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https://github.com/onejune2018/Awesome-Medical-Healthcare-Dataset-For-LLM
A curated list of popular Datasets, Models and Papers for LLMs in Medical/Healthcare
https://github.com/onejune2018/Awesome-Medical-Healthcare-Dataset-For-LLM
List: Awesome-Medical-Healthcare-Dataset-For-LLM
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A curated list of popular Datasets, Models and Papers for LLMs in Medical/Healthcare
- Host: GitHub
- URL: https://github.com/onejune2018/Awesome-Medical-Healthcare-Dataset-For-LLM
- Owner: onejune2018
- License: mit
- Created: 2023-08-16T02:27:26.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2024-04-30T04:12:43.000Z (5 months ago)
- Last Synced: 2024-05-19T03:59:40.352Z (4 months ago)
- Size: 131 KB
- Stars: 110
- Watchers: 3
- Forks: 9
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Awesome-Medical-Healthcare-Dataset-For-LLM
A curated list of popular Datasets, Models and Papers for LLMs in Medical/Healthcare.
## Datasets
### 中文
| 数据集名称 | 内容概述 | 获取链接 | 数据大小 |
|----------|--------|---------|---------|
| MedDialog | MedDialog数据集（中文）包含了医生和患者之间的对话（中文）。它有110万个对话和400万个话语。数据还在不断增长，会有更多的对话加入。原始对话来自好大夫网。 | [下载链接](https://huggingface.co/datasets/medical_dialog) | 3.3GB |
|Chinese medical dialogue data 中文医疗对话数据集 | 数据中有六个科室的医学问答数据:
**** 94596个问答对 **** 220606个问答对 **** 183751个问答对**** 75553个问答对 **** 101602个问答对 **** 115991个问答对 总计 792099个问答对 | [下载链接](https://github.com/Toyhom/Chinese-medical-dialogue-data) | 800k 条，330MB |
| Huatuo-26M | Huatuo-26M 是迄今为止最大的中医问答数据集。该数据集包含超过2600万对高质量的医学问答对，涵盖疾病、症状、治疗和药物信息等广泛主题。 | [下载链接](https://github.com/FreedomIntelligence/Huatuo-26M) | 4.54GB |
| huatuo_encyclopedia_qa | 该数据集共有364,420条医疗QA数据，其中一些数据以不同的方式包含多个问题。我们从纯文本(例如，医学百科全书和医学文章)中提取医学QA对。我们在中文维基百科上收集了8699个疾病百科条目和2736个药物百科条目。此外，我们还从钱文健康网站抓取了226432篇高质量的医学文章。| [下载链接](https://huggingface.co/datasets/FreedomIntelligence/huatuo_encyclopedia_qa) | 605MB |
| 中文医疗对话数据集(华佗项目) | 22万条中文医疗对话数据集(华佗项目)：FreedomIntelligence/HuatuoGPT-sft-data-v1 | [下载链接](https://huggingface.co/datasets/FreedomIntelligence/HuatuoGPT-sft-data-v1) | 333MB |
|医疗大模型数据集(包括预训练、指令微调和奖励数据集) | 240万条中文医疗数据集(包括预训练、指令微调和奖励数据集) | [下载链接](https://huggingface.co/datasets/shibing624/medical) | 2.1GB |
|外科问诊数据BillGPT/Chinese-medical-dialogue-data | 60.8K条外科问诊数据，示例："患者:新癀片有什么用,想问一下新癀片吃了有什么作用呀？ 医生:病情分析：您好：新癀片主要是可以清热解毒，活血化瘀，消肿止痛。用于热毒瘀血所致的咽喉肿痛、牙痛、痹痛、胁痛、黄疸、无名肿毒等症。指导意见：如果您有咽喉疼痛等症状服用效果是很好的，但是有胃炎的朋友尽量不要服用，有一定的胃肠反应，里面也含有对胃有刺激成分。" | [下载链接](https://huggingface.co/datasets/BillGPT/Chinese-medical-dialogue-data) | 936MB |
|中文医学指令精调/指令微调数据集(Instruct-tuning)| 采用了公开和自建的中文医学知识库，主要参考了cMeKG。 医学知识库围绕疾病、药物、检查指标等构建，字段包括并发症，高危因素，组织学检查，临床症状，药物治疗，辅助治疗等。利用GPT3.5接口围绕医学知识库构建问答数据，设置了多种Prompt形式来充分利用知识。 | [下载链接](https://github.com/SCIR-HI/Med-ChatGLM) | 7.6K条 |
|MeChat：中文心理健康支持对话大模型与数据集 | 数据集通过 ChatGPT 改写真实的心理互助 QA 为多轮的心理健康支持多轮对话（single-turn to multi-turn inclusive language expansion via ChatGPT），该数据集含有 56k 个多轮对话，其对话主题、词汇和篇章语义更加丰富多样，更加符合在长程多轮对话的应用场景。 | [下载链接](https://github.com/qiuhuachuan/smile) | 56k条 |
| CMB-Chinese Medical Benchmark |CMB是一个全方位多层次的中文医疗模型评估平台。它共包含280839道多项选择题和74例复杂病例问诊题，涵盖了所有医学临床工种和不同职业级别的考试，综合考察模型的医学知识和临床问诊能力 | [下载链接](https://github.com/FreedomIntelligence/CMB) | 30MB|
|ChatMed_Consult_Dataset | ChatMed_Consult_Dataset 中的query(或者是prompt)来自于互联网上的医疗问诊问题(110,113)，反映了真实世界的不同用户/患者的医疗问诊需求。目前response都是由OpenAI GPT-3.5引擎回答的。我们后续会对互联网上的医生回答与患者回答进行筛选甄别，择优选择，构建质量更优的数据集。| [下载链接](https://huggingface.co/datasets/michaelwzhu/ChatMed_Consult_Dataset) | 395MB |
