arXiv subjects

Edward Choi

Publications and source records attributed to Edward Choi.

At least 37 records · Page 2Linked to original sources

arXiv2026

EHRSQL: A Practical Text-to-SQL Benchmark for Electronic Health Records

We present a new text-to-SQL dataset for electronic health records (EHRs). The utterances were collected from 222 hospital staff members, including physicians, nurses, and insurance review and health records teams. To construct the QA dataset on structured EHR data, we conducted a poll at a university hospital and used the responses to create seed questions. We then manually linked these questions to two open-source EHR databases, MIMIC-III and eICU, and included various time expressions and held-out unanswerable questions in the dataset, which were also collected from the poll. Our dataset poses a unique set of challenges: the model needs to 1) generate SQL queries that reflect a wide range of needs in the hospital, including simple retrieval and complex operations such as calculating survival rate, 2) understand various time expressions to answer time-sensitive questions in healthcare, and 3) distinguish whether a given question is answerable or unanswerable. We believe our dataset, EHRSQL, can serve as a practical benchmark for developing and assessing QA models on structured EHR data and take a step further towards bridging the gap between text-to-SQL research and its real-life deployment in healthcare. EHRSQL is available at https://github.com/glee4810/EHRSQL.

cs.CL↗

arXiv2026

Generating Multi-Table Time Series EHR from Latent Space with Minimal Preprocessing

Electronic Health Records (EHR) are time-series relational databases that record patient interactions and medical events over time, serving as a critical resource for healthcare research and applications. However, privacy concerns and regulatory restrictions limit the sharing and utilization of such sensitive data, necessitating the generation of synthetic EHR datasets. Unlike previous EHR synthesis methods, which typically generate medical records consisting of expert-chosen features (e.g. a few vital signs or structured codes only), we introduce RawMed, the first framework to synthesize multi-table, time-series EHR data that closely resembles raw EHRs. Using text-based representation and compression techniques, RawMed captures complex structures and temporal dynamics with minimal preprocessing. We also propose a new evaluation framework for multi-table time-series synthetic EHRs, assessing distributional similarity, inter-table relationships, temporal dynamics, and privacy. Validated on two open-source EHR datasets, RawMed outperforms baseline models in fidelity and utility. The code is available at https://github.com/eunbyeol-cho/RawMed.

cs.LG↗

arXiv2026

From Conversation to Query Execution: Benchmarking User and Tool Interactions for EHR Database Agents

Despite the impressive performance of LLM-powered agents, their adoption for Electronic Health Record (EHR) data access remains limited by the absence of benchmarks that adequately capture real-world clinical data access flows. In practice, two core challenges hinder deployment: query ambiguity from vague user questions and value mismatch between user terminology and database entries. To address this, we introduce EHR-ChatQA, an interactive database question answering benchmark that evaluates the end-to-end workflow of database agents: clarifying user questions, using tools to resolve value mismatches, and generating correct SQL to deliver accurate answers. To cover diverse patterns of query ambiguity and value mismatch, EHR-ChatQA assesses agents in a simulated environment with an LLM-based user across two interaction flows: Incremental Query Refinement (IncreQA), where users add constraints to existing queries, and Adaptive Query Refinement (AdaptQA), where users adjust their search goals mid-conversation. Experiments with state-of-the-art LLMs (e.g., o4-mini and Gemini-2.5-Flash) over five i.i.d. trials show that while the best-performing agents achieve Pass@5 of over 90% (at least one of five trials) on IncreQA and 60-70% on AdaptQA, their Pass^5 (consistent success across all five trials) is substantially lower, with gaps of up to about 60%. These results underscore the need to build agents that are not only performant but also robust for the safety-critical EHR domain. Finally, we provide diagnostic insights into common failure modes to guide future agent development. Our code and data are publicly available at https://github.com/glee4810/EHR-ChatQA.

cs.AI↗

arXiv2026

Modeling Clinical Uncertainty in Radiology Reports: from Explicit Uncertainty Markers to Implicit Reasoning Pathways

