rng_key, z, pe
def _discrete_gibbs_proposal_body_fn(z_init_flat, unravel_fn, pe_init,
potential_fn, idx, i, val):
rng_key, z, pe, log_weight_sum = val
rng_key, rng_transition = random.split(rng_key)
proposal = jnp.where(i >= z_init_flat[idx], i + 1, i)
z_new_flat = ops.index_update(z_init_flat, idx, proposal)
z_new = unravel_fn(z_new_flat)
pe_new = potential_fn(z_new)
log_weight_new = pe_init - pe_new
# Handles the NaN case...
log_weight_new = jnp.where(jnp.isfinite(log_weight_new), log_weight_new,
-jnp.inf)
# transition_prob = e^weight_new / (e^weight_logsumexp + e^weight_new)
transition_prob = expit(log_weight_new - log_weight_sum)
z, pe = cond(random.bernoulli(rng_transition, transition_prob),
(z_new, pe_new), identity, (z, pe), identity)
log_weight_sum = jnp.logaddexp(log_weight_new, log_weight_sum)
return rng_key, z, pe, log_weight_sum
def sample(self, state, model_args, model_kwargs):
model_kwargs = {} if model_kwargs is None else model_kwargs.copy()
rng_key, rng_gibbs = random.split(state.rng_key)
def potential_fn(z_gibbs, gibbs_state, z_hmc):
return self.inner_kernel._potential_fn_gen(
*model_args,
_gibbs_sites=z_gibbs,
_gibbs_state=gibbs_state,
**model_kwargs,
)(z_hmc)
z_gibbs = {
k: v
for k, v in state.z.items() if k not in state.hmc_state.z
}
z_gibbs_new, gibbs_state_new = self._gibbs_update(
rng_key, z_gibbs, state.gibbs_state)
# given a fixed hmc_sites, pe_new - pe_curr = loglik_new - loglik_curr
pe = state.hmc_state.potential_energy
pe_new = potential_fn(z_gibbs_new, gibbs_state_new, state.hmc_state.z)
accept_prob = jnp.clip(jnp.exp(pe - pe_new), a_max=1.0)
transition = random.bernoulli(rng_key, accept_prob)
grad_ = jacfwd if self.inner_kernel._forward_mode_differentiation else grad
z_gibbs, gibbs_state, pe, z_grad = cond(
transition,
(z_gibbs_new, gibbs_state_new, pe_new),
lambda vals: vals + (grad_(partial(potential_fn, vals[0], vals[1]))
(state.hmc_state.z), ),
(z_gibbs, state.gibbs_state, pe, state.hmc_state.z_grad),
identity,
)
hmc_state = state.hmc_state._replace(z_grad=z_grad,
potential_energy=pe)
model_kwargs["_gibbs_sites"] = z_gibbs
model_kwargs["_gibbs_state"] = gibbs_state
hmc_state = self.inner_kernel.sample(hmc_state, model_args,
model_kwargs)
z = {**z_gibbs, **hmc_state.z}
return HMCECSState(z, hmc_state, rng_key, gibbs_state, accept_prob)
def _hmc_next(step_size, inverse_mass_matrix, vv_state, rng_key):
num_steps = _get_num_steps(step_size, trajectory_len)
vv_state_new = fori_loop(
0, num_steps,
lambda i, val: vv_update(step_size, inverse_mass_matrix, val),
vv_state)
energy_old = vv_state.potential_energy + kinetic_fn(
inverse_mass_matrix, vv_state.r)
energy_new = vv_state_new.potential_energy + kinetic_fn(
inverse_mass_matrix, vv_state_new.r)
delta_energy = energy_new - energy_old
delta_energy = np.where(np.isnan(delta_energy), np.inf, delta_energy)
accept_prob = np.clip(np.exp(-delta_energy), a_max=1.0)
diverging = delta_energy > max_delta_energy
transition = random.bernoulli(rng_key, accept_prob)
vv_state, energy = cond(transition, (vv_state_new, energy_new),
lambda args: args, (vv_state, energy_old),
lambda args: args)
return vv_state, energy, num_steps, accept_prob, diverging
def sample(self, state, model_args, model_kwargs):
"""
Given the current `state`, return the next `state` using the given
transition kernel.