| 中医药指令数据集ChatMed_TCM_Dataset | 以开源的[中医药知识图谱] (https://github.com/ywjawmw/TCM_KG) 为基础，采用以实体为中心的自指令方法(entity-centric self-instruct)，调用ChatGPT得到11w+的围绕中医药的指令数据。 | [下载链接](https://huggingface.co/datasets/michaelwzhu/ShenNong_TCM_Dataset) | 110MB |
| cMedQA中文社区医学问答数据集 |华人社区医疗问答的数据集，该数据集是1.0版本，提供方将不时更新和扩充数据库。为了保护隐私，数据是匿名的，不包括个人信息。| [下载链接](https://github.com/zhangsheng93/cMedQA2) | 80MB |
| WebMedQA 线上医学QA | WebMedQA是一个从百度医生和120Ask等在线健康咨询网站收集的真实中国医学问答数据集。用户首先填写个人信息表格，然后描述他们的疾病和健康问题。这些问题对所有注册的临床医生和用户开放，直到问题提出者选择最满意的答案并结束问题。医生和热心的用户可以在发布的问题下提供诊断和建议，他们的标题和专业与他们的答案一起显示。提问者也可以进一步询问他们是否对其中一个答案感兴趣。每个问题所属的类别也由其提出者选择。 | [下载链接](https://tianchi.aliyun.com/dataset/90202) | 75MB |
| ChineseBLUE基准 | ChineseBLUE基准由不同的带有语料库的生物医学文本挖掘任务组成。这些任务涵盖了各种文本类型(生物医学网络数据和临床笔记)、数据集大小和难度，更重要的是，突出了常见的生物医学文本挖掘挑战。 | [下载链接](https://github.com/CBLUEbenchmark/CBLUE) | 400MB |
| Yidu-S4K | 命名实体识别,实体及属性抽取 | [下载链接](http://openkg.cn/dataset/yidu-s4k) | 4K条 |
| Yidu-N7K | 临床语标准化 | [下载链接](http://openkg.cn/dataset/yidu-n7k ) | 7K条 |
| HealthCareMagic-100k | 来自HealthCareMagic.com的10万次病人和医生之间的真实对话 | [下载链接](https://drive.google.com/file/d/1lyfqIwlLSClhgrCutWuEe_IACNq6XNUt/view?usp=sharing) |137MB|
| icliniq-10k | 来自icliniq.com网站的病人和医生之间的10K条真实对话 | [下载链接](https://drive.google.com/file/d/1ZKbqgYqWc7DJHs3N9TQYQVPdDQmZaClA/view) | 20MB |
| GenMedGPT-5k |5k从ChatGPT GenMedGPT-5k和疾病数据库中生成了患者和医生之间的对话。| [下载链接](https://drive.google.com/file/d/1nDTKZ3wZbZWTkFMBkxlamrzbNz0frugg/view?usp=sharing) | 5K条 |
### 英文
| **数据集名称** | **内容概述** | **获取链接** | **数据大小** |
|--------------------|---------------------|---------------------|--------------------|
| MIMIC-III | EHR | https://mimic.mit.edu/docs/iii/ | 58,976 hospital admissions for 38,597 patients |
| MIMIC-IV | EHR | https://mimic.mit.edu/docs/iv/ | covering a decade of admissions between 2008 and 2019 |
| CPRD | EHR | https://cprd.com/data | over 2,000 primary care practices and include 60 million patients |
| PubMed | Scientific Literature | https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/ | 35M citations and abstracts of biomedical literature |
| PMC | Scientific Literature | https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk | 8 million full-text article records |
| RCT | Scientific Literature | https://github.com/bwallace/RCT-summarization-data | 4,528 abstract |
| MS$\hat{~}$2 | Scientific Literature | https://github.com/allenai/ms2/ | 470,402 abstract |
| CDSR | Scientific Literature | https://github.com/qiuweipku/Plain\_language\_summarization | 7,805 abstract |
| SumPubMed | Scientific Literature | https://github.com/vgupta123/sumpubmed | 33,772 abstract |
| The Pile | Scientific Literature | https://pile.eleuther.ai/ | 825 GB English text |
| S2ORC | Scientific Literature | https://github.com/jbshp/GenCompareSum | 63,709 abstract |
| CORD-19 | Scientific Literature | https://github.com/allenai/cord19 | 1M papers |
| MeQSum | Medical Question Summarization | https://github.com/abachaa/MeQSum | 1000 instances |
| CHQ-Sum | Medical Question Summarization | https://github.com/shwetanlp/Yahoo-CHQ-Summ | 1507 instances |
| UMLS | Knowledge Base | https://www.nlm.nih.gov/research/umls/index.html | 2M entities for 900K concepts |
| COMETA | Web Data (social media) | https://github.com/cambridgeltl/cometa | 800K Reddit posts |
