/MedLLMsPracticalGuide

A curated list of practical guide resources of Medical LLMs (Medical LLMs Tree, Tables, and Papers)

The Practical Guides for Medical Large Language Models

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This is an actively updated list of practical guide resources for medical large language models (LLMs). It's based on our survey paper: A Survey of Large Language Models in Medicine: Progress, Application, and Challenge.

⚡ Contributing

If you want to add your work or model to this list, please do not hesitate to email fenglin.liu@eng.ox.ac.uk and xyzou@uwaterloo.ca or pull requests. Markdown format:

- [**Name of Conference or Journal + Year**] Paper Name. [[pdf]](link) [[code]](link)

🤗 Highlights

This repository aims to provide an overview of the progress, application, and challenge of LLMs in medicine, aiming to promote further research and exploration in this interdisciplinary field.

📣 Update Notes

[2023-11-09] We released the repository.

Table of Contents

🔥 Practical Guide for Building Pipeline

Pre-training from Scratch

  • BioBERT: A pre-trained biomedical language representation model for biomedical text mining. 2020. paper
  • PubMedBERT：Domain-specific language model pretraining for biomedical natural language processing. 2021. paper
  • SciBERT：A pretrained language model for scientific text. 2019. paper
  • ClinicalBERT：Publicly available clinical BERT embeddings. 2019. paper
  • BlueBERT：Transfer learning in biomedical natural language processing: an evaluation of BERT and ELMo on ten benchmarking datasets. 2019. paper
  • BioCPT：Contrastive pre-trained transformers with large-scale pubmed search logs for zero-shot biomedical information retrieval. 2023. paper
  • BioGPT：generative pre-trained transformer for biomedical text generation and mining. 2022. paper
  • OphGLM：Training an Ophthalmology Large Language-and-Vision Assistant based on Instructions and Dialogue. 2023. paper
  • GatorTron：A large language model for electronic health records. 2022. paper
  • GatorTronGPT：A Study of Generative Large Language Model for Medical Research and Healthcare. 2023. paper

Fine-tuning General LLMs

  • ChatGLM-Med：ChatGLM-Med: 基于中文医学知识的ChatGLM模型微调. 2023. github
  • DoctorGLM：Fine-tuning your chinese doctor is not a herculean task. 2023. paper
  • BianQue：Balancing the Questioning and Suggestion Ability of Health LLMs with Multi-turn Health Conversations Polished by ChatGPT. 2023. paper
  • ClinicalGPT：Large Language Models Finetuned with Diverse Medical Data and Comprehensive Evaluation. 2023. paper
  • Qilin-Med：Multi-stage Knowledge Injection Advanced Medical Large Language Model. 2023. paper
  • Qilin-Med-VL：Towards Chinese Large Vision-Language Model for General Healthcare. 2023. paper
  • ChatDoctor：A Medical Chat Model Fine-Tuned on a Large Language Model Meta-AI (LLaMA) Using Medical Domain Knowledge. 2023. paper
  • BenTsao：Tuning llama model with chinese medical knowledge. 2023. paper
  • HuatuoGPT: HuatuoGPT, towards Taming Language Model to Be a Doctor. 2023. paper
  • LLaVA-Med: Training a large language-and-vision assistant for biomedicine in one day. 2023. paper
  • Baize-healthcare: An open-source chat model with parameter-efficient tuning on self-chat data. 2023. paper
  • Visual Med-Alpeca: A parameter-efficient biomedical llm with visual capabilities. 2023. Repo
  • PMC-LLaMA: Further finetuning llama on medical papers. 2023. paper
  • Clinical Camel: An Open-Source Expert-Level Medical Language Model with Dialogue-Based Knowledge Encoding. 2023. paper
  • MedPaLM 2: Towards expert-level medical question answering with large language models. 2023. paper
  • MedPaLM M: Towards generalist biomedical ai. 2023. paper
  • CPLLM: Clinical Prediction with Large Language Models. 2023. paper

Prompting General LLMs

  • DelD-GPT: Zero-shot medical text de-identification by gpt-4. 2023. paper
  • ChatCAD: Interactive computer-aided diagnosis on medical image using large language models. 2023. paper
  • Dr. Knows: Leveraging a medical knowledge graph into large language models for diagnosis prediction. 2023. paper
  • MedPaLM: Large language models encode clinical knowledge. 2022. paper

📊 Practical Guide for Medical Data

Clinical Knowledge Bases

Pre-training Data

  • PubMed: National Institutes of Health. PubMed Data. In National Library of Medicine. 2022. database
  • Literature: Construction of the literature graph in semantic scholar. 2018. paper
  • MIMIC-III: MIMIC-III, a freely accessible critical care database. 2016. paper
  • PubMed: The pile: An 800gb dataset of diverse text for language modeling. 2020. paper
  • MedDialog: Meddialog: Two large-scale medical dialogue datasets. 2020. paper
  • EHRs: A large language model for electronic health records. 2022. paper
  • EHRs: A Study of Generative Large Language Model for Medical Research and Healthcare. 2023. paper

