Source code for botorch.models.transforms.outcome

#!/usr/bin/env python3
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This source code is licensed under the MIT license found in the
# LICENSE file in the root directory of this source tree.

r"""
Outcome transformations for automatically transforming and un-transforming
model outputs. Outcome transformations are typically part of a Model and
applied (i) within the model constructor to transform the train observations
to the model space, and (ii) in the `Model.posterior` call to untransform
the model posterior back to the original space.
"""

from __future__ import annotations

from abc import ABC, abstractmethod
from collections import OrderedDict
from typing import List, Optional, Tuple

import torch
from botorch.models.transforms.utils import (
    norm_to_lognorm_mean,
    norm_to_lognorm_variance,
)
from botorch.posteriors import GPyTorchPosterior, Posterior, TransformedPosterior
from botorch.utils.transforms import normalize_indices
from gpytorch.lazy import CholLazyTensor, DiagLazyTensor
from torch import Tensor
from torch.nn import Module, ModuleDict


[docs]class OutcomeTransform(Module, ABC): r"""Abstract base class for outcome transforms."""
[docs] @abstractmethod def forward( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Transform the outcomes in a model's training targets Args: Y: A `batch_shape x n x m`-dim tensor of training targets. Yvar: A `batch_shape x n x m`-dim tensor of observation noises associated with the training targets (if applicable). Returns: A two-tuple with the transformed outcomes: - The transformed outcome observations. - The transformed observation noise (if applicable). """ pass # pragma: no cover
[docs] def subset_output(self, idcs: List[int]) -> OutcomeTransform: r"""Subset the transform along the output dimension. This functionality is used to properly treat outcome transformations in the `subset_model` functionality. Args: idcs: The output indices to subset the transform to. Returns: The current outcome transform, subset to the specified output indices. """ raise NotImplementedError( f"{self.__class__.__name__} does not implement the " "`subset_output` method" )
[docs] def untransform( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Un-transform previously transformed outcomes Args: Y: A `batch_shape x n x m`-dim tensor of transfomred training targets. Yvar: A `batch_shape x n x m`-dim tensor of transformed observation noises associated with the training targets (if applicable). Returns: A two-tuple with the un-transformed outcomes: - The un-transformed outcome observations. - The un-transformed observation noise (if applicable). """ raise NotImplementedError( f"{self.__class__.__name__} does not implement the `untransform` method" )
[docs] def untransform_posterior(self, posterior: Posterior) -> Posterior: r"""Un-transform a posterior Args: posterior: A posterior in the transformed space. Returns: The un-transformed posterior. """ raise NotImplementedError( f"{self.__class__.__name__} does not implement the " "`untransform_posterior` method" )
[docs]class ChainedOutcomeTransform(OutcomeTransform, ModuleDict): r"""An outcome transform representing the chaining of individual transforms""" def __init__(self, **transforms: OutcomeTransform) -> None: r"""Chaining of outcome transforms. Args: transforms: The transforms to chain. Internally, the names of the kwargs are used as the keys for accessing the individual transforms on the module. """ super().__init__(OrderedDict(transforms))
[docs] def forward( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Transform the outcomes in a model's training targets Args: Y: A `batch_shape x n x m`-dim tensor of training targets. Yvar: A `batch_shape x n x m`-dim tensor of observation noises associated with the training targets (if applicable). Returns: A two-tuple with the transformed outcomes: - The transformed outcome observations. - The transformed observation noise (if applicable). """ for tf in self.values(): Y, Yvar = tf.forward(Y, Yvar) return Y, Yvar
[docs] def subset_output(self, idcs: List[int]) -> OutcomeTransform: r"""Subset the transform along the output dimension. Args: idcs: The output indices to subset the transform to. Returns: The current outcome transform, subset to the specified output indices. """ return self.__class__( **{name: tf.subset_output(idcs=idcs) for name, tf in self.items()} )
