Papers by Yongqi Fan
MedOdyssey: A Medical Domain Benchmark for Long Context Evaluation Up to 200K Tokens (2025.findings-naacl)
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| Challenge: | Existing benchmarks in the generic domain have evaluated long-context capabilities for LLMs. |
| Approach: | They propose a medical long-context benchmark with seven length levels ranging from 4K to 200K tokens. |
| Outcome: | The proposed benchmarks have seven length levels ranging from 4K to 200K tokens. |
RRNorm: A Novel Framework for Chinese Disease Diagnoses Normalization via LLM-Driven Terminology Component Recognition and Reconstruction (2024.findings-acl)
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| Challenge: | Clinical Terminology Normalization (CTN) aims at finding standard terms from a given termbase for mentions extracted from clinical texts. |
| Approach: | They propose a method that leverages reasoning capability of large language models to recognize components of terms and automate decomposition. |
| Outcome: | The proposed strategy achieves state-of-the-art on the experimental dataset. |
Balancing Knowledge Breadth and Task Depth for Effective Domain Adaptation Fine-Tuning (2026.findings-acl)
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| Challenge: | a lack of knowledge breadth and task depth can hinder curriculum learning in domains such as medicine and finance. |
| Approach: | They propose a two-dimensional curriculum learning framework that coordinates model training along two orthogonal axes: the knowledge dimension and the task dimension. |
| Outcome: | The proposed framework improves accuracy on medical evaluations by 2.49% and on financial evaluations 1.2% compared with the second-best method. |
Travel on the ICD Tree: Benchmarking Agentic Reasoning for ICD Coding from Chinese Electronic Medical Records (2026.findings-acl)
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| Challenge: | Accurate International Classification of Diseases (ICD) coding is crucial for hospital management and healthcare data governance. |
| Approach: | They propose a framework to evaluate ICD coding based on complete EMRs . they use a dataset of 560 real clinical records covering 434 common diseases . |
| Outcome: | The proposed framework explores the capability boundaries of large language models under different paradigms. |
ClinicalMC: A Benchmark for Multi-Course Clinical Decision-Making with Large Language Models (2026.findings-acl)
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| Challenge: | Existing benchmarks assess LLM performance in single-course settings and lack systematic evaluation in multi-course scenarios, where a patient’s condition evolves over time. |
| Approach: | They propose to use large language models to assess their performance in multi-course clinical decision-making scenarios where a patient’s condition evolves over time. |
| Outcome: | The proposed model includes 1,275 Chinese and 5,804 English samples across four stages from admission to discharge. |
PEToolLLM: Towards Personalized Tool Learning in Large Language Models (2025.findings-acl)
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| Challenge: | Existing tool learning studies focus on general-purpose tool-use capability, but ignore the importance of personalized tool-user preferences. |
| Approach: | They propose a framework to adapt Large Language Models to personalized tool learning task, which is trained through supervised fine-tuning and direct preference optimization. |
| Outcome: | Extensive experiments on PEToolBench show that the proposed framework outperforms existing LLMs in the personalized tool learning task. |
CMQCIC-Bench: A Chinese Benchmark for Evaluating Large Language Models in Medical Quality Control Indicator Calculation (2025.findings-acl)
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Guangya Yu, Yanhao Li, Zongying Jiang, Yuxiong Jin, Li Dai, Yupian Lin, Ruihui Hou, Weiyan Zhang, Yongqi Fan, Qi Ye, Jingping Liu, Tong Ruan
| Challenge: | Medical quality control indicators are essential to assess the qualifications of healthcare institutions for medical services. |
| Approach: | They propose a Chinese electronic medical records-based dataset for MQCIC and propose CF-IR method that disentangles clinical fact verification and inferential rule reasoning actions. |
| Outcome: | The proposed method outperforms Chain-of-Thought methods on 20 representative LLMs, covering general and medical models. |
MinosEval: Distinguishing Factoid and Non-Factoid for Tailored Open-Ended QA Evaluation with LLMs (2025.findings-acl)
