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https://github.com/hicai-zju/kano-mindspore

MindSpore implementation for paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt"
https://github.com/hicai-zju/kano-mindspore

graph-neural-networks knowledge-graph mindspore molecule pretrained-models

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MindSpore implementation for paper "Knowledge graph-enhanced molecular contrastive learning with functional prompt"

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# Knowledge graph-enhanced molecular contrastive learning with functional prompt



This repository is the official [**MindSpore**](https://www.mindspore.cn/) implementation of **KANO**, which is model proposed in a paper: [**Knowledge graph-enhanced molecular contrastive learning with functional prompt**](https://www.nature.com/articles/s42256-023-00654-0). 



# Brief introduction

We propose a **K**nowledge graph-enhanced molecular contr**A**stive learning with fu**N**ctional pr**O**mpt (**KANO**), exploiting fundamental domain knowledge in both pre-training and fine-tuning.



## 🤖 Model



**Firstly**, we construct a Chemical Element Knowledge Graph (ElementKG) based on the Periodic Table and Wikipedia pages to summarize the class hierarchy, relations and chemical attributes of elements and functional groups. 



**Second**, we propose an element-guided graph augmentation in contrastive-based pre-training to capture deeper associations inside molecular graphs. 



**Third**, to bridge the gap between the pre-training contrastive tasks and downstream molecular property prediction tasks, we propose functional prompts to evoke the downstream task-related knowledge acquired by the pre-trained model.










# 🔬 Requirements



To run our code, please install dependency packages.

```

python          3.7

mindpore        2.0.0

rdkit           2018.09.3

numpy           1.20.3

gensim          4.2.0

nltk            3.4.5

owl2vec-star    0.2.1

Owlready2       0.37

```



# 📚 Overview



This project mainly contains the following parts.



```

├── chemprop_ms                     # molecular graph preprocessing, data splitting, loss function and graph encoder

├── data                            # sore the molecular datasets for pre-training and fine-tuning

│   ├── bace.csv                    # downstream dataset BACE

│   ├── bbbp.csv                    # downstream dataset BBBP

│   ├── clintox.csv                 # downstream dataset ClinTox

│   ├── esol.csv                    # downstream dataset ESOL

│   ├── freesolv.csv                # downstream dataset FreeSolv

│   ├── hiv.csv                     # downstream dataset HIV

│   ├── lipo.csv                    # downstream dataset Lipophilicity

│   ├── muv.csv                     # downstream dataset MUV

│   ├── qm7.csv                     # downstream dataset QM7

│   ├── qm8.csv                     # downstream dataset QM8

│   ├── qm9.csv                     # downstream dataset QM9

│   ├── sider.csv                   # downstream dataset SIDER

│   ├── tox21.csv                   # downstream dataset Tox21

│   ├── toxcast.csv                 # downstream dataset ToxCast

│   └── zinc15_250K.csv             # pre-train dataset ZINC250K

├── ckpt                            # store the checkpoints of the model 

├── finetune.sh                     # conduct fine-tuning

├── initial                         # store the embeddings of ElementKG, and preprocess it for the model

├── KGembedding                     # store ElementKG, and get the embeddings of eneities and relations in ElementKG

├── pretrain.py                     # conduct pre-training

└── train.py                        # training code for fine-tuning



```



# 🚀 Quick start



| Parameter | Description | Default Value |

| --- | --- | --- |

| data_path | Path to downstream tasks data files (.csv) | None |

| metric | Metric to use during evaluation. | Defaults to "auc" for classification and "rmse" for regression. |

| dataset_type | Type of dataset, e.g. classification or regression, this determines the loss function used during training. | 'regression' |

| epochs | Number of epochs to run | 30 |

| num_folds | Number of folds when performing cross validation | 1 |

| gpu | Which GPU to use | None |

| batch_size | Batch size | 50 |

| seed | Random seed to use when splitting data into train/val/test sets. When `num_folds` > 1, the first fold uses this seed and all subsequent folds add 1 to the seed. | 1 |

| init_lr | Initial learning rate | 1e-4 |

| split_type | Method of splitting the data into train/val/test (random/ scaffold splitting/ cluster splitting) | 'random' |

