arXiv subjects

Edward Choi

Publications and source records attributed to Edward Choi.

At least 55 records · Page 3Linked to original sources

arXiv2025

MD-ViSCo: A Unified Model for Multi-Directional Vital Sign Waveform Conversion

Despite the remarkable progress of deep-learning methods generating a target vital sign waveform from a source vital sign waveform, most existing models are designed exclusively for a specific source-to-target pair. This requires distinct model architectures, optimization procedures, and pre-processing pipelines, resulting in multiple models that hinder usability in clinical settings. To address this limitation, we propose the Multi-Directional Vital-Sign Converter (MD-ViSCo), a unified framework capable of generating any target waveform such as electrocardiogram (ECG), photoplethysmogram (PPG), or arterial blood pressure (ABP) from any single input waveform with a single model. MD-ViSCo employs a shallow 1-Dimensional U-Net integrated with a Swin Transformer that leverages Adaptive Instance Normalization (AdaIN) to capture distinct waveform styles. To evaluate the efficacy of MD-ViSCo, we conduct multi-directional waveform generation on two publicly available datasets. Our framework surpasses state-of-the-art baselines (NabNet & PPG2ABP) on average across all waveform types, lowering Mean absolute error (MAE) by 8.8% and improving Pearson correlation (PC) by 4.9% over two datasets. In addition, the generated ABP waveforms satisfy the Association for the Advancement of Medical Instrumentation (AAMI) criterion and achieve Grade B on the British Hypertension Society (BHS) standard, outperforming all baselines. By eliminating the need for developing a distinct model for each task, we believe that this work offers a unified framework that can deal with any kind of vital sign waveforms with a single model in healthcare monitoring.

cs.SD↗

arXiv2025

Towards Predicting Temporal Changes in a Patient's Chest X-ray Images based on Electronic Health Records

Chest X-ray (CXR) is an important diagnostic tool widely used in hospitals to assess patient conditions and monitor changes over time. Recently, generative models, specifically diffusion-based models, have shown promise in generating realistic synthetic CXRs. However, these models mainly focus on conditional generation using single-time-point data, i.e., generating CXRs conditioned on their corresponding reports from a specific time. This limits their clinical utility, particularly for capturing temporal changes. To address this limitation, we propose a novel framework, EHRXDiff, which predicts future CXR images by integrating previous CXRs with subsequent medical events, e.g., prescriptions, lab measures, etc. Our framework dynamically tracks and predicts disease progression based on a latent diffusion model, conditioned on the previous CXR image and a history of medical events. We comprehensively evaluate the performance of our framework across three key aspects, including clinical consistency, demographic consistency, and visual realism. Results show that our framework generates high-quality, realistic future images that effectively capture potential temporal changes. This suggests that our framework could be further developed to support clinical decision-making and provide valuable insights for patient monitoring and treatment planning in the medical field. The code is available at https://github.com/dek924/EHRXDiff.

eess.IV↗

arXiv2025

Single Ground Truth Is Not Enough: Adding Flexibility to Aspect-Based Sentiment Analysis Evaluation

Aspect-based sentiment analysis (ABSA) is a challenging task of extracting sentiments along with their corresponding aspects and opinion terms from the text. The inherent subjectivity of span annotation makes variability in the surface forms of extracted terms, complicating the evaluation process. Traditional evaluation methods often constrain ground truths (GT) to a single term, potentially misrepresenting the accuracy of semantically valid predictions that differ in surface form. To address this limitation, we propose a novel and fully automated pipeline that expands existing evaluation sets by adding alternative valid terms for aspect and opinion. Our approach facilitates an equitable assessment of language models by accommodating multiple-answer candidates, resulting in enhanced human agreement compared to single-answer test sets (achieving up to a 10\%p improvement in Kendall's Tau score). Experimental results demonstrate that our expanded evaluation set helps uncover the capabilities of large language models (LLMs) in ABSA tasks, which is concealed by the single-answer GT sets. Consequently, our work contributes to the development of a flexible evaluation framework for ABSA by embracing diverse surface forms to span extraction tasks in a cost-effective and reproducible manner. Our code and dataset is open at https://github.com/dudrrm/zoom-in-n-out-absa.