| MedDialog | Dialogue | https://github.com/UCSD-AI4H/COVID-Dialogue | 3.66 million conversations |
| CovidDialog | Dialogue | https://github.com/UCSD-AI4H/COVID-Dialogue | 603 consultations |
| Medical Flashcards | Dialogue | https://github.com/kbressem/medalpaca | 33955 instances |
| Wikidoc | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_wikidoc | 67704 instances |
| Wikidoc Patient Information | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_wikidoc\_patient\_information | 5942 instances |
| MEDIQA | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_wikidoc\_patient\_information | 2208 instances |
| CORD-19 | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_cord19 | 1056660 instances |
| MMMLU | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_mmmlu | 3787 instances |
| Pubmed Causal | Dialogue | https://huggingface.co/datasets/medalpaca/medical\_meadow\_pubmed\_causal | 2446 instances |
| ChatDoctor | Dialogue | https://github.com/Kent0n-Li/ChatDoctor | 215000 instances |
| Alpaca-EN-AN | English Instructions | https://github.com/tatsu-lab/stanford\_alpaca/blob/main/alpaca\_data.json | 52K instructions |
| Alpaca-CH-AN | Chinese Instructions | https://github.com/Instruction-Tuning-with-GPT-4/GPT-4-LLM/tree/main/data | 52K instructions |
| ShareGPT | Conversations | https://huggingface.co/datasets/philschmid/sharegpt-raw | 61653 long conversations |
| WebText | Web Data | https://commoncrawl.org/the-data/get-started/ | 40 GB of text |
| OpenWebText | Web Data | https://skylion007.github.io/OpenWebTextCorpus/ | 38 GB of text |
| Colossal Clean Crawled Corpus | Web Data | https://www.tensorflow.org/datasets/catalog/c4 | 806 GB of text |
| OpenI | EHR, Multimodel | https://openi.nlm.nih.gov/faq\#collection | 3.7 million images from about 1.2 million papers |
| U-Xray | Multimodel | https://openi.nlm.nih.gov/ | 3,955 reports and 7,470 images |
| ROCO | Multimodel | https://github.com/razorx89/roco-dataset | 81,000 radiology images and corresponding captions |
| MedICaT | Multimodel | https://github.com/allenai/medicat | 17,000 images includes captions |
| PMC-OA | Multimodel | https://huggingface.co/datasets/axiong/pmc\_oa\_beta | 1.6M image-caption pairs |
| CheXpert | Multimodel | https://aimi.stanford.edu/chexpert-chest-x-rays | 224,316 chest radiographs with associated reports |
| PadChest | Multimodel | http://bimcv.cipf.es/bimcv-projects/padchest/ | 160,000 images with related text |
| MIMIC-CXR | Multimodel | https://mimic.mit.edu/docs/iv/modules/cxr/ | 227,835 imaging studies for 64,588 patients |
| PMC-15M | Multimodel | | 15 million Figure-caption |
| pairs | https://arxiv.org/abs/2303.00915 | | |
| OpenPath | Multimodel | https://laion.ai/blog/laion-5b/ | 208,414 pathology images related descriptions |
## Models
| 模型 | 地址 | 简介 |
| --- | --- | --- |
| DoctorGLM | [DoctorGLM](https://github.com/xionghonglin/DoctorGLM) | 基于 ChatGLM-6B的中文问诊模型，通过中文医疗对话数据集进行微调，实现了包括lora、p-tuningv2等微调及部署 |
| BenTsao | [BenTsao](https://github.com/SCIR-HI/Huatuo-Llama-Med-Chinese) | 开源了经过中文医学指令精调/指令微调(Instruct-tuning) 的LLaMA-7B模型。通过医学知识图谱和GPT3.5 API构建了中文医学指令数据集，并在此基础上对LLaMA进行了指令微调，提高了LLaMA在医疗领域的问答效果。 |
| BianQue | [BianQue](https://github.com/scutcyr/BianQue) | 一个经过指令与多轮问询对话联合微调的医疗对话大模型，基于ClueAI/ChatYuan-large-v2作为底座，使用中文医疗问答指令与多轮问询对话混合数据集进行微调。 |
| HuatuoGPT | [HuatuoGPT](https://github.com/FreedomIntelligence/HuatuoGPT) | 开源了经过中文医学指令精调/指令微调(Instruct-tuning)的一个GPT-like模型 |
