Yongqi Fan

Ruihui Hou, Siyi Zhu, Ziyue Huai et al.

Large language models (LLMs) have been widely adopted in healthcare, yet they still encounter significant challenges in complex clinical decision-making scenarios. Existing benchmarks primarily assess LLM performance in single-course settings and lack systematic evaluation in multi-course scenarios, where a patient's condition evolves over time. To address this gap, we propose ClinicalMC, a benchmark for multi-course clinical decision-making. It includes 1,275 Chinese and 5,804 English samples across four stages from admission to discharge. These stages cover triage, first-course examination/diagnosis/treatment, subsequent multi-course examination/assessment/treatment, and final diagnosis. In ClinicalMC, patients in the English dataset undergo an average of 5.11 clinical courses, whereas those in the Chinese dataset undergo 3.42. To assess LLM performance, we construct a multi-agent evaluation framework that includes patient, examiner, and doctor agents. Based on the benchmark and framework, we design two experimental settings -- a single-turn static setting and a multi-turn dynamic setting -- and assess three categories of LLMs: 1) closed-source LLMs like GPT5-mini; 2) open-source LLMs like DeepSeek-V3.2; and 3) medical LLMs like HuatuoGPT-o1. Through extensive evaluation, we aim to better understand LLM performance in the medical domain and support its effective deployment in healthcare.

Ruihui Hou, Shencheng Chen, Yongqi Fan et al.

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 Chinese clinical diagnostic benchmark, called MSDiagnosis. This benchmark consists of 2,225 cases from 12 departments, covering tasks such as primary diagnosis, differential diagnosis, and final diagnosis. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the large language model to self-evaluate and adjust its diagnostic results. To this end, we test open-source models, closed-source models, and our proposed framework.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.

Cheng Yuan, Xinkai Rui, Yongqi Fan et al.

Despite the remarkable performance of Large Language Models (LLMs) in automated discharge summary generation, they still suffer from hallucination issues, such as generating inaccurate content or fabricating information without valid sources. In addition, electronic medical records (EMRs) typically consist of long-form data, making it challenging for LLMs to attribute the generated content to the sources. To address these challenges, we propose LCDS, a Logic-Controlled Discharge Summary generation system. LCDS constructs a source mapping table by calculating textual similarity between EMRs and discharge summaries to constrain the scope of summarized content. Moreover, LCDS incorporates a comprehensive set of logical rules, enabling it to generate more reliable silver discharge summaries tailored to different clinical fields. Furthermore, LCDS supports source attribution for generated content, allowing experts to efficiently review, provide feedback, and rectify errors. The resulting golden discharge summaries are subsequently recorded for incremental fine-tuning of LLMs. Our project and demo video are in the GitHub repository https://github.com/ycycyc02/LCDS.

Yongqi Fan, Hongli Sun, Kui Xue et al.

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.}

Guangya Yu, Yanhao Li, Zongying Jiang et al.

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.

Zhongzhen Huang, Kui Xue, Yongqi Fan et al.

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.

Nan Wang, Yongqi Fan, yansha zhu et al.

Large Language Models (LLMs) face challenges in knowledge-intensive reasoning tasks like classic multi-hop question and answering, which involves reasoning across multiple facts. This difficulty arises because the chain of thoughts (CoTs) generated by LLMs in such tasks often deviate from real or a priori reasoning paths. In contrast, knowledge graphs (KGs) explicitly represent the logical connections between facts through entities and relationships. This reflects a significant gap. Meanwhile, large reasoning models (LRMs), such as o1, have demonstrated that long-step reasoning significantly enhances the performance of LLMs. Building on these insights, we propose KG-o1, a four-stage approach that integrates KGs to enhance the multi-hop reasoning abilities of LLMs. We first filter out initial entities and generate complex subgraphs. Secondly, we construct logical paths for subgraphs and then use knowledge graphs to build a dataset with a complex and extended brainstorming process, which trains LLMs to imitate long-term reasoning. Finally, we employ rejection sampling to generate a self-improving corpus for direct preference optimization (DPO), further refining the LLMs reasoning abilities. We conducted experiments on two simple and two complex datasets. The results show that KG-o1 models exhibit superior performance across all tasks compared to existing LRMs.

Yongqi Fan, Yating Wang, Guandong Wang et al.

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 \textbf{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.