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GuacaMol Baselines

A series of baseline model implementations for the guacamol benchmark for generative chemistry.
A more in depth explanation of the benchmarks and scores for these baselines is can be found in our paper.

Dependencies

To install all dependencies:

pip install -r requirements.txt

We also provide a Dockerfile which containerizes baselines from this repo. This may be a useful start point when implementing your own generative models.

docker build -f dockers/Dockerfile . -t guacamol-baselines

Dataset

Some baselines require the guacamol dataset to run, to get it run:

bash fetch_guacamol_dataset.sh

Random Sampler

Dummy baseline, always returning random molecules form the guacamol training set.

To execute the goal-directed generation benchmarks:

python -m random_smiles_sampler.goal_directed_generation

To execute the distribution learning benchmarks:

python -m random_smiles_sampler.distribution_learning

Best from ChEMBL

Dummy baseline that simply returns the molecules from the guacamol training set that best satisfy the score of a goal-directed benchmark.
There is no model nor training, its only purpose is to establish a lower bound on the benchmark scores.

To execute the goal-directed generation benchmarks:

python -m best_from_chembl.goal_directed_generation

No distribution learning benchmark available.

SMILES GA

Genetic algorithm on SMILES as described in: https://www.journal.csj.jp/doi/10.1246/cl.180665

Implementation adapted from: https://github.com/tsudalab/ChemGE

To execute the goal-directed generation benchmarks:

python -m smiles_ga.goal_directed_generation

No distribution learning benchmark available.

Graph GA

Genetic algoritm on molecule graphs as described in: https://doi.org/10.26434/chemrxiv.7240751

Implementation adapted from: https://github.com/jensengroup/GB-GA

To execute the goal-directed generation benchmarks:

python -m graph_ga.goal_directed_generation

No distribution learning benchmark available.

Graph MCTS

Monte Carlo Tree Search on molecule graphs as described in: https://doi.org/10.26434/chemrxiv.7240751

Implementation adapted from: https://github.com/jensengroup/GB-GB

To execute the goal-directed generation benchmarks:

python -m graph_mcts.goal_directed_generation

To execute the distribution learning benchmarks:

python -m graph_mcts.distribution_learning

To re-generate the distribution statistics as pickle files:

python -m graph_mcts.analyze_dataset

SMILES LSTM Hill Climbing

Long-short term memory on SMILES as described in: https://arxiv.org/abs/1701.01329

This implementation optimizes using hill climbing algorithm.

Implementation by BenevolentAI

A pre-trained model is provided in: smiles_lstm/pretrained_model

To execute the goal-directed generation benchmarks:

python -m smiles_lstm_hc.goal_directed_generation

To execute the distribution learning benchmark:

python -m smiles_lstm_hc.distribution_learning

To train a model from scratch:

python -m smiles_lstm_hc.train_smiles_lstm_model

SMILES LSTM PPO

Long-short term memory on SMILES as described in: https://arxiv.org/abs/1701.01329

This implementation optimizes using proximal policy optimization algorithm.

Implementation by BenevolentAI

A pre-trained model is provided in: smiles_lstm/pretrained_model

To execute the goal-directed generation benchmarks:

python -m smiles_lstm_ppo.goal_directed_generation

Frag GT

Fragment-based evolutionary algorithm for generating molecules.

See frag-gt readme for install instructions and description.

Implementation by BenevolentAI

Pre-computed fragment libraries are available from Zenodo (https://zenodo.org/record/6038464)

To execute the goal-directed generation benchmarks:

python frag_gt/goal_directed_generation.py --fragstore_path frag_gt/data/fragment_libraries/guacamol_v1_all_fragstore_brics.pkl --smiles_file data/guacamol_v1_all.smiles

Change log

  • 15 Oct 2020: upgrade guacamol version to 0.5.3
  • 10 Nov 2021: upgrade guacamol version to 0.5.4. Migrate RDKit install conda->pip. Update dependencies.
  • 21 Feb 2022: addition of frag-gt baseline.