| Med-ChatGLM | [Med-ChatGLM](https://github.com/SCIR-HI/Med-ChatGLM) | 基于中文医学知识的ChatGLM模型微调，微调数据与BenTsao相同。 |
| QiZhenGPT | [QiZhenGPT](https://github.com/CMKRG/QiZhenGPT) | 该项目利用启真医学知识库构建的中文医学指令数据集，并基于此在LLaMA-7B模型上进行指令精调，大幅提高了模型在中文医疗场景下效果，首先针对药品知识问答发布了评测数据集，后续计划优化疾病、手术、检验等方面的问答效果，并针对医患问答、病历自动生成等应用展开拓展。 |
| ChatMed | [ChatMed](https://github.com/michael-wzhu/ChatMed) | 该项目推出ChatMed系列中文医疗大规模语言模型，模型主干为LlaMA-7b并采用LoRA微调，具体包括ChatMed-Consult : 基于中文医疗在线问诊数据集ChatMed_Consult_Dataset的50w+在线问诊+ChatGPT回复作为训练集；ChatMed-TCM : 基于中医药指令数据集ChatMed_TCM_Dataset，以开源的中医药知识图谱为基础，采用以实体为中心的自指令方法(entity-centric self-instruct)，调用ChatGPT得到2.6w+的围绕中医药的指令数据训练得到。 |
| XrayGLM | [XrayGLM](https://github.com/WangRongsheng/XrayGLM) | 该项目为促进中文领域医学多模态大模型的研究发展，发布了XrayGLM数据集及模型，其在医学影像诊断和多轮交互对话上显示出了非凡的潜力。 |
| MeChat | [MeChat](https://github.com/qiuhuachuan/smile) | 该项目开源的中文心理健康支持通用模型由 ChatGLM-6B LoRA 16-bit 指令微调得到。数据集通过调用gpt-3.5-turbo API扩展真实的心理互助 QA为多轮的心理健康支持多轮对话，提高了通用语言大模型在心理健康支持领域的表现，更加符合在长程多轮对话的应用场景。 |
| MedicalGPT | [MedicalGPT](https://github.com/shibing624/MedicalGPT) | 训练医疗大模型，实现包括二次预训练、有监督微调、奖励建模、强化学习训练。发布中文医疗LoRA模型shibing624/ziya-llama-13b-medical-lora，基于Ziya-LLaMA-13B-v1模型，SFT微调了一版医疗模型，医疗问答效果有提升，发布微调后的LoRA权重。 |
| Sunsimiao | [Sunsimiao](https://github.com/thomas-yanxin/Sunsimiao) | Sunsimiao是一个开源的中文医疗大模型，该模型基于baichuan-7B和ChatGLM-6B底座模型在十万级高质量的中文医疗数据中微调而得。 |
| ShenNong-TCM-LLM | [ShenNong-TCM-LLM](https://github.com/michael-wzhu/ShenNong-TCM-LLM) | 该项目开源了ShenNong中医药大规模语言模型，该模型以LlaMA为底座，采用LoRA (rank=16)微调得到。微调代码与ChatMed代码库相同。此外该项目还开源了中医药指令微调数据集。 |
| SoulChat | [SoulChat](https://github.com/scutcyr/SoulChat) | 该项目开源了经过百万规模心理咨询领域中文长文本指令与多轮共情对话数据联合指令微调的心理健康大模型灵心（SoulChat），该模型以ChatGLM-6B作为初始化模型，进行了全量参数的指令微调。 |
| CareGPT | [CareGPT](https://github.com/WangRongsheng/CareGPT) | 该项目开源了数十个公开可用的医疗微调数据集和开放可用的医疗大语言模型，包含LLM的训练、测评、部署等以促进医疗LLM快速发展。 |
| DISC-MedLLM | [DISC-MedLLM](https://github.com/FudanDISC/DISC-MedLLM) | 该项目是由复旦大学发布的针对医疗健康对话式场景而设计的医疗领域大模型与数据集，该模型由DISC-Med-SFT数据集基于Baichuan-13B-Base指令微调得到。 |
| Taiyi-LLM | [Taiyi-LLM](https://github.com/DUTIR-BioNLP/Taiyi-LLM) | 该项目由大连理工大学信息检索研究室开发的中英双语医学大模型"太一"，收集整理了丰富的中英双语生物医学自然语言处理（BioNLP）训练语料，总共包含38个中文数据集，通过丰富的中英双语任务指令数据（超过100W条样本）进行大模型（Qwen-7B-base）指令微调，使模型具备了出色的中英双语生物医学智能问答、医患对话、报告生成、信息抽取、机器翻译、标题生成、文本分类等多种BioNLP能力。 |
| WiNGPT | [WiNGPT](https://github.com/winninghealth/WiNGPT2) | WiNGPT是一个基于GPT的医疗垂直领域大模型，基于Qwen-7b1作为基础预训练模型，在此技术上进行了继续预训练，指令微调等，该项目具体开源了WiNGPT2-7B-Base与WiNGPT2-7B-Chat模型。 |
| ChiMed-GPT | [ChiMed-GPT](https://github.com/synlp/ChiMed-GPT) | ChiMed-GPT是一个开源中文医学大语言模型，通过在中文医学数据上持续训练 Ziya-v2 构建而成，其中涵盖了预训练、有监督微调 (SFT) 和来自人类反馈的强化学习 (RLHF) 等训练过程。 |
| MindChat | [MindChat](https://github.com/X-D-Lab/MindChat) | 心理大模型——漫谈(MindChat)期望从心理咨询、心理评估、心理诊断、心理治疗四个维度帮助人们纾解心理压力与解决心理困惑，为用户提供隐私、温暖、安全、及时、方便的对话环境，从而帮助用户克服各种困难和挑战，实现自我成长和发展。MindChat是一个基于Qwen作为基础预训练模型，并在此基础上进行指令微调得到的心理垂域大模型。 |
| Title | Institute | Date | Code
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :------------------: | :-----------: | :---------: |
|[DoctorGPT](https://huggingface.co/llSourcell/medllama2_7b) | Sirajraval, GPT School | 2023-08 | [Github](https://github.com/llSourcell/DoctorGPT)
| [CoDoC: Enhancing the reliability and accuracy of AI-enabled diagnosis via complementarity-driven deferral to clinicians](https://www.nature.com/articles/s41591-023-02437-x) | DeepMind, Google