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| Challenge: | Existing evaluation methods overlook the distinction between factoid and non-factoidic questions. |
| Approach: | They propose a method that distinguishes open-ended questions and ranks candidate answers . they propose QA requires longer answer statements and nuanced reasoning processes . |
| Outcome: | The proposed method better aligns with human annotations and offers more interpretable results. |
An LLM-based Framework for Biomedical Terminology Normalization in Social Media via Multi-Agent Collaboration (2025.coling-main)
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| Challenge: | Experimental results indicate that our approach exhibits competitive performance. |
| Approach: | They propose a tuning-free approach to normalize non-standard terms using large language models . they use a search engine and a domain knowledge base to expand the short texts into accurate descriptions . |
| Outcome: | The proposed approach is based on the "Recall and Re-rank" framework . it can be used to identify the standard term in a specified termbase for non-standardized mentions . |
LCDS: A Logic-Controlled Discharge Summary Generation System Supporting Source Attribution and Expert Review (2025.acl-demo)
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| Challenge: | Large language models (LLMs) are capable of generating inaccurate discharge summary content or fabricating information without valid sources. |
| Approach: | They propose a tool for empowering LLMs with Logic-Controlled Discharge Summary generation. |
| Outcome: | The proposed tool identifies the writing logic of discharge summaries and integrates it with EMRs to generate silver discharge summararies. |
MedEureka: A Medical Domain Benchmark for Multi-Granularity and Multi-Data-Type Embedding-Based Retrieval (2025.findings-naacl)
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| Challenge: | Embedding-based retrieval (EBR) is a mainstream approach in information retrieval. |
| Approach: | They propose an enriched benchmark to evaluate retrieval capabilities of embedding models . they use four levels of granularity and six types of medical texts to prompt instruction-fine-tuned embeddable models. |
| Outcome: | The proposed benchmark evaluates the retrieval capabilities of embedding models with multi-granularity and multi-data types. |
MCLE-Mol: Empowering LLM with Molecular Comprehension and Low-Cost Continual Evolution for Interpretable Property Prediction (2026.findings-acl)
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Zhili Pu, Lantian Zhang, Hao Duan, Zhixing Zhang, Keyun Zhu, Yongqi Fan, Ruihui Hou, Tong Ruan, Yun Tang
| Challenge: | Large language models (LLMs) offer a new paradigm for molecular property prediction (MPP), yet a semantic gap between natural language and molecul representations limits their ability to capture structure–activity relationships (SAR). |
| Approach: | They propose an ML–LLM–Rule collaborative framework for MPP that injects ML-derived substructure attribution values into LLMs and calibrates them under specific chemical contexts. |
| Outcome: | The proposed framework outperforms baseline models on multiple benchmark datasets and is highly interpretable. |
Text-to-ES Bench: A Comprehensive Benchmark for Converting Natural Language to Elasticsearch Query (2025.acl-long)
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DonggeXue DonggeXue, Zhili Pu, Zhentao Xia, Hongli Sun, Ruihui Hou, Guangya Yu, Yupian Lin, Yongqi Fan, Jingping Liu, Tong Ruan
| Challenge: | Recent research on text-to-Query has explored using large language models to convert user query intent to executable code. |
| Approach: | They propose a novel semantic parsing task that leverages large language models to generate domain-specific language and post-processing code to support multi-index Elasticsearch queries. |
| Outcome: | The proposed model outperforms DeepSeek-R1 on the large Elasticsearch Dataset (LED) and BirdES datasets. |
TInR: Exploring Tool-Internalized Reasoning in Large Language Models (2026.acl-long)
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| Challenge: | Existing methods rely on external tool documentation during reasoning, leading to tool mastery difficulty, tool size constraints, and inference inefficiency. |
| Approach: | They propose a tool-internalized reasoning framework for unified reasoning and tool usage that integrates external tools into Large Language Models (LLMs) to address these issues, they propose 'tool-internet-based' reasoning. |
| Outcome: | The proposed method achieves superior performance across in-domain and out-of-domain settings, highlighting its effectiveness and efficiency. |