Programming Assignment 5: Bayesian Optimization

CS4787 — Principles of Large-Scale Machine Learning — Spring 2021

Project Due: Monday, May 3, 2021 at 11:59pm

Late Policy: Up to two slip days can be used for the final submission.

Please submit all required documents to CMS.

This is a group project. You can either work alone, or work ONLY with the other members of your group, which may contain AT MOST three people in total. Failure to adhere to this rule (by e.g. copying code) may result in an Academic Integrity Violation.

Overview: In this project, you will be learning how to use Bayesian optimization to automatically tune the hyperparameters of a machine learning algorithm. This project involves a combination of the skills you've previously developed from working with TensorFlow and the tehnical skills you've learned in class about Bayesian optimization. Note that while Project 4 explored TensorFlow's high-level support for deep learning with Keras, here we'll see some more low-level aspects of TensorFlow as we use it to compute gradients for the inner optimization problem of Bayesian optimization.

Background: In class, we discussed the Gaussian process prior for Bayesian optimization. The Gaussian process we described in class used a prior that was determined by a kernel, such as the RBF kernel, for which \(K(x, x) = 1\). This implicitly assumes that if we evaluate the objective function multiple times with the same parameters \(x\), then the value will be exactly the same (i.e. the variance of the difference between different evaluations is \(0\)). This also implicitly assumes that for values of \(x\) and \(z\) that are very close together \( K(x, z) \) becomes arbitrarily close to \(1\), and so, the variance of \(f(x) - f(z)\) also becomes small, implying that they are very close together as well. More explicitly, \[ \begin{aligned} \mathbf{E}\left[ \left( f(x) - f(z) \right)^2 \right] &= \mathbf{E}\left[ f(x)^2 \right] - 2 \mathbf{E}\left[ f(x) f(z) \right] + \mathbf{E}\left[ f(z)^2 \right] \\ &= K(x, x) - 2 K(x, z) + K(z, z) \\ &= 2 - 2 K(x,z) \\ &= 2 - 2 \cdot \exp\left( -\gamma \| x - z \|^2 \right) \end{aligned} \] which comes arbitrarily close to zero as \( x \) approaches \( z \). But for a randomized process like training a ML model, this is not necessarily the case, and the objective measurements \(f(x)\) can be noisy or discontinuous (which is particularly the case for metrics like error that take on discrete values). To better handle this situation, it is common to model the observations of the objective \(f(x)\) as noisy with some noise parameter \(\sigma^2\): this is discussed in more detail in the "Additive Gaussian Noise" section of this old CS4780 lecture on Gaussian processes. Using this noisy observations assumption, the predicted value of the objective observation at a test point \(x_*\) is \[ f(x_*) \sim \mathcal{N}(\mathbf{k}_*^T (\Sigma + \sigma^2 I)^{-1} y, K(x_*, x_*) + \sigma^2 - \mathbf{k}_*^T (\Sigma + \sigma^2 I)^{-1} \mathbf{k}_*). \] Using this assumption can improve the behavior of Bayesian optimization by making the matrix inverses in this expression better-behaved (since nothing ensures that \(\Sigma\) is invertible but \(\Sigma + \sigma^2 I\) certainly will be if \(\sigma^2 > 0\)). So we will be using this formulation with a nonzero \(\sigma^2\) in this assignment.

There are many ways to solve the inner optimization problem to choose the next point \(x_*\) at which we are going to evaluate the objective. In this assignment, we are going to the following a simple heuristic. First, choose a random starting point from some distribution and run gradient descent with a fixed learning rate for some fixed number of steps. Then choose another random starting point and repeat some number of times. Finally, return the parameter vector \(x_*\) that has the smallest value for the acquisition function among all the parameter values arrived at at the end of gradient descent.

Please do not wait until the last minute to do this assignment! Just as in Programming Assignment 4, actually training the models that we will be exploring can take some time, depending on the machine you run on.

Instructions: This project is split into three parts: the implementation of Bayesian optimization for general objective functions, the exploration of its performance for a synthetic objective function, and the investigation of how Bayesian optimization can be used to automatically set the hyperparameters of models you've previously explored.

Part 1: Bayesian Optimization.

  1. Implement a function rbf_kernel_matrix that computes a Gaussian RBF kernel matrix. The function should take in two matrix inputs \( X \in \mathbb{R}^{d \times m} \) and \( Z \in \mathbb{R}^{d \times n} \) and one scalar input \( \gamma \in \mathbb{R} \), and it should return a matrix \( \Sigma \in \mathbb{R}^{m \times n} \) such that \( \Sigma_{ij} = K(X_i, Z_j) = \exp(-\gamma \cdot \| X_i - Z_j \|^2 ) \) where \( X_i \) denotes the \(i\)th column of \( X \) and similarly for \( Z_j \).
  2. Now implement a function gp_prediction that computes the distribution predicted by the Gaussian process using an RBF kernel. This function should take as input the observations you've already made, the parameter \(\gamma\) of the RBF kernel, the parameter \(\sigma^2\) of the noise as described above, and the point \(x_*\) at which we want to make a prediction. Importantly, we will want to make predictions for many different points \(x_*\), and there is a lot of computation (e.g. the forming of the covariance matrix \(\Sigma\)) that be shared among these many predictions. To enable this sharing, your function gp_prediction should use currying in the sense that it takes as input the observations already made and the kernel parameters \(\gamma\) and \(\sigma^2\), performs any precomputation that is necessary on those parameters, and then returns a second function that takes as input \(x_*\) and returns the prediction made by the GP.
  3. Now implement the three acquisition functions we discussed in class.
  4. Finally, implement a function bayes_opt that runs the Bayesian optimization algorithm. This function should take as input You may find the provided gradient_descent function helpful for evaluating the inner minimization problem.

