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.

A multi-perspective combined recall and rank framework for Chinese procedure terminology normalization

Medical terminology normalization aims to map the clinical mention to terminologies come from a knowledge base, which plays an important role in analyzing Electronic Health Record(EHR) and many downstream tasks. In this paper, we focus on Chinese procedure terminology normalization. The expression of terminologies are various and one medical mention may be linked to multiple terminologies. Previous study explores some methods such as multi-class classification or learning to rank(LTR) to sort the terminologies by literature and semantic information. However, these information is inadequate to find the right terminologies, particularly in multi-implication cases. In this work, we propose a combined recall and rank framework to solve the above problems. This framework is composed of a multi-task candidate generator(MTCG), a keywords attentive ranker(KAR) and a fusion block(FB). MTCG is utilized to predict the mention implication number and recall candidates with semantic similarity. KAR is based on Bert with a keywords attentive mechanism which focuses on keywords such as procedure sites and procedure types. FB merges the similarity come from MTCG and KAR to sort the terminologies from different perspectives. Detailed experimental analysis shows our proposed framework has a remarkable improvement on both performance and efficiency.

Fine-tuning BERT for Joint Entity and Relation Extraction in Chinese Medical Text

Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the same time, the language model has achieved excellent results in more and more natural language processing tasks. In this paper, we present a focused attention model for the joint entity and relation extraction task. Our model integrates well-known BERT language model into joint learning through dynamic range attention mechanism, thus improving the feature representation ability of shared parameter layer. Experimental results on coronary angiography texts collected from Shuguang Hospital show that the F1-score of named entity recognition and relation classification tasks reach 96.89% and 88.51%, which are better than state-of-the-art methods 1.65% and 1.22%, respectively.

Question Answering based Clinical Text Structuring Using Pre-trained Language Model

Clinical text structuring is a critical and fundamental task for clinical research. Traditional methods such as taskspecific end-to-end models and pipeline models usually suffer from the lack of dataset and error propagation. In this paper, we present a question answering based clinical text structuring (QA-CTS) task to unify different specific tasks and make dataset shareable. A novel model that aims to introduce domain-specific features (e.g., clinical named entity information) into pre-trained language model is also proposed for QA-CTS task. Experimental results on Chinese pathology reports collected from Ruijing Hospital demonstrate our presented QA-CTS task is very effective to improve the performance on specific tasks. Our proposed model also competes favorably with strong baseline models in specific tasks.