arXiv subjects

Ruey-Ling Weng

Publications and source records attributed to Ruey-Ling Weng.

6 recordsLinked to original sources

arXiv2026

Foundation Models to Unlock Real-World Evidence from Nationwide Medical Claims

Evidence derived from large-scale real-world data (RWD) is increasingly informing regulatory evaluation and healthcare decision-making. Administrative claims provide population-scale, longitudinal records of healthcare utilization, expenditure, and detailed coding of diagnoses, procedures, and medications, yet their potential as a substrate for healthcare foundation models remains largely unexplored. Here we present ReClaim, a generative transformer trained from scratch on 43.8 billion medical events from more than 200 million enrollees in the MarketScan claims data spanning 2008-2022. ReClaim models longitudinal trajectories across diagnoses, procedures, medications, and expenditure, and was scaled to 140 million, 700 million, and 1.7 billion parameters. Across over 1,000 disease-onset prediction tasks, ReClaim achieved a mean AUC of 75.6%, substantially outperforming disease-specific LightGBM (66.3%) and the transformer-based Delphi model (69.4%), with the largest gains for rare diseases. These advantages held across retrospective and prospective evaluations and in external validation on two independent datasets. Performance improved monotonically with scale, and post-training added 13.8 percentage points over pre-training alone. Beyond disease prediction, ReClaim captured financial outcomes and improved real-world evidence (RWE) analyses: for healthcare expenditure forecasting it increased explained variance from 0.28 to 0.37 relative to LightGBM, and in a target trial emulation it reduced systematic bias by 72% on average relative to Delphi. Together, these results establish administrative claims as a scalable substrate for healthcare foundation models and show that learned representations generalize across time periods and data sources, supporting disease surveillance, expenditure forecasting, and RWE generation.

cs.AI↗

arXiv2026

EHRNavigator: A Multi-Agent System for Patient-Level Clinical Question Answering over Heterogeneous Electronic Health Records

Clinical decision-making increasingly relies on timely and context-aware access to patient information within Electronic Health Records (EHRs), yet most existing natural language question-answering (QA) systems are evaluated solely on benchmark datasets, limiting their practical relevance. To overcome this limitation, we introduce EHRNavigator, a multi-agent framework that harnesses AI agents to perform patient-level question answering across heterogeneous and multimodal EHR data. We assessed its performance using both public benchmark and institutional datasets under realistic hospital conditions characterized by diverse schemas, temporal reasoning demands, and multimodal evidence integration. Through quantitative evaluation and clinician-validated chart review, EHRNavigator demonstrated strong generalization, achieving 86% accuracy on real-world cases while maintaining clinically acceptable response times. Overall, these findings confirm that EHRNavigator effectively bridges the gap between benchmark evaluation and clinical deployment, offering a robust, adaptive, and efficient solution for real-world EHR question answering.

cs.CL↗

arXiv2025

Open-FinLLMs: Open Multimodal Large Language Models for Financial Applications

Financial LLMs hold promise for advancing financial tasks and domain-specific applications. However, they are limited by scarce corpora, weak multimodal capabilities, and narrow evaluations, making them less suited for real-world application. To address this, we introduce \textit{Open-FinLLMs}, the first open-source multimodal financial LLMs designed to handle diverse tasks across text, tabular, time-series, and chart data, excelling in zero-shot, few-shot, and fine-tuning settings. The suite includes FinLLaMA, pre-trained on a comprehensive 52-billion-token corpus; FinLLaMA-Instruct, fine-tuned with 573K financial instructions; and FinLLaVA, enhanced with 1.43M multimodal tuning pairs for strong cross-modal reasoning. We comprehensively evaluate Open-FinLLMs across 14 financial tasks, 30 datasets, and 4 multimodal tasks in zero-shot, few-shot, and supervised fine-tuning settings, introducing two new multimodal evaluation datasets. Our results show that Open-FinLLMs outperforms afvanced financial and general LLMs such as GPT-4, across financial NLP, decision-making, and multi-modal tasks, highlighting their potential to tackle real-world challenges. To foster innovation and collaboration across academia and industry, we release all codes (https://anonymous.4open.science/r/PIXIU2-0D70/B1D7/LICENSE) and models under OSI-approved licenses.

