OrthogonalAdditiveGP with component-wise inference (meta-pytorch#3187)

Summary:

This commit adds a new additive Gaussian process model `OrthogonalAdditiveGP`, which leverages the `OrthogonalAdditiveKernel`, and importantly, posterior inference of individual additive components, conditioned on noisy observations of the sum.

This is enabled with the refactored GPyTorch posterior inference stack via `_get_test_prior_mean_and_covariances`.

This relies on having an additional batch dimension for the test-test and train-test covariance, corresponding to the kernel matrices of each additive component, while the batch dimension has to be absent on the training set, because we are observing the *sum* of the additive components.

Reviewed By: hvarfner

Differential Revision: D92461397

Author: SebastianAment

botorch/models/__init__.py

@@ -4,6 +4,7 @@
 # This source code is licensed under the MIT license found in the
 # LICENSE file in the root directory of this source tree.
 
+from botorch.models.additive_gp import OrthogonalAdditiveGP
 from botorch.models.approximate_gp import (
     ApproximateGPyTorchModel,
     SingleTaskVariationalGP,
@@ -44,6 +45,7 @@
     "ModelList",
     "ModelListGP",
     "MultiTaskGP",
+    "OrthogonalAdditiveGP",
     "PairwiseGP",
     "PairwiseLaplaceMarginalLogLikelihood",
     "PosteriorMeanModel",