[docs] def untransform( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Un-transform previously transformed outcomes Args: Y: A `batch_shape x n x m`-dim tensor of transfomred training targets. Yvar: A `batch_shape x n x m`-dim tensor of transformed observation noises associated with the training targets (if applicable). Returns: A two-tuple with the un-transformed outcomes: - The un-transformed outcome observations. - The un-transformed observation noise (if applicable). """ for tf in reversed(self.values()): Y, Yvar = tf.untransform(Y, Yvar) return Y, Yvar
[docs] def untransform_posterior(self, posterior: Posterior) -> Posterior: r"""Un-transform a posterior Args: posterior: A posterior in the transformed space. Returns: The un-transformed posterior. """ for tf in reversed(self.values()): posterior = tf.untransform_posterior(posterior) return posterior
[docs]class Standardize(OutcomeTransform): r"""Standardize outcomes (zero mean, unit variance). This module is stateful: If in train mode, calling forward updates the module state (i.e. the mean/std normalizing constants). If in eval mode, calling forward simply applies the standardization using the current module state. """ def __init__( self, m: int, outputs: Optional[List[int]] = None, batch_shape: torch.Size = torch.Size(), # noqa: B008 min_stdv: float = 1e-8, ) -> None: r"""Standardize outcomes (zero mean, unit variance). Args: m: The output dimension. outputs: Which of the outputs to standardize. If omitted, all outputs will be standardized. batch_shape: The batch_shape of the training targets. min_stddv: The minimum standard deviation for which to perform standardization (if lower, only de-mean the data). """ super().__init__() self.register_buffer("means", torch.zeros(*batch_shape, 1, m)) self.register_buffer("stdvs", torch.zeros(*batch_shape, 1, m)) self.register_buffer("_stdvs_sq", torch.zeros(*batch_shape, 1, m)) self._outputs = normalize_indices(outputs, d=m) self._m = m self._batch_shape = batch_shape self._min_stdv = min_stdv
[docs] def forward( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Standardize outcomes. If the module is in train mode, this updates the module state (i.e. the mean/std normalizing constants). If the module is in eval mode, simply applies the normalization using the module state. Args: Y: A `batch_shape x n x m`-dim tensor of training targets. Yvar: A `batch_shape x n x m`-dim tensor of observation noises associated with the training targets (if applicable). Returns: A two-tuple with the transformed outcomes: - The transformed outcome observations. - The transformed observation noise (if applicable). """ if self.training: if Y.shape[:-2] != self._batch_shape: raise RuntimeError("wrong batch shape") if Y.size(-1) != self._m: raise RuntimeError("wrong output dimension") stdvs = Y.std(dim=-2, keepdim=True) stdvs = stdvs.where(stdvs >= self._min_stdv, torch.full_like(stdvs, 1.0)) means = Y.mean(dim=-2, keepdim=True) if self._outputs is not None: unused = [i for i in range(self._m) if i not in self._outputs] means[..., unused] = 0.0 stdvs[..., unused] = 1.0 self.means = means self.stdvs = stdvs self._stdvs_sq = stdvs.pow(2) Y_tf = (Y - self.means) / self.stdvs Yvar_tf = Yvar / self._stdvs_sq if Yvar is not None else None return Y_tf, Yvar_tf
[docs] def subset_output(self, idcs: List[int]) -> OutcomeTransform: r"""Subset the transform along the output dimension. Args: idcs: The output indices to subset the transform to. Returns: The current outcome transform, subset to the specified output indices. """ new_m = len(idcs) if new_m > self._m: raise RuntimeError( "Trying to subset a transform have more outputs than " " the original transform." ) nlzd_idcs = normalize_indices(idcs, d=self._m) new_outputs = None if self._outputs is not None: new_outputs = [i for i in self._outputs if i in nlzd_idcs] new_tf = self.__class__( m=new_m, outputs=new_outputs, batch_shape=self._batch_shape, min_stdv=self._min_stdv, ) new_tf.means = self.means[..., nlzd_idcs] new_tf.stdvs = self.stdvs[..., nlzd_idcs] new_tf._stdvs_sq = self._stdvs_sq[..., nlzd_idcs] if not self.training: new_tf.eval() return new_tf
[docs] def untransform( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Un-standardize outcomes. Args: Y: A `batch_shape x n x m`-dim tensor of standardized targets. Yvar: A `batch_shape x n x m`-dim tensor of standardized observation noises associated with the targets (if applicable). Returns: A two-tuple with the un-standardized outcomes: - The un-standardized outcome observations. - The un-standardized observation noise (if applicable). """ Y_utf = self.means + self.stdvs * Y Yvar_utf = self._stdvs_sq * Yvar if Yvar is not None else None return Y_utf, Yvar_utf
