Remove HeteroskedasticSingleTaskGP (#2616)

Summary:

This model has been buggy for quite a long time and we still haven't fixed it. Removing it should be preferable to keeping around a known buggy model. Example bug reports:
- #861
- #933
- #2551

Differential Revision: D65543676

Author: saitcakmak

botorch/acquisition/joint_entropy_search.py

@@ -29,12 +29,10 @@
 from botorch import settings
 from botorch.acquisition.acquisition import AcquisitionFunction, MCSamplerMixin
 from botorch.acquisition.objective import PosteriorTransform
-
 from botorch.models.fully_bayesian import SaasFullyBayesianSingleTaskGP
-from botorch.models.gp_regression import MIN_INFERRED_NOISE_LEVEL
 from botorch.models.model import Model
-
 from botorch.models.utils import check_no_nans, fantasize as fantasize_flag
+from botorch.models.utils.gpytorch_modules import MIN_INFERRED_NOISE_LEVEL
 from botorch.sampling.normal import SobolQMCNormalSampler
 from botorch.utils.transforms import concatenate_pending_points, t_batch_mode_transform
 from torch import Tensor

botorch/models/__init__.py

@@ -17,7 +17,7 @@
 from botorch.models.fully_bayesian import SaasFullyBayesianSingleTaskGP
 from botorch.models.fully_bayesian_multitask import SaasFullyBayesianMultiTaskGP
 
-from botorch.models.gp_regression import HeteroskedasticSingleTaskGP, SingleTaskGP
+from botorch.models.gp_regression import SingleTaskGP
 from botorch.models.gp_regression_fidelity import SingleTaskMultiFidelityGP
 from botorch.models.gp_regression_mixed import MixedSingleTaskGP
 from botorch.models.higher_order_gp import HigherOrderGP
@@ -33,7 +33,6 @@
     "SaasFullyBayesianSingleTaskGP",
     "SaasFullyBayesianMultiTaskGP",
     "GenericDeterministicModel",
-    "HeteroskedasticSingleTaskGP",
     "HigherOrderGP",
     "KroneckerMultiTaskGP",
     "MixedSingleTaskGP",

botorch/models/converter.py

@@ -17,7 +17,6 @@
 from botorch.exceptions import UnsupportedError
 from botorch.exceptions.warnings import BotorchWarning
 from botorch.models import SingleTaskGP
-from botorch.models.gp_regression import HeteroskedasticSingleTaskGP
 from botorch.models.gp_regression_fidelity import SingleTaskMultiFidelityGP
 from botorch.models.gp_regression_mixed import MixedSingleTaskGP
 from botorch.models.gpytorch import BatchedMultiOutputGPyTorchModel
@@ -84,12 +83,6 @@ def _check_compatibility(models: ModuleList) -> None:
             "All models must be of type BatchedMultiOutputGPyTorchModel."
         )
 
-    # TODO: Add support for HeteroskedasticSingleTaskGP.
-    if any(isinstance(m, HeteroskedasticSingleTaskGP) for m in models):
-        raise NotImplementedError(
-            "Conversion of HeteroskedasticSingleTaskGP is currently unsupported."
-        )
-
     # TODO: Add support for custom likelihoods.
     if any(getattr(m, "_is_custom_likelihood", False) for m in models):
         raise NotImplementedError(
@@ -289,11 +282,6 @@ def batched_to_model_list(batch_model: BatchedMultiOutputGPyTorchModel) -> Model
     warnings.warn(DEPRECATION_MESSAGE, DeprecationWarning, stacklevel=2)
     was_training = batch_model.training
     batch_model.train()
-    # TODO: Add support for HeteroskedasticSingleTaskGP.
-    if isinstance(batch_model, HeteroskedasticSingleTaskGP):
-        raise NotImplementedError(
-            "Conversion of HeteroskedasticSingleTaskGP is currently not supported."
-        )
     if isinstance(batch_model, MixedSingleTaskGP):
         raise NotImplementedError(
             "Conversion of MixedSingleTaskGP is currently not supported."
@@ -393,12 +381,7 @@ def batched_multi_output_to_single_output(
     warnings.warn(DEPRECATION_MESSAGE, DeprecationWarning, stacklevel=2)
     was_training = batch_mo_model.training
     batch_mo_model.train()
-    # TODO: Add support for HeteroskedasticSingleTaskGP.
-    if isinstance(batch_mo_model, HeteroskedasticSingleTaskGP):
-        raise NotImplementedError(
-            "Conversion of HeteroskedasticSingleTaskGP currently not supported."
-        )
-    elif not isinstance(batch_mo_model, BatchedMultiOutputGPyTorchModel):
+    if not isinstance(batch_mo_model, BatchedMultiOutputGPyTorchModel):
         raise UnsupportedError("Only BatchedMultiOutputGPyTorchModels are supported.")
     # TODO: Add support for custom likelihoods.
     elif getattr(batch_mo_model, "_is_custom_likelihood", False):

botorch/models/gp_regression.py

@@ -10,58 +10,47 @@
 These models are often a good starting point and are further documented in the
 tutorials.
 
