arXiv subjects

Hong Yu

Publications and source records attributed to Hong Yu.

At least 55 records · Page 3Linked to original sources

arXiv2025

SynthEHR-Eviction: Enhancing Eviction SDoH Detection with LLM-Augmented Synthetic EHR Data

Eviction is a significant yet understudied social determinants of health (SDoH), linked to housing instability, unemployment, and mental health. While eviction appears in unstructured electronic health records (EHRs), it is rarely coded in structured fields, limiting downstream applications. We introduce SynthEHR-Eviction, a scalable pipeline combining LLMs, human-in-the-loop annotation, and automated prompt optimization (APO) to extract eviction statuses from clinical notes. Using this pipeline, we created the largest public eviction-related SDoH dataset to date, comprising 14 fine-grained categories. Fine-tuned LLMs (e.g., Qwen2.5, LLaMA3) trained on SynthEHR-Eviction achieved Macro-F1 scores of 88.8% (eviction) and 90.3% (other SDoH) on human validated data, outperforming GPT-4o-APO (87.8%, 87.3%), GPT-4o-mini-APO (69.1%, 78.1%), and BioBERT (60.7%, 68.3%), while enabling cost-effective deployment across various model sizes. The pipeline reduces annotation effort by over 80%, accelerates dataset creation, enables scalable eviction detection, and generalizes to other information extraction tasks.

cs.CL↗

arXiv2025

RADAR: Benchmarking Language Models on Imperfect Tabular Data

Language models (LMs) are increasingly being deployed to perform autonomous data analyses. However, their data awareness -- the ability to recognize, reason over, and appropriately handle data artifacts such as missing values, outliers, and logical inconsistencies -- remains underexplored. These artifacts are especially common in real-world tabular data and, if mishandled, can significantly compromise the validity of analytical conclusions. To address this gap, we present RADAR, a benchmark for systematically evaluating data-aware reasoning on tabular data. We develop a framework to simulate data artifacts via programmatic perturbations to enable targeted evaluation of model behavior. RADAR comprises 2980 table query pairs, grounded in real-world data spanning 9 domains and 5 data artifact types. In addition to evaluating artifact handling, RADAR systematically varies table size to study how reasoning performance holds when increasing table size. Our evaluation reveals that, despite decent performance on tables without data artifacts, frontier models degrade significantly when data artifacts are introduced, exposing critical gaps in their capacity for robust, data-aware analysis. Designed to be flexible and extensible, RADAR supports diverse perturbation types and controllable table sizes, offering a valuable resource for advancing tabular reasoning.

cs.DB↗

arXiv2025

Evaluating Evaluation Metrics -- The Mirage of Hallucination Detection

Hallucinations pose a significant obstacle to the reliability and widespread adoption of language models, yet their accurate measurement remains a persistent challenge. While many task- and domain-specific metrics have been proposed to assess faithfulness and factuality concerns, the robustness and generalization of these metrics are still untested. In this paper, we conduct a large-scale empirical evaluation of 6 diverse sets of hallucination detection metrics across 4 datasets, 37 language models from 5 families, and 5 decoding methods. Our extensive investigation reveals concerning gaps in current hallucination evaluation: metrics often fail to align with human judgments, take an overtly myopic view of the problem, and show inconsistent gains with parameter scaling. Encouragingly, LLM-based evaluation, particularly with GPT-4, yields the best overall results, and mode-seeking decoding methods seem to reduce hallucinations, especially in knowledge-grounded settings. These findings underscore the need for more robust metrics to understand and quantify hallucinations, and better strategies to mitigate them.

cs.CL↗

arXiv2025

Enhancing LLMs for Identifying and Prioritizing Important Medical Jargons from Electronic Health Record Notes Utilizing Data Augmentation: A Comparative Study