| step | Training phases (pre-training, fine-tuning with functional prompts or with other architectures) | 'functional_prompt' |

| exp_name | Experiment name | None |

| exp_id | Experiment ID | None |

| checkpoint_path | Path to pre-trained model checkpoint (.pt file) | None |



Note that if you change the `data_path`, don't forget to change the corresponding `metric`, `dataset_type` and `split_type`! For example:

```sh

>> python run_train.py \

    --data_path ./data/qm7.csv \

    --metric 'mae' \

    --dataset_type regression \

    --epochs 100 \

    --num_folds 20 \

    --gpu 1 \

    --batch_size 256 \

    --seed 43 \

    --init_lr 1e-4  \

    --split_type 'scaffold_balanced' \

    --step 'functional_prompt' \

    --exp_name finetune \

    --exp_id qm7 \

    --checkpoint_path "./ckpt/model_original37.ckpt"

```



# ⚙ Step-by-step guidelines



### ElementKG and its embedding

ElementKG is stored in [`KGembedding/elementkg.owl`](KGembedding/elementkg.owl). If you want to train the model yourself to obtain the embeddings of eneities and relations in ElementKG, please run `$ python run.py`. This may take a few minutes to complete. For your convenience, we provide the trained representaions, stored in [`initial/elementkgontology.embeddings.txt`](initial/elementkgontology.embeddings.txt)



After obtaining the embeddings of ElementKG, we need to preprocess it in order to utilize it in pre-training. Please excute `cd KANO/initial` and run `$ python get_dict.py` to get the processed file. Of course, we also provide processed files in [`initial`](initial), so that you can directly proceed to the next step.



### Contrastive-based pre-training

We collect 250K unlabeled molecules sampled from the ZINC 15 datasets to pre-train KANO. The pre-training data can be found in [`data/zinc15_250K.csv`](data/zinc15_250K.csv). If you want to pre-train the model with the pre-training data, please run:



```sh

>> python pretrain.py --exp_name 'pre-train' --exp_id 1 --step pretrain

```



| Parameter | Description | Default Value |

| --- | --- | --- |

| data_path | Path to pre-training data files (.csv) | None |

| epochs | Number of epochs to run | 30 |

| gpu | Which GPU to use | None |

| batch_size | Batch size | 50 |



You can change these parameters directly in `pretrain.py`. In our setting, we set `epochs` and `batch_size` to `50` and `1024`, respectively. We also provided pre-trained models, which you can download from [`ckpt/model_original37.ckpt`](ckpt/model_original37.ckpt). 



### Prompt-enhanced fine-tuning



The operational details of this part are the same as the section **Quick start**.



# 💡 Other functions



We also provide other options in this code repository.



### Cluster splitting

Our code supports using cluster splitting to split downstream datasets, as detailed in the paper. You can set the``split_type`` parameter to ``cluster_balanced`` to perform cluster splitting.



### Other ways to incorporate functional group knowledge

Besides functional prompts, we also support testing other ways of incorporating functional group knowledge. By setting the ``step`` parameter to ``finetune_add`` or ``finetune_concat``, you achieve adding or concatenating functional group knowledge with the original molecular representation, respectively.



### Conducting experiments on a specified dataset

We also support specifying a dataset as the input for the train/val/test sets by setting the parameters ``data_path``, ``separate_test_path`` and ``separate_val_path`` to the location of the specified train/val/test data.



# 🫱🏻‍🫲🏾 Acknowledgements

Thanks for the following released code bases:

>[chemprop](https://github.com/chemprop/chemprop), [torchlight](https://github.com/RamonYeung/torchlight), [RDKit](https://github.com/rdkit/rdkit), [KCL](https://github.com/ZJU-Fangyin/KCL), [KANO](https://github.com/HICAI-ZJU/KANO)



# References

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



```bibtex

@article{fang2023knowledge,

  title={Knowledge graph-enhanced molecular contrastive learning with functional prompt},

  author={Fang, Yin and Zhang, Qiang and Zhang, Ningyu and Chen, Zhuo and Zhuang, Xiang and Shao, Xin and Fan, Xiaohui and Chen, Huajun},

  journal={Nature Machine Intelligence},

  pages={1--12},

  year={2023},

  publisher={Nature Publishing Group UK London}

}

```