Radiology reports are invaluable for clinical decision-making and hold great potential for automated analysis when structured into machine-readable formats. These reports often contain uncertainty, which we categorize into two distinct types: (i) Explicit uncertainty reflects doubt about the presence or absence of findings, conveyed through hedging phrases. These vary in meaning depending on the context, making rule-based systems insufficient to quantify the level of uncertainty for specific findings; (ii) Implicit uncertainty arises when radiologists omit parts of their reasoning, recording only key findings or diagnoses. Here, it is often unclear whether omitted findings are truly absent or simply unmentioned for brevity. We address these challenges with a two-part framework. We quantify explicit uncertainty by creating an expert-validated, LLM-based reference ranking of common hedging phrases, and mapping each finding to a probability value based on this reference. In addition, we model implicit uncertainty through an expansion framework that systematically adds characteristic sub-findings derived from expert-defined diagnostic pathways for 14 common diagnoses. Using these methods, we release Lunguage++, an expanded, uncertainty-aware version of the Lunguage benchmark of fine-grained structured radiology reports. This enriched resource enables uncertainty-aware image classification, faithful diagnostic reasoning, and new investigations into the clinical impact of diagnostic uncertainty.

cs.CL↗

arXiv2026

ProPerSim: Developing Proactive and Personalized AI Assistants through User-Assistant Simulation

As large language models (LLMs) become increasingly integrated into daily life, there is growing demand for AI assistants that are not only reactive but also proactive and personalized. While recent advances have pushed forward proactivity and personalization individually, their combination remains underexplored. To bridge this gap, we introduce ProPerSim, a new task and simulation framework for developing assistants capable of making timely, personalized recommendations in realistic home scenarios. In our simulation environment, a user agent with a rich persona interacts with the assistant, providing ratings on how well each suggestion aligns with its preferences and context. The assistant's goal is to use these ratings to learn and adapt to achieve higher scores over time. Built on ProPerSim, we propose ProPerAssistant, a retrieval-augmented, preference-aligned assistant that continually learns and adapts through user feedback. Experiments across 32 diverse personas show that ProPerAssistant adapts its strategy and steadily improves user satisfaction, highlighting the promise of uniting proactivity and personalization.

cs.CL↗

arXiv2026

KorMedMCQA-V: A Multimodal Benchmark for Evaluating Vision-Language Models on the Korean Medical Licensing Examination

We introduce KorMedMCQA-V, a Korean medical licensing-exam-style multimodal multiple-choice question answering benchmark for evaluating vision-language models (VLMs). The dataset consists of 1,534 questions with 2,043 associated images from Korean Medical Licensing Examinations (2012-2023), with about 30% containing multiple images requiring cross-image evidence integration. Images cover clinical modalities including X-ray, computed tomography (CT), electrocardiography (ECG), ultrasound, endoscopy, and other medical visuals. We benchmark over 50 VLMs across proprietary and open-source categories-spanning general-purpose, medical-specialized, and Korean-specialized families-under a unified zero-shot evaluation protocol. The best proprietary model (Gemini-3.0-Pro) achieves 96.9% accuracy, the best open-source model (Qwen3-VL-32B-Thinking) 83.7%, and the best Korean-specialized model (VARCO-VISION-2.0-14B) only 43.2%. We further find that reasoning-oriented model variants gain up to +20 percentage points over instruction-tuned counterparts, medical domain specialization yields inconsistent gains over strong general-purpose baselines, all models degrade on multi-image questions, and performance varies notably across imaging modalities. By complementing the text-only KorMedMCQA benchmark, KorMedMCQA-V forms a unified evaluation suite for Korean medical reasoning across text-only and multimodal conditions. The dataset is available via Hugging Face Datasets: https://huggingface.co/datasets/seongsubae/KorMedMCQA-V.

cs.CV↗

arXiv2026

Federated Learning for Heterogeneous Electronic Health Record Systems with Cost Effective Participant Selection

The increasing volume of electronic health records (EHRs) presents the opportunity to improve the accuracy and robustness of models in clinical prediction tasks. Unlike traditional centralized approaches, federated learning enables training on data from multiple institutions while preserving patient privacy and complying with regulatory constraints. In practice, healthcare institutions (i.e., hosts) often need to build predictive models tailored to their specific needs (e.g., creatinine-level prediction, N-day readmission prediction) using federated learning. When building a federated learning model for a single healthcare institution, two key challenges arise: (1) ensuring compatibility across heterogeneous EHR systems, and (2) managing federated learning costs within budget constraints. Specifically, heterogeneity in EHR systems across institutions hinders compatible modeling, while the computational costs of federated learning can exceed practical budget limits for healthcare institutions. To address these challenges, we propose EHRFL, a federated learning framework designed for building a cost-effective, host-specific predictive model using patient EHR data. EHRFL consists of two components: (1) text-based EHR modeling, which facilitates cross-institution compatibility without costly data standardization, and (2) a participant selection strategy based on averaged patient embedding similarity to reduce the number of participants without degrading performance. Our participant selection strategy sharing averaged patient embeddings is differentially private, ensuring patient privacy. Experiments on multiple open-source EHR datasets demonstrate the effectiveness of both components. With our framework, healthcare institutions can build institution-specific predictive models under budgetary constraints with reduced costs and time.