botorch/models/additive_gp.py

@@ -0,0 +1,314 @@
+#!/usr/bin/env python3
+# Copyright (c) Meta Platforms, Inc. and affiliates.
+#
+# This source code is licensed under the MIT license found in the
+# LICENSE file in the root directory of this source tree.
+
+# pyre-strict
+from contextlib import contextmanager
+from typing import Iterator
+
+import torch
+from botorch.models.gp_regression import SingleTaskGP
+from botorch.models.kernels.orthogonal_additive_kernel import OrthogonalAdditiveKernel
+from botorch.models.transforms.input import InputTransform
+from botorch.models.transforms.outcome import OutcomeTransform
+from botorch.posteriors.gpytorch import GPyTorchPosterior
+from botorch.utils.types import _DefaultType, DEFAULT
+from gpytorch.distributions import Distribution, MultivariateNormal
+from gpytorch.kernels import RBFKernel
+from gpytorch.likelihoods import Likelihood
+from gpytorch.means import Mean
+from linear_operator.operators import LinearOperator
+from torch import Tensor
+
+
+class OrthogonalAdditiveGP(SingleTaskGP):
+    """A Gaussian Process with Orthogonal Additive Kernel for interpretable modeling.
+
+    This GP model uses an OrthogonalAdditiveKernel which decomposes the function into
+    interpretable additive components: a bias term, first-order effects for each input
+    dimension, and optionally second-order interaction terms.
+
+    The model supports posterior inference of individual additive components when
+    `infer_all_components=True` is passed to the `posterior` method.
+    """
+
+    # Class-level default for inference mode (avoids __init__ override)
+    _infer_all_components: bool = False
+
+    def __init__(
+        self,
+        train_X: Tensor,
+        train_Y: Tensor,
+        covar_module: OrthogonalAdditiveKernel | None = None,
+        second_order: bool = False,
+        likelihood: Likelihood | None = None,
+        mean_module: Mean | None = None,
+        outcome_transform: OutcomeTransform | _DefaultType | None = DEFAULT,
+        input_transform: InputTransform | None = None,
+    ) -> None:
+        """Initialize the OrthogonalAdditiveGP.
+
+        Args:
+            train_X: Training inputs (batch_shape x n x d) in [0, 1]^d.
+            train_Y: Training outputs (batch_shape x n x 1).
+            covar_module: An OrthogonalAdditiveKernel instance. If None, creates a
+                default kernel with dim inferred from train_X.
+            second_order: If True and covar_module is None, enables second-order
+                interactions in the default kernel. Ignored if covar_module is provided.
+            likelihood: Optional likelihood (defaults to GaussianLikelihood).
+            mean_module: Optional mean module (defaults to ConstantMean).
+            outcome_transform: Optional outcome transform.
+            input_transform: Optional input transform.
+
+        Raises:
+            TypeError: If covar_module is provided but is not an
+                OrthogonalAdditiveKernel.
+        """
+        if covar_module is None:
+            covar_module = OrthogonalAdditiveKernel(
+                base_kernel=RBFKernel(),
+                dim=train_X.shape[-1],
+                second_order=second_order,
+                dtype=train_X.dtype,
+                device=train_X.device,
+            )
+        elif not isinstance(covar_module, OrthogonalAdditiveKernel):
+            raise TypeError(
+                f"covar_module must be an OrthogonalAdditiveKernel, "
+                f"got {type(covar_module).__name__}"
+            )
+
+        super().__init__(
+            train_X=train_X,
+            train_Y=train_Y,
+            likelihood=likelihood,
+            covar_module=covar_module,
+            mean_module=mean_module,
+            outcome_transform=outcome_transform,
+            input_transform=input_transform,
+        )
+
+    @contextmanager
+    def _component_inference_context(
+        self, infer_all_components: bool = False
+    ) -> Iterator[None]:
+        """Context manager that temporarily sets component inference mode.
+
+        Args:
+            infer_all_components: If True, enables per-component posterior inference.
+
+        Yields:
+            None. The context manager sets internal state that is checked by
+            `_get_test_prior_mean_and_covariances` to dispatch to the appropriate
+            covariance computation.
+        """
+        prev_state = self._infer_all_components
+        self._infer_all_components = infer_all_components
+        try:
+            yield
+        finally:
+            self._infer_all_components = prev_state
+
+    def posterior(
+        self,
+        X: Tensor,
+        output_indices: list[int] | None = None,
+        observation_noise: bool = False,
+        posterior_transform=None,
+        infer_all_components: bool = False,
+    ) -> GPyTorchPosterior:
+        """Posterior inference of the additive Gaussian process.
+
+        Args:
+            X: The input tensor of shape (batch_shape x n x d).
+            output_indices: Not supported for this model.
+            observation_noise: Whether to add observation noise to the posterior.
+            posterior_transform: Optional posterior transform.
+            infer_all_components: If True, returns a posterior with a batch
+                dimension corresponding to each additive component (bias, first-order
+                effects, and optionally second-order interactions). The number of
+                components is 1 + d (first-order only) or 1 + d + d*(d-1)/2
+                (with second-order interactions).
+
+        Returns:
+            The posterior distribution at X.
+        """
+        # Use context manager to set inference mode, then delegate to GPyTorch
+        with self._component_inference_context(infer_all_components):
+            return super().posterior(
+                X=X,
+                output_indices=output_indices,
+                observation_noise=observation_noise,
+                posterior_transform=posterior_transform,
+            )
+
+    def _get_test_prior_mean_and_covariances(
+        self,
+        train_inputs: list[Tensor],
+        test_inputs: list[Tensor],
+        **kwargs,
+    ) -> tuple[
+        Tensor,
+        LinearOperator,
+        LinearOperator,
+        torch.Size,
+        torch.Size,
+        type[Distribution],
+    ]:
+        """Dispatches to appropriate covariance computation based on inference mode.
+
