Merge branch 'main' into barker-inverse-mm2

blackjax/__init__.py

@@ -35,6 +35,7 @@
 from .sgmcmc import sgnht as _sgnht
 from .smc import adaptive_tempered
 from .smc import inner_kernel_tuning as _inner_kernel_tuning
+from .smc import partial_posteriors_path as _partial_posteriors_smc
 from .smc import tempered
 from .vi import meanfield_vi as _meanfield_vi
 from .vi import pathfinder as _pathfinder
@@ -119,8 +120,9 @@ def generate_top_level_api_from(module):
 adaptive_tempered_smc = generate_top_level_api_from(adaptive_tempered)
 tempered_smc = generate_top_level_api_from(tempered)
 inner_kernel_tuning = generate_top_level_api_from(_inner_kernel_tuning)
+partial_posteriors_smc = generate_top_level_api_from(_partial_posteriors_smc)
 
-smc_family = [tempered_smc, adaptive_tempered_smc]
+smc_family = [tempered_smc, adaptive_tempered_smc, partial_posteriors_smc]
 "Step_fn returning state has a .particles attribute"
 
 # stochastic gradient mcmc

blackjax/smc/__init__.py

@@ -6,4 +6,5 @@
     "tempered",
     "inner_kernel_tuning",
     "extend_params",
+    "partial_posteriors_path",
 ]

blackjax/smc/base.py

@@ -156,3 +156,31 @@ def extend_params(params):
     """
 
     return jax.tree.map(lambda x: jnp.asarray(x)[None, ...], params)
+
+
+def update_and_take_last(
+    mcmc_init_fn,
+    tempered_logposterior_fn,
+    shared_mcmc_step_fn,
+    num_mcmc_steps,
+    n_particles,
+):
+    """Given N particles, runs num_mcmc_steps of a kernel starting at each particle, and
+    returns the last values, waisting the previous num_mcmc_steps-1
+    samples per chain.
+    """
+
+    def mcmc_kernel(rng_key, position, step_parameters):
+        state = mcmc_init_fn(position, tempered_logposterior_fn)
+
+        def body_fn(state, rng_key):
+            new_state, info = shared_mcmc_step_fn(
+                rng_key, state, tempered_logposterior_fn, **step_parameters
+            )
+            return new_state, info
+
+        keys = jax.random.split(rng_key, num_mcmc_steps)
+        last_state, info = jax.lax.scan(body_fn, state, keys)
+        return last_state.position, info
+
+    return jax.vmap(mcmc_kernel), n_particles

blackjax/smc/from_mcmc.py

@@ -0,0 +1,64 @@
+from functools import partial
+from typing import Callable
+
+import jax
+
+from blackjax import smc
+from blackjax.smc.base import SMCState, update_and_take_last
+from blackjax.types import PRNGKey
+
+
+def build_kernel(
+    mcmc_step_fn: Callable,
+    mcmc_init_fn: Callable,
+    resampling_fn: Callable,
+    update_strategy: Callable = update_and_take_last,
+):
+    """SMC step from MCMC kernels.
+    Builds MCMC kernels from the input parameters, which may change across iterations.
+    Moreover, it defines the way such kernels are used to update the particles. This layer
+    adapts an API defined in terms of kernels (mcmc_step_fn and mcmc_init_fn) into an API
+    that depends on an update function over the set of particles.
+    Returns
+    -------
+    A callable that takes a rng_key and a state with .particles and .weights and returns a base.SMCState
+    and base.SMCInfo pair.
+
+    """
+
+    def step(
+        rng_key: PRNGKey,
+        state,
+        num_mcmc_steps: int,
+        mcmc_parameters: dict,
+        logposterior_fn: Callable,
+        log_weights_fn: Callable,
+    ) -> tuple[smc.base.SMCState, smc.base.SMCInfo]:
+        shared_mcmc_parameters = {}
+        unshared_mcmc_parameters = {}
+        for k, v in mcmc_parameters.items():
+            if v.shape[0] == 1:
+                shared_mcmc_parameters[k] = v[0, ...]
+            else:
+                unshared_mcmc_parameters[k] = v
+
+        shared_mcmc_step_fn = partial(mcmc_step_fn, **shared_mcmc_parameters)
+
+        update_fn, num_resampled = update_strategy(
+            mcmc_init_fn,
+            logposterior_fn,
+            shared_mcmc_step_fn,
+            n_particles=state.weights.shape[0],
+            num_mcmc_steps=num_mcmc_steps,
+        )
+
+        return smc.base.step(
+            rng_key,
+            SMCState(state.particles, state.weights, unshared_mcmc_parameters),
+            update_fn,
+            jax.vmap(log_weights_fn),
+            resampling_fn,
+            num_resampled,
+        )
+
+    return step