OpenNotes gives patients access to their EHR notes, but dense medical jargon limits comprehension. We evaluate closed-source and open-source LLMs for extracting and prioritizing the jargon terms most relevant to individual patients, using 90 expert-annotated EHR notes. We test combinations of general vs. structured prompts, zero-shot vs. few-shot prompting, fine-tuning, and GPT-4o-based data augmentation, the last paired with a ranking technique to refine training in low-resource settings. To assess the effect of dataset size, we fine-tune on augmented datasets scaled from 10 to 9,995 examples. All settings are evaluated with 10-fold cross-validation, reporting F1 and Mean Reciprocal Rank (MRR) under two string-matching criteria (relaxed matching and Jaccard Index), followed by an error analysis of model outputs. Open-source models performed best when fine-tuned on the gold-standard dataset: under Jaccard-based matching, DeepSeek 8B achieved the top F1 (0.431, SD 0.046) and BioMistral 7B the top MRR (0.577, SD 0.109). Under relaxed matching, however, open-source models did not match closed-source performance even with augmentation or fine-tuning. Few-shot prompting offered no advantage over zero-shot in vanilla models; prompting style substantially affected results; fine-tuning on a small gold-standard set improved performance; and data augmentation matched or exceeded fine-tuning, though its benefit depended heavily on augmented-data quality. These findings show that prompting strategy, fine-tuning, and data augmentation each meaningfully improve LLM performance on patient-centered jargon extraction in low-resource clinical settings.

cs.CL↗

arXiv2024

RARE: Retrieval-Augmented Reasoning Enhancement for Large Language Models

This work introduces RARE (Retrieval-Augmented Reasoning Enhancement), a versatile extension to the mutual reasoning framework (rStar), aimed at enhancing reasoning accuracy and factual integrity across large language models (LLMs) for complex, knowledge-intensive tasks such as commonsense and medical reasoning. RARE incorporates two innovative actions within the Monte Carlo Tree Search (MCTS) framework: A6, which generates search queries based on the initial problem statement, performs information retrieval using those queries, and augments reasoning with the retrieved data to formulate the final answer; and A7, which leverages information retrieval specifically for generated sub-questions and re-answers these sub-questions with the relevant contextual information. Additionally, a Retrieval-Augmented Factuality Scorer is proposed to replace the original discriminator, prioritizing reasoning paths that meet high standards of factuality. Experimental results with LLaMA 3.1 show that RARE enables open-source LLMs to achieve competitive performance with top open-source models like GPT-4 and GPT-4o. This research establishes RARE as a scalable solution for improving LLMs in domains where logical coherence and factual integrity are critical.

cs.CL↗

arXiv2024

CRTRE: Causal Rule Generation with Target Trial Emulation Framework

Causal inference and model interpretability are gaining increasing attention, particularly in the biomedical domain. Despite recent advance, decorrelating features in nonlinear environments with human-interpretable representations remains underexplored. In this study, we introduce a novel method called causal rule generation with target trial emulation framework (CRTRE), which applies randomize trial design principles to estimate the causal effect of association rules. We then incorporate such association rules for the downstream applications such as prediction of disease onsets. Extensive experiments on six healthcare datasets, including synthetic data, real-world disease collections, and MIMIC-III/IV, demonstrate the model's superior performance. Specifically, our method achieved a $β$ error of 0.907, outperforming DWR (1.024) and SVM (1.141). On real-world datasets, our model achieved accuracies of 0.789, 0.920, and 0.300 for Esophageal Cancer, Heart Disease, and Cauda Equina Syndrome prediction task, respectively, consistently surpassing baseline models. On the ICD code prediction tasks, it achieved AUC Macro scores of 92.8 on MIMIC-III and 96.7 on MIMIC-IV, outperforming the state-of-the-art models KEPT and MSMN. Expert evaluations further validate the model's effectiveness, causality, and interpretability.

