Source code for deephyper.skopt.acquisition

import numpy as np
import warnings

from scipy.stats import norm


[docs] def gaussian_acquisition_1D( X, model, y_opt=None, acq_func="LCB", acq_func_kwargs=None, return_grad=True, ): """A wrapper around the acquisition function that is called by fmin_l_bfgs_b. This is because lbfgs allows only 1-D input. """ return _gaussian_acquisition( np.expand_dims(X, axis=0), model, y_opt, acq_func=acq_func, acq_func_kwargs=acq_func_kwargs, return_grad=return_grad, )
def _gaussian_acquisition( X, model, y_opt=None, acq_func="LCB", return_grad=False, acq_func_kwargs=None, ): """Wrapper so that the output of this function can be directly passed to a minimizer. """ # Check inputs X = np.asarray(X) if X.ndim != 2: raise ValueError( "X is {}-dimensional, however," " it must be 2-dimensional.".format(X.ndim) ) # Check if the deterministic acquisition function variant should be used deterministic = False if "d" == acq_func[-1]: deterministic = True acq_func = acq_func[:-1] if acq_func_kwargs is None: acq_func_kwargs = dict() xi = acq_func_kwargs.get("xi", 0.01) kappa = acq_func_kwargs.get("kappa", 1.96) # Evaluate acquisition function per_second = acq_func.endswith("ps") if per_second: model, time_model = model.estimators_ if acq_func in ["LCB"]: func_and_grad = gaussian_lcb( X, model, kappa, return_grad, deterministic=deterministic ) if return_grad: acq_vals, acq_grad = func_and_grad else: acq_vals = func_and_grad elif acq_func in ["EI", "PI", "EIps", "PIps"]: if acq_func in ["EI", "EIps"]: func_and_grad = gaussian_ei( X, model, y_opt, xi, return_grad, deterministic=deterministic ) else: func_and_grad = gaussian_pi( X, model, y_opt, xi, return_grad, deterministic=deterministic ) if return_grad: acq_vals = -func_and_grad[0] acq_grad = -func_and_grad[1] else: acq_vals = -func_and_grad if acq_func in ["EIps", "PIps"]: if return_grad: mu, std, mu_grad, std_grad = time_model.predict( X, return_std=True, return_mean_grad=True, return_std_grad=True ) else: mu, std = time_model.predict(X, return_std=True) # acq = acq / E(t) inv_t = np.exp(-mu + 0.5 * std**2) acq_vals *= inv_t # grad = d(acq_func) * inv_t + (acq_vals *d(inv_t)) # inv_t = exp(g) # d(inv_t) = inv_t * grad(g) # d(inv_t) = inv_t * (-mu_grad + std * std_grad) if return_grad: acq_grad *= inv_t acq_grad += acq_vals * (-mu_grad + std * std_grad) elif acq_func in ["MES"]: acq_vals = -gaussian_mes(X, model, deterministic=deterministic) if return_grad: raise NotImplementedError( "Gradient not implemented for MES acquisition function." ) else: raise ValueError("Acquisition function not implemented.") if return_grad: return acq_vals, acq_grad return acq_vals
[docs] def gaussian_lcb(X, model, kappa=1.96, return_grad=False, deterministic=False): """Use the lower confidence bound to estimate the acquisition values. The trade-off between exploitation and exploration is left to be controlled by the user through the parameter ``kappa``. Parameters ---------- X : array-like, shape (n_samples, n_features) Values where the acquisition function should be computed. model : sklearn estimator that implements predict with ``return_std`` The fit estimator that approximates the function through the method ``predict``. It should have a ``return_std`` parameter that returns the standard deviation. kappa : float, default 1.96 or 'inf' Controls how much of the variance in the predicted values should be taken into account. If set to be very high, then we are favouring exploration over exploitation and vice versa. If set to 'inf', the acquisition function will only use the variance which is useful in a pure exploration setting. Useless if ``method`` is not set to "LCB". return_grad : boolean, optional Whether or not to return the grad. Implemented only for the case where ``X`` is a single sample. Returns: ------- values : array-like, shape (X.shape[0],) Acquisition function values computed at X. grad : array-like, shape (n_samples, n_features) Gradient at X. """ # Compute posterior. with warnings.catch_warnings(): warnings.simplefilter("ignore") if return_grad: mu, std, mu_grad, std_grad = model.predict( X, return_std=True, return_mean_grad=True, return_std_grad=True ) if kappa == "inf": return -std, -std_grad return mu - kappa * std, mu_grad - kappa * std_grad else: if deterministic: mu, std_al, std_ep = model.predict( X, return_std=True, disentangled_std=True ) std = std_ep else: mu, std = model.predict(X, return_std=True) if kappa == "inf": return -std return mu - kappa * std