-`SingleTaskGP` and `HeteroskedasticSingleTaskGP` are single-task exact GP models,
-differing in how they treat noise. They use relatively strong priors on the Kernel
-hyperparameters, which work best when covariates are normalized to the unit cube
-and outcomes are standardized (zero mean, unit variance). By default, these models
-use a `Standardize` outcome transform, which applies this standardization. However,
-they do not (yet) use an input transform by default.
-
-These models all work in batch mode (each batch having its own hyperparameters).
-When the training observations include multiple outputs, these models use
+`SingleTaskGP` is a single-task exact GP model that uses relatively strong priors on
+the Kernel hyperparameters, which work best when covariates are normalized to the unit
+cube and outcomes are standardized (zero mean, unit variance). By default, this model
+uses a `Standardize` outcome transform, which applies this standardization. However,
+it does not (yet) use an input transform by default.
+
+`SingleTaskGP` model works in batch mode (each batch having its own hyperparameters).
+When the training observations include multiple outputs, `SingleTaskGP` uses
 batching to model outputs independently.
 
-These models all support multiple outputs. However, as single-task models,
-`SingleTaskGP` and `HeteroskedasticSingleTaskGP` should be used only when the
-outputs are independent and all use the same training data. If outputs are
-independent and outputs have different training data, use the `ModelListGP`.
-When modeling correlations between outputs, use a multi-task model like `MultiTaskGP`.
+`SingleTaskGP` supports multiple outputs. However, as a single-task model,
+`SingleTaskGP` should be used only when the outputs are independent and all
+use the same training inputs. If outputs are independent but they have different
+training inputs, use the `ModelListGP`. When modeling correlations between outputs,
+use a multi-task model like `MultiTaskGP`.
 """
 
 from __future__ import annotations
 
 import warnings
-from typing import NoReturn
 
 import torch
 from botorch.models.gpytorch import BatchedMultiOutputGPyTorchModel
 from botorch.models.model import FantasizeMixin
 from botorch.models.transforms.input import InputTransform
-from botorch.models.transforms.outcome import Log, OutcomeTransform, Standardize
+from botorch.models.transforms.outcome import OutcomeTransform, Standardize
 from botorch.models.utils import validate_input_scaling
 from botorch.models.utils.gpytorch_modules import (
     get_covar_module_with_dim_scaled_prior,
     get_gaussian_likelihood_with_lognormal_prior,
-    MIN_INFERRED_NOISE_LEVEL,
 )
 from botorch.utils.containers import BotorchContainer
 from botorch.utils.datasets import SupervisedDataset
 from botorch.utils.types import _DefaultType, DEFAULT
-from gpytorch.constraints.constraints import GreaterThan
 from gpytorch.distributions.multivariate_normal import MultivariateNormal
-from gpytorch.likelihoods.gaussian_likelihood import (
-    _GaussianLikelihoodBase,
-    FixedNoiseGaussianLikelihood,
-    GaussianLikelihood,
-)
+from gpytorch.likelihoods.gaussian_likelihood import FixedNoiseGaussianLikelihood
 from gpytorch.likelihoods.likelihood import Likelihood
-from gpytorch.likelihoods.noise_models import HeteroskedasticNoise
 from gpytorch.means.constant_mean import ConstantMean
 from gpytorch.means.mean import Mean
-from gpytorch.mlls.noise_model_added_loss_term import NoiseModelAddedLossTerm
 from gpytorch.models.exact_gp import ExactGP
 from gpytorch.module import Module
-from gpytorch.priors.smoothed_box_prior import SmoothedBoxPrior
 from torch import Tensor
 