cs.LG↗

arXiv2024

Data Extraction Attacks in Retrieval-Augmented Generation via Backdoors

Despite significant advancements, large language models (LLMs) still struggle with providing accurate answers when lacking domain-specific or up-to-date knowledge. Retrieval-Augmented Generation (RAG) addresses this limitation by incorporating external knowledge bases, but it also introduces new attack surfaces. In this paper, we investigate data extraction attacks targeting RAG's knowledge databases. We show that previous prompt injection-based extraction attacks largely rely on the instruction-following capabilities of LLMs. As a result, they fail on models that are less responsive to such malicious prompts -- for example, our experiments show that state-of-the-art attacks achieve near-zero success on Gemma-2B-IT. Moreover, even for models that can follow these instructions, we found fine-tuning may significantly reduce attack performance. To further reveal the vulnerability, we propose to backdoor RAG, where a small portion of poisoned data is injected during the fine-tuning phase to create a backdoor within the LLM. When this compromised LLM is integrated into a RAG system, attackers can exploit specific triggers in prompts to manipulate the LLM to leak documents from the retrieval database. By carefully designing the poisoned data, we achieve both verbatim and paraphrased document extraction. For example, on Gemma-2B-IT, we show that with only 5\% poisoned data, our method achieves an average success rate of 94.1\% for verbatim extraction (ROUGE-L score: 82.1) and 63.6\% for paraphrased extraction (average ROUGE score: 66.4) across four datasets. These results underscore the privacy risks associated with the supply chain when deploying RAG systems.

cs.CR↗

arXiv2024

README: Bridging Medical Jargon and Lay Understanding for Patient Education through Data-Centric NLP

The advancement in healthcare has shifted focus toward patient-centric approaches, particularly in self-care and patient education, facilitated by access to Electronic Health Records (EHR). However, medical jargon in EHRs poses significant challenges in patient comprehension. To address this, we introduce a new task of automatically generating lay definitions, aiming to simplify complex medical terms into patient-friendly lay language. We first created the README dataset, an extensive collection of over 50,000 unique (medical term, lay definition) pairs and 300,000 mentions, each offering context-aware lay definitions manually annotated by domain experts. We have also engineered a data-centric Human-AI pipeline that synergizes data filtering, augmentation, and selection to improve data quality. We then used README as the training data for models and leveraged a Retrieval-Augmented Generation method to reduce hallucinations and improve the quality of model outputs. Our extensive automatic and human evaluations demonstrate that open-source mobile-friendly models, when fine-tuned with high-quality data, are capable of matching or even surpassing the performance of state-of-the-art closed-source large language models like ChatGPT. This research represents a significant stride in closing the knowledge gap in patient education and advancing patient-centric healthcare solutions.

cs.CL↗

arXiv2024

SemiHVision: Enhancing Medical Multimodal Models with a Semi-Human Annotated Dataset and Fine-Tuned Instruction Generation

Multimodal large language models (MLLMs) have made significant strides, yet they face challenges in the medical domain due to limited specialized knowledge. While recent medical MLLMs demonstrate strong performance in lab settings, they often struggle in real-world applications, highlighting a substantial gap between research and practice. In this paper, we seek to address this gap at various stages of the end-to-end learning pipeline, including data collection, model fine-tuning, and evaluation. At the data collection stage, we introduce SemiHVision, a dataset that combines human annotations with automated augmentation techniques to improve both medical knowledge representation and diagnostic reasoning. For model fine-tuning, we trained PMC-Cambrian-8B-AN over 2400 H100 GPU hours, resulting in performance that surpasses public medical models like HuatuoGPT-Vision-34B (79.0% vs. 66.7%) and private general models like Claude3-Opus (55.7%) on traditional benchmarks such as SLAKE and VQA-RAD. In the evaluation phase, we observed that traditional benchmarks cannot accurately reflect realistic clinical task capabilities. To overcome this limitation and provide more targeted guidance for model evaluation, we introduce the JAMA Clinical Challenge, a novel benchmark specifically designed to evaluate diagnostic reasoning. On this benchmark, PMC-Cambrian-AN achieves state-of-the-art performance with a GPT-4 score of 1.29, significantly outperforming HuatuoGPT-Vision-34B (1.13) and Claude3-Opus (1.17), demonstrating its superior diagnostic reasoning abilities.

