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Comparative Evaluation of Clinical Large Language Models and Machine Learning to Predict Antimicrobial Resistance in Hospital-Onset Sepsis. 临床大语言模型和机器学习预测医院源性败血症抗菌素耐药性的比较评价
Pub Date : 2025-06-01 Epub Date: 2025-06-23 DOI: 10.1007/978-3-031-95838-0_7
Scott A Cohen, Ziyi Chen, Jiang Bian, Christina Boucher, Yonghui Wu, Mattia Prosperi

Approaches to guide empiric antimicrobial therapy are needed, especially in critically ill populations with prevalent antimicrobial resistance (AMR). While artificial intelligence shows promise in predicting AMR, scalable and generalizable prediction models are essential for broad clinical adoption. We utilized a publicly available clinical large language model (LLM), Gatortron, in comparison to traditional machine learning, to predict AMR and methicillin-resistant Staphylococcus aureus (MRSA)-specific patterns within a hospital-onset sepsis cohort using electronic health record (EHR) data available at time of illness onset. EHR data from approximately 150,000 hospitalizations with a documented bacterial infection at a large tertiary care healthcare system between 2010 and 2023 were examined. Among 2,019 eligible hospital-onset sepsis encounters, an AMR pathogen was identified in 911 (45%) and MRSA was isolated in 234 (26%). LLMs outperformed traditional models in predicting MRSA, achieving an AUC of 0.73 compared to 0.66 for the best traditional ML model, with superior F1 scores (0.43 vs. 0.16 for ML). Negative predictive value for MRSA prediction using LLM was at least 90% across majority of infection presentations. The LLM's superior prediction using a relatively simplified feature set demonstrates the potential of leveraging EHR data for early resistance prediction, though further refinement is needed to enhance sensitivity and clinical applicability.

需要指导经验性抗菌素治疗的方法,特别是在普遍存在抗菌素耐药性(AMR)的重症人群中。虽然人工智能在预测抗菌素耐药性方面显示出前景,但可扩展和可推广的预测模型对于广泛的临床应用至关重要。与传统机器学习相比,我们利用公开的临床大语言模型Gatortron,利用发病时可用的电子健康记录(EHR)数据,预测医院发病脓毒症队列中的AMR和耐甲氧西林金黄色葡萄球菌(MRSA)特异性模式。对2010年至2023年大型三级医疗保健系统中约15万例记录在案的细菌感染住院患者的电子病历数据进行了检查。在2019例符合条件的医院发生的败血症中,911例(45%)鉴定出AMR病原体,234例(26%)分离出MRSA。LLMs在预测MRSA方面优于传统模型,AUC为0.73,而最佳传统ML模型的AUC为0.66,F1得分更高(0.43比0.16)。在大多数感染表现中,使用LLM预测MRSA的阴性预测值至少为90%。LLM使用相对简化的特征集进行优越的预测,表明利用EHR数据进行早期耐药预测的潜力,尽管需要进一步改进以提高敏感性和临床适用性。
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引用次数: 0
Reinforcement Learning on Dyads to Enhance Medication Adherence. 强化学习对提高药物依从性的影响。
Pub Date : 2025-06-01 Epub Date: 2025-06-23 DOI: 10.1007/978-3-031-95838-0_48
Ziping Xu, Hinal Jajal, Sung Won Choi, Inbal Nahum-Shani, Guy Shani, Alexandra M Psihogios, Pei-Yao Hung, Susan A Murphy

Medication adherence is critical for the recovery of adolescents and young adults (AYAs) who have undergone hematopoietic cell transplantation. However, maintaining adherence is challenging for AYAs after hospital discharge, who experience both individual (e.g. physical and emotional symptoms) and interpersonal barriers (e.g., relational difficulties with their care partner, who is often involved in medication management). To optimize the effectiveness of a three-component digital intervention targeting both members of the dyad as well as their relationship, we propose a novel Multi-Agent Reinforcement Learning (MARL) approach to personalize the delivery of interventions. By incorporating the domain knowledge, the MARL framework, where each agent is responsible for the delivery of one intervention component, allows for faster learning compared with a flattened agent. Evaluation using a dyadic simulator environment, based on real clinical data, shows a significant improvement in medication adherence (approximately 3%) compared to purely random intervention delivery. The effectiveness of this approach will be further evaluated in an upcoming trial.

药物依从性对于接受了造血细胞移植的青少年和年轻人(AYAs)的康复至关重要。然而,对于在出院后经历个人(例如身体和情绪症状)和人际障碍(例如与其护理伙伴的关系困难,后者通常参与药物管理)的助理护士来说,保持坚持是具有挑战性的。为了优化针对两组成员及其关系的三组分数字干预的有效性,我们提出了一种新的多智能体强化学习(MARL)方法来个性化干预的交付。通过整合领域知识,与扁平的代理相比,每个代理负责交付一个干预组件的MARL框架允许更快的学习。基于真实临床数据,使用二元模拟环境的评估显示,与纯随机干预相比,药物依从性有显著改善(约3%)。这种方法的有效性将在即将进行的试验中进一步评估。
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引用次数: 0
Augmentation-Free Contrastive Learning for EKG Classification. 无增强对比学习在心电图分类中的应用。
Pub Date : 2025-01-01 Epub Date: 2025-06-23 DOI: 10.1007/978-3-031-95838-0_46
Junheng Wang, Milos Hauskrecht

Electrocardiogram (ECG/EKG) analysis is a vital diagnostic tool for assessing heart conditions, extensively used in clinical applications such as patient monitoring, surgical support, and heart disease research. With the rising demand for automated EKG interpretation, particularly for disease diagnosis and waveform labeling, machine learning models have become essential. However, the scarcity of large, well-labeled EKG datasets poses a significant challenge for training EKG classification models in the supervised form. This has shifted the attention towards unsupervised model pre-training, which often outperforms pure supervised methods when only a limited number of labeled data is available. This study explores the adaptation of the contrastive representation learning framework for EKG classification. Traditional contrastive learning methods rely on data augmentations to create diverse views of the same sample, but these augmentations are domain-specific, difficult to design, and can unpredictably impact model performance across different tasks. In this work, we address these limitations by proposing a novel, augmentation-free approach that integrates seamlessly with existing contrastive frameworks by eliminating their dependence on augmentations and hence their potential drawbacks. We evaluate our approach on the PTB-XL [1] dataset, and demonstrate its benefits in the unsupervised model pre-training step. Our solution offers a promising pathway for enhancing cardiac disease diagnostics in data-constrained environments.