cs.CL↗

arXiv2024

EHRCon: Dataset for Checking Consistency between Unstructured Notes and Structured Tables in Electronic Health Records

Electronic Health Records (EHRs) are integral for storing comprehensive patient medical records, combining structured data (e.g., medications) with detailed clinical notes (e.g., physician notes). These elements are essential for straightforward data retrieval and provide deep, contextual insights into patient care. However, they often suffer from discrepancies due to unintuitive EHR system designs and human errors, posing serious risks to patient safety. To address this, we developed EHRCon, a new dataset and task specifically designed to ensure data consistency between structured tables and unstructured notes in EHRs. EHRCon was crafted in collaboration with healthcare professionals using the MIMIC-III EHR dataset, and includes manual annotations of 4,101 entities across 105 clinical notes checked against database entries for consistency. EHRCon has two versions, one using the original MIMIC-III schema, and another using the OMOP CDM schema, in order to increase its applicability and generalizability. Furthermore, leveraging the capabilities of large language models, we introduce CheckEHR, a novel framework for verifying the consistency between clinical notes and database tables. CheckEHR utilizes an eight-stage process and shows promising results in both few-shot and zero-shot settings. The code is available at https://github.com/dustn1259/EHRCon.

cs.CL↗

arXiv2024

Ensembling Large Language Models with Process Reward-Guided Tree Search for Better Complex Reasoning

Despite recent advances in large language models, open-source models often struggle to consistently perform well on complex reasoning tasks. Existing ensemble methods, whether applied at the token or output levels, fail to address these challenges. In response, we present Language model Ensemble with Monte Carlo Tree Search (LE-MCTS), a novel framework for process-level ensembling of language models. LE-MCTS formulates step-by-step reasoning with an ensemble of language models as a Markov decision process. In this framework, states represent intermediate reasoning paths, while actions consist of generating the next reasoning step using one of the language models selected from a predefined pool. Guided by a process-based reward model, LE-MCTS performs a tree search over the reasoning steps generated by different language models, identifying the most accurate reasoning chain. Experimental results on five mathematical reasoning benchmarks demonstrate that our approach outperforms both single language model decoding algorithms and language model ensemble methods. Notably, LE-MCTS improves performance by 3.6% and 4.3% on the MATH and MQA datasets, respectively, highlighting its effectiveness in solving complex reasoning problems.

cs.CL↗

arXiv2024

KorMedMCQA: Multi-Choice Question Answering Benchmark for Korean Healthcare Professional Licensing Examinations

We present KorMedMCQA, the first Korean Medical Multiple-Choice Question Answering benchmark, derived from professional healthcare licensing examinations conducted in Korea between 2012 and 2024. The dataset contains 7,469 questions from examinations for doctor, nurse, pharmacist, and dentist, covering a wide range of medical disciplines. We evaluate the performance of 59 large language models, spanning proprietary and open-source models, multilingual and Korean-specialized models, and those fine-tuned for clinical applications. Our results show that applying Chain of Thought (CoT) reasoning can enhance the model performance by up to 4.5% compared to direct answering approaches. We also investigate whether MedQA, one of the most widely used medical benchmarks derived from the U.S. Medical Licensing Examination, can serve as a reliable proxy for evaluating model performance in other regions-in this case, Korea. Our correlation analysis between model scores on KorMedMCQA and MedQA reveals that these two benchmarks align no better than benchmarks from entirely different domains (e.g., MedQA and MMLU-Pro). This finding underscores the substantial linguistic and clinical differences between Korean and U.S. medical contexts, reinforcing the need for region-specific medical QA benchmarks. To support ongoing research in Korean healthcare AI, we publicly release the KorMedMCQA via Huggingface.

cs.CL↗

arXiv2024

Forecasting Future International Events: A Reliable Dataset for Text-Based Event Modeling