cs.CL↗

arXiv2024

MCQG-SRefine: Multiple Choice Question Generation and Evaluation with Iterative Self-Critique, Correction, and Comparison Feedback

Automatic question generation (QG) is essential for AI and NLP, particularly in intelligent tutoring, dialogue systems, and fact verification. Generating multiple-choice questions (MCQG) for professional exams, like the United States Medical Licensing Examination (USMLE), is particularly challenging, requiring domain expertise and complex multi-hop reasoning for high-quality questions. However, current large language models (LLMs) like GPT-4 struggle with professional MCQG due to outdated knowledge, hallucination issues, and prompt sensitivity, resulting in unsatisfactory quality and difficulty. To address these challenges, we propose MCQG-SRefine, an LLM self-refine-based (Critique and Correction) framework for converting medical cases into high-quality USMLE-style questions. By integrating expert-driven prompt engineering with iterative self-critique and self-correction feedback, MCQG-SRefine significantly enhances human expert satisfaction regarding both the quality and difficulty of the questions. Furthermore, we introduce an LLM-as-Judge-based automatic metric to replace the complex and costly expert evaluation process, ensuring reliable and expert-aligned assessments.

cs.CL↗

arXiv2024

RiTeK: A Dataset for Large Language Models Complex Reasoning over Textual Knowledge Graphs in Medicine

Answering complex real-world questions in the medical domain often requires accurate retrieval from medical Textual Knowledge Graphs (medical TKGs), as the relational path information from TKGs could enhance the inference ability of Large Language Models (LLMs). However, the main bottlenecks lie in the scarcity of existing medical TKGs, the limited expressiveness of their topological structures, and the lack of comprehensive evaluations of current retrievers for medical TKGs. To address these challenges, we first develop a Dataset1 for LLMs Complex Reasoning over medical Textual Knowledge Graphs (RiTeK), covering a broad range of topological structures. Specifically, we synthesize realistic user queries integrating diverse topological structures, relational information, and complex textual descriptions. We conduct a rigorous medical expert evaluation process to assess and validate the quality of our synthesized queries. RiTeK also serves as a comprehensive benchmark dataset for evaluating the capabilities of retrieval systems built upon LLMs. By assessing 11 representative retrievers on this benchmark, we observe that existing methods struggle to perform well, revealing notable limitations in current LLM-driven retrieval approaches. These findings highlight the pressing need for more effective retrieval systems tailored for semi-structured data in the medical domain.

cs.CL↗

arXiv2024

Blocks Architecture (BloArk): Efficient, Cost-Effective, and Incremental Dataset Architecture for Wikipedia Revision History

Wikipedia (Wiki) is one of the most widely used and publicly available resources for natural language processing (NLP) applications. Wikipedia Revision History (WikiRevHist) shows the order in which edits were made to any Wiki page since its first modification. While the most up-to-date Wiki has been widely used as a training source, WikiRevHist can also be valuable resources for NLP applications. However, there are insufficient tools available to process WikiRevHist without having substantial computing resources, making additional customization, and spending extra time adapting others' works. Therefore, we report Blocks Architecture (BloArk), an efficiency-focused data processing architecture that reduces running time, computing resource requirements, and repeated works in processing WikiRevHist dataset. BloArk consists of three parts in its infrastructure: blocks, segments, and warehouses. On top of that, we build the core data processing pipeline: builder and modifier. The BloArk builder transforms the original WikiRevHist dataset from XML syntax into JSON Lines (JSONL) format for improving the concurrent and storage efficiency. The BloArk modifier takes previously-built warehouses to operate incremental modifications for improving the utilization of existing databases and reducing the cost of reusing others' works. In the end, BloArk can scale up easily in both processing Wikipedia Revision History and incrementally modifying existing dataset for downstream NLP use cases. The source code, documentations, and example usages are publicly available online and open-sourced under GPL-2.0 license.