:param state: A `pytree <https://jax.readthedocs.io/en/latest/pytrees.html>`_
class representing the state for the kernel. For HMC, this is given
by :data:`~numpyro.infer.hmc.HMCStkernel0ate`. In general, this could be any
class that supports `getattr`.
:param model_args: Arguments provided to the model.
:param model_kwargs: Keyword arguments provided to the model.
:return: Next `state`.
"""
return cond(state.itr % 2 == 0,
state,
lambda s: self._kernel0.sample(
s, model_args, model_kwargs),
state,
lambda s: self._kernel1.sample(s, model_args, model_kwargs))
def sample_kernel(hmc_state, model_args=(), model_kwargs=None):
"""
Given an existing :data:`~numpyro.infer.mcmc.HMCState`, run HMC with fixed (possibly adapted)
step size and return a new :data:`~numpyro.infer.mcmc.HMCState`.
:param hmc_state: Current sample (and associated state).
:param tuple model_args: Model arguments if `potential_fn_gen` is specified.
:param dict model_kwargs: Model keyword arguments if `potential_fn_gen` is specified.
:return: new proposed :data:`~numpyro.infer.mcmc.HMCState` from simulating
Hamiltonian dynamics given existing state.
"""
model_kwargs = {} if model_kwargs is None else model_kwargs
rng_key, rng_key_momentum, rng_key_transition = random.split(
hmc_state.rng_key, 3)
r = momentum_generator(hmc_state.z,
hmc_state.adapt_state.mass_matrix_sqrt,
rng_key_momentum)
vv_state = IntegratorState(hmc_state.z, r, hmc_state.potential_energy,
hmc_state.z_grad)
vv_state, energy, num_steps, accept_prob, diverging = _next(
hmc_state.adapt_state.step_size,
hmc_state.adapt_state.inverse_mass_matrix, vv_state, model_args,
model_kwargs, rng_key_transition)
# not update adapt_state after warmup phase
adapt_state = cond(
hmc_state.i < wa_steps,
(hmc_state.i, accept_prob, vv_state, hmc_state.adapt_state),
lambda args: wa_update(*args), hmc_state.adapt_state, identity)
itr = hmc_state.i + 1
n = jnp.where(hmc_state.i < wa_steps, itr, itr - wa_steps)
mean_accept_prob = hmc_state.mean_accept_prob + (
accept_prob - hmc_state.mean_accept_prob) / n
return HMCState(itr, vv_state.z, vv_state.z_grad,
vv_state.potential_energy, energy, num_steps,
accept_prob, mean_accept_prob, diverging, adapt_state,
rng_key)
def _hmc_next(step_size, inverse_mass_matrix, vv_state,
model_args, model_kwargs, rng_key):
if potential_fn_gen:
nonlocal vv_update
pe_fn = potential_fn_gen(*model_args, **model_kwargs)
_, vv_update = velocity_verlet(pe_fn, kinetic_fn)
num_steps = _get_num_steps(step_size, trajectory_len)
vv_state_new = fori_loop(0, num_steps,
lambda i, val: vv_update(step_size, inverse_mass_matrix, val),
vv_state)
energy_old = vv_state.potential_energy + kinetic_fn(inverse_mass_matrix, vv_state.r)
energy_new = vv_state_new.potential_energy + kinetic_fn(inverse_mass_matrix, vv_state_new.r)
delta_energy = energy_new - energy_old
delta_energy = jnp.where(jnp.isnan(delta_energy), jnp.inf, delta_energy)
accept_prob = jnp.clip(jnp.exp(-delta_energy), a_max=1.0)
diverging = delta_energy > max_delta_energy
transition = random.bernoulli(rng_key, accept_prob)
vv_state, energy = cond(transition,
(vv_state_new, energy_new), identity,
(vv_state, energy_old), identity)
return vv_state, energy, num_steps, accept_prob, diverging
def gibbs_fn(rng_key, gibbs_sites, hmc_sites):
