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TCMChat: A Generative Large Language Model for Traditional Chinese Medicine
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
git clone https://github.com/ZJUFanLab/TCMChat
cd TCMChat
Create a conda environment
conda create -n baichuan2 python=3.10 -y
First install the dependency package. python environment 3.10+ is recommended.
pip install -r requirements.txt
Weights download
- 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
Retrain
Dataset Download
Note: Before performing pre-training, fine-tuning, and inference, please modify the relevant paths for your model, data, and other related files.
Pre-training
## Slurm cluster
sbatch scripts/pretrain/baichuan2_7b_chat.slurm
## or
bash scripts/pretrain/baichuan2_7b_chat.sh
Fine-tuning
## 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
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
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
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
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
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
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
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
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