[docs] def gaussian_pi(X, model, y_opt=0.0, xi=0.01, return_grad=False, deterministic=False): """Use the probability of improvement to calculate the acquisition values. The conditional probability `P(y=f(x) | x)` form a gaussian with a certain mean and standard deviation approximated by the model. The PI condition is derived by computing ``E[u(f(x))]`` where ``u(f(x)) = 1``, if ``f(x) < y_opt`` and ``u(f(x)) = 0``, if``f(x) > y_opt``. This means that the PI condition does not care about how "better" the predictions are than the previous values, since it gives an equal reward to all of them. Note that the value returned by this function should be maximized to obtain the ``X`` with maximum improvement. Parameters ---------- X : array-like, shape=(n_samples, n_features) Values where the acquisition function should be computed. model : sklearn estimator that implements predict with ``return_std`` The fit estimator that approximates the function through the method ``predict``. It should have a ``return_std`` parameter that returns the standard deviation. y_opt : float, default 0 Previous minimum value which we would like to improve upon. xi : float, default=0.01 Controls how much improvement one wants over the previous best values. Useful only when ``method`` is set to "EI" return_grad : boolean, optional Whether or not to return the grad. Implemented only for the case where ``X`` is a single sample. Returns: ------- values : [array-like, shape=(X.shape[0],) Acquisition function values computed at X. """ with warnings.catch_warnings(): warnings.simplefilter("ignore") if return_grad: mu, std, mu_grad, std_grad = model.predict( X, return_std=True, return_mean_grad=True, return_std_grad=True ) else: if deterministic: mu, std_al, std_ep = model.predict( X, return_std=True, disentangled_std=True ) std = std_ep else: mu, std = model.predict(X, return_std=True) # check dimensionality of mu, std so we can divide them below if (mu.ndim != 1) or (std.ndim != 1): raise ValueError( "mu and std are {}-dimensional and {}-dimensional, " "however both must be 1-dimensional. Did you train " "your model with an (N, 1) vector instead of an " "(N,) vector?".format(mu.ndim, std.ndim) ) values = np.zeros_like(mu) mask = std > 0 improve = y_opt - xi - mu[mask] scaled = improve / std[mask] values[mask] = norm.cdf(scaled) if return_grad: if not np.all(mask): return values, np.zeros_like(std_grad) # Substitute (y_opt - xi - mu) / sigma = t and apply chain rule. # improve_grad is the gradient of t wrt x. improve_grad = -mu_grad * std - std_grad * improve improve_grad /= std**2 return values, improve_grad * norm.pdf(scaled) return values
[docs] def gaussian_ei(X, model, y_opt=0.0, xi=0.01, return_grad=False, deterministic=False): """Use the expected improvement to calculate the acquisition values. The conditional probability `P(y=f(x) | x)` form a gaussian with a certain mean and standard deviation approximated by the model. The EI condition is derived by computing ``E[u(f(x))]`` where ``u(f(x)) = 0``, if ``f(x) > y_opt`` and ``u(f(x)) = y_opt - f(x)``, if``f(x) < y_opt``. This solves one of the issues of the PI condition by giving a reward proportional to the amount of improvement got. Note that the value returned by this function should be maximized to obtain the ``X`` with maximum improvement. Parameters ---------- X : array-like, shape=(n_samples, n_features) Values where the acquisition function should be computed. model : sklearn estimator that implements predict with ``return_std`` The fit estimator that approximates the function through the method ``predict``. It should have a ``return_std`` parameter that returns the standard deviation. y_opt : float, default 0 Previous minimum value which we would like to improve upon. xi : float, default=0.01 Controls how much improvement one wants over the previous best values. Useful only when ``method`` is set to "EI" return_grad : boolean, optional Whether or not