assert set(gibbs_sites) == set(plate_sizes)
u_new = {}
for name in gibbs_sites:
size, subsample_size = plate_sizes[name]
rng_key, subkey, block_key = random.split(rng_key, 3)
block_size = subsample_size // num_blocks
chosen_block = random.randint(block_key,
shape=(),
minval=0,
maxval=num_blocks)
new_idx = random.randint(subkey,
minval=0,
maxval=size,
shape=(subsample_size, ))
block_mask = jnp.arange(
subsample_size) // block_size == chosen_block
u_new[name] = jnp.where(block_mask, new_idx, gibbs_sites[name])
u_loglik = log_likelihood(_wrap_model(model),
hmc_sites,
*model_args,
batch_ndims=0,
**model_kwargs,
_gibbs_sites=gibbs_sites)
u_loglik = sum(v.sum() for v in u_loglik.values())
u_new_loglik = log_likelihood(_wrap_model(model),
hmc_sites,
*model_args,
batch_ndims=0,
**model_kwargs,
_gibbs_sites=u_new)
u_new_loglik = sum(v.sum() for v in u_new_loglik.values())
accept_prob = jnp.clip(jnp.exp(u_new_loglik - u_loglik), a_max=1.0)
return cond(random.bernoulli(rng_key, accept_prob), u_new, identity,
gibbs_sites, identity)
def _body_fn(state):
current_tree, _, r_ckpts, r_sum_ckpts, rng = state
rng, transition_rng = random.split(rng)
z, r, z_grad = _get_leaf(current_tree, going_right)
new_leaf = _build_basetree(vv_update, kinetic_fn, z, r, z_grad, inverse_mass_matrix, step_size,
going_right, energy_current, max_delta_energy)
new_tree = _combine_tree(current_tree, new_leaf, inverse_mass_matrix, going_right,
transition_rng, False)
leaf_idx = current_tree.num_proposals
ckpt_idx_min, ckpt_idx_max = _leaf_idx_to_ckpt_idxs(leaf_idx)
r, _ = ravel_pytree(new_leaf.r_right)
r_sum, _ = ravel_pytree(new_tree.r_sum)
# we update checkpoints when leaf_idx is even
r_ckpts, r_sum_ckpts = cond(leaf_idx % 2 == 0,
(r_ckpts, r_sum_ckpts),
lambda x: (index_update(x[0], ckpt_idx_max, r),
index_update(x[1], ckpt_idx_max, r_sum)),
(r_ckpts, r_sum_ckpts),
lambda x: x)
turning = _is_iterative_turning(inverse_mass_matrix, r, r_sum, r_ckpts, r_sum_ckpts,
ckpt_idx_min, ckpt_idx_max)
return new_tree, turning, r_ckpts, r_sum_ckpts, rng
def _discrete_modified_gibbs_proposal(rng_key,
z_discrete,
pe,
potential_fn,
idx,
support_size,
stay_prob=0.):
assert isinstance(stay_prob, float) and stay_prob >= 0. and stay_prob < 1
z_discrete_flat, unravel_fn = ravel_pytree(z_discrete)
body_fn = partial(_discrete_gibbs_proposal_body_fn, z_discrete_flat,
unravel_fn, pe, potential_fn, idx)
# like gibbs_step but here, weight of the current value is 0
init_val = (rng_key, z_discrete, pe, jnp.array(-jnp.inf))
rng_key, z_new, pe_new, log_weight_sum = fori_loop(0, support_size - 1,
body_fn, init_val)
rng_key, rng_stay = random.split(rng_key)
z_new, pe_new = cond(random.bernoulli(rng_stay, stay_prob),
(z_discrete, pe), identity, (z_new, pe_new), identity)
# here we calculate the MH correction: (1 - P(z)) / (1 - P(z_new))
# where 1 - P(z) ~ weight_sum
# and 1 - P(z_new) ~ 1 + weight_sum - z_new_weight
log_accept_ratio = log_weight_sum - jnp.log(
jnp.exp(log_weight_sum) - jnp.expm1(pe - pe_new))
return rng_key, z_new, pe_new, log_accept_ratio
def _get_leaf(tree, going_right):
return cond(going_right, tree, lambda tree:
(tree.z_right, tree.r_right, tree.z_right_grad), tree,
lambda tree: (tree.z_left, tree.r_left, tree.z_left_grad))
def sample(self, state, model_args, model_kwargs):