 | 2023-07 | [Github](https://github.com/deepmind/codoc/tree/main)
| [Med-PaLM 2: Towards Expert-Level Medical Question Answering with Large Language Models](https://arxiv.org/pdf/2305.09617.pdf) | Google
 | 2023-05 | -
| [Capabilities of GPT-4 on Medical Challenge Problems](https://arxiv.org/pdf/2303.13375.pdf) | Microsoft, OpenAI
 | 2023-03 | -
| [BioMedLM-PubMedGPT: A purpose-built AI model trained to interpret biomedical language](https://crfm.stanford.edu/2022/12/15/biomedlm.html) | Stanford CRFM, MosaicML | 2022-12 | [HuggingFace](https://huggingface.co/stanford-crfm/BioMedLM)
| [Med-PaLM: Large Language Models Encode Clinical Knowledge](https://arxiv.org/pdf/2212.13138.pdf) | Google
 | 2022-12 | [Github](https://github.com/conceptofmind/PaLM)
| [ClinicalT5: A Generative Language Model for Clinical Text](https://aclanthology.org/2022.findings-emnlp.398.pdf) | University of Oregon, Baidu
 | 2022-12 | [HuggingFace](https://huggingface.co/luqh/ClinicalT5-large)
| [GatorTron: A large language model for electronic health records](https://www.nature.com/articles/s41746-022-00742-2) | University of Florida, NVIDIA
 | 2022-12 | [HuggingFace](https://huggingface.co/UFNLP/gatortron-base)
| [BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining](https://aclanthology.org/2020.clinicalnlp-1.17/) | Microsoft Research
 | 2022-09 | [HuggingFace](https://huggingface.co/microsoft/biogpt)
| [BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model](https://arxiv.org/pdf/2204.03905.pdf) | Tsinghua University
 | 2022-04 | [HuggingFace](https://huggingface.co/GanjinZero/biobart-v2-base)
| [KeBioLM: Improving Biomedical Pretrained Language Models with Knowledge](https://aclanthology.org/2021.bionlp-1.20.pdf) | Tsinghua, Alibaba
 | 2021-04 | [Github](https://github.com/GanjinZero/KeBioLM)
| [Pretrained Language Models for Biomedical and Clinical Tasks: Understanding and Extending the State-of-the-Art](https://aclanthology.org/2020.clinicalnlp-1.17/) | Meta
 | 2020-11 | [Github](https://github.com/facebookresearch/bio-lm)
| [BioMegatron: Larger Biomedical Domain Language Model](https://aclanthology.org/2020.emnlp-main.379.pdf) | NVIDIA
 | 2020-10 | [HuggingFace](https://huggingface.co/EMBO/BioMegatron345mUncased)
| [PubMedBERT: Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://arxiv.org/pdf/2007.15779.pdf) | Microsoft Research
 | 2020-07 | [HuggingFace](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext)
| [Publicly Available Clinical BERT Embeddings](https://arxiv.org/pdf/1904.03323.pdf) | MIT CSAIL
 | 2019-04 | [HuggingFace](https://huggingface.co/emilyalsentzer/Bio_ClinicalBERT)
| [ClinicalBERT: Modeling Clinical Notes and Predicting Hospital Readmission](https://arxiv.org/pdf/1904.05342.pdf) | Harvard, Princeton, NYU
 | 2019-04 | [Github](https://github.com/kexinhuang12345/clinicalBERT)
| [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://arxiv.org/pdf/1901.08746) | Korea University
 | 2019-01 | [Github](https://github.com/dmis-lab/biobert)
## Popular LLMs
| **Model Name** | **Base** | **Para. (B)** | **Features** | **Date** | **Link** |
|--------------------------------------------|----------------|-------------------|-------------------------------------------------|----------|------------------------------------------------------------------------|
| GatorTron | Transformer | 0.345, 3.9, 8.9 | Training from scratch | 06/2022 | https://github.com/uf-hobi-informatics-lab/GatorTron |