to return the grad. Implemented only for the case where ``X`` is a single sample. Returns: ------- values : array-like, shape=(X.shape[0],) Acquisition function values computed at X. """ with warnings.catch_warnings(): warnings.simplefilter("ignore") if return_grad: mu, std, mu_grad, std_grad = model.predict( X, return_std=True, return_mean_grad=True, return_std_grad=True ) else: if deterministic: mu, std_al, std_ep = model.predict( X, return_std=True, disentangled_std=True ) std = std_ep else: mu, std = model.predict(X, return_std=True) # check dimensionality of mu, std so we can divide them below if (mu.ndim != 1) or (std.ndim != 1): raise ValueError( "mu and std are {}-dimensional and {}-dimensional, " "however both must be 1-dimensional. Did you train " "your model with an (N, 1) vector instead of an " "(N,) vector?".format(mu.ndim, std.ndim) ) values = np.zeros_like(mu) mask = std > 0 improve = y_opt - xi - mu[mask] scaled = improve / std[mask] cdf = norm.cdf(scaled) pdf = norm.pdf(scaled) exploit = improve * cdf explore = std[mask] * pdf values[mask] = exploit + explore if return_grad: if not np.all(mask): return values, np.zeros_like(std_grad) # Substitute (y_opt - xi - mu) / sigma = t and apply chain rule. # improve_grad is the gradient of t wrt x. improve_grad = -mu_grad * std - std_grad * improve improve_grad /= std**2 cdf_grad = improve_grad * pdf pdf_grad = -improve * cdf_grad exploit_grad = -mu_grad * cdf - pdf_grad explore_grad = std_grad * pdf + pdf_grad grad = exploit_grad + explore_grad return values, grad return values
[docs] def gaussian_mes(X, model, k_samples=10, deterministic=False): """Use the max-value entropy to calculate the acquisition values. Article: https://arxiv.org/abs/1703.01968 Source implementation: https://github.com/zi-w/Max-value-Entropy-Search/blob/master/acFuns/evaluateMES.m The conditional probability `P(y=f(x) | x)` form a gaussian with a certain mean and standard deviation approximated by the model. The EI condition is derived by computing ``E[u(f(x))]`` where ``u(f(x)) = 0``, if ``f(x) > y_opt`` and ``u(f(x)) = y_opt - f(x)``, if``f(x) < y_opt``. This solves one of the issues of the PI condition by giving a reward proportional to the amount of improvement got. Note that the value returned by this function should be maximized to obtain the ``X`` with maximum improvement. Parameters ---------- X : array-like, shape=(n_samples, n_features) Values where the acquisition function should be computed. model : sklearn estimator that implements predict with ``return_std`` The fit estimator that approximates the function through the method ``predict``. It should have a ``return_std`` parameter that returns the standard deviation. y_opt : float, default 0 Previous minimum value which we would like to improve upon. xi : float, default=0.01 Controls how much improvement one wants over the previous best values. Useful only when ``method`` is set to "EI" return_grad : boolean, optional Whether or not to return the grad. Implemented only for the case where ``X`` is a single sample. Returns: ------- values : array-like, shape=(X.shape[0],) Acquisition function values computed at X. """ with warnings.catch_warnings(): warnings.simplefilter("ignore") if deterministic: mu, std_al, std_ep = model.predict( X, return_std=True, disentangled_std=True ) std = std_ep else: mu, std = model.predict(X, return_std=True) # MES is defined for a maximization problem but the model prediction are for minimization # we map minimization to maximization by multiplying by -1 mu *= -1 # check dimensionality of mu, std so we can divide them below if (mu.ndim != 1) or (std.ndim != 1): raise ValueError( "mu, std_al, std_ep are {}-dimensional and {}-dimensional, " "however both must be 1-dimensional. Did you train " "your model with an (N, 1) vector instead of an " "(N,) vector?".format(mu.ndim, std.ndim) ) values = np.zeros_like(mu) eps = 1e-10 std = np.maximum(std, eps) for _ in range(k_samples): y_sample = norm.rvs(loc=mu, scale=std) gamma = (np.max(y_sample) - mu) / std pdfgamma = np.maximum(norm.pdf(gamma), eps) cdfgamma = np.maximum(norm.cdf(gamma), eps) values += 0.5 * gamma * pdfgamma / cdfgamma - np.log(cdfgamma) values /= k_samples return values