Showing 1–7 of 7 results for author: Wong, A I

Performance of Large Language Models in Answering Critical Care Medicine Questions

Authors: Mahmoud Alwakeel, Aditya Nagori, An-Kwok Ian Wong, Neal Chaisson, Vijay Krishnamoorthy, Rishikesan Kamaleswaran

Abstract: Large Language Models have been tested on medical student-level questions, but their performance in specialized fields like Critical Care Medicine (CCM) is less explored. This study evaluated Meta-Llama 3.1 models (8B and 70B parameters) on 871 CCM questions. Llama3.1:70B outperformed 8B by 30%, with 60% average accuracy. Performance varied across domains, highest in Research (68.4%) and lowest in… ▽ More Large Language Models have been tested on medical student-level questions, but their performance in specialized fields like Critical Care Medicine (CCM) is less explored. This study evaluated Meta-Llama 3.1 models (8B and 70B parameters) on 871 CCM questions. Llama3.1:70B outperformed 8B by 30%, with 60% average accuracy. Performance varied across domains, highest in Research (68.4%) and lowest in Renal (47.9%), highlighting the need for broader future work to improve models across various subspecialty domains. △ Less

Submitted 16 September, 2025; originally announced September 2025.

Predicting Antibiotic Resistance Patterns Using Sentence-BERT: A Machine Learning Approach

Authors: Mahmoud Alwakeel, Michael E. Yarrington, Rebekah H. Wrenn, Ethan Fang, Jian Pei, Anand Chowdhury, An-Kwok Ian Wong

Abstract: Antibiotic resistance poses a significant threat in in-patient settings with high mortality. Using MIMIC-III data, we generated Sentence-BERT embeddings from clinical notes and applied Neural Networks and XGBoost to predict antibiotic susceptibility. XGBoost achieved an average F1 score of 0.86, while Neural Networks scored 0.84. This study is among the first to use document embeddings for predict… ▽ More Antibiotic resistance poses a significant threat in in-patient settings with high mortality. Using MIMIC-III data, we generated Sentence-BERT embeddings from clinical notes and applied Neural Networks and XGBoost to predict antibiotic susceptibility. XGBoost achieved an average F1 score of 0.86, while Neural Networks scored 0.84. This study is among the first to use document embeddings for predicting antibiotic resistance, offering a novel pathway for improving antimicrobial stewardship. △ Less

Submitted 16 September, 2025; originally announced September 2025.

Evaluating Large Language Models for Automated Clinical Abstraction in Pulmonary Embolism Registries: Performance Across Model Sizes, Versions, and Parameters

Authors: Mahmoud Alwakeel, Emory Buck, Jonathan G. Martin, Imran Aslam, Sudarshan Rajagopal, Jian Pei, Mihai V. Podgoreanu, Christopher J. Lindsell, An-Kwok Ian Wong

Abstract: Pulmonary embolism (PE) registries accelerate practice-improving research but depend on resource-intensive manual abstraction of radiology reports. We evaluated whether openly available large-language models (LLMs) can automate concept extraction from computed-tomography PE (CTPE) reports without sacrificing data quality. Four Llama-3 (L3) variants (3.0 8 B, 3.1 8 B, 3.1 70 B, 3.3 70 B) and two re… ▽ More Pulmonary embolism (PE) registries accelerate practice-improving research but depend on resource-intensive manual abstraction of radiology reports. We evaluated whether openly available large-language models (LLMs) can automate concept extraction from computed-tomography PE (CTPE) reports without sacrificing data quality. Four Llama-3 (L3) variants (3.0 8 B, 3.1 8 B, 3.1 70 B, 3.3 70 B) and two reviewer models Phi-4 (P4) 14 B and Gemma-3 27 B (G3) were tested on 250 dual-annotated CTPE reports each from MIMIC-IV and Duke University. Outcomes were accuracy, positive predictive value (PPV), and negative predictive value (NPV) versus a human gold standard across model sizes, temperature settings, and shot counts. Mean accuracy across all concepts increased with scale: 0.83 (L3-0 8 B), 0.91 (L3-1 8 B), and 0.96 for both 70 B variants; P4 14 B achieved 0.98; G3 matched. Accuracy differed by < 0.03 between datasets, underscoring external robustness. In dual-model concordance analysis (L3 70 B + P4 14 B), PE-presence PPV was >= 0.95 and NPV >= 0.98, while location, thrombus burden, right-heart strain, and image-quality artifacts each maintained PPV >= 0.90 and NPV >= 0.95. Fewer than 4% of individual concept annotations were discordant, and complete agreement was observed in more than 75% of reports. G3 performed comparably. LLMs therefore offer a scalable, accurate solution for PE registry abstraction, and a dual-model review workflow can further safeguard data quality with minimal human oversight. △ Less

Submitted 11 August, 2025; v1 submitted 26 March, 2025; originally announced March 2025.