| Codex-Med | GPT-3.5 | 175 | CoT, Zero-shot | 07/2022 | https://github.com/vlievin/medical-reasoning |
| Galactica | Transformer | 1.3, 6.4, 30, 120 | Reasoning, Multidisciplinary | 11/2022 | https://galactica.org |
| Med-PaLM | Flan-PaLM/PaLM | 540 | CoT, Self-consistency | 12/2022 | - |
| GPT-4-Med | GPT-4 | - | no specialized prompt crafting | 03/2023 | - |
| DeID-GPT | GPT-4 | - | De-identifying | 03/2023 | https://github.com/yhydhx/ChatGPT-API |
| ChatDoctor | LLaMA | 7 | Retrieve online, external knowledge | 03/2023 | https://github.com/Kent0n-Li/ChatDoctor |
| DoctorGLM | ChatGLM | 6 | Extra prompt designer | 04/2023 | https://github.com/xionghonglin/DoctorGLM |
| MedAlpaca | LLaMA | 7, 13 | Adapt to Medicine | 04/2023 | https://github.com/kbressem/medAlpaca |
| BenTsao | LLaMA | 7 | Knowledge graph | 04/2023 | https://github.com/SCIR-HI/ Huatuo-Llama-Med-Chinese |
| PMC-LLaMA | LLaMA | 7 | Adapt to Medicine | 04/2023 | https://github.com/chaoyi-wu/PMC-LLaMA |
| Visual Med-Alpaca | LLaMA | 7 | multimodal generative model, Self-Instruct | 04/2023 | https://github.com/cambridgeltl/visual-med-alpaca |
| BianQue~ | ChatGLM | 6 | Chain of Questioning | 04/2023 | https://github.com/scutcyr/BianQue |
| Med-PaLM 2 | PaLM 2 | 340 | Ensemble refinement, CoT, Self-consistency | 05/2023 | - |
| GatorTronGPT | GPT-3 | 5, 20 | Training from scratch for medicine | 05/2023 | https://github.com/uf-hobi-informatics-lab/GatorTronGPT |
| HuatuoGPT | Bloomz | 7 | Reinforced learning from AI feedback | 05/2023 | https://github.com/FreedomIntelligence/HuatuoGPT |
| ClinicalGPT | BLOOM | 7 | multi-round dialogue consultations | 06/2023 | - |
| MedAGI | MiniGPT-4 | - | multimodal, AGI | 06/2023 | https://github.com/JoshuaChou2018/MedAGI |
| LLaVA-Med | LLaVA | 13 | multimodal, self-instruct, curriculum learning | 06/2023 | https://github.com/microsoft/LLaVA-Med |
| OphGLM | ChatGLM | 6 | multimodal, Ophthalmology LLM | 06/2023 | https://github.com/ML-AILab/OphGLM |
| SoulChat | ChatGLM | 6 | Mental Healthcare | 06/2023 | https://github.com/scutcyr/SoulChat |
| Med-Flamingo | Flamingo | 80 | multimodal, Few-Shot generative medical VQA | 07/2023 | https://github.com/snap-stanford/med-flamingo |
## Papers
- Med-PaLM 2: Towards Expert-Level Medical Question Answering with Large Language Models [[Paper]](https://arxiv.org/pdf/2305.09617.pdf)
- KeBioLM: Improving Biomedical Pretrained Language Models with Knowledge [[Paper]](https://arxiv.org/abs/2104.10344)
- BioELMo: Probing Biomedical Embeddings from Language Models [[Paper]](https://arxiv.org/abs/1904.02181)
- BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model [[Paper]](https://aclanthology.org/2022.bionlp-1.9.pdf)
- ClinicalT5: A Generative Language Model for Clinical Text [[Paper]](https://aclanthology.org/2022.findings-emnlp.398.pdf)
- GatorTron: A Large Clinical Language Model to Unlock Patient Information from Unstructured Electronic Health Records [[Paper]](https://arxiv.org/pdf/2203.03540v2.pdf)
- ChatCAD: Interactive Computer-Aided Diagnosis on Medical Image using Large Language Models [[Paper]](https://arxiv.org/pdf/2302.07257.pdf) [[Code]](https://github.com/zhaozh10/ChatCAD)
- DeID-GPT: Zero-shot Medical Text De-Identification by GPT-4 [[Paper]](https://arxiv.org/pdf/2303.11032.pdf)
- Capabilities of GPT-4 on Medical Challenge Problems [[Paper]](https://arxiv.org/pdf/2303.13375.pdf)