cs.CL↗

arXiv2025

Retrieval-augmented Large Language Models for Financial Time Series Forecasting

Accurately forecasting stock price movements is critical for informed financial decision-making, supporting applications ranging from algorithmic trading to risk management. However, this task remains challenging due to the difficulty of retrieving subtle yet high-impact patterns from noisy financial time-series data, where conventional retrieval methods, whether based on generic language models or simplistic numeric similarity, often fail to capture the intricate temporal dependencies and context-specific signals essential for precise market prediction. To bridge this gap, we introduce FinSrag, the first retrieval-augmented generation (RAG) framework with a novel domain-specific retriever FinSeer for financial time-series forecasting. FinSeer leverages a candidate selection mechanism refined by LLM feedback and a similarity-driven training objective to align queries with historically influential sequences while filtering out financial noise. Such training enables FinSeer to identify the most relevant time-series data segments for downstream forecasting tasks, unlike embedding or distance-based retrieval methods used in existing RAG frameworks. The retrieved patterns are then fed into StockLLM, a 1B-parameter LLM fine-tuned for stock movement prediction, which serves as the generative backbone. Beyond the retrieval method, we enrich the retrieval corpus by curating new datasets that integrate a broader set of financial indicators, capturing previously overlooked market dynamics. Experiments demonstrate that FinSeer outperforms existing textual retrievers and traditional distance-based retrieval approaches in enhancing the prediction accuracy of StockLLM, underscoring the importance of domain-specific retrieval frameworks in handling the complexity of financial time-series data.

cs.CL↗

arXiv2025

Information Extraction from Clinical Notes: Are We Ready to Switch to Large Language Models?

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We investigated Named Entity Recognition (NER) and Relation Extraction (RE) using 1,588 clinical notes from four sources (UT Physicians, MTSamples, MIMIC-III, and i2b2). We developed an annotated corpus covering 4 clinical entities and 16 modifiers, and compared instruction-tuned LLaMA-2 and LLaMA-3 against BERT in terms of performance, generalizability, computational resources, and throughput to BERT. Results: LLaMA models outperformed BERT across datasets. With sufficient training data, LLaMA showed modest improvements (1% on NER, 1.5-3.7% on RE); improvements were larger with limited training data. On unseen i2b2 data, LLaMA-3-70B outperformed BERT by 7% (F1) on NER and 4% on RE. However, LLaMA models required more computing resources and ran up to 28 times slower. We implemented "Kiwi," a clinical IE package featuring both models, available at https://kiwi.clinicalnlp.org/. Conclusion: This study is among the first to develop and evaluate a comprehensive clinical IE system using open-source LLMs. Results indicate that LLaMA models outperform BERT for clinical NER and RE but with higher computational costs and lower throughputs. These findings highlight that choosing between LLMs and traditional deep learning methods for clinical IE applications should remain task-specific, taking into account both performance metrics and practical considerations such as available computing resources and the intended use case scenarios.

cs.CL↗

arXiv2024

CDEMapper: Enhancing NIH Common Data Element Normalization using Large Language Models

Common Data Elements (CDEs) standardize data collection and sharing across studies, enhancing data interoperability and improving research reproducibility. However, implementing CDEs presents challenges due to the broad range and variety of data elements. This study aims to develop an effective and efficient mapping tool to bridge the gap between local data elements and National Institutes of Health (NIH) CDEs. We propose CDEMapper, a large language model (LLM) powered mapping tool designed to assist in mapping local data elements to NIH CDEs. CDEMapper has three core modules: (1) CDE indexing and embeddings. NIH CDEs were indexed and embedded to support semantic search; (2) CDE recommendations. The tool combines Elasticsearch (BM25 similarity methods) with state of the art GPT services to recommend candidate CDEs and their permissible values; and (3) Human review. Users review and select the NIH CDEs and values that best match their data elements and value sets. We evaluate the tool recommendation accuracy against manually annotated mapping results. CDEMapper offers a publicly available, LLM-powered, and intuitive user interface that consolidates essential and advanced mapping services into a streamlined pipeline. It provides a step by step, quality assured mapping workflow designed with a user-centered approach. The evaluation results demonstrated that augmenting BM25 with GPT embeddings and a ranker consistently enhances CDEMapper mapping accuracy in three different mapping settings across four evaluation datasets. This work opens up the potential of using LLMs to assist with CDE recommendation and human curation when aligning local data elements with NIH CDEs. Additionally, this effort enhances clinical research data interoperability and helps researchers better understand the gaps between local data elements and NIH CDEs.

cs.IR↗