cs.LG↗

arXiv2026

ECG-Agent: On-Device Tool-Calling Agent for ECG Multi-Turn Dialogue

Recent advances in Multimodal Large Language Models have rapidly expanded to electrocardiograms, focusing on classification, report generation, and single-turn QA tasks. However, these models fall short in real-world scenarios, lacking multi-turn conversational ability, on-device efficiency, and precise understanding of ECG measurements such as the PQRST intervals. To address these limitations, we introduce ECG-Agent, the first LLM-based tool-calling agent for multi-turn ECG dialogue. To facilitate its development and evaluation, we also present ECG-Multi-Turn-Dialogue (ECG-MTD) dataset, a collection of realistic user-assistant multi-turn dialogues for diverse ECG lead configurations. We develop ECG-Agents in various sizes, from on-device capable to larger agents. Experimental results show that ECG-Agents outperform baseline ECG-LLMs in response accuracy. Furthermore, on-device agents achieve comparable performance to larger agents in various evaluations that assess response accuracy, tool-calling ability, and hallucinations, demonstrating their viability for real-world applications.

cs.AI↗

arXiv2025

SCARE: A Benchmark for SQL Correction and Question Answerability Classification for Reliable EHR Question Answering

Recent advances in Large Language Models (LLMs) have enabled the development of text-to-SQL models that allow clinicians to query structured data stored in Electronic Health Records (EHRs) using natural language. However, deploying these models for EHR question answering (QA) systems in safety-critical clinical environments remains challenging: incorrect SQL queries-whether caused by model errors or problematic user inputs-can undermine clinical decision-making and jeopardize patient care. While prior work has mainly focused on improving SQL generation accuracy or filtering questions before execution, there is a lack of a unified benchmark for evaluating independent post-hoc verification mechanisms (i.e., a component that inspects and validates the generated SQL before execution), which is crucial for safe deployment. To fill this gap, we introduce SCARE, a benchmark for evaluating methods that function as a post-hoc safety layer in EHR QA systems. SCARE evaluates the joint task of (1) classifying question answerability (i.e., determining whether a question is answerable, ambiguous, or unanswerable) and (2) verifying or correcting candidate SQL queries. The benchmark comprises 4,200 triples of questions, candidate SQL queries, and expected model outputs, grounded in the MIMIC-III, MIMIC-IV, and eICU databases. It covers a diverse set of questions and corresponding candidate SQL queries generated by seven different text-to-SQL models, ensuring a realistic and challenging evaluation. Using SCARE, we benchmark a range of approaches-from two-stage methods to agentic frameworks. Our experiments reveal a critical trade-off between question classification and SQL error correction, highlighting key challenges and outlining directions for future research.

cs.CL↗

arXiv2025

FHIR-AgentBench: Benchmarking LLM Agents for Realistic Interoperable EHR Question Answering

The recent shift toward the Health Level Seven Fast Healthcare Interoperability Resources (HL7 FHIR) standard opens a new frontier for clinical AI, demanding LLM agents to navigate complex, resource-based data models instead of conventional structured health data. However, existing benchmarks have lagged behind this transition, lacking the realism needed to evaluate recent LLMs on interoperable clinical data. To bridge this gap, we introduce FHIR-AgentBench, a benchmark that grounds 2,931 real-world clinical questions in the HL7 FHIR standard. Using this benchmark, we systematically evaluate agentic frameworks, comparing different data retrieval strategies (direct FHIR API calls vs. specialized tools), interaction patterns (single-turn vs. multi-turn), and reasoning strategies (natural language vs. code generation). Our experiments highlight the practical challenges of retrieving data from intricate FHIR resources and the difficulty of reasoning over them, both of which critically affect question answering performance. We publicly release the FHIR-AgentBench dataset and evaluation suite (https://github.com/glee4810/FHIR-AgentBench) to promote reproducible research and the development of robust, reliable LLM agents for clinical applications.

cs.CL↗

arXiv2025

R2-KG: General-Purpose Dual-Agent Framework for Reliable Reasoning on Knowledge Graphs

