Show code cell source
MAKE_BOOK_FIGURES=False
import numpy as np
import scipy.stats as st
import matplotlib as mpl
import matplotlib.pyplot as plt
%matplotlib inline
import matplotlib_inline
matplotlib_inline.backend_inline.set_matplotlib_formats('svg')
import seaborn as sns
sns.set_context("paper")
sns.set_style("ticks")
def set_book_style():
plt.style.use('seaborn-v0_8-white')
sns.set_style("ticks")
sns.set_palette("deep")
mpl.rcParams.update({
# Font settings
'font.family': 'serif', # For academic publishing
'font.size': 8, # As requested, 10pt font
'axes.labelsize': 8,
'axes.titlesize': 8,
'xtick.labelsize': 7, # Slightly smaller for better readability
'ytick.labelsize': 7,
'legend.fontsize': 7,
# Line and marker settings for consistency
'axes.linewidth': 0.5,
'grid.linewidth': 0.5,
'lines.linewidth': 1.0,
'lines.markersize': 4,
# Layout to prevent clipped labels
'figure.constrained_layout.use': True,
# Default DPI (will override when saving)
'figure.dpi': 600,
'savefig.dpi': 600,
# Despine - remove top and right spines
'axes.spines.top': False,
'axes.spines.right': False,
# Remove legend frame
'legend.frameon': False,
# Additional trim settings
'figure.autolayout': True, # Alternative to constrained_layout
'savefig.bbox': 'tight', # Trim when saving
'savefig.pad_inches': 0.1 # Small padding to ensure nothing gets cut off
})
def set_notebook_style():
plt.style.use('seaborn-v0_8-white')
sns.set_style("ticks")
sns.set_palette("deep")
mpl.rcParams.update({
# Font settings - using default sizes
'font.family': 'serif',
'axes.labelsize': 10,
'axes.titlesize': 10,
'xtick.labelsize': 9,
'ytick.labelsize': 9,
'legend.fontsize': 9,
# Line and marker settings
'axes.linewidth': 0.5,
'grid.linewidth': 0.5,
'lines.linewidth': 1.0,
'lines.markersize': 4,
# Layout settings
'figure.constrained_layout.use': True,
# Remove only top and right spines
'axes.spines.top': False,
'axes.spines.right': False,
# Remove legend frame
'legend.frameon': False,
# Additional settings
'figure.autolayout': True,
'savefig.bbox': 'tight',
'savefig.pad_inches': 0.1
})
def save_for_book(fig, filename, is_vector=True, **kwargs):
"""
Save a figure with book-optimized settings.
Parameters:
-----------
fig : matplotlib figure
The figure to save
filename : str
Filename without extension
is_vector : bool
If True, saves as vector at 1000 dpi. If False, saves as raster at 600 dpi.
**kwargs : dict
Additional kwargs to pass to savefig
"""
# Set appropriate DPI and format based on figure type
if is_vector:
dpi = 1000
ext = '.pdf'
else:
dpi = 600
ext = '.tif'
# Save the figure with book settings
fig.savefig(f"{filename}{ext}", dpi=dpi, **kwargs)
def make_full_width_fig():
return plt.subplots(figsize=(4.7, 2.9), constrained_layout=True)
def make_half_width_fig():
return plt.subplots(figsize=(2.35, 1.45), constrained_layout=True)
if MAKE_BOOK_FIGURES:
set_book_style()
else:
set_notebook_style()
make_full_width_fig = make_full_width_fig if MAKE_BOOK_FIGURES else lambda: plt.subplots()
make_half_width_fig = make_half_width_fig if MAKE_BOOK_FIGURES else lambda: plt.subplots()
Show code cell source
!pip install gpytorch
import torch
import gpytorch
from gpytorch.kernels import ScaleKernel, RBFKernel
class ExactGP(gpytorch.models.ExactGP):
"""Exact Gaussian Process model.
Arguments
train_x -- The training inputs.
train_y -- The training labels.
mean_module -- The mean module. Defaults to a constant mean.
covar_module-- The covariance module. Defaults to a RBF kernel.
likelihood -- The likelihood function. Defaults to Gaussian.
