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

OpenNotes enables patients to access EHR notes, but medical jargon can hinder comprehension. To improve understanding, we evaluated closed- and open-source LLMs for extracting and prioritizing key medical terms using prompting, fine-tuning, and data augmentation. We assessed LLMs on 106 expert-annotated EHR notes, experimenting with (i) general vs. structured prompts, (ii) zero-shot vs. few-shot prompting, (iii) fine-tuning, and (iv) data augmentation. To enhance open-source models in low-resource settings, we used ChatGPT for data augmentation and applied ranking techniques. We incrementally increased the augmented dataset size (10 to 10,000) and conducted 5-fold cross-validation, reporting F1 score and Mean Reciprocal Rank (MRR). Our result show that fine-tuning and data augmentation improved performance over other strategies. GPT-4 Turbo achieved the highest F1 (0.433), while Mistral7B with data augmentation had the highest MRR (0.746). Open-source models, when fine-tuned or augmented, outperformed closed-source models. Notably, the best F1 and MRR scores did not always align. Few-shot prompting outperformed zero-shot in vanilla models, and structured prompts yielded different preferences across models. Fine-tuning improved zero-shot performance but sometimes degraded few-shot performance. Data augmentation performed comparably or better than other methods. Our evaluation highlights the effectiveness of prompting, fine-tuning, and data augmentation in improving model performance for medical jargon extraction in low-resource scenarios.

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.

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 $\beta$ 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.

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 the knowledge databases of RAG systems. We demonstrate that previous attacks on RAG largely depend on the instruction-following capabilities of LLMs, and that simple fine-tuning can reduce the success rate of such attacks to nearly zero. This makes these attacks impractical since fine-tuning is a common practice when deploying LLMs in specific domains. 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. We show that with only 3\% poisoned data, our method achieves an average success rate of 79.7\% in verbatim extraction on Llama2-7B, with a ROUGE-L score of 64.21, and a 68.6\% average success rate in paraphrased extraction, with an average ROUGE score of 52.6 across four datasets. These results underscore the privacy risks associated with the supply chain when deploying RAG systems.

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.

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

Answering complex real-world questions often requires accurate retrieval from textual knowledge graphs (TKGs). The scarcity of annotated data, along with intricate topological structures, makes this task particularly challenging. As the nature of relational path information could enhance the inference ability of Large Language Models (LLMs), efficiently retrieving more complex relational path information from TKGs presents another key challenge. To tackle these challenges, we first develop a Dataset for LLMs Complex Reasoning over Textual Knowledge Graphs (RiTeK) with a broad topological structure coverage.We synthesize realistic user queries that integrate diverse topological structures, relational information, and complex textual descriptions. We conduct rigorous expert evaluation to validate the quality of our synthesized queries. And then, we introduce an enhanced Monte Carlo Tree Search (MCTS) method, Relational MCTS, to automatically extract relational path information from textual graphs for specific queries. Our dataset mainly covers the medical domain as the relation types and entity are complex and publicly available. Experimental results indicate that RiTeK poses significant challenges for current retrieval and LLM systems, while the proposed Relational MCTS method enhances LLM inference ability and achieves state-of-the-art performance on RiTeK.

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.

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.

MedQA-CS: Benchmarking Large Language Models Clinical Skills Using an AI-SCE Framework

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.

Large Language Model-based Role-Playing for Personalized Medical Jargon Extraction

Previous studies reveal that Electronic Health Records (EHR), which have been widely adopted in the U.S. to allow patients to access their personal medical information, do not have high readability to patients due to the prevalence of medical jargon. Tailoring medical notes to individual comprehension by identifying jargon that is difficult for each person will enhance the utility of generative models. We present the first quantitative analysis to measure the impact of role-playing in LLM in medical term extraction. By comparing the results of Mechanical Turk workers over 20 sentences, our study demonstrates that LLM role-playing improves F1 scores in 95% of cases across 14 different socio-demographic backgrounds. Furthermore, applying role-playing with in-context learning outperformed the previous state-of-the-art models. Our research showed that ChatGPT can improve traditional medical term extraction systems by utilizing role-play to deliver personalized patient education, a potential that previous models had not achieved.