Update the default SingleTaskGP prior (pytorch#2449)

Summary:
Pull Request resolved: pytorch#2449

Update of the default hyperparameter priors for the SingleTaskGP.

Switch from the conventional Scale-Matern kernel with Gamma(3, 6) lengthscale prior is substituted for an RBF Kernel (without a ScaleKernel), and a change from the high-noise Gamma(1.1, 0.05) noise prior of the GaussianLikelihood to a LogNormal prior that prefers lower values. The change is made in accordance with the findings of [1].

 The change is made to improve the out-of-the-box performance of the BoTorch models on high-dimensional problems.

[1] Carl Hvarfner, Erik Orm Hellsten, Luigi Nardi. _Vanilla Bayesian Optimization Performs Great in High Dimensions_. ICML, 2024.

Reviewed By: saitcakmak

Differential Revision: D60080819

botorch/models/gp_regression.py

@@ -40,8 +40,8 @@
 from botorch.models.transforms.outcome import Log, OutcomeTransform
 from botorch.models.utils import validate_input_scaling
 from botorch.models.utils.gpytorch_modules import (
- get_gaussian_likelihood_with_gamma_prior,
- get_matern_kernel_with_gamma_prior,
+ get_covar_module_with_dim_scaled_prior,
+ get_gaussian_likelihood_with_lognormal_prior,
  MIN_INFERRED_NOISE_LEVEL,
 )
 from botorch.utils.containers import BotorchContainer
@@ -174,7 +174,7 @@ def __init__(
  )
  if likelihood is None:
  if train_Yvar is None:
- likelihood = get_gaussian_likelihood_with_gamma_prior(
+ likelihood = get_gaussian_likelihood_with_lognormal_prior(
  batch_shape=self._aug_batch_shape
  )
  else:
@@ -190,14 +190,13 @@ def __init__(
  mean_module = ConstantMean(batch_shape=self._aug_batch_shape)
  self.mean_module = mean_module
  if covar_module is None:
- covar_module = get_matern_kernel_with_gamma_prior(
+ covar_module = get_covar_module_with_dim_scaled_prior(
  ard_num_dims=transformed_X.shape[-1],
  batch_shape=self._aug_batch_shape,
  )
  self._subset_batch_dict = {
  "mean_module.raw_constant": -1,
- "covar_module.raw_outputscale": -1,
- "covar_module.base_kernel.raw_lengthscale": -3,
+ "covar_module.raw_lengthscale": -3,
  }
  if train_Yvar is None:
  self._subset_batch_dict["likelihood.noise_covar.raw_noise"] = -2

botorch/utils/gp_sampling.py

@@ -143,10 +143,9 @@ def __init__(
  """
  if not isinstance(kernel, ScaleKernel):
  base_kernel = kernel
- outputscale = torch.tensor(
- 1.0,
- dtype=base_kernel.lengthscale.dtype,
- device=base_kernel.lengthscale.device,
+ outputscale = torch.ones(kernel.batch_shape).to(
+ dtype=kernel.lengthscale.dtype,
+ device=kernel.lengthscale.device,
  )
  else:
  base_kernel = kernel.base_kernel

