NLE with multiple iid conditions

sbi/inference/potentials/likelihood_based_potential.py

@@ -1,7 +1,8 @@
 # This file is part of sbi, a toolkit for simulation-based inference. sbi is licensed
 # under the Apache License Version 2.0, see <https://www.apache.org/licenses/>
 
-from typing import Callable, Optional, Tuple
+import warnings
+from typing import Callable, List, Optional, Tuple
 
 import torch
 from torch import Tensor
@@ -115,6 +116,52 @@
                 )
             return log_likelihood_batches + self.prior.log_prob(theta)  # type: ignore
 
+    def condition_on_theta(
+        self, theta_condition: Tensor, dims_to_sample: List[int]
+    ) -> Callable:
+        """Returns a potential function conditioned on a subset of theta dimensions.
+
+        The condition is a part of theta, but is assumed to correspond to a batch of iid
+        x_o. For example, it can be a batch of experimental conditions that corresponds
+        to a batch of i.i.d. trials in x_o.
+
+        Args:
+            theta_condition: The condition values to be conditioned.
+            dims_to_sample: The indices of the columns in theta that will be sampled,
+                i.e., that *not* conditioned. For example, if original theta has shape
+                `(batch_dim, 3)`, and `dims_to_sample=[0, 1]`, then the potential will
+                set `theta[:, 3] = theta_condition` at inference time.
+
+        Returns:
+            A potential function conditioned on the theta_condition.
+        """
+
+        assert self.x_is_iid, "Conditioning is only supported for iid data."
+
+        def conditioned_potential(
+            theta: Tensor, x_o: Optional[Tensor] = None, track_gradients: bool = True
+        ) -> Tensor:
+            assert (
+                len(dims_to_sample) == theta.shape[1]
+            ), "dims_to_sample must match the number of parameters to sample."
+            theta_without_condition = theta[:, dims_to_sample]
+            x_o = x_o if x_o is not None else self.x_o
+            # x needs shape (sample_dim (iid), batch_dim (xs), *event_shape)
+            if x_o.dim() < 3:
+                x_o = reshape_to_sample_batch_event(
+                    x_o, event_shape=x_o.shape[1:], leading_is_sample=self.x_is_iid
+                )
+
+            return _log_likelihood_over_iid_conditions(
+                x=x_o,
+                theta_without_condition=theta_without_condition,
+                condition=theta_condition,
+                estimator=self.likelihood_estimator,
+                track_gradients=track_gradients,
+            )
+
+        return conditioned_potential
+
 
 def _log_likelihoods_over_trials(
     x: Tensor,
@@ -172,6 +219,78 @@
     return log_likelihood_trial_sum
 
 
+def _log_likelihood_over_iid_conditions(
+    x: Tensor,
+    theta_without_condition: Tensor,
+    condition: Tensor,
+    estimator: ConditionalDensityEstimator,
+    track_gradients: bool = False,
+) -> Tensor:
+    """Returns $\\log(p(x_o|\theta, condition)$, where x_o is a batch of iid data, and
+    condition is a matching batch of conditions.
+
+    This function is different from `_log_likelihoods_over_trials` in that it moves the
+    iid batch dimension of `x` onto the batch dimension of `theta`. This is needed when
+    the likelihood estimator is conditioned on a batch of conditions that are iid with
+    the batch of `x`. It avoids the evaluation of the likelihood for every combination
+    of `x` and `condition`. Instead, it manually constructs a batch covering all
+    combination of iid trials and theta batch and reshapes to sum over the iid
+    likelihoods.
+
+    Args:
+        x: data with shape `(sample_dim, x_batch_dim, *x_event_shape)`, where sample_dim
+            holds the i.i.d. trials and batch_dim holds a batch of xs, e.g., non-iid
+            observations.
+        theta_without_condition: Batch of parameters `(theta_batch_dim,
+            num_parameters)`.
+        condition: Batch of conditions of shape `(sample_dim, num_conditions)`, must
+            match x's `sample_dim`.
+        estimator: DensityEstimator.
+        track_gradients: Whether to track gradients.
+
+    Returns:
+        log_likelihood: log likelihood for each x in x_batch_dim, for each theta in
+            theta_batch_dim, summed over all i.i.d. trials. Shape
+            `(x_batch_dim, theta_batch_dim)`.
+    """
+    assert x.dim() > 2, "x must have shape (sample_dim, batch_dim, *event_shape)."
+    assert (
+        condition.dim() == 2
+    ), "condition must have shape (sample_dim, num_conditions)."
+    assert (
+        theta_without_condition.dim() == 2
+    ), "theta must have shape (batch_dim, num_parameters)."
+    num_trials, num_xs = x.shape[:2]
+    num_thetas = theta_without_condition.shape[0]
+    assert (
+        condition.shape[0] == num_trials
+    ), "Condition batch size must match the number of iid trials in x."
+
+    # move the iid batch dimension onto the batch dimension of theta and repeat it there
+    x_repeated = torch.transpose(x, 0, 1).repeat_interleave(num_thetas, dim=1)
+
+    # construct theta and condition to cover all trial-theta combinations
+    theta_with_condition = torch.cat(
+        [
+            theta_without_condition.repeat(num_trials, 1),  # repeat ABAB
+            condition.repeat_interleave(num_thetas, dim=0),  # repeat AABB
+        ],
+        dim=-1,
+    )
+
+    with torch.set_grad_enabled(track_gradients):
+        # Calculate likelihood in one batch. Returns (1, num_trials * num_theta)
+        log_likelihood_trial_batch = estimator.log_prob(
+            x_repeated, condition=theta_with_condition
+        )
+        # Reshape to (x-trials x parameters), sum over trial-log likelihoods.
+        log_likelihood_trial_sum = log_likelihood_trial_batch.reshape(
+            num_xs, num_trials, num_thetas
+        ).sum(1)
+
+    return log_likelihood_trial_sum
+
+
 def mixed_likelihood_estimator_based_potential(
     likelihood_estimator: MixedDensityEstimator,
     prior: Distribution,
@@ -192,6 +311,13 @@
         to unconstrained space.
     """
 