cs.CL↗

arXiv2024

Large Language Models are In-context Teachers for Knowledge Reasoning

In this work, we study in-context teaching (ICT), where a teacher provides in-context example rationales to teach a student to reason over unseen cases. Human teachers are usually required to craft in-context demonstrations, which are costly and have high variance. We ask whether a large language model (LLM) can serve as a more effective in-context teacher for itself or other LLMs, compared to humans. Inspired by the Encoding Specificity Hypothesis from human episodic memory, we hypothesize that in-context exemplars crafted by the teacher should match the training data of the student. This hypothesis motivates us to propose Self-Explain where an LLM's self-elicited explanations are used as in-context demonstrations for prompting it as they are generalized from the model's training examples. Self-Explain is shown to significantly outperform using human-crafted exemplars and other baselines. Furthermore, we reveal that for ICT, rationales from different teacher LLMs or human experts that more resemble the student LLM's self-explanations are better in-context demonstrations. This supports our encoding specificity hypothesis. We then propose Teach-Back that aligns a teacher LLM with the student to enhance the ICT performance. For example, Teach-Back enables a 7B model to teach the much larger GPT-3.5 in context, surpassing human teachers by around 5% in test accuracy on medical question answering.

cs.CL↗

arXiv2024

SYNFAC-EDIT: Synthetic Imitation Edit Feedback for Factual Alignment in Clinical Summarization

Large Language Models (LLMs) such as GPT & Llama have demonstrated significant achievements in summarization tasks but struggle with factual inaccuracies, a critical issue in clinical NLP applications where errors could lead to serious consequences. To counter the high costs and limited availability of expert-annotated data for factual alignment, this study introduces an innovative pipeline that utilizes >100B parameter GPT variants like GPT-3.5 & GPT-4 to act as synthetic experts to generate high-quality synthetics feedback aimed at enhancing factual consistency in clinical note summarization. Our research primarily focuses on edit feedback generated by these synthetic feedback experts without additional human annotations, mirroring and optimizing the practical scenario in which medical professionals refine AI system outputs. Although such 100B+ parameter GPT variants have proven to demonstrate expertise in various clinical NLP tasks, such as the Medical Licensing Examination, there is scant research on their capacity to act as synthetic feedback experts and deliver expert-level edit feedback for improving the generation quality of weaker (<10B parameter) LLMs like GPT-2 (1.5B) & Llama 2 (7B) in clinical domain. So in this work, we leverage 100B+ GPT variants to act as synthetic feedback experts offering expert-level edit feedback, that is used to reduce hallucinations and align weaker (<10B parameter) LLMs with medical facts using two distinct alignment algorithms (DPO & SALT), endeavoring to narrow the divide between AI-generated content and factual accuracy. This highlights the substantial potential of LLM-based synthetic edits in enhancing the alignment of clinical factuality.

cs.CL↗

arXiv2024

MedQA-CS: Objective Structured Clinical Examination (OSCE)-Style Benchmark for Evaluating LLM Clinical Skills

Artificial intelligence (AI) and large language models (LLMs) in healthcare require advanced clinical skills (CS), yet current benchmarks fail to evaluate these comprehensively. We introduce MedQA-CS, an AI-SCE framework inspired by medical education's Objective Structured Clinical Examinations (OSCEs), to address this gap. MedQA-CS evaluates LLMs through two instruction-following tasks, LLM-as-medical-student and LLM-as-CS-examiner, designed to reflect real clinical scenarios. Our contributions include developing MedQA-CS, a comprehensive evaluation framework with publicly available data and expert annotations, and providing the quantitative and qualitative assessment of LLMs as reliable judges in CS evaluation. Our experiments show that MedQA-CS is a more challenging benchmark for evaluating clinical skills than traditional multiple-choice QA benchmarks (e.g., MedQA). Combined with existing benchmarks, MedQA-CS enables a more comprehensive evaluation of LLMs' clinical capabilities for both open- and closed-source LLMs.