Predicting future international events from textual information, such as news articles, has tremendous potential for applications in global policy, strategic decision-making, and geopolitics. However, existing datasets available for this task are often limited in quality, hindering the progress of related research. In this paper, we introduce WORLDREP (WORLD Relationship and Event Prediction), a novel dataset designed to address these limitations by leveraging the advanced reasoning capabilities of large-language models (LLMs). Our dataset features high-quality scoring labels generated through advanced prompt modeling and rigorously validated by domain experts in political science. We showcase the quality and utility of WORLDREP for real-world event prediction tasks, demonstrating its effectiveness through extensive experiments and analysis. Furthermore, we publicly release our dataset along with the full automation source code for data collection, labeling, and benchmarking, aiming to support and advance research in text-based event prediction.

cs.CL↗

arXiv2024

EHRNoteQA: An LLM Benchmark for Real-World Clinical Practice Using Discharge Summaries

Discharge summaries in Electronic Health Records (EHRs) are crucial for clinical decision-making, but their length and complexity make information extraction challenging, especially when dealing with accumulated summaries across multiple patient admissions. Large Language Models (LLMs) show promise in addressing this challenge by efficiently analyzing vast and complex data. Existing benchmarks, however, fall short in properly evaluating LLMs' capabilities in this context, as they typically focus on single-note information or limited topics, failing to reflect the real-world inquiries required by clinicians. To bridge this gap, we introduce EHRNoteQA, a novel benchmark built on the MIMIC-IV EHR, comprising 962 different QA pairs each linked to distinct patients' discharge summaries. Every QA pair is initially generated using GPT-4 and then manually reviewed and refined by three clinicians to ensure clinical relevance. EHRNoteQA includes questions that require information across multiple discharge summaries and covers eight diverse topics, mirroring the complexity and diversity of real clinical inquiries. We offer EHRNoteQA in two formats: open-ended and multi-choice question answering, and propose a reliable evaluation method for each. We evaluate 27 LLMs using EHRNoteQA and examine various factors affecting the model performance (e.g., the length and number of discharge summaries). Furthermore, to validate EHRNoteQA as a reliable proxy for expert evaluations in clinical practice, we measure the correlation between the LLM performance on EHRNoteQA, and the LLM performance manually evaluated by clinicians. Results show that LLM performance on EHRNoteQA have higher correlation with clinician-evaluated performance (Spearman: 0.78, Kendall: 0.62) compared to other benchmarks, demonstrating its practical relevance in evaluating LLMs in clinical settings.

cs.CL↗

arXiv2024

ThreatKG: An AI-Powered System for Automated Open-Source Cyber Threat Intelligence Gathering and Management

Open-source cyber threat intelligence (OSCTI) has become essential for keeping up with the rapidly changing threat landscape. However, current OSCTI gathering and management solutions mainly focus on structured Indicators of Compromise (IOC) feeds, which are low-level and isolated, providing only a narrow view of potential threats. Meanwhile, the extensive and interconnected knowledge found in the unstructured text of numerous OSCTI reports (e.g., security articles, threat reports) available publicly is still largely underexplored. To bridge the gap, we propose ThreatKG, an automated system for OSCTI gathering and management. ThreatKG efficiently collects a large number of OSCTI reports from multiple sources, leverages specialized AI-based techniques to extract high-quality knowledge about various threat entities and their relationships, and constructs and continuously updates a threat knowledge graph by integrating new OSCTI data. ThreatKG features a modular and extensible design, allowing for the addition of components to accommodate diverse OSCTI report structures and knowledge types. Our extensive evaluations demonstrate ThreatKG's practical effectiveness in enhancing threat knowledge gathering and management.

cs.CR↗

arXiv2024

Significantly improving zero-shot X-ray pathology classification via fine-tuning pre-trained image-text encoders

Deep neural networks are increasingly used in medical imaging for tasks such as pathological classification, but they face challenges due to the scarcity of high-quality, expert-labeled training data. Recent efforts have utilized pre-trained contrastive image-text models like CLIP, adapting them for medical use by fine-tuning the model with chest X-ray images and corresponding reports for zero-shot pathology classification, thus eliminating the need for pathology-specific annotations. However, most studies continue to use the same contrastive learning objectives as in the general domain, overlooking the multi-labeled nature of medical image-report pairs. In this paper, we propose a new fine-tuning strategy that includes positive-pair loss relaxation and random sentence sampling. We aim to improve the performance of zero-shot pathology classification without relying on external knowledge. Our method can be applied to any pre-trained contrastive image-text encoder and easily transferred to out-of-domain datasets without further training, as it does not use external data. Our approach consistently improves overall zero-shot pathology classification across four chest X-ray datasets and three pre-trained models, with an average macro AUROC increase of 4.3%. Additionally, our method outperforms the state-of-the-art and marginally surpasses board-certified radiologists in zero-shot classification for the five competition pathologies in the CheXpert dataset.

