Local Latent Bayesian Optimization (LOLBO)

Official implementation of Local Latent Space Bayesian Optimization over Structured Inputs https://arxiv.org/abs/2201.11872

This repository includes base code to run LOLBO, along with full implementation for GuacaMol and Penalized logP Molecular Optimization tasks to replicate results in Figure 1 left and Figure 2 in the original paper. The base code is also set up to allow LOLBO to be run on any other latent space optimization task. Please contact the authors if you need any help with applying the LOLBO to run the other two tasks from the paper (Arithmetic Expressions, DRD3 Receptor Docking Affinity), or any other latent space optimization task.

Weights and Biases (wandb) tracking

This repo it set up to automatically track optimization progress using the Weights and Biases (wandb) API. Wandb stores and updates data during optimization and automatically generates live plots of progress. If you are unfamiliar with wandb, we recommend creating a free account here: https://wandb.ai/site Otherwise, the code can also be run without wandb tracking by simply setting the argument --track_with_wandb False (see example commands below).

Getting Started

Cloning the Repo (Git Lfs)

This repository uses git lfs to store larger data files and model checkpoints. Git lfs must therefore be installed before cloning the repository.

conda install -c conda-forge git-lfs

Environment Setup (Conda)

Follow the steps below to install all dependencies to run LOLBO. Execute in the repository ROOT.

conda env create -f lolbo_env.yml
conda activate lolbo_conda_env1
pip install molsets==0.3.1 --no-deps

The resultant environment will have all imports necessary to run LOLBO on the example GuacaMol and Penalized Log P molecular optimization tasks in this repo.

How to Run LOLBO on Our Example Molecular Optimization Tasks

In this section we provide commands that can be used to start a LOLBO optimization after the environment has been set up.

Args:

To start an molecule optimization run, run scripts/molecule_optimization.py with desired command line arguments. To get a list of command line args specifically for the molecule optimization tasks with the SELFIES VAE, run the following:

cd scripts/

python3 molecule_optimization.py -- --help

For a list of the remaining possible args that are the more general LOLBO args (not specific to molecule tasks) run the following:

cd scripts/

python3 optimize.py -- --help

The above commands will give defaults for each arg and a description of each. The only required argument is --task_id, which is the string id that determines the optimization task.

Task IDs

GuacaMol Task IDs

This code base provides support for the following 12 GuacaMol Optimization Tasks:

task_id	Full Task Name
med1	Median molecules 1
med2	Median molecules 2
pdop	Perindopril MPO
osmb	Osimertinib MPO
adip	Amlodipine MPO
siga	Sitagliptin MPO
zale	Zaleplon MPO
valt	Valsartan SMARTS
dhop	Deco Hop
shop	Scaffold Hop
rano	Ranolazine MPO
fexo	Fexofenadine MPO

The original LOLBO paper features results on zale, pdop, and rano. For descriptions of these and the other GuacaMol objectives listed, as well as a leaderboard for each of these tasks, see https://www.benevolent.com/guacamol

Penalized Log P Task ID

To run on Penalized Log P instead of one of the above GuacaMOl tasks, use the following four-letter task id:

logp --> Penalized Log P

Example Command to Optimize Penalized Log P with LOLBO

(Replicates Result in Figure 1 Left of Paper)

cd scripts/

CUDA_VISIBLE_DEVICES=0 python3 molecule_optimization.py --task_id logp --max_n_oracle_calls 500 --bsz 1 --k 10 - run_lolbo - done 

Command Modified to Run With Weights and Biases (wandb) Tracking

CUDA_VISIBLE_DEVICES=0 python3 molecule_optimization.py --task_id logp --max_n_oracle_calls 500 --bsz 1 --k 10 --track_with_wandb True --wandb_entity $YOUR_WANDB_USERNAME - run_lolbo - done 

Example Command to GuacaMol Objectives with LOLBO

To replicate the result in Figure 2 of the paper, simply run the below command three times - once each with --task_id pdop, --task_id rano, and --task_id zale (modify as above to run with wandb tracking):

cd scripts/

CUDA_VISIBLE_DEVICES=0 python3 molecule_optimization.py --task_id zale --max_string_length 400 --max_n_oracle_calls 120000 --bsz 10 - run_lolbo - done 

How to Run LOLBO on Other Tasks

To run LOLBO on other tasks, you'll need to write two new classes:

1. Objective Class

Create a new child class of LatentSpaceObjective (see lolbo/latent_space_objective.py) which all outlined methods defined.

See example objective class for molecule tasks: lolbo/molecule_objective.py

2. Top Level Optimization Class

Create a new child class of Optimize (see scripts/optimize.py) which defines the two methods specific to the optimization task. The first is the initialize_objective method, which defines the variable self.objective to be an object of the new objective class created in step 1. The second is the load_train_data method which loads in the available training data that will be used to initialize the optimization run.

See example optimization class for molecule tasks: scripts/molecule_optimization.py