 
@@ -253,107 +242,3 @@ def forward(self, x: Tensor) -> MultivariateNormal:
         mean_x = self.mean_module(x)
         covar_x = self.covar_module(x)
         return MultivariateNormal(mean_x, covar_x)
-
-
-class HeteroskedasticSingleTaskGP(BatchedMultiOutputGPyTorchModel, ExactGP):
-    r"""A single-task exact GP model using a heteroskedastic noise model.
-
-    This model differs from `SingleTaskGP` with observed observation noise
-    variances (`train_Yvar`) in that it can predict noise levels out of sample.
-    This is achieved by internally wrapping another GP (a `SingleTaskGP`) to model
-    the (log of) the observation noise. Noise levels must be provided to
-    `HeteroskedasticSingleTaskGP` as `train_Yvar`.
-
-    Examples of cases in which noise levels are known include online
-    experimentation and simulation optimization.
-
-    Example:
-        >>> train_X = torch.rand(20, 2)
-        >>> train_Y = torch.sin(train_X).sum(dim=1, keepdim=True)
-        >>> se = torch.linalg.norm(train_X, dim=1, keepdim=True)
-        >>> train_Yvar = 0.1 + se * torch.rand_like(train_Y)
-        >>> model = HeteroskedasticSingleTaskGP(train_X, train_Y, train_Yvar)
-    """
-
-    def __init__(
-        self,
-        train_X: Tensor,
-        train_Y: Tensor,
-        train_Yvar: Tensor,
-        outcome_transform: OutcomeTransform | None = None,
-        input_transform: InputTransform | None = None,
-    ) -> None:
-        r"""
-        Args:
-            train_X: A `batch_shape x n x d` tensor of training features.
-            train_Y: A `batch_shape x n x m` tensor of training observations.
-            train_Yvar: A `batch_shape x n x m` tensor of observed measurement
-                noise.
-            outcome_transform: An outcome transform that is applied to the
-                training data during instantiation and to the posterior during
-                inference (that is, the `Posterior` obtained by calling
-                `.posterior` on the model will be on the original scale).
-                Note that the noise model internally log-transforms the
-                variances, which will happen after this transform is applied.
-            input_transform: An input transfrom that is applied in the model's
-                forward pass.
-        """
-        if outcome_transform is not None:
-            train_Y, train_Yvar = outcome_transform(train_Y, train_Yvar)
-        self._validate_tensor_args(X=train_X, Y=train_Y, Yvar=train_Yvar)
-        validate_input_scaling(train_X=train_X, train_Y=train_Y, train_Yvar=train_Yvar)
-        self._set_dimensions(train_X=train_X, train_Y=train_Y)
-        noise_likelihood = GaussianLikelihood(
-            noise_prior=SmoothedBoxPrior(-3, 5, 0.5, transform=torch.log),
-            batch_shape=self._aug_batch_shape,
-            noise_constraint=GreaterThan(
-                MIN_INFERRED_NOISE_LEVEL, transform=None, initial_value=1.0
-            ),
-        )
-        # Likelihood will always get evaluated with transformed X, so we need to
-        # transform the training data before constructing the noise model.
-        with torch.no_grad():
-            transformed_X = self.transform_inputs(
-                X=train_X, input_transform=input_transform
-            )
-        noise_model = SingleTaskGP(
-            train_X=transformed_X,
-            train_Y=train_Yvar,
-            likelihood=noise_likelihood,
-            outcome_transform=Log(),
-        )
-        likelihood = _GaussianLikelihoodBase(HeteroskedasticNoise(noise_model))
-        # This is hacky -- this class used to inherit from SingleTaskGP, but it
-        # shouldn't so this is a quick fix to enable getting rid of that
-        # inheritance
-        SingleTaskGP.__init__(
-            # pyre-fixme[6]: Incompatible parameter type
-            self,
-            train_X=train_X,
-            train_Y=train_Y,
-            likelihood=likelihood,
-            outcome_transform=None,
-            input_transform=input_transform,
-        )
-        self.register_added_loss_term("noise_added_loss")
-        self.update_added_loss_term(
-            "noise_added_loss", NoiseModelAddedLossTerm(noise_model)
-        )
-        if outcome_transform is not None:
-            self.outcome_transform = outcome_transform
-        self.to(train_X)
-
-    # pyre-fixme[15]: Inconsistent override
-    def condition_on_observations(self, *_, **__) -> NoReturn:
-        raise NotImplementedError
-
-    # pyre-fixme[15]: Inconsistent override
-    def subset_output(self, idcs) -> NoReturn:
-        raise NotImplementedError
-
-    def forward(self, x: Tensor) -> MultivariateNormal:
-        if self.training:
-            x = self.transform_inputs(x)
-        mean_x = self.mean_module(x)
-        covar_x = self.covar_module(x)
-        return MultivariateNormal(mean_x, covar_x)