cs.LG↗

arXiv2024

UniHPF : Universal Healthcare Predictive Framework with Zero Domain Knowledge

Despite the abundance of Electronic Healthcare Records (EHR), its heterogeneity restricts the utilization of medical data in building predictive models. To address this challenge, we propose Universal Healthcare Predictive Framework (UniHPF), which requires no medical domain knowledge and minimal pre-processing for multiple prediction tasks. Experimental results demonstrate that UniHPF is capable of building large-scale EHR models that can process any form of medical data from distinct EHR systems. We believe that our findings can provide helpful insights for further research on the multi-source learning of EHRs.

cs.LG↗

arXiv2024

Time is Not Enough: Time-Frequency based Explanation for Time-Series Black-Box Models

Despite the massive attention given to time-series explanations due to their extensive applications, a notable limitation in existing approaches is their primary reliance on the time-domain. This overlooks the inherent characteristic of time-series data containing both time and frequency features. In this work, we present Spectral eXplanation (SpectralX), an XAI framework that provides time-frequency explanations for time-series black-box classifiers. This easily adaptable framework enables users to "plug-in" various perturbation-based XAI methods for any pre-trained time-series classification models to assess their impact on the explanation quality without having to modify the framework architecture. Additionally, we introduce Feature Importance Approximations (FIA), a new perturbation-based XAI method. These methods consist of feature insertion, deletion, and combination techniques to enhance computational efficiency and class-specific explanations in time-series classification tasks. We conduct extensive experiments in the generated synthetic dataset and various UCR Time-Series datasets to first compare the explanation performance of FIA and other existing perturbation-based XAI methods in both time-domain and time-frequency domain, and then show the superiority of our FIA in the time-frequency domain with the SpectralX framework. Finally, we conduct a user study to confirm the practicality of our FIA in SpectralX framework for class-specific time-frequency based time-series explanations. The source code is available in https://github.com/gustmd0121/Time_is_not_Enough

cs.LG↗

arXiv2024

EHR-SeqSQL : A Sequential Text-to-SQL Dataset For Interactively Exploring Electronic Health Records

In this paper, we introduce EHR-SeqSQL, a novel sequential text-to-SQL dataset for Electronic Health Record (EHR) databases. EHR-SeqSQL is designed to address critical yet underexplored aspects in text-to-SQL parsing: interactivity, compositionality, and efficiency. To the best of our knowledge, EHR-SeqSQL is not only the largest but also the first medical text-to-SQL dataset benchmark to include sequential and contextual questions. We provide a data split and the new test set designed to assess compositional generalization ability. Our experiments demonstrate the superiority of a multi-turn approach over a single-turn approach in learning compositionality. Additionally, our dataset integrates specially crafted tokens into SQL queries to improve execution efficiency. With EHR-SeqSQL, we aim to bridge the gap between practical needs and academic research in the text-to-SQL domain. EHR-SeqSQL is available at https://github.com/seonhee99/EHR-SeqSQL.

cs.CL↗

arXiv2024

Publicly Shareable Clinical Large Language Model Built on Synthetic Clinical Notes