test/models/test_converter.py

@@ -23,7 +23,7 @@
 from botorch.models.transforms.outcome import Standardize
 from botorch.utils.test_helpers import SimpleGPyTorchModel
 from botorch.utils.testing import BotorchTestCase
-from gpytorch.kernels import RBFKernel
+from gpytorch.kernels import MaternKernel, RBFKernel
 from gpytorch.likelihoods import GaussianLikelihood
 from gpytorch.likelihoods.gaussian_likelihood import FixedNoiseGaussianLikelihood
 from gpytorch.priors import LogNormalPrior
@@ -134,13 +134,17 @@ def test_model_list_to_batched(self):
  model_list_to_batched(ModelListGP(gp1, gp2))
  # check scalar agreement
  gp2 = SingleTaskGP(train_X, train_Y2)
- gp2.likelihood.noise_covar.noise_prior.rate.fill_(1.0)
+
+ # modified to check the scalar agreement in a parameter that is accessible
+ # since the error is going to slip through for the non-parametrizable
+ # priors regardless (like the LogNormal)
+ gp2.likelihood.noise_covar.raw_noise_constraint.lower_bound.fill_(1e-3)
  with self.assertRaises(UnsupportedError):
  model_list_to_batched(ModelListGP(gp1, gp2))
  # check tensor shape agreement
  gp2 = SingleTaskGP(train_X, train_Y2)
- gp2.covar_module.raw_outputscale = torch.nn.Parameter(
- torch.tensor([0.0], device=self.device, dtype=dtype)
+ gp2.likelihood.noise_covar.raw_noise = torch.nn.Parameter(
+ torch.tensor([[0.42]], device=self.device, dtype=dtype)
  )
  with self.assertRaises(UnsupportedError):
  model_list_to_batched(ModelListGP(gp1, gp2))
@@ -155,14 +159,15 @@ def test_model_list_to_batched(self):
  with self.assertRaises(NotImplementedError):
  model_list_to_batched(ModelListGP(gp2))
  # test non-default kernel
- gp1 = SingleTaskGP(train_X, train_Y1, covar_module=RBFKernel())
- gp2 = SingleTaskGP(train_X, train_Y2, covar_module=RBFKernel())
+ gp1 = SingleTaskGP(train_X, train_Y1, covar_module=MaternKernel())
+ gp2 = SingleTaskGP(train_X, train_Y2, covar_module=MaternKernel())
  list_gp = ModelListGP(gp1, gp2)
  batch_gp = model_list_to_batched(list_gp)
- self.assertEqual(type(batch_gp.covar_module), RBFKernel)
+ self.assertEqual(type(batch_gp.covar_module), MaternKernel)
  # test error when component GPs have different kernel types
- gp1 = SingleTaskGP(train_X, train_Y1, covar_module=RBFKernel())
- gp2 = SingleTaskGP(train_X, train_Y2)
+ # added types for both default and non-default kernels for clarity
+ gp1 = SingleTaskGP(train_X, train_Y1, covar_module=MaternKernel())
+ gp2 = SingleTaskGP(train_X, train_Y2, covar_module=RBFKernel())
  list_gp = ModelListGP(gp1, gp2)
  with self.assertRaises(UnsupportedError):
  model_list_to_batched(list_gp)

test/models/test_deterministic.py

@@ -172,7 +172,7 @@ def test_FixedSingleSampleModel(self):
  post = model.posterior(test_X)
  original_output = post.mean + post.variance.sqrt() * w
  fss_output = fss_model(test_X)
- self.assertTrue(torch.equal(original_output, fss_output))
+ self.assertAllClose(original_output, fss_output)
 
  self.assertTrue(hasattr(fss_model, "num_outputs"))
 

test/models/test_gp_regression.py

@@ -23,7 +23,7 @@
 from botorch.utils.sampling import manual_seed
 from botorch.utils.test_helpers import get_pvar_expected
 from botorch.utils.testing import _get_random_data, BotorchTestCase
-from gpytorch.kernels import MaternKernel, RBFKernel, ScaleKernel
+from gpytorch.kernels import RBFKernel
 from gpytorch.likelihoods import (
  _GaussianLikelihoodBase,
  FixedNoiseGaussianLikelihood,
@@ -33,7 +33,7 @@
 from gpytorch.means import ConstantMean, ZeroMean
 from gpytorch.mlls.exact_marginal_log_likelihood import ExactMarginalLogLikelihood
 from gpytorch.mlls.noise_model_added_loss_term import NoiseModelAddedLossTerm
-from gpytorch.priors import GammaPrior
+from gpytorch.priors import LogNormalPrior
 
 
 class TestGPRegressionBase(BotorchTestCase):
@@ -96,10 +96,10 @@ def test_gp(self, double_only: bool = False):
 
  # test init
  self.assertIsInstance(model.mean_module, ConstantMean)
- self.assertIsInstance(model.covar_module, ScaleKernel)
- matern_kernel = model.covar_module.base_kernel
- self.assertIsInstance(matern_kernel, MaternKernel)
- self.assertIsInstance(matern_kernel.lengthscale_prior, GammaPrior)
+ self.assertIsInstance(model.covar_module, RBFKernel)
+ rbf_kernel = model.covar_module
+ self.assertIsInstance(rbf_kernel, RBFKernel)
+ self.assertIsInstance(rbf_kernel.lengthscale_prior, LogNormalPrior)
  if use_octf:
  self.assertIsInstance(model.outcome_transform, Standardize)
  if use_intf:

test/models/test_model_list_gp_regression.py

@@ -25,7 +25,7 @@
 from botorch.sampling.normal import IIDNormalSampler
 from botorch.utils.testing import _get_random_data, BotorchTestCase
 from gpytorch.distributions import MultitaskMultivariateNormal, MultivariateNormal
-from gpytorch.kernels import MaternKernel, ScaleKernel
+from gpytorch.kernels import RBFKernel
 from gpytorch.likelihoods import LikelihoodList
 from gpytorch.likelihoods.gaussian_likelihood import (
  FixedNoiseGaussianLikelihood,
@@ -34,7 +34,7 @@
 from gpytorch.means import ConstantMean
 from gpytorch.mlls import SumMarginalLogLikelihood
 from gpytorch.mlls.exact_marginal_log_likelihood import ExactMarginalLogLikelihood
-from gpytorch.priors import GammaPrior
+from gpytorch.priors import LogNormalPrior
 from torch import Tensor
 