Fine-tuning Data

  • cMeKG：Chinese Medical Knowledge Graph. 2023. github
  • CMD.: Chinese medical dialogue data. 2023. repo
  • BianQueCorpus: BianQue: Balancing the Questioning and Suggestion Ability of Health LLMs with Multi-turn Health Conversations Polished by ChatGPT. 2023. paper
  • MD-EHR: ClinicalGPT: Large Language Models Finetuned with Diverse Medical Data and Comprehensive Evaluation. 2023. paper
  • VariousMedQA: Multi-scale attentive interaction networks for chinese medical question answer selection. 2018. paper
  • VariousMedQA: What disease does this patient have? a large-scale open domain question answering dataset from medical exams. 2021. paper
  • MedDialog: Meddialog: Two large-scale medical dialogue datasets. 2020. paper
  • ChiMed: Qilin-Med: Multi-stage Knowledge Injection Advanced Medical Large Language Model. 2023. paper
  • ChiMed-VL: Qilin-Med-VL: Towards Chinese Large Vision-Language Model for General Healthcare. 2023. paper
  • Healthcare Magic: Healthcare Magic. platform
  • ICliniq: ICliniq. platform
  • Hybrid SFT: HuatuoGPT, towards Taming Language Model to Be a Doctor. 2023. paper
  • PMC-15M: Large-scale domain-specific pretraining for biomedical vision-language processing. 2023. paper
  • MedQuAD: A question-entailment approach to question answering. 2019. paper
  • VariousMedQA: Visual med-alpaca: A parameter-efficient biomedical llm with visual capabilities. 2023. repo
  • MTB: Med-flamingo: a multimodal medical few-shot learner. 2023. paper
  • PMC-OA: Pmc-clip: Contrastive language-image pre-training using biomedical documents. 2023. paper
  • Medical Meadow: MedAlpaca--An Open-Source Collection of Medical Conversational AI Models and Training Data. 2023. paper
  • Literature: S2ORC: The semantic scholar open research corpus. 2019. paper
  • MedC-I: Pmc-llama: Further finetuning llama on medical papers. 2023. paper
  • ShareGPT: Sharegpt. 2023. platform
  • PubMed: National Institutes of Health. PubMed Data. In National Library of Medicine. 2022. database
  • MedQA: What disease does this patient have? a large-scale open domain question answering dataset from medical exams. 2021. paper
  • MultiMedQA: Towards expert-level medical question answering with large language models. 2023. paper
  • MultiMedBench: Towards generalist biomedical ai. 2023. paper

✨ Practical Guide for Clinical Applications

Medical Diagnosis

  • Designing a Deep Learning-Driven Resource-Efficient Diagnostic System for Metastatic Breast Cancer: Reducing Long Delays of Clinical Diagnosis and Improving Patient Survival in Developing Countries. 2023. paper
  • AI in health and medicine. 2022. paper
  • Large language models in medicine. 2023. paper
  • Leveraging a medical knowledge graph into large language models for diagnosis prediction. 2023. paper
  • Chatcad: Interactive computer-aided diagnosis on medical image using large language models. 2023. paper

Formatting and ICD-Coding

  • Applying large language model artificial intelligence for retina International Classification of Diseases (ICD) coding. 2023. paper
  • PLM-ICD: automatic ICD coding with pretrained language models. 2022. paper

Clinical Report Generation

  • Using ChatGPT to write patient clinic letters. 2023. paper
  • ChatGPT: the future of discharge summaries?. 2023. paper
  • Chatcad: Interactive computer-aided diagnosis on medical image using large language models. 2023. paper
  • Can GPT-4V (ision) Serve Medical Applications? Case Studies on GPT-4V for Multimodal Medical Diagnosis. 2023. paper
  • Qilin-Med-VL: Towards Chinese Large Vision-Language Model for General Healthcare. 2023. paper
  • Customizing General-Purpose Foundation Models for Medical Report Generation. 2023. paper
  • Towards generalist foundation model for radiology. 2023. paper
  • Clinical Text Summarization: Adapting Large Language Models Can Outperform Human Experts. 2023. paper

Medical Education

  • Large Language Models in Medical Education: Opportunities, Challenges, and Future Directions. 2023. paper
  • The Advent of Generative Language Models in Medical Education. 2023. paper
  • The impending impacts of large language models on medical education. 2023. paper

Medical Robotics

  • A Nested U-Structure for Instrument Segmentation in Robotic Surgery. 2023. paper
  • The multi-trip autonomous mobile robot scheduling problem with time windows in a stochastic environment at smart hospitals. 2023. paper
  • Advanced robotics for medical rehabilitation. 2016. paper
  • GRID: Scene-Graph-based Instruction-driven Robotic Task Planning. 2023. paper
  • Trust in Construction AI-Powered Collaborative Robots: A Qualitative Empirical Analysis. 2023. paper

