MSDiagnosis: An EMR-based Dataset for Clinical Multi-Step Diagnosis

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

MedOdyssey: A Medical Domain Benchmark for Long Context Evaluation Up to 200K Tokens

Numerous advanced Large Language Models (LLMs) now support context lengths up to 128K, and some extend to 200K. Some benchmarks in the generic domain have also followed up on evaluating long-context capabilities. In the medical domain, tasks are distinctive due to the unique contexts and need for domain expertise, necessitating further evaluation. However, despite the frequent presence of long texts in medical scenarios, evaluation benchmarks of long-context capabilities for LLMs in this field are still rare. In this paper, we propose MedOdyssey, the first medical long-context benchmark with seven length levels ranging from 4K to 200K tokens. MedOdyssey consists of two primary components: the medical-context "needles in a haystack" task and a series of tasks specific to medical applications, together comprising 10 datasets. The first component includes challenges such as counter-intuitive reasoning and novel (unknown) facts injection to mitigate knowledge leakage and data contamination of LLMs. The second component confronts the challenge of requiring professional medical expertise. Especially, we design the ``Maximum Identical Context'' principle to improve fairness by guaranteeing that different LLMs observe as many identical contexts as possible. Our experiment evaluates advanced proprietary and open-source LLMs tailored for processing long contexts and presents detailed performance analyses. This highlights that LLMs still face challenges and need for further research in this area. Our code and data are released in the repository: \url{https://github.com/JOHNNY-fans/MedOdyssey.}

Medical Dialogue: A Survey of Categories, Methods, Evaluation and Challenges

This paper surveys and organizes research works on medical dialog systems, which is an important yet challenging task. Although these systems have been surveyed in the medical community from an application perspective, a systematic review from a rigorous technical perspective has to date remained noticeably absent. As a result, an overview of the categories, methods, and evaluation of medical dialogue systems remain limited and underspecified, hindering the further improvement of this area. To fill this gap, we investigate an initial pool of 325 papers from well-known computer science, and natural language processing conferences and journals, and make an overview. Recently, large language models have shown strong model capacity on downstream tasks, which also reshaped medical dialog systems' foundation. Despite the alluring practical application value, current medical dialogue systems still suffer from problems. To this end, this paper lists the grand challenges of medical dialog systems, especially of large language models.

Tool Calling: Enhancing Medication Consultation via Retrieval-Augmented Large Language Models

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new \textit{Distill-Retrieve-Read} framework instead of the previous \textit{Retrieve-then-Read}. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

OpenMEDLab: An Open-source Platform for Multi-modality Foundation Models in Medicine

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

MedDM:LLM-executable clinical guidance tree for clinical decision-making

It is becoming increasingly emphasis on the importance of LLM participating in clinical diagnosis decision-making. However, the low specialization refers to that current medical LLMs can not provide specific medical advice, which are more like a medical Q\&A. And there is no suitable clinical guidance tree data set that can be used directly with LLM. To address this issue, we first propose LLM-executavle clinical guidance tree(CGT), which can be directly used by large language models, and construct medical diagnostic decision-making dataset (MedDM), from flowcharts in clinical practice guidelines. We propose an approach to screen flowcharts from medical literature, followed by their identification and conversion into standardized diagnostic decision trees. Constructed a knowledge base with 1202 decision trees, which came from 5000 medical literature and covered 12 hospital departments, including internal medicine, surgery, psychiatry, and over 500 diseases.Moreover, we propose a method for reasoning on LLM-executable CGT and a Patient-LLM multi-turn dialogue framework.

