Merge branch 'master' into enhance_optimizers

Author: icouckuy

GPflowOpt/__init__.py

@@ -20,3 +20,4 @@
 from . import transforms
 from . import scaling
 from . import objective
+from . import pareto

GPflowOpt/acquisition/__init__.py

@@ -20,7 +20,8 @@
 from .poi import ProbabilityOfImprovement
 from .lcb import LowerConfidenceBound
 
-# Multi-objective
+# Multiobjective
+from .hvpoi import HVProbabilityOfImprovement
 
-# Black-box constraints
+# Black-box constraint
 from .pof import ProbabilityOfFeasibility

GPflowOpt/acquisition/hvpoi.py

@@ -0,0 +1,136 @@
+# Copyright 2017 Joachim van der Herten, Ivo Couckuyt
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from .acquisition import Acquisition
+from ..pareto import Pareto
+
+from GPflow.param import DataHolder
+from GPflow import settings
+
+import numpy as np
+import tensorflow as tf
+
+stability = settings.numerics.jitter_level
+float_type = settings.dtypes.float_type
+
+
+class HVProbabilityOfImprovement(Acquisition):
+    """
+    Hypervolume-based Probability of Improvement.
+
+    A multiobjective acquisition function for multiobjective optimization. It is used to identify a complete Pareto set
+    of non-dominated solutions.
+    
+    Key reference:
+
+     ::
+
+        @article{Couckuyt:2014,
+            title={Fast calculation of multiobjective probability of improvement and expected improvement criteria for Pareto optimization},
+            author={Couckuyt, Ivo and Deschrijver, Dirk and Dhaene, Tom},
+            journal={Journal of Global Optimization},
+            volume={60},
+            number={3},
+            pages={575--594},
+            year={2014},
+            publisher={Springer}
+        }
+
+    For a Pareto set :math:`\\mathcal{P}`, the non-dominated section of the objective space is denoted by :math:`A`.
+    The :meth:`~..pareto.Pareto.hypervolume` of the dominated part of the space is denoted by :math:`\\mathcal{H}`
+    and can be used as indicator for the optimality of the Pareto set (the higher the better).
+
+    .. math::
+       \\boldsymbol{\\mu} &= \\left[ \\mathbb{E} \\left[ f^{(1)}_{\\star}\\,|\\, \\mathbf x, \\mathbf y, \\mathbf x_{\\star} \\right],
+       ..., \\mathbb{E} \\left[ f^{(p)}_{\\star}\\,|\\, \\mathbf x, \\mathbf y, \\mathbf x_{\\star} \\right]\\right] \\\\
+       I\\left(\\boldsymbol{\\mu}, \\mathcal{P}\\right) &=
+       \\begin{cases} \\left( \\mathcal{H} \\left( \\mathcal{P} \\cup \\boldsymbol{\\mu} \\right) - \\mathcal{H}
+       \\left( \\mathcal{P} \\right)) \\right) ~ if ~ \\boldsymbol{\\mu} \\in A
+       \\\\ 0 ~ \\mbox{otherwise} \\end{cases} \\\\
+       \\alpha(\\mathbf x_{\\star}) &= I\\left(\\boldsymbol{\\mu}, \\mathcal{P}\\right) p\\left(\\mathbf x_{\\star} \\in A \\right)
+
+    Attributes:
+        pareto: An instance of :class:`~..pareto.Pareto`.
+    """
+
+    def __init__(self, models):
+        """
+        :param models: A list of (possibly multioutput) GPflow representing our belief of the objectives.
+        """
+        super(HVProbabilityOfImprovement, self).__init__(models)
+        assert self.data[1].shape[1] > 1
+        self.pareto = Pareto(np.hstack((m.predict_f(self.data[0])[0] for m in self.models)))
+        self.reference = DataHolder(self._estimate_reference())
+
+    def _estimate_reference(self):
+        pf = self.pareto.front.value
+        f = np.max(pf, axis=0, keepdims=True) - np.min(pf, axis=0, keepdims=True)
+        return np.max(pf, axis=0, keepdims=True) + 2 * f / pf.shape[0]
+
+    def setup(self):
+        """
+        Pre-computes the Pareto set and cell bounds for integrating over the non-dominated region.
+        """
+        super(HVProbabilityOfImprovement, self).setup()
+
+        # Obtain hypervolume cell bounds, use prediction mean
