Elasticsearch (ES) is a distributed RESTful search engine optimized for large-scale and long-text search scenarios. Recent research on text-to-Query has explored using large language models (LLMs) to convert user query intent to executable code, making it an increasingly popular research topic. To our knowledge, we are the first to introduce the novel semantic parsing task text-to-ES. To bridge the gap between LLM and ES, in detail, we leverage LLMs and employ domain experts to generate ES query bodies, which are Domain-Specific Language (DSL), along with the corresponding post-processing code to support multi-index ES queries. Consequently, we propose the text-to-ES benchmark that consists of two datasets: Large Elasticsearch Dataset (LED), containing 26,207 text-ES pairs derived from a 224.9GB schema-free database, and ElasticSearch (BirdES)with 10,926 pairs sourced from the Bird dataset on a 33.4GB schema-fixed database. Compared with fourteen advanced LLMs and six code-based LLMs, the model we trained outperformed DeepSeek-R1 by 15.64% on the LED dataset, setting a new state-of-the-art, and achieved 78% of DeepSeek-R1’s performance on the BirdES dataset. Additionally, we provide in-depth experimental analyses and suggest future research directions for this task. Our datasets are available at https://huggingface.co/datasets/Barry1915/Text-to-ES.

Despite the remarkable performance of Large Language Models (LLMs) in automated discharge summary generation, they still suffer from generating inaccurate content or fabricating information without valid sources. To address these issues, we propose LCDS, a tool for empowering LLMs with Logic-Controlled Discharge Summary generation. LCDS constructs a source mapping table by calculating the textual similarity between electronic medical records (EMRs) and discharge summaries, providing a structured reference for generation. Based on a comprehensive set of logical rules, LCDS identifies the structured writing logic of discharge summaries and integrates it with EMRs to generate silver discharge summaries. Furthermore, LCDS traces the provenance of generated content, allowing experts to review, provide feedback, and rectify errors to produce golden discharge summaries, which are subsequently recorded for the incremental fine-tuning of LLMs.Our project and demo video are in the GitHub repository https://github.com/ycycyc02/LCDS.

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.

Medical quality control indicators are essential to assess the qualifications of healthcare institutions for medical services. With the impressive performance of large language models (LLMs) like GPT-4 in the medical field, leveraging these technologies for the Medical Quality Control Indicator Calculation (MQCIC) presents a promising approach. In this work, (1) we introduce a real-world task MQCIC and propose an open-source Chinese electronic medical records (EMRs)-based dataset (CMQCIC-Bench) comprising 785 instances and 76 indicators. (2) We propose a semi-automatic method to enhance the rule representation. Then we propose the Clinical Facts-based Inferential Rule (CF-IR) method that disentangles the clinical fact verification and inferential rule reasoning actions. (3) We conduct comprehensive experiments on 20 representative LLMs, covering general and medical models. Our findings reveal that CF-IR outperforms Chain-of-Thought methods in MQCIC tasks. (4) We conduct an error analysis and investigate the capabilities of clinical fact verification and inferential rule reasoning, providing insights to improve performance in the MQCIC further. The dataset and code is available in this repository https://github.com/YuY-2001/C-MQCIC.

Open-ended question answering (QA) is a key task for evaluating the capabilities of large language models (LLMs). Compared to closed-ended QA, it demands longer answer statements, more nuanced reasoning processes, and diverse expressions, making refined and interpretable automatic evaluation both crucial and challenging. Traditional metrics like ROUGE and BERTScore struggle to capture semantic similarities due to different patterns between model responses and reference answers. Current LLM-based evaluation approaches, such as pairwise or listwise comparisons of candidate answers, lack intuitive interpretability. While pointwise scoring of each response provides some descriptions, it fails to adapt across different question contents. Most notably, existing methods overlook the distinction between factoid and non-factoid questions. To address these challenges, we propose MinosEval, a novel evaluation method that first distinguishes open-ended questions and then ranks candidate answers using different evaluation strategies. For factoid questions, it applies an adaptive key-point scoring strategy, while for non-factoid questions, it uses an instance-aware listwise ranking strategy. Experiments on multiple open-ended QA datasets, including self-built ones with more candidate responses to complement community resources, show that MinosEval better aligns with human annotations and offers more interpretable results.

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.