The development of large language models tailored for handling patients' clinical notes is often hindered by the limited accessibility and usability of these notes due to strict privacy regulations. To address these challenges, we first create synthetic large-scale clinical notes using publicly available case reports extracted from biomedical literature. We then use these synthetic notes to train our specialized clinical large language model, Asclepius. While Asclepius is trained on synthetic data, we assess its potential performance in real-world applications by evaluating it using real clinical notes. We benchmark Asclepius against several other large language models, including GPT-3.5-turbo and other open-source alternatives. To further validate our approach using synthetic notes, we also compare Asclepius with its variants trained on real clinical notes. Our findings convincingly demonstrate that synthetic clinical notes can serve as viable substitutes for real ones when constructing high-performing clinical language models. This conclusion is supported by detailed evaluations conducted by both GPT-4 and medical professionals. All resources including weights, codes, and data used in the development of Asclepius are made publicly accessible for future research. (https://github.com/starmpcc/Asclepius)

cs.CL↗

arXiv2024

General-Purpose Retrieval-Enhanced Medical Prediction Model Using Near-Infinite History

Machine learning (ML) has recently shown promising results in medical predictions using electronic health records (EHRs). However, since ML models typically have a limited capability in terms of input sizes, selecting specific medical events from EHRs for use as input is necessary. This selection process, often relying on expert opinion, can cause bottlenecks in development. We propose Retrieval-Enhanced Medical prediction model (REMed) to address such challenges. REMed can essentially evaluate unlimited medical events, select the relevant ones, and make predictions. This allows for an unrestricted input size, eliminating the need for manual event selection. We verified these properties through experiments involving 27 clinical prediction tasks across four independent cohorts, where REMed outperformed the baselines. Notably, we found that the preferences of REMed align closely with those of medical experts. We expect our approach to significantly expedite the development of EHR prediction models by minimizing clinicians' need for manual involvement.

cs.LG↗

arXiv2024

TrustSQL: Benchmarking Text-to-SQL Reliability with Penalty-Based Scoring

Text-to-SQL enables users to interact with databases using natural language, simplifying the retrieval and synthesis of information. Despite the remarkable success of large language models (LLMs) in translating natural language questions into SQL queries, widespread deployment remains limited due to two primary challenges. First, the effective use of text-to-SQL models depends on users' understanding of the model's capabilities-the scope of questions the model can correctly answer. Second, the absence of abstention mechanisms can lead to incorrect SQL generation going unnoticed, thereby undermining trust in the model's output. To enable wider deployment, it is crucial to address these challenges in model design and enhance model evaluation to build trust in the model's output. To this end, we introduce TrustSQL, a novel comprehensive benchmark designed to evaluate text-to-SQL reliability-defined as a model's ability to correctly handle any type of input question by generating correct SQL queries for feasible questions and abstaining from generating infeasible ones (e.g., due to schema incompatibility or functionalities beyond SQL). We evaluate existing methods using a novel penalty-based scoring metric with two modeling approaches: (1) pipeline-based methods combining SQL generators with infeasible question detectors and SQL error detectors for abstention; and (2) unified methods using a single model for the entire task. Our experimental results reveal that achieving high scores under severe penalties requires significant effort and provide a new perspective on developing text-to-SQL models for safer deployment. TrustSQL is available at https://github.com/glee4810/TrustSQL.

cs.AI↗

arXiv2024

Overview of the EHRSQL 2024 Shared Task on Reliable Text-to-SQL Modeling on Electronic Health Records

Electronic Health Records (EHRs) are relational databases that store the entire medical histories of patients within hospitals. They record numerous aspects of patients' medical care, from hospital admission and diagnosis to treatment and discharge. While EHRs are vital sources of clinical data, exploring them beyond a predefined set of queries requires skills in query languages like SQL. To make information retrieval more accessible, one strategy is to build a question-answering system, possibly leveraging text-to-SQL models that can automatically translate natural language questions into corresponding SQL queries and use these queries to retrieve the answers. The EHRSQL 2024 shared task aims to advance and promote research in developing a question-answering system for EHRs using text-to-SQL modeling, capable of reliably providing requested answers to various healthcare professionals to improve their clinical work processes and satisfy their needs. Among more than 100 participants who applied to the shared task, eight teams were formed and completed the entire shared task requirement and demonstrated a wide range of methods to effectively solve this task. In this paper, we describe the task of reliable text-to-SQL modeling, the dataset, and the methods and results of the participants. We hope this shared task will spur further research and insights into developing reliable question-answering systems for EHRs.

cs.CL↗

arXiv2024

Vision-Language Generative Model for View-Specific Chest X-ray Generation

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

eess.IV↗