- BioBERT: a pre-trained biomedical language representation model for biomedical text mining [[Paper]](https://arxiv.org/pdf/1901.08746.pdf)
- Publicly Available Clinical BERT Embeddings [[Paper]](https://arxiv.org/pdf/1904.03323.pdf)
- BioMegatron: Larger Biomedical Domain Language Model [[Paper]](https://arxiv.org/pdf/2010.06060.pdf)
- Don’t Stop Pretraining: Adapt Language Models to Domains and Tasks [[Paper]](https://aclanthology.org/2020.acl-main.740.pdf)
- Med-BERT: pretrained contextualized embeddings on large-scale structured electronic health records for disease prediction [[Paper]](https://www.nature.com/articles/s41746-021-00455-y)
- DoctorGLM: Fine-tuning your chinese doctor is not a herculean task [[Paper]](https://arxiv.org/abs/2304.01097) [[Code]](https://github.com/xionghonglin/DoctorGLM)
- HuatuoGPT, Towards Taming Language Models To Be a Doctor [[Paper]](https://arxiv.org/abs/2305.15075) [[Code]](https://github.com/FreedomIntelligence/HuatuoGPT)
- BioELECTRA:Pretrained Biomedical text Encoder using Discriminators [[Paper]](https://aclanthology.org/2021.bionlp-1.16.pdf)
- LinkBERT: Pretraining Language Models with Document Links [[Paper]](https://arxiv.org/pdf/2203.15827.pdf)
- BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining [[Paper]](https://arxiv.org/pdf/2210.10341.pdf)
- Large Language Models Encode Clinical Knowledge [[Paper]](https://arxiv.org/pdf/2212.13138.pdf)
- A large language model for electronic health records [[Paper]](https://www.nature.com/articles/s41746-022-00742-2)
- Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing [[Paper]](https://arxiv.org/pdf/2007.15779.pdf)
- BEHRT: Transformer for Electronic Health Records [[Paper]](https://www.nature.com/articles/s41598-020-62922-y)
- Federated Learning of Medical Concepts Embedding using BEHRT [[Paper]](https://arxiv.org/abs/2305.13052) [[Code]](https://github.com/nadavlab/FederatedBEHRT)
- RadBERT: Adapting Transformer-based Language Models to Radiology [[paper]](https://pubs.rsna.org/doi/epdf/10.1148/ryai.210258) [[HuggingFace]](https://huggingface.co/UCSD-VA-health/RadBERT-RoBERTa-4m)
- Highly accurate protein structure prediction with AlphaFold [[Paper]](https://www.nature.com/articles/s41586-021-03819-2) [[Code]](https://github.com/deepmind/alphafold)
- Accurate prediction of protein structures and interactions using a three-track neural network [[Paper]](https://www.science.org/doi/full/10.1126/science.abj8754?casa_token=tleEHPOOSr8AAAAA%3AT0eToIMPW0oN1jjIGLs8aPyQK8qbcFIByjT1x4k90tvBAj03SZUzpEinCPe_t-g4ECmjJ9wlj8OwQBs)
- Protein complex prediction with AlphaFold-Multimer [[Paper]](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2.abstract)
- FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours [[Paper]](https://arxiv.org/abs/2203.00854) [[Code]](https://github.com/hpcaitech/fastfold)
- HelixFold: An Efficient Implementation of AlphaFold2 using PaddlePaddle [[Paper]](https://arxiv.org/abs/2207.05477) [[Code]](https://github.com/PaddlePaddle/PaddleHelix)
- Uni-Fold: An Open-Source Platform for Developing Protein Folding Models beyond AlphaFold [[Paper]](https://www.biorxiv.org/content/10.1101/2022.08.04.502811v3.abstract) [[Code]](https://github.com/dptech-corp/Uni-Fold)
- OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization [[Paper]](https://www.biorxiv.org/content/10.1101/2022.11.20.517210v2.abstract) [[Code]](https://github.com/aqlaboratory/openfold)