model_kwargs = {} if model_kwargs is None else model_kwargs
num_discretes = self._support_sizes_flat.shape[0]
def potential_fn(z_gibbs, z_hmc):
return self.inner_kernel._potential_fn_gen(*model_args,
_gibbs_sites=z_gibbs,
**model_kwargs)(z_hmc)
def update_discrete(idx, rng_key, hmc_state, z_discrete, ke_discrete,
delta_pe_sum):
# Algo 1, line 19: get a new discrete proposal
(
rng_key,
z_discrete_new,
pe_new,
log_accept_ratio,
) = self._discrete_proposal_fn(
rng_key,
z_discrete,
hmc_state.potential_energy,
partial(potential_fn, z_hmc=hmc_state.z),
idx,
self._support_sizes_flat[idx],
)
# Algo 1, line 20: depending on reject or refract, we will update
# the discrete variable and its corresponding kinetic energy. In case of
# refract, we will need to update the potential energy and its grad w.r.t. hmc_state.z
ke_discrete_i_new = ke_discrete[idx] + log_accept_ratio
grad_ = jacfwd if self.inner_kernel._forward_mode_differentiation else grad
z_discrete, pe, ke_discrete_i, z_grad = lax.cond(
ke_discrete_i_new > 0,
(z_discrete_new, pe_new, ke_discrete_i_new),
lambda vals: vals + (grad_(partial(potential_fn, vals[0]))
(hmc_state.z), ),
(
z_discrete,
hmc_state.potential_energy,
ke_discrete[idx],
hmc_state.z_grad,
),
identity,
)
delta_pe_sum = delta_pe_sum + pe - hmc_state.potential_energy
ke_discrete = ops.index_update(ke_discrete, idx, ke_discrete_i)
hmc_state = hmc_state._replace(potential_energy=pe, z_grad=z_grad)
return rng_key, hmc_state, z_discrete, ke_discrete, delta_pe_sum
def update_continuous(hmc_state, z_discrete):
model_kwargs_ = model_kwargs.copy()
model_kwargs_["_gibbs_sites"] = z_discrete
hmc_state_new = self.inner_kernel.sample(hmc_state, model_args,
model_kwargs_)
# each time a sub-trajectory is performed, we need to reset i and adapt_state
# (we will only update them at the end of HMCGibbs step)
# For `num_steps`, we will record its cumulative sum for diagnostics
hmc_state = hmc_state_new._replace(
i=hmc_state.i,
adapt_state=hmc_state.adapt_state,
num_steps=hmc_state.num_steps + hmc_state_new.num_steps,
)
return hmc_state
def body_fn(i, vals):
(
rng_key,
hmc_state,
z_discrete,
ke_discrete,
delta_pe_sum,
arrival_times,
) = vals
idx = jnp.argmin(arrival_times)
# NB: length of each sub-trajectory is scaled from the current min(arrival_times)
# (see the note at total_time below)
trajectory_length = arrival_times[idx] * time_unit
arrival_times = arrival_times - arrival_times[idx]
arrival_times = ops.index_update(arrival_times, idx, 1.0)
# this is a trick, so that in a sub-trajectory of HMC, we always accept the new proposal
pe = jnp.inf
hmc_state = hmc_state._replace(trajectory_length=trajectory_length,
potential_energy=pe)
# Algo 1, line 7: perform a sub-trajectory
hmc_state = update_continuous(hmc_state, z_discrete)
# Algo 1, line 8: perform a discrete update
rng_key, hmc_state, z_discrete, ke_discrete, delta_pe_sum = update_discrete(
idx, rng_key, hmc_state, z_discrete, ke_discrete, delta_pe_sum)
return (
rng_key,
hmc_state,
z_discrete,
ke_discrete,
delta_pe_sum,
arrival_times,
)
z_discrete = {
k: v
for k, v in state.z.items() if k not in state.hmc_state.z
}
rng_key, rng_ke, rng_time, rng_r, rng_accept = random.split(
state.rng_key, 5)
# Algo 1, line 2: sample discrete kinetic energy
ke_discrete = random.exponential(rng_ke, (num_discretes, ))