Recent studies have combined Large Language Models (LLMs) with Knowledge Graphs (KGs) to enhance reasoning, improving inference accuracy without additional training while mitigating hallucination. However, existing frameworks still suffer two practical drawbacks: they must be re-tuned whenever the KG or reasoning task changes, and they depend on a single, high-capacity LLM for reliable (i.e., trustworthy) reasoning. To address this, we introduce R2-KG, a plug-and-play, dual-agent framework that separates reasoning into two roles: an Operator (a low-capacity LLM) that gathers evidence and a Supervisor (a high-capacity LLM) that makes final judgments. This design is cost-efficient for LLM inference while still maintaining strong reasoning accuracy. Additionally, R2-KG employs an Abstention mechanism, generating answers only when sufficient evidence is collected from KG, which significantly enhances reliability. Experiments across five diverse benchmarks show that R2-KG consistently outperforms baselines in both accuracy and reliability, regardless of the inherent capability of LLMs used as the Operator. Further experiments reveal that the single-agent version of R2-KG, equipped with a strict self-consistency strategy, achieves significantly higher-than-baseline reliability with reduced inference cost but increased abstention rate in complex KGs. Our findings establish R2-KG as a flexible and cost-effective solution for KG-based reasoning, reducing reliance on high-capacity LLMs while ensuring trustworthy inference. The code is available at https://github.com/ekrxjwh2009/R2-KG/.

cs.CL↗

arXiv2025

Reflections from Research Roundtables at the Conference on Health, Inference, and Learning (CHIL) 2025

The 6th Annual Conference on Health, Inference, and Learning (CHIL 2025), hosted by the Association for Health Learning and Inference (AHLI), was held in person on June 25-27, 2025, at the University of California, Berkeley, in Berkeley, California, USA. As part of this year's program, we hosted Research Roundtables to catalyze collaborative, small-group dialogue around critical, timely topics at the intersection of machine learning and healthcare. Each roundtable was moderated by a team of senior and junior chairs who fostered open exchange, intellectual curiosity, and inclusive engagement. The sessions emphasized rigorous discussion of key challenges, exploration of emerging opportunities, and collective ideation toward actionable directions in the field. In total, eight roundtables were held by 19 roundtable chairs on topics of "Explainability, Interpretability, and Transparency," "Uncertainty, Bias, and Fairness," "Causality," "Domain Adaptation," "Foundation Models," "Learning from Small Medical Data," "Multimodal Methods," and "Scalable, Translational Healthcare Solutions."

cs.LG↗

arXiv2025

PatientSim: A Persona-Driven Simulator for Realistic Doctor-Patient Interactions

Doctor-patient consultations require multi-turn, context-aware communication tailored to diverse patient personas. Training or evaluating doctor LLMs in such settings requires realistic patient interaction systems. However, existing simulators often fail to reflect the full range of personas seen in clinical practice. To address this, we introduce PatientSim, a patient simulator that generates realistic and diverse patient personas for clinical scenarios, grounded in medical expertise. PatientSim operates using: 1) clinical profiles, including symptoms and medical history, derived from real-world data in the MIMIC-ED and MIMIC-IV datasets, and 2) personas defined by four axes: personality, language proficiency, medical history recall level, and cognitive confusion level, resulting in 37 unique combinations. We evaluate eight LLMs for factual accuracy and persona consistency. The top-performing open-source model, Llama 3.3 70B, is validated by four clinicians to confirm the robustness of our framework. As an open-source, customizable platform, PatientSim provides a reproducible and scalable solution that can be customized for specific training needs. Offering a privacy-compliant environment, it serves as a robust testbed for evaluating medical dialogue systems across diverse patient presentations and shows promise as an educational tool for healthcare. The code is available at https://github.com/dek924/PatientSim.

cs.AI↗

arXiv2025

CXReasonBench: A Benchmark for Evaluating Structured Diagnostic Reasoning in Chest X-rays

Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the publicly available MIMIC-CXR-JPG dataset. CheXStruct automatically derives a sequence of intermediate reasoning steps directly from chest X-rays, such as segmenting anatomical regions, deriving anatomical landmarks and diagnostic measurements, computing diagnostic indices, and applying clinical thresholds. CXReasonBench leverages this pipeline to evaluate whether models can perform clinically valid reasoning steps and to what extent they can learn from structured guidance, enabling fine-grained and transparent assessment of diagnostic reasoning. The benchmark comprises 18,988 QA pairs across 12 diagnostic tasks and 1,200 cases, each paired with up to 4 visual inputs, and supports multi-path, multi-stage evaluation including visual grounding via anatomical region selection and diagnostic measurements. Even the strongest of 12 evaluated LVLMs struggle with structured reasoning and generalization, often failing to link abstract knowledge with anatomically grounded visual interpretation. The code is available at https://github.com/ttumyche/CXReasonBench

cs.CV↗

arXiv2025

Trans-EnV: A Framework for Evaluating the Linguistic Robustness of LLMs Against English Varieties

