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README.md

@@ -1,47 +1,157 @@
 ---
-license: Apache License 2.0
+license: apache-2.0
-
-#model-type:
-##如 gpt、phi、llama、chatglm、baichuan 等
-#- gpt
-
-#domain:
-##如 nlp、cv、audio、multi-modal
-#- nlp
-
-#language:
-##语言代码列表 https://help.aliyun.com/document_detail/215387.html?spm=a2c4g.11186623.0.0.9f8d7467kni6Aa
-#- cn 
-
-#metrics:
-##如 CIDEr、Blue、ROUGE 等
-#- CIDEr
-
-#tags:
-##各种自定义，包括 pretrained、fine-tuned、instruction-tuned、RL-tuned 等训练方法和其他
-#- pretrained
-
-#tools:
-##如 vllm、fastchat、llamacpp、AdaSeq 等
-#- vllm
 ---
-### 当前模型的贡献者未提供更加详细的模型介绍。模型文件和权重，可浏览“模型文件”页面获取。
+# Multilingual Medicine: Model, Dataset, Benchmark, Code
-#### 您可以通过如下git clone命令，或者ModelScope SDK来下载模型
 
-SDK下载
+Covering English, Chinese, French, Hindi, Spanish, Hindi, Arabic So far
-```bash
+
-#安装ModelScope
+
-pip install modelscope
+<p align="center">
+   👨🏻‍💻<a href="https://github.com/FreedomIntelligence/Apollo" target="_blank">Github</a> •📃 <a href="https://arxiv.org/abs/2403.03640" target="_blank">Paper</a> • 🌐 <a href="https://apollo.llmzoo.com/" target="_blank">Demo</a> • 🤗 <a href="https://huggingface.co/datasets/FreedomIntelligence/ApolloCorpus" target="_blank">ApolloCorpus</a> • 🤗 <a href="https://huggingface.co/datasets/FreedomIntelligence/XMedbench" target="_blank">XMedBench</a> 
+   <br>  <a href="./README_zh.md"> 中文 </a> | <a href="./README.md"> English
+</p>
+
+![Apollo](assets/apollo_medium_final.png)
+
+## 🌈 Update
+
+* **[2024.04.25]** [MedJamba](https://huggingface.co/FreedomIntelligence/Apollo-MedJamba) released, train and evaluation code refer to [repo](https://github.com/FreedomIntelligence/MedJamba).
+* **[2024.03.07]** [Paper](https://arxiv.org/abs/2403.03640) released.
+* **[2024.02.12]** <a href="https://huggingface.co/datasets/FreedomIntelligence/ApolloCorpus" target="_blank">ApolloCorpus</a> and  <a href="https://huggingface.co/datasets/FreedomIntelligence/XMedbench" target="_blank">XMedBench</a>  is published！🎉
+* **[2024.01.23]** Apollo repo is published！🎉
+
+
+## Results
+   🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-0.5B" target="_blank">Apollo-0.5B</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-1.8B" target="_blank">Apollo-1.8B</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-2B" target="_blank">Apollo-2B</a>  • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-6B" target="_blank">Apollo-6B</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-7B" target="_blank">Apollo-7B</a>  • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-34B" target="_blank">Apollo-34B</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-72B" target="_blank">Apollo-72B</a>  
+   
+   🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-MedJamba" target="_blank">MedJamba</a>
+
+   🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-0.5B-GGUF" target="_blank">Apollo-0.5B-GGUF</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-2B-GGUF" target="_blank">Apollo-2B-GGUF</a>  • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-6B-GGUF" target="_blank">Apollo-6B-GGUF</a> • 🤗 <a href="https://huggingface.co/FreedomIntelligence/Apollo-7B-GGUF" target="_blank">Apollo-7B-GGUF</a> 
+   
+   
+   
+   ![Apollo](assets/result.png)
+      
+
+## Usage Format
+
+User:{query}\nAssistant:{response}<|endoftext|>
+
+
+## Dataset & Evaluation
+
+- Dataset
+  🤗 <a href="https://huggingface.co/datasets/FreedomIntelligence/ApolloCorpus" target="_blank">ApolloCorpus</a>
+  
+  <details><summary>Click to expand</summary>
+
+    ![Apollo](assets/dataset.png)
+
+    - [Zip File](https://huggingface.co/datasets/FreedomIntelligence/ApolloCorpus/blob/main/ApolloCorpus.zip)
+    - [Data category](https://huggingface.co/datasets/FreedomIntelligence/ApolloCorpus/tree/main/train)
+       - Pretrain:
+         - data item:
+            - json_name: {data_source}_{language}_{data_type}.json
+            - data_type: medicalBook, medicalGuideline, medicalPaper, medicalWeb(from online forum), medicalWiki
+            - language: en(English), zh(chinese), es(spanish), fr(french), hi(Hindi)
+            - data_type: qa(generated qa from text)
+            - data_type==text: list of string
               ```
-```python
+              [
-#SDK模型下载
+                "string1",
-from modelscope import snapshot_download
+                "string2",
-model_dir = snapshot_download('FreedomIntelligence/Apollo-0.5B')
+                ...
+              ]
               ```
-Git下载
+            - data_type==qa: list of qa pairs(list of string)
               ```
-#Git模型下载
+              [
-git clone https://www.modelscope.cn/FreedomIntelligence/Apollo-0.5B.git
+                [
+                  "q1",
+                  "a1",
+                  "q2",
+                  "a2",
+                  ...
+                ],
+                ...
+              ]
+              ```
+      - SFT:
+          - json_name: {data_source}_{language}.json
+          - data_type: code, general, math, medicalExam, medicalPatient
+          - data item: list of qa pairs(list of string)
+            ```
+              [
+                [
+                  "q1",
+                  "a1",
+                  "q2",
+                  "a2",
+                  ...
+                ],
+                ...
+              ]
             ```
 
