Bayesian optimization for guided chemical design

Notebooks and scripts to support the materials delivered at the Sargent Centre for Process Systems Engineering 2024 BO Summer School and the 2024 AIchemy BO for Chemistry workshop.

overview • installation instructions • case study descriptions • additional resources •

overview

This repo contains tutorial notebooks featuring BO for two chemical tasks. We explore implementing BO using several available packages, including BayBE, BOFire, and BOTorch.

installation instructions

We encourage you to take advantage of Google colab to run the tutorial notebooks included in this repository. Should you wish to run them locally, please follow the installation instructions below:

foo@bar:~$ git clone https://github.com/austin-mroz/2024-BO-summer-school
foo@bar:~$ cd 2024-BO-summer-school
foo@bar:~$ conda env create -p ./.venv -f environment.yml
foo@bar:~$ conda activate ./.venv

case study descriptions

catalysis

To help you get familiar with all that Web-BO has to offer, we provide an optimization case study that takes advantage of existing reaction emulators to acquire the experimental measurements.

This case study concerns optimizing the coupling of 3-bromoquinoline with 3,5-dimethylisoxazole-4-boronic acid pinacol ester in the presence of 1,8-diazobicyclo[5.4.0]undec-7-ene (DBU) and THF/water, Figure 1.

Figure 1. Suzuki-Miyaura cross-coupling reaction involved in this case study.

The parameter space involved in this optimisation task is detailed in Figure 2.

Figure 2. Parameter space spanned by this case study includes 3 continuous variables (catalyst loading, temperature, and residence time) and 1 categorical variable (catalyst).

The catalyst options are presented in Figure 3.

Figure 3. The catalyst options included in this study.

This case study takes advantage of the experiment emulators offered by the Summit package. Specifically, the Suzuki-Miyaura Cross Coupling Emulator.

covalent-organic framework design

additional resources

There are a wealth of additional tutorials on the general BO framework, as well as materials specifically featuring BO for chemical tasks. (This is not an exhaustive list)

general BO tutorials and notebooks

• GPs hands-on code tutorial

chemistry-specific tutorials and examples

GAUCHE tutorials

• Bayesian Optimisation Over Molecules
• Multioutput Gaussian Processes for Multitask Learning

BO for COFs

• BO for COFs
• MFBO for COFs