- ManyFold: an efficient and flexible library for training and validating protein folding models [[Paper]](https://academic.oup.com/bioinformatics/article/39/1/btac773/6887136) [[Code]](https://github.com/instadeepai/manyfold)
- ColabFold: making protein folding accessible to all [[Paper]](https://www.nature.com/articles/s41592-022-01488-1) [[Code]](https://github.com/sokrypton/ColabFold)
- Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences [[Paper]](https://www.pnas.org/doi/abs/10.1073/pnas.2016239118) [[Code]](https://github.com/facebookresearch/esm)
- ProGen: Language Modeling for Protein Generation [[Paper]](https://arxiv.org/abs/2004.03497) [[Code]](https://github.com/lucidrains/progen)
- ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing [[Paper]](https://arxiv.org/abs/2007.06225) [[Code]](https://github.com/agemagician/ProtTrans)
- Evolutionary-scale prediction of atomic level protein structure with a language model [[Paper]](https://www.science.org/doi/full/10.1126/science.ade2574)
- High-resolution de novo structure prediction from primary sequence [[Paper]](https://www.biorxiv.org/content/10.1101/2022.07.21.500999v1.abstract) [[Code]](https://github.com/HeliXonProtein/OmegaFold)
- Single-sequence protein structure prediction using a language model and deep learning [[Paper]](https://www.nature.com/articles/s41587-022-01432-w)
- Improved the Protein Complex Prediction with Protein Language Models [[Paper]](https://www.biorxiv.org/content/10.1101/2022.09.15.508065v2.abstract)
- MSA Transformer [[Paper]](http://proceedings.mlr.press/v139/rao21a.html) [[Code]](https://github.com/The-AI-Summer/self-attention-cv)
- Deciphering antibody affinity maturation with language models and weakly supervised learning [[Paper]](https://arxiv.org/abs/2112.07782)
- xTrimoABFold: De novo Antibody Structure Prediction without MSA [[Paper]](https://arxiv.org/abs/2212.00735)
- scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data [[Paper]](https://arxiv.org/abs/2212.00735) [[Code]](https://github.com/TencentAILabHealthcare/scBERT)
- Interpretable RNA Foundation Model from Unannotated Data for Highly Accurate RNA Structure and Function Predictions [[Paper]](https://www.biorxiv.org/content/10.1101/2022.08.06.503062v2.abstract) [[Code]](https://github.com/ml4bio/rna-fm)
- E2Efold-3D: End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction [[Paper]](https://www.biorxiv.org/content/10.1101/2022.08.06.503062v2.abstract) [[Code]](https://github.com/ml4bio/rna-fm)
## Other Awesome List
[LLM-for-Healthcare](https://github.com/KaiHe-better/LLM-for-Healthcare) - A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics.
## Licenses
[](https://lbesson.mit-license.org/)
本项目遵循 [MIT License](https://lbesson.mit-license.org/).
[](http://creativecommons.org/licenses/by-nc-sa/4.0/)
本项目遵循 [Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-nc-sa/4.0/).
## 引用
如果本项目对您有帮助，请引用我们的项目。
```
@misc{medllmdata2023,
author = {Jun Wang, Changyu Hou, Pengyong Li, Jingjing Gong ,Chen Song, Qi Shen, Guotong Xie},
title = {Awesome Dataset for Medical LLM: A curated list of popular Datasets, Models and Papers for LLMs in Medical/Healthcare},
year = {2023},
publisher = {GitHub},
journal = {GitHub repository},
howpublished = {\url{https://github.com/onejune2018/Awesome-Medical-Healthcare-Dataset-For-LLM}},
}
```