-<p style="color: lightgrey;">如果您是本模型的贡献者，我们邀请您根据<a href="https://modelscope.cn/docs/ModelScope%E6%A8%A1%E5%9E%8B%E6%8E%A5%E5%85%A5%E6%B5%81%E7%A8%8B%E6%A6%82%E8%A7%88" style="color: lightgrey; text-decoration: underline;">模型贡献文档</a>，及时完善模型卡片内容。</p>
+
+   </details>
+
+
+
+- Evaluation
+  🤗 <a href="https://huggingface.co/datasets/FreedomIntelligence/XMedbench" target="_blank">XMedBench</a>
+
+  <details><summary>Click to expand</summary>
+  
+     - EN:
+       - [MedQA-USMLE](https://huggingface.co/datasets/GBaker/MedQA-USMLE-4-options) 
+       - [MedMCQA](https://huggingface.co/datasets/medmcqa/viewer/default/test)
+       - [PubMedQA](https://huggingface.co/datasets/pubmed_qa): Because the results fluctuated too much, they were not used in the paper.
+       - [MMLU-Medical](https://huggingface.co/datasets/cais/mmlu)
+         - Clinical knowledge, Medical genetics, Anatomy, Professional medicine, College biology, College medicine
+     - ZH:
+       - [MedQA-MCMLE](https://huggingface.co/datasets/bigbio/med_qa/viewer/med_qa_zh_4options_bigbio_qa/test)
+       - [CMB-single](https://huggingface.co/datasets/FreedomIntelligence/CMB): Not used in the paper
+         - Randomly sample 2,000 multiple-choice questions with single answer.
+       - [CMMLU-Medical](https://huggingface.co/datasets/haonan-li/cmmlu)
+         - Anatomy, Clinical_knowledge, College_medicine, Genetics, Nutrition, Traditional_chinese_medicine, Virology
+       - [CExam](https://github.com/williamliujl/CMExam): Not used in the paper
+         - Randomly sample 2,000 multiple-choice questions
+
+
+     - ES: [Head_qa](https://huggingface.co/datasets/head_qa)
+     - FR: [Frenchmedmcqa](https://github.com/qanastek/FrenchMedMCQA)
+     - HI: [MMLU_HI](https://huggingface.co/datasets/FreedomIntelligence/MMLU_Arabic)
+        - Clinical knowledge, Medical genetics, Anatomy, Professional medicine, College biology, College medicine
+     - AR: [MMLU_Ara](https://huggingface.co/datasets/FreedomIntelligence/MMLU_Hindi)
+        - Clinical knowledge, Medical genetics, Anatomy, Professional medicine, College biology, College medicine
+
+
+   </details>
+
+
+## Results reproduction
+   <details><summary>Click to expand</summary>
+
+   **Waiting for Update**
+      
+
+
+   </details>
+
+
+
+
+##  Citation
+Please use the following citation if you intend to use our dataset for training or evaluation:
+
+```
+@misc{wang2024apollo,
+   title={Apollo: Lightweight Multilingual Medical LLMs towards Democratizing Medical AI to 6B People},
+   author={Xidong Wang and Nuo Chen and Junyin Chen and Yan Hu and Yidong Wang and Xiangbo Wu and Anningzhe Gao and Xiang Wan and Haizhou Li and Benyou Wang},
+   year={2024},
+   eprint={2403.03640},
+   archivePrefix={arXiv},
+   primaryClass={cs.CL}
+}
+```

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+  "<|im_start|>": 151644
+}

config.json

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+  "_name_or_path": "apollo-0.5B",
+  "architectures": [
+    "Qwen2ForCausalLM"
+  ],
+  "attention_dropout": 0.0,
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+  "hidden_act": "silu",
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+  "max_position_embeddings": 32768,
+  "max_window_layers": 21,
+  "model_type": "qwen2",
+  "num_attention_heads": 16,
+  "num_hidden_layers": 24,
+  "num_key_value_heads": 16,
+  "rms_norm_eps": 1e-06,
+  "rope_theta": 1000000.0,
+  "sliding_window": 32768,
+  "tie_word_embeddings": true,
+  "torch_dtype": "float32",
+  "transformers_version": "4.38.2",
+  "use_cache": true,
+  "use_sliding_window": false,
+  "vocab_size": 151936
+}

configuration.json

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generation_config.json

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+  "eos_token_id": 151643,
+  "max_new_tokens": 2048,
+  "transformers_version": "4.38.2"
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+    "<|im_end|>"
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