+        This method is called by GPyTorch's ExactGP.__call__ during posterior
+        computation. When `_infer_all_components` is True (set via the context
+        manager), it returns per-component covariances with an extra batch dimension.
+        Otherwise, it uses the standard kernel forward pass which sums over components.
+        """
+        if self._infer_all_components:
+            return self._get_test_prior_mean_and_covariances_per_component(
+                train_inputs, test_inputs, **kwargs
+            )
+        return super()._get_test_prior_mean_and_covariances(
+            train_inputs=train_inputs, test_inputs=test_inputs, **kwargs
+        )
+
+    def _get_test_prior_mean_and_covariances_per_component(
+        self,
+        train_inputs: list[Tensor],
+        test_inputs: list[Tensor],
+        **kwargs,
+    ) -> tuple[
+        Tensor,
+        LinearOperator,
+        LinearOperator,
+        torch.Size,
+        torch.Size,
+        type[Distribution],
+    ]:
+        """Computes mean and covariances with a batch dimension for each component.
+
+        This enables posterior inference of individual additive components by returning
+        covariance matrices with an extra leading batch dimension for each component.
+
+        Returns:
+            A tuple containing:
+            - test_mean: The mean evaluated on the test set (batch_shape x n_test)
+            - test_test_covar: Covariance between test points
+                (num_components x batch_shape x n_test x n_test)
+            - test_train_covar: Covariance between test and train points
+                (num_components x batch_shape x n_test x n_train)
+            - batch_shape: The batch shape of the model
+            - test_shape: Shape (n_test,)
+            - posterior_class: The class of the posterior to be instantiated
+        """
+        if len(train_inputs) != 1 or len(test_inputs) != 1:
+            raise ValueError(
+                "OrthogonalAdditiveGP expects a single input X, but received "
+                f"{len(train_inputs)=}, and {len(test_inputs)=}."
+            )
+
+        X_train = train_inputs[0]
+        X_test = test_inputs[0]
+
+        # Batch shape includes the component dimension as the leading dimension
+        # This is needed so GPyTorch correctly reshapes the predictive mean
+        num_components = self.covar_module.num_components
+        batch_shape = torch.Size([num_components]) + X_train.shape[:-2]
+
+        # Get component-wise covariances using _non_reduced_forward
+        # Shape: (num_components x batch_shape x n_test x n_test)
+        test_test_covar = self.covar_module._non_reduced_forward(X_test, X_test)
+        # Shape: (num_components x batch_shape x n_test x n_train)
+        test_train_covar = self.covar_module._non_reduced_forward(X_test, X_train)
+
+        # Prior mean: Only the bias component (index 0) should have the prior mean.
+        # All other components represent deviations from the mean, so their prior
+        # mean should be zero. This ensures that when we sum over all components,
+        # we get the correct total posterior mean (prior mean added once).
+        n_test = X_test.shape[-2]
+        # Create a (num_components, n_test) tensor of zeros
+        test_mean = torch.zeros(
+            num_components, n_test, dtype=X_test.dtype, device=X_test.device
+        )
+        # Set the bias component's mean to the actual prior mean
+        test_mean[0, :] = self.mean_module(X_test)
+        test_shape = torch.Size([n_test])
+
+        return (
+            test_mean,
+            test_test_covar,
+            test_train_covar,
+            batch_shape,
+            test_shape,
+            MultivariateNormal,
+        )
+
+    @property
+    def component_indices(self) -> dict[str, Tensor]:
+        """Returns component indices from the OrthogonalAdditiveKernel."""
+        return self.covar_module.component_indices
+
+    def evaluate_first_order_on_grid(
+        self,
+        grid_1d: Tensor,
+    ) -> tuple[tuple[Tensor, Tensor], tuple[Tensor, Tensor]]:
+        r"""Evaluate first-order component posteriors on 1D grids.
+
+        Uses diagonal test inputs with the existing GPyTorch posterior
+        infrastructure. Each first-order component is evaluated on its
+        own independent 1D grid.
+
+        Args:
+            grid_1d: 1D tensor of m points in [0, 1].
+
+        Returns:
+            Tuple of:
+            - bias: (mean, variance) - scalar values
+            - first_order: ((d, m) means, (d, m) variances) on 1D grids
+
+        Example:
+            >>> grid = torch.linspace(0, 1, 50)
+            >>> (bias_mean, bias_var), (fo_mean, fo_var) = \\
+            ...     model.evaluate_first_order_on_grid(grid)
+            >>> # fo_mean[i, :] is component i's posterior mean on the 1D grid
+        """
+        self.eval()
+        m = len(grid_1d)
+        d = self.covar_module.dim
+
+        # Diagonal test inputs: X[k, :] = [t_k, t_k, ..., t_k]
+        # Each first-order component i sees its own 1D grid on dimension i
+        X_diag = grid_1d.unsqueeze(-1).expand(m, d)
+
+        # Use existing posterior with all-components mode
+        posterior = self.posterior(X_diag, infer_all_components=True)
+
+        # Squeeze output dimension (last dim) since this is single-output
+        mean = posterior.mean.squeeze(-1)  # (num_components, m)
+        variance = posterior.variance.squeeze(-1)  # (num_components, m)
+
+        # Extract bias (component 0) - should be constant across grid
+        bias_mean = mean[0, :].mean()
+        bias_var = variance[0, :].mean()
+
+        # Extract first-order (components 1 to d)
+        first_order_means = mean[1 : d + 1, :]  # (d, m)
+        first_order_vars = variance[1 : d + 1, :]  # (d, m)
+
+        return (bias_mean, bias_var), (first_order_means, first_order_vars)
+
+    @property
+    def num_components(self) -> int:
+        """Total number of additive components (bias + first-order [+ second-order])."""
+        return self.covar_module.num_components
+
+    def get_component_index(
+        self,
+        component_type: str,
+        dim_index: int | tuple[int, int] | None = None,
+    ) -> int:
+        """Returns the component index for a given component type and dimension.
+
+        See OrthogonalAdditiveKernel.get_component_index for details.
+        """
+        return self.covar_module.get_component_index(component_type, dim_index)