[docs] def untransform_posterior(self, posterior: Posterior) -> Posterior: r"""Un-standardize the posterior. Args: posterior: A posterior in the standardized space. Returns: The un-standardized posterior. If the input posterior is a MVN, the transformed posterior is again an MVN. """ if self._outputs is not None: raise NotImplementedError( "Standardize does not yet support output selection for " "untransform_posterior" ) is_mtgp_posterior = False if isinstance(posterior, GPyTorchPosterior): is_mtgp_posterior = posterior._is_mt if not self._m == posterior.event_shape[-1] and not is_mtgp_posterior: raise RuntimeError( "Incompatible output dimensions encountered for transform " f"{self._m} and posterior {posterior.event_shape[-1]}." ) if not isinstance(posterior, GPyTorchPosterior): # fall back to TransformedPosterior return TransformedPosterior( posterior=posterior, sample_transform=lambda s: self.means + self.stdvs * s, mean_transform=lambda m, v: self.means + self.stdvs * m, variance_transform=lambda m, v: self._stdvs_sq * v, ) # GPyTorchPosterior (TODO: Should we Lazy-evaluate the mean here as well?) mvn = posterior.mvn offset = self.means scale_fac = self.stdvs if not posterior._is_mt: mean_tf = offset.squeeze(-1) + scale_fac.squeeze(-1) * mvn.mean scale_fac = scale_fac.squeeze(-1).expand_as(mean_tf) else: mean_tf = offset + scale_fac * mvn.mean reps = mean_tf.shape[-2:].numel() // scale_fac.size(-1) scale_fac = scale_fac.squeeze(-2) if mvn._interleaved: scale_fac = scale_fac.repeat(*[1 for _ in scale_fac.shape[:-1]], reps) else: scale_fac = torch.repeat_interleave(scale_fac, reps, dim=-1) if ( not mvn.islazy # TODO: Figure out attribute namming weirdness here or mvn._MultivariateNormal__unbroadcasted_scale_tril is not None ): # if already computed, we can save a lot of time using scale_tril covar_tf = CholLazyTensor(mvn.scale_tril * scale_fac.unsqueeze(-1)) else: lcv = mvn.lazy_covariance_matrix # allow batch-evaluation of the model scale_mat = DiagLazyTensor(scale_fac.expand(lcv.shape[:-1])) covar_tf = scale_mat @ lcv @ scale_mat kwargs = {"interleaved": mvn._interleaved} if posterior._is_mt else {} mvn_tf = mvn.__class__(mean=mean_tf, covariance_matrix=covar_tf, **kwargs) return GPyTorchPosterior(mvn_tf)
[docs]class Log(OutcomeTransform): r"""Log-transform outcomes. Useful if the targets are modeled using a (multivariate) log-Normal distribution. This means that we can use a standard GP model on the log-transformed outcomes and un-transform the model posterior of that GP. """ def __init__(self, outputs: Optional[List[int]] = None) -> None: r"""Log-transform outcomes. Args: outputs: Which of the outputs to log-transform. If omitted, all outputs will be standardized. """ super().__init__() self._outputs = outputs
[docs] def subset_output(self, idcs: List[int]) -> OutcomeTransform: r"""Subset the transform along the output dimension. Args: idcs: The output indices to subset the transform to. Returns: The current outcome transform, subset to the specified output indices. """ new_outputs = None if self._outputs is not None: if min(self._outputs + idcs) < 0: raise NotImplementedError( f"Negative indexing not supported for {self.__class__.__name__} " "when subsetting outputs and only transforming some outputs." ) new_outputs = [i for i in self._outputs if i in idcs] new_tf = self.__class__(outputs=new_outputs) if not self.training: new_tf.eval() return new_tf
[docs] def forward( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Log-transform outcomes. Args: Y: A `batch_shape x n x m`-dim tensor of training targets. Yvar: A `batch_shape x n x m`-dim tensor of observation noises associated with the training targets (if applicable). Returns: A two-tuple with the transformed outcomes: - The transformed outcome observations. - The transformed observation noise (if applicable). """ Y_tf = torch.log(Y) outputs = normalize_indices(self._outputs, d=Y.size(-1)) if outputs is not None: Y_tf = torch.stack( [ Y_tf[..., i] if i in outputs else Y[..., i] for i in range(Y.size(-1)) ], dim=-1, ) if Yvar is not None: # TODO: Delta method, possibly issue warning raise NotImplementedError( "Log does not yet support transforming observation noise" ) return Y_tf, Yvar