+        F = np.hstack((m.predict_f(self.data[0])[0] for m in self.models))
+        self.pareto.update(F)
+
+        # Calculate reference point.
+        self.reference = self._estimate_reference()
+
+    def build_acquisition(self, Xcand):
+        outdim = tf.shape(self.data[1])[1]
+        num_cells = tf.shape(self.pareto.bounds.lb)[0]
+        N = tf.shape(Xcand)[0]
+
+        # Extended Pareto front
+        pf_ext = tf.concat([-np.inf * tf.ones([1, outdim], dtype=float_type), self.pareto.front, self.reference], 0)
+
+        # Predictions for candidates, concatenate columns
+        preds = [m.build_predict(Xcand) for m in self.models]
+        candidate_mean, candidate_var = (tf.concat(moment, 1) for moment in zip(*preds))
+        candidate_var = tf.maximum(candidate_var, stability)  # avoid zeros
+
+        # Calculate the cdf's for all candidates for every predictive distribution in the data points
+        normal = tf.contrib.distributions.Normal(candidate_mean, tf.sqrt(candidate_var))
+        Phi = tf.transpose(normal.cdf(tf.expand_dims(pf_ext, 1)), [1, 0, 2])  # N x pf_ext_size x outdim
+
+        # tf.gather_nd indices for bound points
+        col_idx = tf.tile(tf.range(outdim), (num_cells,))
+        ub_idx = tf.stack((tf.reshape(self.pareto.bounds.ub, [-1]), col_idx), axis=1)  # (num_cells*outdim x 2)
+        lb_idx = tf.stack((tf.reshape(self.pareto.bounds.lb, [-1]), col_idx), axis=1)  # (num_cells*outdim x 2)
+
+        # Calculate PoI
+        P1 = tf.transpose(tf.gather_nd(tf.transpose(Phi, perm=[1, 2, 0]), ub_idx))  # N x num_cell*outdim
+        P2 = tf.transpose(tf.gather_nd(tf.transpose(Phi, perm=[1, 2, 0]), lb_idx))  # N x num_cell*outdim
+        P = tf.reshape(P1 - P2, [N, num_cells, outdim])
+        PoI = tf.reduce_sum(tf.reduce_prod(P, axis=2), axis=1, keep_dims=True)  # N x 1
+
+        # Calculate Hypervolume contribution of points Y
+        ub_points = tf.reshape(tf.gather_nd(pf_ext, ub_idx), [num_cells, outdim])
+        lb_points = tf.reshape(tf.gather_nd(pf_ext, lb_idx), [num_cells, outdim])
+
+        splus_valid = tf.reduce_all(tf.tile(tf.expand_dims(ub_points, 1), [1, N, 1]) > candidate_mean,
+                                    axis=2)  # num_cells x N
+        splus_idx = tf.expand_dims(tf.cast(splus_valid, dtype=float_type), -1)  # num_cells x N x 1
+        splus_lb = tf.tile(tf.expand_dims(lb_points, 1), [1, N, 1])  # num_cells x N x outdim
+        splus_lb = tf.maximum(splus_lb, candidate_mean)  # num_cells x N x outdim
+        splus_ub = tf.tile(tf.expand_dims(ub_points, 1), [1, N, 1])  # num_cells x N x outdim
+        splus = tf.concat([splus_idx, splus_ub - splus_lb], axis=2)  # num_cells x N x (outdim+1)
+        Hv = tf.transpose(tf.reduce_sum(tf.reduce_prod(splus, axis=2), axis=0, keep_dims=True))  # N x 1
+
+        # return HvPoI
+        return tf.multiply(Hv, PoI)

GPflowOpt/bo.py

@@ -21,7 +21,7 @@
 from .optim import Optimizer, SciPyOptimizer
 from .objective import ObjectiveWrapper
 from .design import Design, EmptyDesign
-
+from .pareto import non_dominated_sort
 
 class BayesianOptimizer(Optimizer):
     """
@@ -123,9 +123,12 @@ def _create_bo_result(self, success, message):
         valid_Y = Y[valid, :]
         valid_Yo = valid_Y[:, self.acquisition.objective_indices()]
 
-        # Here is the place to plug in pareto front if valid_Y.shape[1] > 1
-        # else
-        idx = np.argmin(valid_Yo)
+        # Differentiate between single- and multiobjective optimization results
+        if valid_Y.shape[1] > 1:
+            _, dom = non_dominated_sort(valid_Yo)
+            idx = dom == 0  # Return the non-dominated points
+        else:
+            idx = np.argmin(valid_Yo)
 
         return OptimizeResult(x=valid_X[idx, :],
                               success=success,