LLM-Mini-CEX: Automatic Evaluation of Large Language Model for Diagnostic Conversation

There is an increasing interest in developing LLMs for medical diagnosis to improve diagnosis efficiency. Despite their alluring technological potential, there is no unified and comprehensive evaluation criterion, leading to the inability to evaluate the quality and potential risks of medical LLMs, further hindering the application of LLMs in medical treatment scenarios. Besides, current evaluations heavily rely on labor-intensive interactions with LLMs to obtain diagnostic dialogues and human evaluation on the quality of diagnosis dialogue. To tackle the lack of unified and comprehensive evaluation criterion, we first initially establish an evaluation criterion, termed LLM-specific Mini-CEX to assess the diagnostic capabilities of LLMs effectively, based on original Mini-CEX. To address the labor-intensive interaction problem, we develop a patient simulator to engage in automatic conversations with LLMs, and utilize ChatGPT for evaluating diagnosis dialogues automatically. Experimental results show that the LLM-specific Mini-CEX is adequate and necessary to evaluate medical diagnosis dialogue. Besides, ChatGPT can replace manual evaluation on the metrics of humanistic qualities and provides reproducible and automated comparisons between different LLMs.

CBEAF-Adapting: Enhanced Continual Pretraining for Building Chinese Biomedical Language Model

Continual pretraining is a standard way of building a domain-specific pretrained language model from a general-domain language model. However, sequential task training may cause catastrophic forgetting, which affects the model performance in downstream tasks. In this paper, we propose a continual pretraining method for the BERT-based model, named CBEAF-Adapting (Chinese Biomedical Enhanced Attention-FFN Adapting). Its main idea is to introduce a small number of attention heads and hidden units inside each self-attention layer and feed-forward network. Using the Chinese biomedical domain as a running example, we trained a domain-specific language model named CBEAF-RoBERTa. We conduct experiments by applying models to downstream tasks. The results demonstrate that with only about 3% of model parameters trained, our method could achieve about 0.5%, 2% average performance gain compared to the best performing model in baseline and the domain-specific model, PCL-MedBERT, respectively. We also examine the forgetting problem of different pretraining methods. Our method alleviates the problem by about 13% compared to fine-tuning.

FL-Tuning: Layer Tuning for Feed-Forward Network in Transformer

Prompt tuning is an emerging way of adapting pre-trained language models to downstream tasks. However, the existing studies are mainly to add prompts to the input sequence. This way would not work as expected due to the intermediate multi-head self-attention and feed-forward network computation, making model optimization not very smooth. Hence, we propose a novel tuning way called layer tuning, aiming to add learnable parameters in Transformer layers. Specifically, we focus on layer tuning for feed-forward network in the Transformer, namely FL-tuning. It introduces additional units into the hidden layer of each feed-forward network. We conduct extensive experiments on the public CLUE benchmark. The results show that: 1) Our FL-tuning outperforms prompt tuning methods under both full-data and few-shot settings in almost all cases. In particular, it improves accuracy by 17.93% (full-data setting) on WSC 1.0 and F1 by 16.142% (few-shot setting) on CLUENER over P-tuning v2. 2) Our FL-tuning is more stable and converges about 1.17 times faster than P-tuning v2. 3) With only about 3% of Transformer's parameters to be trained, FL-tuning is comparable with fine-tuning on most datasets, and significantly outperforms fine-tuning (e.g., accuracy improved by 12.9% on WSC 1.1) on several datasets. The source codes are available at https://github.com/genggui001/FL-Tuning.

Prompt-based Generative Approach towards Multi-Hierarchical Medical Dialogue State Tracking

The medical dialogue system is a promising application that can provide great convenience for patients. The dialogue state tracking (DST) module in the medical dialogue system which interprets utterances into the machine-readable structure for downstream tasks is particularly challenging. Firstly, the states need to be able to represent compound entities such as symptoms with their body part or diseases with degrees of severity to provide enough information for decision support. Secondly, these named entities in the utterance might be discontinuous and scattered across sentences and speakers. These also make it difficult to annotate a large corpus which is essential for most methods. Therefore, we first define a multi-hierarchical state structure. We annotate and publish a medical dialogue dataset in Chinese. To the best of our knowledge, there are no publicly available ones before. Then we propose a Prompt-based Generative Approach which can generate slot values with multi-hierarchies incrementally using a top-down approach. A dialogue style prompt is also supplemented to utilize the large unlabeled dialogue corpus to alleviate the data scarcity problem. The experiments show that our approach outperforms other DST methods and is rather effective in the scenario with little data.