blackjax/smc/partial_posteriors_path.py

@@ -0,0 +1,127 @@
+from typing import Callable, NamedTuple, Optional, Tuple
+
+import jax
+import jax.numpy as jnp
+
+from blackjax import SamplingAlgorithm, smc
+from blackjax.smc.base import update_and_take_last
+from blackjax.smc.from_mcmc import build_kernel as smc_from_mcmc
+from blackjax.types import Array, ArrayLikeTree, ArrayTree, PRNGKey
+
+
+class PartialPosteriorsSMCState(NamedTuple):
+    """Current state for the tempered SMC algorithm.
+
+    particles: PyTree
+        The particles' positions.
+    weights:
+        Weights of the particles, so that they represent a probability distribution
+    data_mask:
+        A 1D boolean array to indicate which datapoints to include
+        in the computation of the observed likelihood.
+    """
+
+    particles: ArrayTree
+    weights: Array
+    data_mask: Array
+
+
+def init(particles: ArrayLikeTree, num_datapoints: int) -> PartialPosteriorsSMCState:
+    """num_datapoints are the number of observations that could potentially be
+    used in a partial posterior. Since the initial data_mask is all 0s, it
+    means that no likelihood term will be added (only prior).
+    """
+    num_particles = jax.tree_util.tree_flatten(particles)[0][0].shape[0]
+    weights = jnp.ones(num_particles) / num_particles
+    return PartialPosteriorsSMCState(particles, weights, jnp.zeros(num_datapoints))
+
+
+def build_kernel(
+    mcmc_step_fn: Callable,
+    mcmc_init_fn: Callable,
+    resampling_fn: Callable,
+    num_mcmc_steps: Optional[int],
+    mcmc_parameters: ArrayTree,
+    partial_logposterior_factory: Callable[[Array], Callable],
+    update_strategy=update_and_take_last,
+) -> Callable:
+    """Build the Partial Posteriors (data tempering) SMC kernel.
+    The distribution's trajectory includes increasingly adding more
+    datapoints to the likelihood. See Section 2.2 of https://arxiv.org/pdf/2007.11936
+    Parameters
+    ----------
+    mcmc_step_fn
+        A function that computes the log density of the prior distribution
+    mcmc_init_fn
+        A function that returns the probability at a given position.
+    resampling_fn
+        A random function that resamples generated particles based of weights
+    num_mcmc_steps
+        Number of iterations in the MCMC chain.
+    mcmc_parameters
+        A dictionary of parameters to be used by the inner MCMC kernels
+    partial_logposterior_factory:
+        A callable that given an array of 0 and 1, returns a function logposterior(x).
+        The array represents which values to include in the logposterior calculation. The logposterior
+        must be jax compilable.
+
+    Returns
+    -------
+    A callable that takes a rng_key and PartialPosteriorsSMCState and selectors for
+    the current and previous posteriors, and takes a data-tempered SMC state.
+    """
+    delegate = smc_from_mcmc(mcmc_step_fn, mcmc_init_fn, resampling_fn, update_strategy)
+
+    def step(
+        key, state: PartialPosteriorsSMCState, data_mask: Array
+    ) -> Tuple[PartialPosteriorsSMCState, smc.base.SMCInfo]:
+        logposterior_fn = partial_logposterior_factory(data_mask)
+
+        previous_logposterior_fn = partial_logposterior_factory(state.data_mask)
+
+        def log_weights_fn(x):
+            return logposterior_fn(x) - previous_logposterior_fn(x)
+
+        state, info = delegate(
+            key, state, num_mcmc_steps, mcmc_parameters, logposterior_fn, log_weights_fn
+        )
+
+        return (
+            PartialPosteriorsSMCState(state.particles, state.weights, data_mask),
+            info,
+        )
+
+    return step
+
+
+def as_top_level_api(
+    mcmc_step_fn: Callable,
+    mcmc_init_fn: Callable,
+    mcmc_parameters: dict,
+    resampling_fn: Callable,
+    num_mcmc_steps,
+    partial_logposterior_factory: Callable,
+    update_strategy=update_and_take_last,
+) -> SamplingAlgorithm:
+    """A factory that wraps the kernel into a SamplingAlgorithm object.
+    See build_kernel for full documentation on the parameters.
+    """
+
+    kernel = build_kernel(
+        mcmc_step_fn,
+        mcmc_init_fn,
+        resampling_fn,
+        num_mcmc_steps,
+        mcmc_parameters,
+        partial_logposterior_factory,
+        update_strategy,
+    )
+
+    def init_fn(position: ArrayLikeTree, num_observations, rng_key=None):
+        del rng_key
+        return init(position, num_observations)
+
+    def step(key: PRNGKey, state: PartialPosteriorsSMCState, data_mask: Array):
+        return kernel(key, state, data_mask)
+
+    return SamplingAlgorithm(init_fn, step)  # type: ignore[arg-type]