# Algo 1, line 4 and 5: sample the initial amount of time that each discrete site visits
# the point 0/1. The logic in GetStepSizesNSteps(...) is more complicated but does
# the same job: the sub-trajectory length eta_t * M_t is the lag between two arrival time.
arrival_times = random.uniform(rng_time, (num_discretes, ))
# compute the amount of time to make `num_discrete_updates` discrete updates
total_time = (self._num_discrete_updates -
1) // num_discretes + jnp.sort(arrival_times)[
(self._num_discrete_updates - 1) % num_discretes]
# NB: total_time can be different from the HMC trajectory length, so we need to scale
# the time unit so that total_time * time_unit = hmc_trajectory_length
time_unit = state.hmc_state.trajectory_length / total_time
# Algo 1, line 2: sample hmc momentum
r = momentum_generator(state.hmc_state.r,
state.hmc_state.adapt_state.mass_matrix_sqrt,
rng_r)
hmc_state = state.hmc_state._replace(r=r, num_steps=0)
hmc_ke = euclidean_kinetic_energy(
hmc_state.adapt_state.inverse_mass_matrix, r)
# Algo 1, line 10: compute the initial energy
energy_old = hmc_ke + hmc_state.potential_energy
# Algo 1, line 3: set initial values
delta_pe_sum = 0.0
init_val = (
rng_key,
hmc_state,
z_discrete,
ke_discrete,
delta_pe_sum,
arrival_times,
)
# Algo 1, line 6-9: perform the update loop
rng_key, hmc_state_new, z_discrete_new, _, delta_pe_sum, _ = fori_loop(
0, self._num_discrete_updates, body_fn, init_val)
# Algo 1, line 10: compute the proposal energy
hmc_ke = euclidean_kinetic_energy(
hmc_state.adapt_state.inverse_mass_matrix, hmc_state_new.r)
energy_new = hmc_ke + hmc_state_new.potential_energy
# Algo 1, line 11: perform MH correction
delta_energy = energy_new - energy_old - delta_pe_sum
delta_energy = jnp.where(jnp.isnan(delta_energy), jnp.inf,
delta_energy)
accept_prob = jnp.clip(jnp.exp(-delta_energy), a_max=1.0)
# record the correct new num_steps
hmc_state = hmc_state._replace(num_steps=hmc_state_new.num_steps)
# reset the trajectory length
hmc_state_new = hmc_state_new._replace(
trajectory_length=hmc_state.trajectory_length)
hmc_state, z_discrete = cond(
random.bernoulli(rng_key, accept_prob),
(hmc_state_new, z_discrete_new),
identity,
(hmc_state, z_discrete),
identity,
)
# perform hmc adapting (similar to the implementation in hmc)
adapt_state = cond(
hmc_state.i < self._num_warmup,
(hmc_state.i, accept_prob, (hmc_state.z, ), hmc_state.adapt_state),
lambda args: self._wa_update(*args),
hmc_state.adapt_state,
identity,
)
itr = hmc_state.i + 1
n = jnp.where(hmc_state.i < self._num_warmup, itr,
itr - self._num_warmup)
mean_accept_prob_prev = state.hmc_state.mean_accept_prob
mean_accept_prob = (mean_accept_prob_prev +
(accept_prob - mean_accept_prob_prev) / n)
hmc_state = hmc_state._replace(
i=itr,
accept_prob=accept_prob,
mean_accept_prob=mean_accept_prob,
adapt_state=adapt_state,
)
z = {**z_discrete, **hmc_state.z}
return MixedHMCState(z, hmc_state, rng_key, accept_prob)
def _combine_tree(current_tree, new_tree, inverse_mass_matrix, going_right,
rng_key, biased_transition):