"""
def __init__(
self,
train_x,
train_y,
mean_module=gpytorch.means.ConstantMean(),
covar_module = ScaleKernel(RBFKernel()),
likelihood=gpytorch.likelihoods.GaussianLikelihood(
noise_constraint=gpytorch.constraints.GreaterThan(0.0)
)
):
super().__init__(train_x, train_y, likelihood)
self.mean_module = mean_module
self.covar_module = covar_module
def forward(self, x):
mean_x = self.mean_module(x)
covar_x = self.covar_module(x)
return gpytorch.distributions.MultivariateNormal(mean_x, covar_x)
def plot_1d_regression(
x_star,
model,
ax=None,
f_true=None,
num_samples=10
):
"""Plot the posterior predictive.
Arguments
x_start -- The test points on which to evaluate.
model -- The trained model.
Keyword Arguments
ax -- An axes object to write on.
f_true -- The true function.
num_samples -- The number of samples.
"""
f_star = model(x_star)
m_star = f_star.mean
v_star = f_star.variance
y_star = model.likelihood(f_star)
yv_star = y_star.variance
f_lower = (
m_star - 2.0 * torch.sqrt(v_star)
)
f_upper = (
m_star + 2.0 * torch.sqrt(v_star)
)
y_lower = m_star - 2.0 * torch.sqrt(yv_star)
y_upper = m_star + 2.0 * torch.sqrt(yv_star)
if ax is None:
fig, ax = plt.subplots()
ax.plot(model.train_inputs[0].flatten().detach(),
model.train_targets.detach(),
'kx',
markersize=10,
markeredgewidth=2,
label='Observations'
)
ax.plot(
x_star,
m_star.detach(),
lw=2,
label='$m_n(x)$',
color=sns.color_palette()[0]
)
ax.fill_between(
x_star.flatten().detach(),
f_lower.flatten().detach(),
f_upper.flatten().detach(),
alpha=0.5,
label=r'$f(\mathbf{x}^*)$ 95% pred.',
color=sns.color_palette()[0]
)
ax.fill_between(
x_star.detach().flatten(),
y_lower.detach().flatten(),
f_lower.detach().flatten(),
color=sns.color_palette()[1],
alpha=0.5,
label='$y^*$ 95% pred.'
)
ax.fill_between(
x_star.detach().flatten(),
f_upper.detach().flatten(),
y_upper.detach().flatten(),
color=sns.color_palette()[1],
alpha=0.5,
label=None
)
if f_true is not None:
ax.plot(
x_star,
f_true(x_star),
'm-.',
label='True function'
)
if num_samples > 0:
f_post_samples = f_star.sample(
sample_shape=torch.Size([10])
)
ax.plot(
x_star,
f_post_samples.T.detach(),
color="red",
lw=0.5
)
# This is just to add the legend entry
ax.plot(
[],
[],
color="red",
lw=0.5,
label="Posterior samples"
)
ax.set_xlabel('$x$')
ax.set_ylabel('$y$')
plt.legend(loc='best', frameon=False)
sns.despine(trim=True)
return m_star, v_star
def plot_iaf(
x_star,
gpr,
alpha,
alpha_params={},
ax=None,
f_true=None
):
"""Plot the information acquisition function.
Arguments
x_star -- A set of points to plot on.
gpr -- A rained Gaussian process regression
object.
alpha -- The information acquisition function.
This assumed to be a function of the
posterior mean and standard deviation.
Keyword Arguments
ax -- An axes object to plot on.
f_true -- The true function - if available.