WorldMedQA-V: a multilingual, multimodal medical examination dataset for multimodal language models evaluation

Authors: João Matos, Shan Chen, Siena Placino, Yingya Li, Juan Carlos Climent Pardo, Daphna Idan, Takeshi Tohyama, David Restrepo, Luis F. Nakayama, Jose M. M. Pascual-Leone, Guergana Savova, Hugo Aerts, Leo A. Celi, A. Ian Wong, Danielle S. Bitterman, Jack Gallifant

Abstract: Multimodal/vision language models (VLMs) are increasingly being deployed in healthcare settings worldwide, necessitating robust benchmarks to ensure their safety, efficacy, and fairness. Multiple-choice question and answer (QA) datasets derived from national medical examinations have long served as valuable evaluation tools, but existing datasets are largely text-only and available in a limited su… ▽ More Multimodal/vision language models (VLMs) are increasingly being deployed in healthcare settings worldwide, necessitating robust benchmarks to ensure their safety, efficacy, and fairness. Multiple-choice question and answer (QA) datasets derived from national medical examinations have long served as valuable evaluation tools, but existing datasets are largely text-only and available in a limited subset of languages and countries. To address these challenges, we present WorldMedQA-V, an updated multilingual, multimodal benchmarking dataset designed to evaluate VLMs in healthcare. WorldMedQA-V includes 568 labeled multiple-choice QAs paired with 568 medical images from four countries (Brazil, Israel, Japan, and Spain), covering original languages and validated English translations by native clinicians, respectively. Baseline performance for common open- and closed-source models are provided in the local language and English translations, and with and without images provided to the model. The WorldMedQA-V benchmark aims to better match AI systems to the diverse healthcare environments in which they are deployed, fostering more equitable, effective, and representative applications. △ Less

Submitted 16 October, 2024; originally announced October 2024.

Comments: submitted for review, total of 14 pages

Evaluating the Impact of Pulse Oximetry Bias in Machine Learning under Counterfactual Thinking

Authors: Inês Martins, João Matos, Tiago Gonçalves, Leo A. Celi, A. Ian Wong, Jaime S. Cardoso

Abstract: Algorithmic bias in healthcare mirrors existing data biases. However, the factors driving unfairness are not always known. Medical devices capture significant amounts of data but are prone to errors; for instance, pulse oximeters overestimate the arterial oxygen saturation of darker-skinned individuals, leading to worse outcomes. The impact of this bias in machine learning (ML) models remains uncl… ▽ More Algorithmic bias in healthcare mirrors existing data biases. However, the factors driving unfairness are not always known. Medical devices capture significant amounts of data but are prone to errors; for instance, pulse oximeters overestimate the arterial oxygen saturation of darker-skinned individuals, leading to worse outcomes. The impact of this bias in machine learning (ML) models remains unclear. This study addresses the technical challenges of quantifying the impact of medical device bias in downstream ML. Our experiments compare a "perfect world", without pulse oximetry bias, using SaO2 (blood-gas), to the "actual world", with biased measurements, using SpO2 (pulse oximetry). Under this counterfactual design, two models are trained with identical data, features, and settings, except for the method of measuring oxygen saturation: models using SaO2 are a "control" and models using SpO2 a "treatment". The blood-gas oximetry linked dataset was a suitable test-bed, containing 163,396 nearly-simultaneous SpO2 - SaO2 paired measurements, aligned with a wide array of clinical features and outcomes. We studied three classification tasks: in-hospital mortality, respiratory SOFA score in the next 24 hours, and SOFA score increase by two points. Models using SaO2 instead of SpO2 generally showed better performance. Patients with overestimation of O2 by pulse oximetry of > 3% had significant decreases in mortality prediction recall, from 0.63 to 0.59, P < 0.001. This mirrors clinical processes where biased pulse oximetry readings provide clinicians with false reassurance of patients' oxygen levels. A similar degradation happened in ML models, with pulse oximetry biases leading to more false negatives in predicting adverse outcomes. △ Less

Submitted 8 August, 2024; originally announced August 2024.

Comments: 10 pages; accepted at MICCAI's Third Workshop on Applications of Medical AI (2024)

EHRmonize: A Framework for Medical Concept Abstraction from Electronic Health Records using Large Language Models

Authors: João Matos, Jack Gallifant, Jian Pei, A. Ian Wong

Abstract: Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize,… ▽ More Electronic health records (EHRs) contain vast amounts of complex data, but harmonizing and processing this information remains a challenging and costly task requiring significant clinical expertise. While large language models (LLMs) have shown promise in various healthcare applications, their potential for abstracting medical concepts from EHRs remains largely unexplored. We introduce EHRmonize, a framework leveraging LLMs to abstract medical concepts from EHR data. Our study uses medication data from two real-world EHR databases to evaluate five LLMs on two free-text extraction and six binary classification tasks across various prompting strategies. GPT-4o's with 10-shot prompting achieved the highest performance in all tasks, accompanied by Claude-3.5-Sonnet in a subset of tasks. GPT-4o achieved an accuracy of 97% in identifying generic route names, 82% for generic drug names, and 100% in performing binary classification of antibiotics. While EHRmonize significantly enhances efficiency, reducing annotation time by an estimated 60%, we emphasize that clinician oversight remains essential. Our framework, available as a Python package, offers a promising tool to assist clinicians in EHR data abstraction, potentially accelerating healthcare research and improving data harmonization processes. △ Less

Submitted 28 June, 2024; originally announced July 2024.

Comments: submitted for review, total of 10 pages

Benchmarking emergency department triage prediction models with machine learning and large public electronic health records

Authors: Feng Xie, Jun Zhou, Jin Wee Lee, Mingrui Tan, Siqi Li, Logasan S/O Rajnthern, Marcel Lucas Chee, Bibhas Chakraborty, An-Kwok Ian Wong, Alon Dagan, Marcus Eng Hock Ong, Fei Gao, Nan Liu

Abstract: The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have acce… ▽ More The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care. △ Less

Submitted 20 March, 2022; v1 submitted 22 November, 2021; originally announced November 2021.