 
@@ -104,10 +104,8 @@ def _base_test_ModelListGP(
  self.assertEqual(model.num_outputs, 2)
  for m in model.models:
  self.assertIsInstance(m.mean_module, ConstantMean)
- self.assertIsInstance(m.covar_module, ScaleKernel)
- matern_kernel = m.covar_module.base_kernel
- self.assertIsInstance(matern_kernel, MaternKernel)
- self.assertIsInstance(matern_kernel.lengthscale_prior, GammaPrior)
+ self.assertIsInstance(m.covar_module, RBFKernel)
+ self.assertIsInstance(m.covar_module.lengthscale_prior, LogNormalPrior)
  if outcome_transform != "None":
  self.assertIsInstance(
  m.outcome_transform, (Log, Standardize, ChainedOutcomeTransform)

test/optim/test_fit.py

@@ -29,9 +29,9 @@ def setUp(self) -> None:
  self.mlls = {}
  with torch.random.fork_rng():
  torch.manual_seed(0)
- train_X = torch.linspace(0, 1, 10).unsqueeze(-1)
- train_Y = torch.sin((2 * math.pi) * train_X)
- train_Y = train_Y + 0.1 * torch.randn_like(train_Y)
+ train_X = torch.linspace(0, 1, 30).unsqueeze(-1)
+ train_Y = torch.sin((6 * math.pi) * train_X)
+ train_Y = train_Y + 0.01 * torch.randn_like(train_Y)
 
  model = SingleTaskGP(
  train_X=train_X,

test/optim/utils/test_model_utils.py

@@ -6,6 +6,7 @@
 
 from __future__ import annotations
 
+import itertools
 import re
 import warnings
 from copy import deepcopy
@@ -16,6 +17,10 @@
 import torch
 from botorch import settings
 from botorch.models import SingleTaskGP
+from botorch.models.utils.gpytorch_modules import (
+ get_covar_module_with_dim_scaled_prior,
+ get_matern_kernel_with_gamma_prior,
+)
 from botorch.optim.utils import (
  get_data_loader,
  get_name_filter,
@@ -158,10 +163,18 @@ def test__get_name_filter(self) -> None:
 
 class TestSampleAllPriors(BotorchTestCase):
  def test_sample_all_priors(self):
- for dtype in (torch.float, torch.double):
+ for dtype, covar_module in itertools.product(
+ (torch.float, torch.double),
+ (
+ get_covar_module_with_dim_scaled_prior(ard_num_dims=5),
+ get_matern_kernel_with_gamma_prior(ard_num_dims=5),
+ ),
+ ):
  train_X = torch.rand(3, 5, device=self.device, dtype=dtype)
  train_Y = torch.rand(3, 1, device=self.device, dtype=dtype)
- model = SingleTaskGP(train_X=train_X, train_Y=train_Y)
+ model = SingleTaskGP(
+ train_X=train_X, train_Y=train_Y, covar_module=covar_module
+ )
  mll = ExactMarginalLogLikelihood(model.likelihood, model)
  mll.to(device=self.device, dtype=dtype)
  original_state_dict = dict(deepcopy(mll.model.state_dict()))
@@ -173,7 +186,10 @@ def test_sample_all_priors(self):
  != original_state_dict["likelihood.noise_covar.raw_noise"]
  )
  # check that lengthscales are all different
- ls = model.covar_module.base_kernel.raw_lengthscale.view(-1).tolist()
+ if isinstance(model.covar_module, ScaleKernel):
+ ls = model.covar_module.base_kernel.raw_lengthscale.view(-1).tolist()
+ else:
+ ls = model.covar_module.raw_lengthscale.view(-1).tolist()
  self.assertTrue(all(ls[0] != ls[i]) for i in range(1, len(ls)))
 
  # change one of the priors to a dummy prior that does not support sampling

test/test_fit.py

@@ -27,7 +27,7 @@
 from botorch.settings import debug
 from botorch.utils.context_managers import module_rollback_ctx, TensorCheckpoint
 from botorch.utils.testing import BotorchTestCase
-from gpytorch.kernels import MaternKernel
+from gpytorch.kernels import RBFKernel
 from gpytorch.mlls import ExactMarginalLogLikelihood, VariationalELBO
 from linear_operator.utils.errors import NotPSDError
 
