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⚗️ MolGen

Domain-Agnostic Molecular Generation with Chemical Feedback

📃 Paper • 🤗 Model • 🔬 Space

Pytorch license

🔔 News

📕 Requirements

To run the codes, You can configure dependencies by restoring our environment:

conda env create -f MolGen/environment.yml -n $Your_env_name$

and then:

conda activate $Your_env_name$

📚 Resource Download

You can download the pre-trained and fine-tuned models via Huggingface: MolGen-large and MolGen-large-opt.

Moreover, the dataset used for downstream tasks can be found here.

The expected structure of files is:

moldata
├── checkpoint 
│   ├── molgen.pkl              # pre-trained model
│   ├── syn_qed_model.pkl       # fine-tuned model for QED optimization on synthetic data
│   ├── syn_plogp_model.pkl     # fine-tuned model for p-logP optimization on synthetic data
│   ├── np_qed_model.pkl        # fine-tuned model for QED optimization on natural product data
│   ├── np_plogp_model.pkl      # fine-tuned model for p-logP optimization on natural product data
├── finetune
│   ├── np_test.csv             # nature product test data
│   ├── np_train.csv            # nature product train data
│   ├── plogp_test.csv          # synthetic test data for plogp optimization
│   ├── qed_test.csv            # synthetic test data for plogp optimization
│   └── zinc250k.csv            # synthetic train data
├── generate                    # generate molecules
├── output                      # molecule candidates
└── vocab_list
    └── zinc.npy                # SELFIES alphabet

🚀 How to run

  • Fine-tune

    • First, preprocess the finetuning dataset by generating candidate molecules using our pre-trained model. The preprocessed data will be stored in the folder output.
        cd MolGen
        bash preprocess.sh
    • Then utilize the self-feedback paradigm. The fine-tuned model will be stored in the folder checkpoint.
        bash finetune.sh
  • Generate

    To generate molecules, run this script. Please specify the checkpoint_path to determine whether to use the pre-trained model or the fine-tuned model.

    cd MolGen
    bash generate.sh

🥽 Experiments

We conduct experiments on well-known benchmarks to confirm MolGen's optimization capabilities, encompassing penalized logP, QED, and molecular docking properties. For detailed experimental settings and analysis, please refer to our paper.

  • MolGen captures real-word molecular distributions

image
  • MolGen mitigates molecular hallucinations

Targeted molecule discovery

image image image

Constrained molecular optimization

image

Citation

If you use or extend our work, please cite the paper as follows:

@inproceedings{fang2023domain,
  author       = {Yin Fang and
                  Ningyu Zhang and
                  Zhuo Chen and
                  Xiaohui Fan and
                  Huajun Chen},
  title        = {Domain-Agnostic Molecular Generation with Chemical feedback},
  booktitle    = {{ICLR}},
  publisher    = {OpenReview.net},
  year         = {2024},
  url          = {https://openreview.net/pdf?id=9rPyHyjfwP}
}

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