The evaluation of the information acquisition function
is as follows:
af_values = alpha(mu, sigma, y_max, **alpha_params)
"""
if ax is None:
fig, ax = plt.subplots()
ax.set_title(
", ".join(
f"{n}={k:.2f}"
for n, k in alpha_params.items()
)
)
m, v = plot_1d_regression(
x_star,
gpr,
ax=ax,
f_true=f_true,
num_samples=0
)
sigma = torch.sqrt(v)
af_values = alpha(m, sigma, Y.max(), **alpha_params)
next_id = torch.argmax(af_values)
next_x = x_star[next_id]
af_max = af_values[next_id]
ax2 = ax.twinx()
ax2.plot(x_star, af_values.detach(), color=sns.color_palette()[1])
ax2.set_ylabel(
'Maximum Upper Interval',
color=sns.color_palette()[1]
)
plt.setp(
ax2.get_yticklabels(),
color=sns.color_palette()[1]
)
ax2.plot(
next_x * np.ones(100),
torch.linspace(0, af_max.item(), 100),
color=sns.color_palette()[1],
linewidth=1
)
def maximize(
f,
model,
X_design,
alpha,
alpha_params={},
max_it=10,
optimize=False,
plot=False,
**kwargs
):
"""Optimize a function using a limited number of evaluations.
Arguments
f -- The function to optimize.
gpr -- A Gaussian process model to use for representing
our state of knowledge.
X_design -- The set of candidate points for identifying the
maximum.
alpha -- The information acquisition function.
This assumed to be a function of the
posterior mean and standard deviation.
Keyword Arguments
alpha_params -- Extra parameters to the information
acquisition function.
max_it -- The maximum number of iterations.
optimize -- Whether or not to optimize the hyper-parameters.
plot -- Determines how often to plot. Make it one
to plot at each iteration. Make it max_it
to plot at the last iteration.
The rest of the keyword arguments are passed to plot_iaf().
"""
af_all = []
for count in range(max_it):
# Predict
f_design = model(X_design)
m = f_design.mean
sigma2 = f_design.variance
sigma = torch.sqrt(sigma2)
# Evaluate information acquisition function
y_train = model.train_targets.numpy()
af_values = alpha(
m,
sigma,
y_train.max(),
**alpha_params
)
# Find best point to include
i = torch.argmax(af_values)
af_all.append(af_values[i])
new_x = X_design[i:(i+1)].float()
new_y = f(new_x)
train_x = torch.cat([model.train_inputs[0], new_x[:, None]])
train_y = torch.cat([model.train_targets, new_y])
model.set_train_data(train_x, train_y, strict=False)
if optimize:
train(model, train_x, train_y, n_iter=100, lr=0.1)
else:
model.train()
model.eval()
# Plot if required
if count % plot == 0:
if "ax" in kwargs:
ax = kwargs[ax]
else:
fig, ax = plt.subplots()
plot_iaf(
X_design,
model,
alpha,
alpha_params=alpha_params,
f_true=f,
ax=ax
)
ax.set_title(
f"N={count}, " + ax.get_title()
)
return af_all
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Probability of Improvement#
We develop intuition about an information acquisition function using the probability of improvement. Let’s reintroduce the same running example as the previous hands-on activity.
Show code cell source
def f(x):
"""A function to optimize."""
return -4 * (1. - np.sin(6 * x + 8 * np.exp(6 * x - 7.)))
np.random.seed(12345)
n_init = 3
X = np.random.rand(n_init)
Y = f(X)
plt.plot(X, Y, 'kx', markersize=10, markeredgewidth=2)
plt.xlabel('$x$')
plt.ylabel('$y$')
sns.despine(trim=True);
Just like in the previous hands-on activity, assume that we have made some observations and that we have used them to do Gaussian process regression, resulting in the point-predictive distribution:
\[
p(y|\mathbf{x},\mathcal{D}_{n}) = \mathcal{N}\left(y|m_{n}(\mathbf{x}), \sigma^2_{n}(\mathbf{x})\right),
\]
where \(m_{n}(\mathbf{x})\) and \(\sigma^2_{n}(\mathbf{x})\) are the predictive mean and variance respectively. Here is the code for this:
train_x = torch.from_numpy(X).float()
train_y = torch.from_numpy(Y).float()
model = ExactGP(train_x, train_y)
# It is not a good idea to train the model when we don't have enough data
# So we fix the hyperparameters to something reasonable
model.covar_module.base_kernel.lengthscale = 0.15
model.covar_module.outputscale = 4.0
model.likelihood.noise = 0.0
model.eval()
x = torch.linspace(0, 1, 100)
plot_1d_regression(
x,
model,
f_true=f
);
What if you try to find the point that maximizes the probability of getting an observation greater than the ones you have so far? Let’s derive this. First, let’s call \(y_n^*\) the current maximum in your dataset, i.e.,
\[
y_n^* = \max_{1\le i\le n}y_i.