botorch_community/acquisition/scorebo.py

@@ -31,8 +31,8 @@
 )
 from botorch.acquisition.objective import ScalarizedPosteriorTransform
 from botorch.models.fully_bayesian import MCMC_DIM, SaasFullyBayesianSingleTaskGP
-from botorch.models.gp_regression import MIN_INFERRED_NOISE_LEVEL
 from botorch.models.utils import fantasize as fantasize_flag
+from botorch.models.utils.gpytorch_modules import MIN_INFERRED_NOISE_LEVEL
 from botorch.utils.transforms import concatenate_pending_points, t_batch_mode_transform
 from botorch_community.acquisition.bayesian_active_learning import DISTANCE_METRICS
 from torch import Tensor

docs/models.md

@@ -72,8 +72,8 @@ Noise can be treated in several different ways:
   if you know your observations are noiseless (by passing a zero noise level).
 
 - _Heteroskedastic_: Noise is provided as an input and is modeled to allow for
-  predicting noise out-of-sample. Models like `HeteroskedasticSingleTaskGP` take
-  this approach.
+  predicting noise out-of-sample. BoTorch does not implement a model that
+  supports this out of the box.
 
 ## Standard BoTorch Models
 
@@ -90,10 +90,6 @@ instead.
 - [`SingleTaskGP`](../api/models.html#botorch.models.gp_regression.SingleTaskGP):
   a single-task exact GP that supports both inferred and observed noise. When
   noise observations are not provided, it infers a homoskedastic noise level.
-- [`HeteroskedasticSingleTaskGP`](../api/models.html#botorch.models.gp_regression.HeteroskedasticSingleTaskGP):
-  a single-task exact GP that differs from `SingleTaskGP` with observed noise in
-  that it models heteroskedastic noise using an additional internal GP model. It
-  requires noise observations.
 - [`MixedSingleTaskGP`](../api/models.html#botorch.models.gp_regression_mixed.MixedSingleTaskGP):
   a single-task exact GP that supports mixed search spaces, which combine
   discrete and continuous features.

test/models/test_converter.py

@@ -7,12 +7,7 @@
 
 import torch
 from botorch.exceptions import UnsupportedError
-from botorch.models import (
-    HeteroskedasticSingleTaskGP,
-    ModelListGP,
-    SingleTaskGP,
-    SingleTaskMultiFidelityGP,
-)
+from botorch.models import ModelListGP, SingleTaskGP, SingleTaskMultiFidelityGP
 from botorch.models.converter import (
     _batched_kernel,
     batched_multi_output_to_single_output,
@@ -58,12 +53,6 @@ def test_batched_to_model_list(self):
                 )
                 list_gp = batched_to_model_list(batch_gp)
                 self.assertIsInstance(list_gp, ModelListGP)
-            # test HeteroskedasticSingleTaskGP
-            batch_gp = HeteroskedasticSingleTaskGP(
-                train_X, train_Y, torch.rand_like(train_Y)
-            )
-            with self.assertRaises(NotImplementedError):
-                batched_to_model_list(batch_gp)
             # test with transforms
             input_tf = Normalize(
                 d=2,
@@ -161,12 +150,6 @@ def test_model_list_to_batched(self):
             )
             with self.assertRaises(UnsupportedError):
                 model_list_to_batched(ModelListGP(gp1, gp2))
-            # test HeteroskedasticSingleTaskGP
-            gp2 = HeteroskedasticSingleTaskGP(
-                train_X, train_Y1, torch.ones_like(train_Y1)
-            )
-            with self.assertRaises(NotImplementedError):
-                model_list_to_batched(ModelListGP(gp2))
             # test custom likelihood
             gp2 = SingleTaskGP(
                 train_X,
@@ -419,11 +402,6 @@ def test_batched_multi_output_to_single_output(self):
             non_batch_model = SimpleGPyTorchModel(train_X, train_Y[:, :1])
             with self.assertRaises(UnsupportedError):
                 batched_multi_output_to_single_output(non_batch_model)
-            gp2 = HeteroskedasticSingleTaskGP(
-                train_X, train_Y, torch.ones_like(train_Y)
-            )
-            with self.assertRaises(NotImplementedError):
-                batched_multi_output_to_single_output(gp2)
             # test custom likelihood
             gp2 = SingleTaskGP(train_X, train_Y, likelihood=GaussianLikelihood())
             with self.assertRaises(NotImplementedError):