Part 2: Evaluating Bayesian Optimization on a Synthetic Objective.

  1. To get a sense of how your method performs, run Bayesian optimization on the provided one-dimensional synthetic objective test_objective \[ f(x) = \cos(8x) - 0.3 + (x - 0.5)^2. \] Use the following parameters: Run Bayesian optimization for each of the three acquisition functions you wrote. For the lower confidence bound acquisition function, use parameter \(\kappa = 2\). Report the best parameter value and objective value returned by Bayesian optimization for each acquisition function.
  2. For at least one of your acquisition functions, use the provided animate_predictions function to visualize what your Gaussian process is predicting at each step of Bayesian optimization. (If you are running on the VM, you may need to install the library ffmpeg by running sudo apt-get update and sudo apt-get install ffmpeg to get this to work.) This function should take in the outputs of your Bayesian optimization function, and generate an animation. Here's an example of the output of this function, plotted for the PI acquisition function.

    In this video, the blue curve represents the true objective function, the red curve represents the mean predicted by Bayesian optimization, the light blue region is a \(2\sigma\)-confidence interval about the mean, and the blue dots are the parameters explored by Bayesian optimization. Briefly report what you observed in this video, and include the video in your submission. (Warning: the video may take some time to render, so start early!)
  3. Now explore how the performance of Bayesian optimization changes as we change the kernel hyperparameter \(\gamma\). Choose one of your three aquisition functions, and observe how the loss changes when \(\gamma\) is changed to values that are much larger or much smaller. Report your conclusions, and justify them by reporting your observations for at least two runs of Bayesian optimization, one with a larger value of \(\gamma\) and one with a smaller value of \(\gamma\).
  4. Now explore how the performance of Bayesian optimization changes as we change the LCB hyperparameter \(\kappa\). Using the LCB aquisition function, observe how the loss changes when \(\kappa\) is changed to values that are much larger or much smaller. Report your conclusions, and justify them by reporting your observations for at least two runs of Bayesian optimization, one with a larger value of \(\kappa\) and one with a smaller value of \(\kappa\).

Part 3: Bayesian Optimization for Learning Hyperparameters.

  1. Now, let's use Bayesian optimization to optimize the hyperparameters for a machine learning task from a previous assignment. Specifically, we're going to look at stochastic gradient descent with minibatching, sequential sampling, and momentum on MNIST, which you explored in Programming Assignment 3. For this assignment, we'll need a validation set, so the provided load_MNIST_dataset_with_validation_split splits the MNIST training set into a new training set of 50000 examples and a validation set of 10000 examples. The hyperparameters we want to set are \(\alpha\), the learning rate, \(\beta\), the momentum parameter, and \(\gamma\), the \(\ell_2\)-regularization constant (not to be confused with the RBF kernel hyperparameter). Since these hyperparameters are all of different scales, we need to rescale them somehow to be on a similar scale. When you're using Bayesian optimization in practice, this is something that you'll need to do based on your intuition about the problem, but for this assignment I've suggested the following parameterization. Let \(x \in \mathbb{R}^3\) be the parameter optimized by Bayesian optimization, and define \[ \gamma = 10^{-8 \cdot x_1}, \; \alpha = 0.5 \cdot x_2, \; \beta = x_3. \] This scales all the parameters such that randomly sampling each coordinate of \(x\) from \([0,1]\) will result in a reasonable setting of the hyperparameters. Implement the function mnist_sgd_mss_with_momentum, which provides an objective function for Bayesian optimization. Specifically, this function trains the classifier using SGD+Momentum with the specified parameters, and then returns the validation error minus \(0.9\). (This is the validation error minus what we expect the validation error would be for random guessing).
  2. Run Bayesian optimization on your objective, using the following parameters:
  3. Report the validation error and test error that result from the best set of hyperparameters returned from Bayesian optimization. This should be your only use of the MNIST test set in this assignment. How does the performance of Bayesian optimization compare to the performance of the other hyperparameter optimization methods you tried in Programming Assignment 3? Briefly explain.
  4. Now design and perform some experiment to measure the fraction of overall wall clock time in your program that is spent on the evaluation of the objective function mnist_sgd_mss_with_momentum (as opposed to the other computations internal to Bayesian optimization). Report your methodology, your observations, and your conclusions about what the fraction is. What does this say about the overhead of Bayesian optimization for this task?

What to submit:

  1. An implementation of the functions in
  2. A lab report containing:
  3. The video you produced in Part 2.2.


  1. Run pip3 install -r requirements.txt to install the required python packages