# Now we combine the current tree and the new tree. Note that outside
# leaves of the combined tree are determined by the direction.
z_left, r_left, z_left_grad, z_right, r_right, r_right_grad = cond(
going_right,
(current_tree, new_tree),
lambda trees: (
trees[0].z_left,
trees[0].r_left,
trees[0].z_left_grad,
trees[1].z_right,
trees[1].r_right,
trees[1].z_right_grad,
),
(new_tree, current_tree),
lambda trees: (
trees[0].z_left,
trees[0].r_left,
trees[0].z_left_grad,
trees[1].z_right,
trees[1].r_right,
trees[1].z_right_grad,
),
)
r_sum = tree_multimap(jnp.add, current_tree.r_sum, new_tree.r_sum)
if biased_transition:
transition_prob = _biased_transition_kernel(current_tree, new_tree)
turning = new_tree.turning | _is_turning(inverse_mass_matrix, r_left,
r_right, r_sum)
else:
transition_prob = _uniform_transition_kernel(current_tree, new_tree)
turning = current_tree.turning
transition = random.bernoulli(rng_key, transition_prob)
z_proposal, z_proposal_pe, z_proposal_grad, z_proposal_energy = cond(
transition,
new_tree,
lambda tree: (
tree.z_proposal,
tree.z_proposal_pe,
tree.z_proposal_grad,
tree.z_proposal_energy,
),
current_tree,
lambda tree: (
tree.z_proposal,
tree.z_proposal_pe,
tree.z_proposal_grad,
tree.z_proposal_energy,
),
)
tree_depth = current_tree.depth + 1
tree_weight = jnp.logaddexp(current_tree.weight, new_tree.weight)
diverging = new_tree.diverging
sum_accept_probs = current_tree.sum_accept_probs + new_tree.sum_accept_probs
num_proposals = current_tree.num_proposals + new_tree.num_proposals
return TreeInfo(
z_left,
r_left,
z_left_grad,
z_right,
r_right,
r_right_grad,
z_proposal,
z_proposal_pe,
z_proposal_grad,
z_proposal_energy,
tree_depth,
tree_weight,
r_sum,
turning,
diverging,
sum_accept_probs,
num_proposals,
)
def update_fn(t, accept_prob, z_info, state):
"""
:param int t: The current time step.
:param float accept_prob: Acceptance probability of the current trajectory.
:param IntegratorState z_info: The new integrator state.
:param state: Current state of the adapt scheme.
:return: new state of the adapt scheme.
"""
(
step_size,
inverse_mass_matrix,
mass_matrix_sqrt,
mass_matrix_sqrt_inv,
ss_state,
mm_state,
window_idx,
rng_key,
) = state
if rng_key is not None:
rng_key, rng_key_ss = random.split(rng_key)
else:
rng_key_ss = None
# update step size state
if adapt_step_size:
ss_state = ss_update(target_accept_prob - accept_prob, ss_state)
# note: at the end of warmup phase, use average of log step_size
log_step_size, log_step_size_avg, *_ = ss_state
step_size = jnp.where(
t == (num_adapt_steps - 1),
jnp.exp(log_step_size_avg),
jnp.exp(log_step_size),
)
# account the the case log_step_size is an extreme number
finfo = jnp.finfo(jnp.result_type(step_size))
step_size = jnp.clip(step_size, a_min=finfo.tiny, a_max=finfo.max)
# update mass matrix state
is_middle_window = (0 < window_idx) & (window_idx < (num_windows - 1))
if adapt_mass_matrix:
z = z_info[0]
mm_state = cond(
is_middle_window,
(z, mm_state),
lambda args: mm_update(*args),
mm_state,
identity,
)
t_at_window_end = t == adaptation_schedule[window_idx, 1]
window_idx = jnp.where(t_at_window_end, window_idx + 1, window_idx)
state = HMCAdaptState(
step_size,
inverse_mass_matrix,
mass_matrix_sqrt,
mass_matrix_sqrt_inv,
ss_state,
mm_state,
window_idx,
rng_key,
)
state = cond(
t_at_window_end & is_middle_window,
(z_info, rng_key_ss, state),
lambda args: _update_at_window_end(*args),
state,
identity,
)
return state