[docs] def untransform( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Un-transform log-transformed outcomes Args: Y: A `batch_shape x n x m`-dim tensor of log-transfomred targets. Yvar: A `batch_shape x n x m`-dim tensor of log- transformed observation noises associated with the training targets (if applicable). Returns: A two-tuple with the un-transformed outcomes: - The exponentiated outcome observations. - The exponentiated observation noise (if applicable). """ Y_utf = torch.exp(Y) outputs = normalize_indices(self._outputs, d=Y.size(-1)) if outputs is not None: Y_utf = torch.stack( [ Y_utf[..., i] if i in outputs else Y[..., i] for i in range(Y.size(-1)) ], dim=-1, ) if Yvar is not None: # TODO: Delta method, possibly issue warning raise NotImplementedError( "Log does not yet support transforming observation noise" ) return Y_utf, Yvar
[docs] def untransform_posterior(self, posterior: Posterior) -> Posterior: r"""Un-transform the log-transformed posterior. Args: posterior: A posterior in the log-transformed space. Returns: The un-transformed posterior. """ if self._outputs is not None: raise NotImplementedError( "Log does not yet support output selection for untransform_posterior" ) return TransformedPosterior( posterior=posterior, sample_transform=torch.exp, mean_transform=norm_to_lognorm_mean, variance_transform=norm_to_lognorm_variance, )
[docs]class Power(OutcomeTransform): r"""Power-transform outcomes. Useful if the targets are modeled using a (multivariate) power transform of a Normal distribution. This means that we can use a standard GP model on the power-transformed outcomes and un-transform the model posterior of that GP. """ def __init__(self, power: float, outputs: Optional[List[int]] = None) -> None: r"""Power-transform outcomes. Args: outputs: Which of the outputs to power-transform. If omitted, all outputs will be standardized. """ super().__init__() self._outputs = outputs self.power = power
[docs] def subset_output(self, idcs: List[int]) -> OutcomeTransform: r"""Subset the transform along the output dimension. Args: idcs: The output indices to subset the transform to. Returns: The current outcome transform, subset to the specified output indices. """ new_outputs = None if self._outputs is not None: if min(self._outputs + idcs) < 0: raise NotImplementedError( f"Negative indexing not supported for {self.__class__.__name__} " "when subsetting outputs and only transforming some outputs." ) new_outputs = [i for i in self._outputs if i in idcs] new_tf = self.__class__(power=self.power, outputs=new_outputs) if not self.training: new_tf.eval() return new_tf
[docs] def forward( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Power-transform outcomes. Args: Y: A `batch_shape x n x m`-dim tensor of training targets. Yvar: A `batch_shape x n x m`-dim tensor of observation noises associated with the training targets (if applicable). Returns: A two-tuple with the transformed outcomes: - The transformed outcome observations. - The transformed observation noise (if applicable). """ Y_tf = Y.pow(self.power) outputs = normalize_indices(self._outputs, d=Y.size(-1)) if outputs is not None: Y_tf = torch.stack( [ Y_tf[..., i] if i in outputs else Y[..., i] for i in range(Y.size(-1)) ], dim=-1, ) if Yvar is not None: # TODO: Delta method, possibly issue warning raise NotImplementedError( "Power does not yet support transforming observation noise" ) return Y_tf, Yvar
[docs] def untransform( self, Y: Tensor, Yvar: Optional[Tensor] = None ) -> Tuple[Tensor, Optional[Tensor]]: r"""Un-transform power-transformed outcomes Args: Y: A `batch_shape x n x m`-dim tensor of power-transfomred targets. Yvar: A `batch_shape x n x m`-dim tensor of power-transformed observation noises associated with the training targets (if applicable). Returns: A two-tuple with the un-transformed outcomes: - The un-power transformed outcome observations. - The un-power transformed observation noise (if applicable). """ Y_utf = Y.pow(1.0 / self.power) outputs = normalize_indices(self._outputs, d=Y.size(-1)) if outputs is not None: Y_utf = torch.stack( [ Y_utf[..., i] if i in outputs else Y[..., i] for i in range(Y.size(-1)) ], dim=-1, ) if Yvar is not None: # TODO: Delta method, possibly issue warning raise NotImplementedError( "Power does not yet support transforming observation noise" ) return Y_utf, Yvar
[docs] def untransform_posterior(self, posterior: Posterior) -> Posterior: r"""Un-transform the power-transformed posterior. Args: posterior: A posterior in the power-transformed space. Returns: The un-transformed posterior. """ if self._outputs is not None: raise NotImplementedError( "Power does not yet support output selection for untransform_posterior" ) return TransformedPosterior( posterior=posterior, sample_transform=lambda x: x.pow(1.0 / self.power), )