\]
We define the following acquisition function:
\[
a_n(\mathbf{x}) = \mathbb{P}[y > y_n^* + \psi | \mathbf{x}, \mathcal{D}_n].
\]
We read that “\(a_n(\mathbf{x})\)” is the probability that we observe at \(x\) a \(y\) that is greater than the currently observed maximum \(y_n^*\) by at least \(\psi>0\). The good thing is that it is possible to get an analytical answer because our point predictive distribution is Gaussian. In particular, we get:
\[\begin{split}
\begin{align}
a_n(\mathbf{x}) &=& \mathbb{P}[y > y_n^* + \psi | x, \mathcal{D}_n]\\
&=& \mathbb{P}\left[\frac{y - \mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})} > \frac{y_n^* + \psi - \mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})} \Big| \mathbf{x}, \mathcal{D}_n\right]\\
&=& 1 - \mathbb{P}\left[\frac{y - \mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})} \le \frac{y_n^* + \psi - \mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})} \Big| \mathbf{x}, \mathcal{D}_n\right]\\
&=& 1 - \Phi\left(\frac{y_n^* + \psi - \mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})} \right)\\
&=& \Phi\left(\frac{\mu_n(\mathbf{x}) - y_n^* - \psi}{\sigma_n(\mathbf{x})} \right),
\end{align}
\end{split}\]
where we used that since \(y_n | \mathbf{x}_n, \mathcal{D}_n\) is Gaussian with mean \(\mu_n(\mathbf{x})\) and variance \(\sigma_n^2(\mathbf{x})\), then \(\frac{y_n-\mu_n(\mathbf{x})}{\sigma_n(\mathbf{x})}\) is a standard normal, and we also used that the CDF of the standard normal satisfies this property:
\[
\Phi(-z) = 1 - \Phi(z).
\]
Here is the code for this activation function:
def poi(m, sigma, ymax, psi=0.):
"""Return the probability of improvement.
Arguments
m -- The predictive mean at the test points.
sigma -- The predictive standard deviation at
the test points.
ymax -- The maximum observed value (so far).
psi -- A parameter that controls exploration.
"""
return torch.distributions.Normal(0, 1).cdf((m - ymax - psi) / sigma)
Let’s visualize this:
plot_iaf(
x,
model,
poi,
alpha_params=dict(psi=2.0)
)
Questions#
Experiment with different values of \(\psi\).
When do you get exploration?
When do you get exploitation?
Bayesian global optimization with the probability of improvement#
Let’s run the Bayesian global optimization algorithm using the probability of improvement as the information acquisition function.
I have included the generic function maximize() from the previous section.
Here is how to use it:
train_x = torch.from_numpy(X).float()
train_y = torch.from_numpy(Y).float()
covar_module = ScaleKernel(RBFKernel())
model = ExactGP(train_x, train_y)
# It is not a good idea to train the model when we don't have enough data
# So we fix the hyperparameters to something reasonable
model.covar_module.base_kernel.lengthscale = 0.15
model.covar_module.outputscale = 4.0
model.likelihood.noise = 1e-2
model.eval()
# Run the algorithm
X_design = torch.linspace(0, 1, 100)
af_all = maximize(
f,
model,
X_design,
poi,
alpha_params=dict(psi=0.1),
max_it=10,
plot=1
)
Show code cell output
Questions#
Repeat the main algorithm using POI for a \(\psi\) that exploits. Does the method converge?
Repeat the main algorithm using POI for a \(\psi\) that explores. Does the method converge?