| --- |
| language: en |
| tags: |
| - TCM |
| - chinese-medicine |
| - conversational |
| license: apache-2.0 |
| datasets: |
| - ZJUFanLab/TCMChat-dataset-600k |
| model-index: |
| - name: TCMChat-dataset-600k |
| results: [] |
| --- |
| [**中文**](./README_ZH.md) | [**English**](./README.md) |
|
|
| <p align="center" width="100%"> |
| <a href="https://github.com/ZJUFanLab/TCMChat" target="_blank"><img src="./logo.png" alt="TCMChat" style="width: 25%; min-width: 300px; display: block; margin: auto;"></a> |
| </p> |
|
|
| # TCMChat: A Generative Large Language Model for Traditional Chinese Medicine |
|
|
| [](https://github.com/SCIR-HI/Huatuo-Llama-Med-Chinese/blob/main/LICENSE) [](https://www.python.org/downloads/release/python-390/) |
|
|
| ## News |
| [2024-11-1] We have fully open-sourced the model weights and training dataset on Huggingface. |
| [2024-5-17] Open source model weight on HuggingFace. |
|
|
| ## Application |
|
|
| ### Install |
| ```shell |
| git clone https://github.com/ZJUFanLab/TCMChat |
| cd TCMChat |
| ``` |
| Create a conda environment |
| ```shell |
| conda create -n baichuan2 python=3.10 -y |
| ``` |
| First install the dependency package. python environment 3.10+ is recommended. |
|
|
| ```shell |
| pip install -r requirements.txt |
| ``` |
|
|
| ### Weights download |
| - [TCMChat](https://huggingface.co/daiyizheng/TCMChat): QA and recommendation of TCM knowledge based on baichuan2-7B-Chat. |
|
|
| ### Inference |
| #### Command line |
|
|
| ``` |
| python cli_infer.py \ |
| --model_name_or_path /your/model/path \ |
| --model_type chat |
| ``` |
|
|
| #### Web demo |
|
|
| ``` |
| python gradio_demo.py |
| ``` |
|
|
| We provide an online tool：[https://xomics.com.cn/tcmchat](https://xomics.com.cn/tcmchat) |
|
|
|
|
| ### Retrain |
| #### Dataset Download |
|
|
| - [Pretrain dataset](https://huggingface.co/datasets/ZJUFanLab/TCMChat-dataset-600k) |
| - [SFT dataset](https://huggingface.co/datasets/ZJUFanLab/TCMChat-dataset-600k) |
| - [Benchmark dataset](https://github.com/ZJUFanLab/TCMChat/tree/master/evaluation/resources) |
|
|
|
|
| > Note: Before performing pre-training, fine-tuning, and inference, please modify the relevant paths for your model, data, and other related files. |
| #### Pre-training |
|
|
| ```shell |
| ## Slurm cluster |
| sbatch scripts/pretrain/baichuan2_7b_chat.slurm |
| ## or |
| bash scripts/pretrain/baichuan2_7b_chat.sh |
| ``` |
|
|
| #### Fine-tuning |
| ```shell |
| ## Slurm cluster |
| sbatch scripts/sft/baichuan2_7b_chat.slurm |
| ## or |
| bash scripts/sft/baichuan2_7b_chat.sh |
| ``` |
| ### Training details |
|
|
| Please refer to the experimental section of the paper for instructions. |
|
|
|
|
| ### Benchmark evaluation |
|
|
| #### Choice Question |
| ```shell |
| python evaluation/choices_evaluate/eval.py --model_path_or_name /your/model/path --model_name baichuan2-7b-chat --few_shot -sz herb --dev_file_path evaluation/resources/choice/single/tcm-herb_dev.csv --val_file_path evaluation/resources/choice/single/choice_herb_500.csv --log_dir logs/choices |
| ``` |
|
|
| #### Reading Comprehension |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| ##BertScore |
| python evaluation/question_rouge_bleu.py/question_bert_score.py |
| ## BLEU METEOR |
| python evaluation/question_rouge_bleu.py/open_question_bleu.py |
| ## ROUGE-x |
| python evaluation/question_rouge_bleu.py/open_question_rouge.py |
| |
| ``` |
|
|
| #### Entity Extraction |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| |
| python evaluation/ner_evaluate/tcm_entity_recognition.py |
| |
| ``` |
|
|
| #### Medical Case Diagnosis |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| |
| python evaluation/acc_evaluate/extract_syndrome.py |
| |
| ``` |
|
|
| #### Herb or Formula Recommendation |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| |
| python evaluation/recommend_evaluate/mrr_ndcg_p_r.py |
| |
| ``` |
| ### ADMET Prediction |
| #### Regression |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| |
| python evaluation/admet_evaluate/rmse_mae_mse.py |
| |
| ``` |
| #### Classification |
| ```shell |
| python infers/baichuan_infer.py \ |
| --model_name_or_path /your/model/path / \ |
| --model_type chat \ |
| --save_path /your/save/data/path \ |
| --data_path /your/data/path |
| |
| python evaluation/admet_evaluate/acc_recall_f1.py |
| |
| ``` |