cs.AI↗

arXiv2024

Bridging Knowledge Gaps in Clinical AI: An Activity Theory Perspective on Interdisciplinary Data Work for Telehealth

Advanced AI technologies are increasingly integrated into clinical domains to advance patient care. The design and development of clinical AI technologies necessitate seamless collaboration between clinical and technical experts. However, such interdisciplinary teams are often unsuccessful, with a lack of systematic analysis of collaboration barriers and coping strategies. This work examines two clinical AI collaborations in the context of speech-language pathology via semi-structured interviews with six clinical and seven technical experts. Using Activity Theory (AT) as our analytical lens, we examine persistent knowledge gaps and collaboration tensions across clinical and technical workflows, and show how clinical data can function as boundary objects while interdisciplinary collaborators may act as knowledge brokers to help address these challenges. Our findings contribute to CSCW research on interdisciplinary teams' data work by showing how shared clinical data, boundary objects, and broker roles shape coordination in early-stage clinical AI collaboration, and by providing insights into best practices for future collaboration.

cs.HC↗

arXiv2024

ReALM: Reference Resolution As Language Modeling

Reference resolution is an important problem, one that is essential to understand and successfully handle context of different kinds. This context includes both previous turns and context that pertains to non-conversational entities, such as entities on the user's screen or those running in the background. While LLMs have been shown to be extremely powerful for a variety of tasks, their use in reference resolution, particularly for non-conversational entities, remains underutilized. This paper demonstrates how LLMs can be used to create an extremely effective system to resolve references of various types, by showing how reference resolution can be converted into a language modeling problem, despite involving forms of entities like those on screen that are not traditionally conducive to being reduced to a text-only modality. We demonstrate large improvements over an existing system with similar functionality across different types of references, with our smallest model obtaining absolute gains of over 5% for on-screen references. We also benchmark against GPT-3.5 and GPT-4, with our smallest model achieving performance comparable to that of GPT-4, and our larger models substantially outperforming it.

cs.CL↗

arXiv2024

Exploring LLM Multi-Agents for ICD Coding

To address the limitations of Large Language Models (LLMs) in the International Classification of Diseases (ICD) coding task, where they often produce inaccurate and incomplete prediction results due to the high-dimensional and skewed distribution of the ICD codes, and often lack interpretability and reliability as well. We introduce an innovative multi-agent approach for ICD coding which mimics the ICD coding assignment procedure in real-world settings, comprising five distinct agents: the patient, physician, coder, reviewer, and adjuster. Each agent utilizes an LLM-based model tailored to their specific role within the coding process. We also integrate the system with Electronic Health Record (HER)'s SOAP (subjective, objective, assessment and plan) structure to boost the performances. We compare our method with a system of agents designed solely by LLMs and other strong baselines and evaluate it using the Medical Information Mart for Intensive Care III (MIMIC-III) dataset. Our multi-agent coding framework significantly outperforms Zero-shot Chain of Thought (CoT) prompting and self-consistency with CoT (CoT-SC) in coding common and rare ICD codes. An ablation study validates the effectiveness of the designated agent roles. it also outperforms the LLM-designed agent system. Moreover, our method achieves comparable results to state-of-the-art ICD coding methods that require extensive pre-training or fine-tuning, and outperforms them in rare code accuracy, and explainability. Additionally, we demonstrate the method's practical applicability by presenting its performance in scenarios not limited by the common or rare ICD code constraints.The proposed multi-agent method for ICD coding effectively mimics the real-world coding process and improves performance on both common and rare codes.

cs.CL↗