def clean_chain(self, scenario: Scenario,
chain_ensemble_state: cdict) -> cdict:
chain_ensemble_state.temperature = chain_ensemble_state.temperature[:,
0]
scenario.temperature = float(chain_ensemble_state.temperature[-1])
chain_ensemble_state.ess = chain_ensemble_state.ess[:, 0]
return chain_ensemble_state
def startup(self, scenario: Scenario, n: int, initial_state: cdict,
initial_extra: cdict, **kwargs) -> Tuple[cdict, cdict]:
if not hasattr(scenario, 'prior_sample'):
raise TypeError(
f'Likelihood tempering requires scenario {scenario.name} to have prior_sample implemented'
)
initial_state, initial_extra = super().startup(scenario, n,
initial_state,
initial_extra, **kwargs)
random_keys = random.split(initial_extra.random_key, 2 * n + 1)
initial_extra.random_key = random_keys[-1]
initial_state.prior_potential = vmap(scenario.prior_potential)(
initial_state.value, random_keys[:n])
initial_state.likelihood_potential = vmap(
scenario.likelihood_potential)(initial_state.value,
random_keys[n:(2 * n)])
initial_state.potential = initial_state.prior_potential
initial_state.temperature = jnp.zeros(n)
initial_state.log_weight = jnp.zeros(n)
initial_state.ess = jnp.zeros(n) + n
scenario.temperature = 0.
return initial_state, initial_extra
def startup(self, scenario: Scenario, n: int, initial_state: cdict,
initial_extra: cdict, **kwargs) -> Tuple[cdict, cdict]:
initial_state, initial_extra = super().startup(scenario, n,
initial_state,
initial_extra, **kwargs)
if not hasattr(initial_state, 'log_weight'):
initial_state.log_weight = jnp.zeros(n)
if not hasattr(initial_state, 'ess'):
initial_state.ess = jnp.zeros(n) + n
return initial_state, initial_extra
def adapt(self, previous_ensemble_state: cdict, previous_extra: cdict,
new_ensemble_state: cdict,
new_extra: cdict) -> Tuple[cdict, cdict]:
n = new_ensemble_state.value.shape[0]
next_temperature = self.next_temperature(new_ensemble_state, new_extra)
new_ensemble_state.temperature = jnp.ones(n) * next_temperature
new_ensemble_state.log_weight = previous_ensemble_state.log_weight \
+ self.log_weight(previous_ensemble_state, previous_extra,
new_ensemble_state, new_extra)
new_ensemble_state.ess = jnp.ones(n) * jnp.exp(
log_ess_log_weight(new_ensemble_state.log_weight))
return new_ensemble_state, new_extra
def adapt(self,
previous_ensemble_state: cdict,
previous_extra: cdict,
new_ensemble_state: cdict,
new_extra: cdict) -> Tuple[cdict, cdict]:
n = new_ensemble_state.value.shape[0]
next_threshold = self.next_threshold(new_ensemble_state, new_extra)
new_ensemble_state.threshold = jnp.ones(n) * next_threshold
new_extra.parameters.threshold = next_threshold
new_ensemble_state.log_weight = self.log_weight(previous_ensemble_state, previous_extra,
new_ensemble_state, new_extra)
new_ensemble_state.ess = jnp.ones(n) * ess_log_weight(new_ensemble_state.log_weight)
alive_inds = previous_ensemble_state.log_weight > -jnp.inf
new_extra.alpha_mean = (new_ensemble_state.alpha * alive_inds).sum() / alive_inds.sum()
new_ensemble_state, new_extra = self.adapt_mcmc_params(previous_ensemble_state, previous_extra,
new_ensemble_state, new_extra)
return new_ensemble_state, new_extra
def startup(self, scenario: Scenario, n: int, initial_state: cdict,
initial_extra: cdict, **kwargs) -> Tuple[cdict, cdict]:
self.mcmc_sampler.correction = check_correction(
self.mcmc_sampler.correction)
initial_state, initial_extra = super().startup(scenario, n,
initial_state,
initial_extra, **kwargs)
first_temp = self.next_temperature(initial_state, initial_extra)
scenario.temperature = first_temp
initial_state.temperature += first_temp
initial_state.potential = initial_state.prior_potential + first_temp * initial_state.likelihood_potential
initial_state.log_weight = -first_temp * initial_state.likelihood_potential
initial_state.ess = jnp.repeat(
jnp.exp(log_ess_log_weight(initial_state.log_weight)), n)
initial_state, initial_extra = vmap(
lambda state: self.mcmc_sampler.startup(
scenario, n, state, initial_extra))(initial_state)
initial_extra = initial_extra[0]
return initial_state, initial_extra
def startup(self,
abc_scenario: ABCScenario,
n: int,
initial_state: cdict,
initial_extra: cdict,
**kwargs) -> Tuple[cdict, cdict]:
initial_state, initial_extra = SMCSampler.startup(self, abc_scenario, n,
initial_state, initial_extra, **kwargs)
n = len(initial_state.value)
if not hasattr(initial_state, 'prior_potential') and is_implemented(abc_scenario.prior_potential):
random_keys = random.split(initial_extra.random_key, n + 1)
initial_extra.random_key = random_keys[-1]
initial_state.prior_potential = vmap(abc_scenario.prior_potential)(initial_state.value,
random_keys[:n])
if not hasattr(initial_state, 'simulated_data'):
random_keys = random.split(initial_extra.random_key, n + 1)
initial_extra.random_key = random_keys[-1]
initial_state.simulated_data = vmap(abc_scenario.likelihood_sample)(initial_state.value,
random_keys[:n])
if not hasattr(initial_state, 'distance'):
initial_state.distance = vmap(abc_scenario.distance_function)(initial_state.simulated_data)
if not hasattr(initial_state, 'threshold'):
if self.threshold_schedule is None:
initial_state.threshold = jnp.zeros(n) + jnp.inf
else:
initial_state.threshold = jnp.zeros(n) + self.threshold_schedule[0]
if not hasattr(initial_state, 'ess'):
initial_state.ess = jnp.zeros(n) + n
return initial_state, initial_extra
def clean_chain(self,
abc_scenario: ABCScenario,
chain_ensemble_state: cdict) -> cdict:
chain_ensemble_state.threshold = chain_ensemble_state.threshold[:, 0]
chain_ensemble_state.ess = chain_ensemble_state.ess[:, 0]
return chain_ensemble_state