Large Language Models (LLMs) are predominantly evaluated on Standard American English (SAE), often overlooking the diversity of global English varieties. This narrow focus may raise fairness concerns as degraded performance on non-standard varieties can lead to unequal benefits for users worldwide. Therefore, it is critical to extensively evaluate the linguistic robustness of LLMs on multiple non-standard English varieties. We introduce Trans-EnV, a framework that automatically transforms SAE datasets into multiple English varieties to evaluate the linguistic robustness. Our framework combines (1) linguistics expert knowledge to curate variety-specific features and transformation guidelines from linguistic literature and corpora, and (2) LLM-based transformations to ensure both linguistic validity and scalability. Using Trans-EnV, we transform six benchmark datasets into 38 English varieties and evaluate seven state-of-the-art LLMs. Our results reveal significant performance disparities, with accuracy decreasing by up to 46.3% on non-standard varieties. These findings highlight the importance of comprehensive linguistic robustness evaluation across diverse English varieties. Each construction of Trans-EnV was validated through rigorous statistical testing and consultation with a researcher in the field of second language acquisition, ensuring its linguistic validity. Our code and datasets are publicly available at https://github.com/jiyounglee-0523/TransEnV and https://huggingface.co/collections/jiyounglee0523/transenv-681eadb3c0c8cf363b363fb1.

cs.CL↗

arXiv2025

DialSim: A Dialogue Simulator for Evaluating Long-Term Multi-Party Dialogue Understanding of Conversational Agents

Recent advancements in Large Language Models (LLMs) have significantly enhanced conversational agents, making them applicable to various fields (e.g., education, entertainment). Despite their progress, the evaluation of the agents often overlooks the complexities of real-world conversations, such as multi-party dialogues and extended contextual dependencies. To bridge this gap, we introduce DialSim, a dialogue simulation-based evaluation framework. In DialSim, an agent assumes the role of a character in a scripted conversation and is evaluated on their ability to answer spontaneous questions using only the dialogue history, while recognizing when they lack sufficient information. To support this framework, we introduce LongDialQA, a new QA dataset constructed from long-running TV shows, comprising over 1,300 dialogue sessions, each paired with more than 1,000 carefully curated questions, totaling over 352,000 tokens. To minimize reliance on prior knowledge, all character names are anonymized or swapped. Our evaluation of state-of-the-art LLM-based conversational agents using DialSim reveals that even models with large context windows or RAG capabilities struggle to maintain accurate comprehension over long-term, multi-party interactions-underscoring the need for more realistic and challenging benchmarks in conversational AI.

cs.CL↗

arXiv2025

LabTOP: A Unified Model for Lab Test Outcome Prediction on Electronic Health Records

Lab tests are fundamental for diagnosing diseases and monitoring patient conditions. However, frequent testing can be burdensome for patients, and test results may not always be immediately available. To address these challenges, we propose LabTOP, a unified model that predicts lab test outcomes by leveraging a language modeling approach on EHR data. Unlike conventional methods that estimate only a subset of lab tests or classify discrete value ranges, LabTOP performs continuous numerical predictions for a diverse range of lab items. We evaluate LabTOP on three publicly available EHR datasets and demonstrate that it outperforms existing methods, including traditional machine learning models and state-of-the-art large language models. We also conduct extensive ablation studies to confirm the effectiveness of our design choices. We believe that LabTOP will serve as an accurate and generalizable framework for lab test outcome prediction, with potential applications in clinical decision support and early detection of critical conditions.

cs.LG↗

arXiv2025

A Large-Scale Real-World Evaluation of LLM-Based Virtual Teaching Assistant

Virtual Teaching Assistants (VTAs) powered by Large Language Models (LLMs) have the potential to enhance student learning by providing instant feedback and facilitating multi-turn interactions. However, empirical studies on their effectiveness and acceptance in real-world classrooms are limited, leaving their practical impact uncertain. In this study, we develop an LLM-based VTA and deploy it in an introductory AI programming course with 477 graduate students. To assess how student perceptions of the VTA's performance evolve over time, we conduct three rounds of comprehensive surveys at different stages of the course. Additionally, we analyze 3,869 student--VTA interaction pairs to identify common question types and engagement patterns. We then compare these interactions with traditional student--human instructor interactions to evaluate the VTA's role in the learning process. Through a large-scale empirical study and interaction analysis, we assess the feasibility of deploying VTAs in real-world classrooms and identify key challenges for broader adoption. Finally, we release the source code of our VTA system, fostering future advancements in AI-driven education: \texttt{https://github.com/sean0042/VTA}.

cs.CY↗