Biomedical Terminology Normalization aims to identify the standard term in a specified termbase for non-standardized mentions from social media or clinical texts, employing the mainstream “Recall and Re-rank” framework. Instead of the traditional pretraining-finetuning paradigm, we would like to explore the possibility of accomplishing this task through a tuning-free paradigm using powerful Large Language Models (LLMs), hoping to address the costs of re-training due to discrepancies of both standard termbases and annotation protocols. Another major obstacle in this task is that both mentions and terms are short texts. Short texts contain an insufficient amount of information that can introduce ambiguity, especially in a biomedical context. Therefore, besides using the advanced embedding model, we implement a Retrieval-Augmented Generation (RAG) based knowledge card generation module. This module introduces an LLM agent that expands the short texts into accurate, harmonized, and more informative descriptions using a search engine and a domain knowledge base. Furthermore, we present an innovative tuning-free agent collaboration framework for the biomedical terminology normalization task in social media. By leveraging the internal knowledge and the reasoning capabilities of LLM, our framework conducts more sophisticated recall, ranking and re-ranking processes with the collaboration of different LLM agents. Experimental results across multiple datasets indicate that our approach exhibits competitive performance. We release our code and data on the github repository JOHNNY-fans/RankNorm.

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: https://github.com/JOHNNY-fans/MedOdyssey.

Embedding-based retrieval (EBR), the mainstream approach in information retrieval (IR), aims to help users obtain relevant information and plays a crucial role in retrieval-augmented generation (RAG) techniques of large language models (LLMs). Numerous methods have been proposed to significantly improve the quality of retrieved content and many generic benchmarks are proposed to evaluate the retrieval abilities of embedding models. However, texts in the medical domain present unique contexts, structures, and language patterns, such as terminology, doctor-patient dialogue, and electronic health records (EHRs). Despite these unique features, specific benchmarks for medical context retrieval are still lacking. In this paper, we propose MedEureka, an enriched benchmark designed to evaluate medical-context retrieval capabilities of embedding models with multi-granularity and multi-data types. MedEureka includes four levels of granularity and six types of medical texts, encompassing 18 datasets, incorporating granularity and data type description to prompt instruction-fine-tuned text embedding models for embedding generation. We also provide the MedEureka Toolkit to support evaluation on the MedEureka test set. Our experiments evaluate state-of-the-art open-source and proprietary embedding models, and fine-tuned classical baselines, providing a detailed performance analysis. This underscores the challenges of using embedding models for medical domain retrieval and the need for further research. Our code and data are released in the repository: https://github.com/JOHNNY-fans/MedEureka.

The Clinical Terminology Normalization aims at finding standard terms from a given termbase for mentions extracted from clinical texts. However, we found that extracted mentions suffer from the multi-implication problem, especially disease diagnoses. The reason for this is that physicians often use abbreviations, conjunctions, and juxtapositions when writing diagnoses, and it is difficult to manually decompose. To address this problem, we propose a Terminology Component Recognition and Reconstruction strategy that leverages the reasoning capability of large language models (LLMs) to recognize the components of terms, enabling automated decomposition and transforming original mentions into multiple atomic mentions. Furthermore, we adopt the mainstream “Recall and Rank” framework to apply the benefits of the above strategy to the task flow. By leveraging the LLM incorporating the advanced sampling strategies, we design a sampling algorithm for atomic mentions and train the recall model using contrastive learning. Besides the information about the components is also used as knowledge to guide the final term ranking and selection. The experimental results show that our proposed strategy effectively improves the performance of the terminology normalization task and our proposed approach achieves state-of-the-art on the experimental dataset. We release our code and data on the repository https://github.com/yuugaochyan/RRNorm.