@@ -136,8 +136,7 @@ def setUp(self, suppress_input_warnings: bool = True) -> None:
  input_transform=Normalize(d=1),
  outcome_transform=Standardize(m=output_dim),
  )
- self.assertIsInstance(model.covar_module.base_kernel, MaternKernel)
- model.covar_module.base_kernel.nu = 2.5
+ self.assertIsInstance(model.covar_module, RBFKernel)
 
  mll = ExactMarginalLogLikelihood(model.likelihood, model)
  for dtype in (torch.float32, torch.float64):

tutorials/constraint_active_search.ipynb

@@ -249,7 +249,7 @@
  " return radius * r * z\n",
  "\n",
  " def _get_base_point_mask(self, X):\n",
- " distance_matrix = self.model.models[0].covar_module.base_kernel.covar_dist(\n",
+ " distance_matrix = self.model.models[0].covar_module.covar_dist(\n",
  " X, self.base_points\n",
  " )\n",
  " return smooth_mask(distance_matrix, self.punchout_radius)\n",
@@ -676,9 +676,18 @@
  "\n",
  "\n",
  "fig, ax = plt.subplots(figsize=(8, 6))\n",
- "h1 = ax.contourf(Xplt.cpu().numpy(), Yplt.cpu().numpy(), Zplt.cpu().numpy(), 20, cmap=\"Blues\", alpha=0.6)\n",
+ "h1 = ax.contourf(\n",
+ " Xplt.cpu().numpy(),\n",
+ " Yplt.cpu().numpy(),\n",
+ " Zplt.cpu().numpy(),\n",
+ " 20,\n",
+ " cmap=\"Blues\",\n",
+ " alpha=0.6,\n",
+ ")\n",
  "fig.colorbar(h1)\n",
- "ax.contour(Xplt.cpu().numpy(), Yplt.cpu().numpy(), Zplt.cpu().numpy(), [0.55, 0.75], colors=\"k\")\n",
+ "ax.contour(\n",
+ " Xplt.cpu().numpy(), Yplt.cpu().numpy(), Zplt.cpu().numpy(), [0.55, 0.75], colors=\"k\"\n",
+ ")\n",
  "\n",
  "feasible_inds = (\n",
  " identify_samples_which_satisfy_constraints(Y, constraints)\n",
@@ -715,10 +724,12 @@
  ],
  "metadata": {
  "fileHeader": "",
+ "fileUid": "cb282d47-f143-4c00-9ae1-b631e97daddb",
+ "isAdHoc": false,
  "kernelspec": {
- "display_name": "python3",
+ "display_name": "Python 3",
  "language": "python",
- "name": "python3"
+ "name": "bento_kernel_default"
  },
  "language_info": {
  "codemirror_mode": {
@@ -732,7 +743,5 @@
  "pygments_lexer": "ipython3",
  "version": "3.9.13"
  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
+ }
 }

tutorials/fit_model_with_torch_optimizer.ipynb

@@ -20,6 +20,7 @@
  "outputs": [],
  "source": [
  "import math\n",
+ "\n",
  "import torch\n",
  "\n",
  "# use a GPU if available\n",
@@ -190,7 +191,7 @@
  " if (epoch + 1) % 10 == 0:\n",
  " print(\n",
  " f\"Epoch {epoch+1:>3}/{NUM_EPOCHS} - Loss: {loss.item():>4.3f} \"\n",
- " f\"lengthscale: {model.covar_module.base_kernel.lengthscale.item():>4.3f} \"\n",
+ " f\"lengthscale: {model.covar_module.lengthscale.item():>4.3f} \"\n",
  " f\"noise: {model.likelihood.noise.item():>4.3f}\"\n",
  " )\n",
  " optimizer.step()"
@@ -215,7 +216,7 @@
  "outputs": [],
  "source": [
  "# set model (and likelihood)\n",
- "model.eval();"
+ "model.eval()"
  ]
  },
  {
@@ -309,12 +310,13 @@
  }
  ],
  "metadata": {
+ "fileHeader": "",
+ "fileUid": "29414a8f-010b-41a8-837d-70d9294b809e",
+ "isAdHoc": false,
  "kernelspec": {
- "display_name": "python3",
+ "display_name": "Python 3",
  "language": "python",
- "name": "python3"
+ "name": "bento_kernel_default"
  }
- },
- "nbformat": 4,
- "nbformat_minor": 1
+ }
 }