+    warnings.warn(
+        "This function is deprecated and will be removed in a future release. Use "
+        "`likelihood_estimator_based_potential` instead.",
+        DeprecationWarning,
+        stacklevel=2,
+    )
+
     device = str(next(likelihood_estimator.discrete_net.parameters()).device)
 
     potential_fn = MixedLikelihoodBasedPotential(
@@ -212,6 +338,13 @@
     ):
         super().__init__(likelihood_estimator, prior, x_o, device)
 
+        warnings.warn(
+            "This function is deprecated and will be removed in a future release. Use "
+            "`LikelihoodBasedPotential` instead.",
+            DeprecationWarning,
+            stacklevel=2,
+        )
+
     def __call__(self, theta: Tensor, track_gradients: bool = True) -> Tensor:
         prior_log_prob = self.prior.log_prob(theta)  # type: ignore
 
@@ -231,7 +364,6 @@
         with torch.set_grad_enabled(track_gradients):
             # Call the specific log prob method of the mixed likelihood estimator as
             # this optimizes the evaluation of the discrete data part.
-            # TODO log_prob_iid
             log_likelihood_trial_batch = self.likelihood_estimator.log_prob(
                 input=x,
                 condition=theta.to(self.device),

sbi/inference/trainers/nle/mnle.py

@@ -7,7 +7,7 @@
 from torch.distributions import Distribution
 
 from sbi.inference.posteriors import MCMCPosterior, RejectionPosterior, VIPosterior
-from sbi.inference.potentials import mixed_likelihood_estimator_based_potential
+from sbi.inference.potentials import likelihood_estimator_based_potential
 from sbi.inference.trainers.nle.nle_base import LikelihoodEstimator
 from sbi.neural_nets.estimators import MixedDensityEstimator
 from sbi.sbi_types import TensorboardSummaryWriter, TorchModule
@@ -155,9 +155,7 @@ def build_posterior(
         (
             potential_fn,
             theta_transform,
-        ) = mixed_likelihood_estimator_based_potential(
-            likelihood_estimator=likelihood_estimator, prior=prior, x_o=None
-        )
+        ) = likelihood_estimator_based_potential(likelihood_estimator, prior, x_o=None)
 
         if sample_with == "mcmc":
             self._posterior = MCMCPosterior(

sbi/utils/conditional_density_utils.py

@@ -293,7 +293,7 @@ def __init__(
             masked outside of prior.
         """
         condition = torch.atleast_2d(condition)
-        if condition.shape[0] != 1:
+        if condition.shape[0] > 1:
             raise ValueError("Condition with batch size > 1 not supported.")
 
         self.potential_fn = potential_fn

sbi/utils/sbiutils.py

@@ -60,8 +60,8 @@ def warn_if_zscoring_changes_data(x: Tensor, duplicate_tolerance: float = 0.1) -
 
         if num_unique_z < num_unique * (1 - duplicate_tolerance):
             warnings.warn(
-                "Z-scoring these simulation outputs resulted in {num_unique_z} unique "
-                "datapoints. Before z-scoring, it had been {num_unique}. This can "
+                f"Z-scoring these simulation outputs resulted in {num_unique_z} unique "
+                f"datapoints. Before z-scoring, it had been {num_unique}. This can "
                 "occur due to numerical inaccuracies when the data covers a large "
                 "range of values. Consider either setting `z_score_x=False` (but "
                 "beware that this can be problematic for training the NN) or exclude "