Medical Language Translation

  • Machine translation of standardised medical terminology using natural language processing: A Scoping Review. 2023. paper
  • The Advent of Generative Language Models in Medical Education. 2023. paper
  • The impending impacts of large language models on medical education. 2023. paper

Mental Health Support

  • ChatCounselor: A Large Language Models for Mental Health Support. 2023. paper
  • Tell me, what are you most afraid of? Exploring the Effects of Agent Representation on Information Disclosure in Human-Chatbot Interaction, 2023, paper
  • A Brief Wellbeing Training Session Delivered by a Humanoid Social Robot: A Pilot Randomized Controlled Trial. 2023. paper
  • Real conversations with artificial intelligence: A comparison between human–human online conversations and human–chatbot conversations. 2015. paper

⚔️ Practical Guide for Challenges

Hallucination

  • Survey of hallucination in natural language generation. 2023. paper
  • Med-halt: Medical domain hallucination test for large language models. 2023. paper
  • A survey of hallucination in large foundation models. 2023. paper
  • Selfcheckgpt: Zero-resource black-box hallucination detection for generative large language models. 2023. paper
  • Retrieval augmentation reduces hallucination in conversation. 2021. paper
  • Chain-of-verification reduces hallucination in large language models. 2023. paper

Lack of Evaluation Benchmarks and Metrics

  • What disease does this patient have? a large-scale open domain question answering dataset from medical exams. 2021. paper
  • Truthfulqa: Measuring how models mimic human falsehoods. 2021. paper
  • HaluEval: A Large-Scale Hallucination Evaluation Benchmark for Large Language Models. 2023. paper

Domain Data Limitations

  • Textbooks Are All You Need. 2023. paper
  • Model Dementia: Generated Data Makes Models Forget. 2023. paper

New Knowledge Adaptation

  • Detecting Edit Failures In Large Language Models: An Improved Specificity Benchmark. 2023. paper
  • Editing Large Language Models: Problems, Methods, and Opportunities. 2023. paper
  • Retrieval-augmented generation for knowledge-intensive nlp tasks. 2020. paper

Behavior Alignment

  • Aligning ai with shared human values. 2020. paper
  • Training a helpful and harmless assistant with reinforcement learning from human feedback. 2022. paper
  • Improving alignment of dialogue agents via targeted human judgements. 2022. paper
  • Webgpt: Browser-assisted question-answering with human feedback. 2021. paper
  • Languages are rewards: Hindsight finetuning using human feedback. 2023. paper

Ethical, Legal, and Safety Concerns

  • ChatGPT utility in healthcare education, research, and practice: systematic review on the promising perspectives and valid concerns. 2023. paper
  • ChatGPT listed as author on research papers: many scientists disapprove. 2023. paper
  • A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics. 2023. paper
  • Multi-step jailbreaking privacy attacks on chatgpt. 2023. paper
  • Jailbroken: How does llm safety training fail?. 2023. paper

🚀 Practical Guide for Future Directions

Introduction of New Benchmarks

  • A comprehensive benchmark study on biomedical text generation and mining with ChatGPT. 2023. paper
  • Creation and adoption of large language models in medicine. 2023. paper

Interdisciplinary Collaborations

  • Creation and adoption of large language models in medicine. 2023. paper
  • ChatGPT and Physicians' Malpractice Risk. 2023. paper

Multi-modal LLM

  • A Survey on Multimodal Large Language Models. 2023. paper
  • Mm-react: Prompting chatgpt for multimodal reasoning and action. 2023. paper
  • ChatGPT for shaping the future of dentistry: the potential of multi-modal large language model. 2023. paper
  • Frozen Language Model Helps ECG Zero-Shot Learning. 2023. paper
  • Exploring and Characterizing Large Language Models For Embedded System Development and Debugging. 2023. paper
  • MME: A Comprehensive Evaluation Benchmark for Multimodal Large Language Models. 2023. paper

LLMs in less established fields of healthcare

  • Large Language Models in Sport Science & Medicine: Opportunities, Risks and Considerations. 2023. paper

👍 Acknowledgement

📑 Citation

Please consider citing 📑 our papers if our repository is helpful to your work, thanks sincerely!

@article{zhou2023survey,
   title={A Survey of Large Language Models in Medicine: Progress, Application, and Challenge},
   author={Hongjian Zhou, Boyang Gu, Xinyu Zou, Yiru Li, Sam S. Chen, Peilin Zhou, Junling Liu, Yining Hua, Chengfeng Mao, Xian Wu, Zheng Li, Fenglin Liu},
   journal={arXiv preprint 2311.05112}
   year={2023}
}