morgancthomas/mol_opt

mol_opt: A Benchmark for Practical Molecular Optimization

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This repository hosts an open-source benchmark for Practical Molecular Optimization (PMO), to facilitate the transparent and reproducible evaluation of algorithmic advances in molecular optimization. This repository supports 25 molecular design algorithms on 23 tasks with a particular focus on sample efficiency (oracle calls). The preprint version of the paper is available at https://arxiv.org/pdf/2206.12411.pdf

Installation

conda create -n molopt python=3.7
conda activate molopt 
pip install torch 
pip install PyTDC 
pip install PyYAML
conda install -c rdkit rdkit 
pip install wandb   
wandb login  ### user need to register wandb

We recommend to use PyTorch 1.10.2 and PyTDC 0.3.6.

Then we can activate conda via following command.

conda activate molopt 

29 Methods

Based the ML methodologies, all the methods are categorized into:

• virtual screening
  • screening randomly search ZINC database.
  • molpal uses molecular property predictor to prioritize the high-scored molecules.
• GA (genetic algorithm)
  • graph_ga based on molecular graph.
  • smiles_ga based on SMILES
  • selfies_ga based on SELFIES
  • stoned based on SELFIES
  • synnet based on synthesis
• VAE (variational auto-encoder)
  • smiles_vae based on SMILES
  • selfies_vae based on SELFIES
  • jt_vae based on junction tree (fragment as building block)
  • dog_ae based on synthesis
• BO (Bayesian optimization)
  • gpbo
• RL (reinforcement learning)
  • reinvent
  • reinvent_selfies
  • graphinvent
  • moldqn
  • smiles_aug_mem
  • smiles_bar
• HC (hill climbing)
  • smiles_lstm_hc is SMILES-level HC.
  • smiles_ahc is SMILES-level augmented HC.
  • selfies_lstm_hc is SELFIES-level HC
  • mimosa is graph-level HC
  • dog_gen is synthesis based HC
• gradient (gradient ascent)
  • dst is based molecular graph.
  • pasithea is based on SELFIES.
• SBM (score-based modeling)
  • gflownet
  • gflownet_al
  • mars

time is the average rough clock time for a single run in our benchmark and do not involve the time for pretraining and data preprocess. We have processed the data, pretrained the model. Both are available in the repository.

	assembly	additional package	time	requires_gpu
screening	-	-	2 min	no
molpal	-	ray, tensorflow, ConfigArgParse, pytorch-lightning	1 hour	no
graph_ga	fragment	joblib	3 min	no
smiles_ga	SMILES	joblib, nltk	2 min	no
stoned	SELFIES	-	3 min	no
selfies_ga	SELFIES	selfies	20 min	no
graph_mcts	atom	-	2 min	no
smiles_lstm_hc	SMILES	guacamol	4 min	no
smiles_ahc	SMILES		4 min	no
selfies_lstm_hc	SELFIES	guacamol, selfies	4 min	yes
smiles_vae	SMILES	botorch	20 min	yes
selfies_vae	SELFIES	botorch, selfies	20 min	yes
jt_vae	fragment	botorch	20 min	yes
gpbo	fragment	botorch, networkx	15 min	no
reinvent	SMILES	pexpect, bokeh	2 min	yes
reinvent_selfies	SELFIES	selfies, pexpect, bokeh	3 min	yes
smiles_aug_mem	SMILES	reinvent-models==0.0.15rc1	2 min	yes
smiles_bar	SMILES	reinvent-models==0.0.15rc1	2 min	yes
reinvent_selfies	SELFIES	selfies	3 min	yes
moldqn	atom	networks, requests	60 min	yes
mimosa	fragment	-	10 min	yes
mars	fragment	chemprop, networkx, dgl	20 min	yes
dog_gen	synthesis	extra conda	120 min	yes
dog_ae	synthesis	extra conda	50 min	yes
synnet	synthesis	dgl, pytorch_lightning, networkx, matplotlib	2-5 hours	yes
pasithea	SELFIES	selfies, matplotlib	50 min	yes
dst	fragment	-	120 min	no
gflownet	fragment	torch_{geometric,sparse,cluster}, pdb	30 min	yes
gflownet_al	fragment	torch_{geometric,sparse,cluster}, pdb	30 min	yes

Run with one-line code

There are three types of runs defined in our code base:

• simple: A single run for testing purposes for each oracle, is the defualt.
• production: Multiple independent runs with various random seeds for each oracle.
• tune: A hyper-parameter tuning over the search space defined in main/MODEL_NAME/hparam_tune.yaml for each oracle.

## run a single test run on qed with wandb logging online
python run.py MODEL_NAME --wandb online
## specify multiple random seeds 
python run.py MODEL_NAME --seed 0 1 2 
## run 5 runs with different random seeds with specific oracle with wandb logging offline
python run.py MODEL_NAME --task production --n_runs 5 --oracles qed 
## run a hyper-parameter tuning starting from smiles in a smi_file, 30 runs in total without wandb logging
python run.py MODEL_NAME --task tune --n_runs 30 --smi_file XX --wandb disabled --other_args XX 

MODEL_NAME are listed in the table above.

Multi-Objective Optimization

Multi-objective optimization is implemented in multiobjective branch. We use "+" to connect multiple properties, please see the command line below.

python run.py MODEL_NAME --oracles qed+jnk3  

Hyperparameters

We separate hyperparameters for task-level control, defined from argparse, and algorithm-level control, defined from hparam_default.yaml. There is no clear boundary for them, but we recommend one keep all hyperparameters in the self._optimize function as task-level.

• running hyperparameter: parser argument.
• default model hyperparameter: hparam_default.yaml
• tuning model hyperparameter: hparam_tune.yaml

For algorithm-level hyperparameters, we adopt the stratforward yaml file format. One should define a default set of hyper-parameters in main/MODEL_NAME/hparam_default.yaml:

population_size: 50
offspring_size: 100
mutation_rate: 0.02
patience: 5
max_generations: 1000

And the search space for hyper-parameter tuning in main/MODEL_NAME/hparam_tune.yaml:

name: graph_ga
method: random
metric:
  goal: maximize
  name: avg_top100
parameters:
  population_size:
    values: [20, 40, 50, 60, 80, 100, 150, 200]
  offspring_size:
    values: [50, 100, 200, 300]
  mutation_rate:
    distribution: uniform
    min: 0
    max: 0.1
  patience:
    value: 5
  max_generations:
    value: 1000

We use the sweep function in wandb for a convenient visualization. The yaml file should follow the format as above. Further detail is in this instruction.

Contribute

Our repository is an open-source initiative. To update a better set of parameters or incldue your model in out benchmark, check our Contribution Guidelines!