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TCMChat

# TCMChat: A Generative Large Language Model for Traditional Chinese Medicine [![Code License](https://img.shields.io/badge/Code%20License-Apache_2.0-green.svg)](https://github.com/SCIR-HI/Huatuo-Llama-Med-Chinese/blob/main/LICENSE) [![Python 3.10.12](https://img.shields.io/badge/python-3.10.12-blue.svg)](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/daiyizheng/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 ```