blackjax/smc/tempered.py

@@ -11,15 +11,15 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-from functools import partial
 from typing import Callable, NamedTuple, Optional
 
 import jax
 import jax.numpy as jnp
 
 import blackjax.smc as smc
+import blackjax.smc.from_mcmc as smc_from_mcmc
 from blackjax.base import SamplingAlgorithm
-from blackjax.smc.base import SMCState
+from blackjax.smc.base import update_and_take_last
 from blackjax.types import Array, ArrayLikeTree, ArrayTree, PRNGKey
 
 __all__ = ["TemperedSMCState", "init", "build_kernel", "as_top_level_api"]
@@ -48,35 +48,6 @@ def init(particles: ArrayLikeTree):
     return TemperedSMCState(particles, weights, 0.0)
 
 
-def update_and_take_last(
-    mcmc_init_fn,
-    tempered_logposterior_fn,
-    shared_mcmc_step_fn,
-    num_mcmc_steps,
-    n_particles,
-):
-    """
-    Given N particles, runs num_mcmc_steps of a kernel starting at each particle, and
-    returns the last values, waisting the previous num_mcmc_steps-1
-    samples per chain.
-    """
-
-    def mcmc_kernel(rng_key, position, step_parameters):
-        state = mcmc_init_fn(position, tempered_logposterior_fn)
-
-        def body_fn(state, rng_key):
-            new_state, info = shared_mcmc_step_fn(
-                rng_key, state, tempered_logposterior_fn, **step_parameters
-            )
-            return new_state, info
-
-        keys = jax.random.split(rng_key, num_mcmc_steps)
-        last_state, info = jax.lax.scan(body_fn, state, keys)
-        return last_state.position, info
-
-    return jax.vmap(mcmc_kernel), n_particles
-
-
 def build_kernel(
     logprior_fn: Callable,
     loglikelihood_fn: Callable,
@@ -121,6 +92,9 @@ def build_kernel(
     information about the transition.
 
     """
+    delegate = smc_from_mcmc.build_kernel(
+        mcmc_step_fn, mcmc_init_fn, resampling_fn, update_strategy
+    )
 
     def kernel(
         rng_key: PRNGKey,
@@ -153,14 +127,6 @@ def kernel(
         """
         delta = lmbda - state.lmbda
 
-        shared_mcmc_parameters = {}
-        unshared_mcmc_parameters = {}
-        for k, v in mcmc_parameters.items():
-            if v.shape[0] == 1:
-                shared_mcmc_parameters[k] = v[0, ...]
-            else:
-                unshared_mcmc_parameters[k] = v
-
         def log_weights_fn(position: ArrayLikeTree) -> float:
             return delta * loglikelihood_fn(position)
 
@@ -169,23 +135,13 @@ def tempered_logposterior_fn(position: ArrayLikeTree) -> float:
             tempered_loglikelihood = state.lmbda * loglikelihood_fn(position)
             return logprior + tempered_loglikelihood
 
-        shared_mcmc_step_fn = partial(mcmc_step_fn, **shared_mcmc_parameters)
-
-        update_fn, num_resampled = update_strategy(
-            mcmc_init_fn,
-            tempered_logposterior_fn,
-            shared_mcmc_step_fn,
-            n_particles=state.weights.shape[0],
-            num_mcmc_steps=num_mcmc_steps,
-        )
-
-        smc_state, info = smc.base.step(
+        smc_state, info = delegate(
             rng_key,
-            SMCState(state.particles, state.weights, unshared_mcmc_parameters),
-            update_fn,
-            jax.vmap(log_weights_fn),
-            resampling_fn,
-            num_resampled,
+            state,
+            num_mcmc_steps,
+            mcmc_parameters,
+            tempered_logposterior_fn,
+            log_weights_fn,
         )
 
         tempered_state = TemperedSMCState(