心电图(ECG/EKG)分析是评估心脏状况的重要诊断工具,广泛用于临床应用,如患者监测,手术支持和心脏病研究。随着对自动心电图解释的需求不断增长,特别是在疾病诊断和波形标记方面,机器学习模型变得至关重要。然而,缺乏大型、标记良好的心电图数据集,这对训练监督形式的心电图分类模型构成了重大挑战。这将注意力转移到无监督模型预训练上,当只有有限数量的标记数据可用时,它通常优于纯监督方法。本研究探讨对比表征学习框架在心电图分类中的适应性。传统的对比学习方法依赖于数据增强来创建相同样本的不同视图,但是这些增强是特定于领域的,难以设计,并且可能不可预测地影响跨不同任务的模型性能。在这项工作中,我们通过提出一种新颖的、无增强的方法来解决这些限制,该方法通过消除现有对比框架对增强的依赖和潜在的缺点,与现有对比框架无缝集成。我们在PTB-XL[1]数据集上评估了我们的方法,并证明了它在无监督模型预训练步骤中的好处。我们的解决方案为在数据受限的环境中增强心脏病诊断提供了一条有希望的途径。
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引用次数: 0
Minimizing Survey Questions for PTSD Prediction Following Acute Trauma. 尽量减少用于预测急性创伤后创伤后应激障碍的调查问题。
Pub Date : 2024-07-01 Epub Date: 2024-07-25 DOI: 10.1007/978-3-031-66538-7_11
Ben Kurzion, Chia-Hao Shih, Hong Xie, Xin Wang, Kevin S Xu

Traumatic experiences have the potential to give rise to post-traumatic stress disorder (PTSD), a debilitating psychiatric condition associated with impairments in both social and occupational functioning. There has been great interest in utilizing machine learning approaches to predict the development of PTSD in trauma patients from clinician assessment or survey-based psychological assessments. However, these assessments require a large number of questions, which is time consuming and not easy to administer. In this paper, we aim to predict PTSD development of patients 3 months post-trauma from multiple survey-based assessments taken within 2 weeks post-trauma. Our objective is to minimize the number of survey questions that patients need to answer while maintaining the prediction accuracy from the full surveys. We formulate this as a feature selection problem and consider 4 different feature selection approaches. We demonstrate that it is possible to achieve up to 72% accuracy for predicting the 3-month PTSD diagnosis from 10 survey questions using a mean decrease in impurity-based feature selector followed by a gradient boosting classifier.

创伤经历有可能导致创伤后应激障碍(PTSD),这是一种使人衰弱的精神疾病,与社会和职业功能受损有关。人们对利用机器学习方法从临床医生的评估或基于调查的心理评估中预测创伤后应激障碍患者的发展非常感兴趣。然而,这些评估需要回答大量问题,既费时又不易操作。在本文中,我们旨在通过创伤后两周内进行的多项基于调查的评估来预测创伤后 3 个月患者的创伤后应激障碍发展情况。我们的目标是尽量减少患者需要回答的调查问题数量,同时保持完整调查的预测准确性。我们将其表述为一个特征选择问题,并考虑了 4 种不同的特征选择方法。我们证明,使用基于不纯度的平均下降特征选择器和梯度提升分类器,从 10 个调查问题中预测 3 个月的创伤后应激障碍诊断的准确率可高达 72%。
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引用次数: 0
Enhancing Hypotension Prediction in Real-time Patient Monitoring Through Deep Learning: A Novel Application of XResNet with Contrastive Learning and Value Attention Mechanisms. 通过深度学习加强实时患者监测中的低血压预测:具有对比学习和价值注意机制的 XResNet 的新应用。
Pub Date : 2024-07-01 Epub Date: 2024-07-25 DOI: 10.1007/978-3-031-66538-7_5
Xiangru Chen, Milos Hauskrecht

The precise prediction of hypotension is vital for advancing preemptive patient care strategies. Traditional machine learning approaches, while instrumental in this field, are hampered by their dependence on structured historical data and manual feature extraction techniques. These methods often fall short of recognizing the intricate patterns present in physiological signals. Addressing this limitation, our study introduces an innovative application of deep learning technologies, utilizing a sophisticated end-to-end architecture grounded in XResNet. This architecture is further enhanced by the integration of contrastive learning and a value attention mechanism, specifically tailored to analyze arterial blood pressure (ABP) waveform signals. Our approach improves the performance of hypotension prediction over the existing state-of-theart ABP model [7]. This research represents a step towards optimizing patient care, embodying the next generation of AI-driven healthcare solutions. Through our findings, we demonstrate the promise of deep learning in overcoming the limitations of conventional prediction models, thereby offering an avenue for enhancing patient outcomes in clinical settings.

精确预测低血压对于推进先发制人的患者护理策略至关重要。传统的机器学习方法虽然在这一领域大有用武之地,但由于依赖于结构化历史数据和人工特征提取技术而受到阻碍。这些方法往往无法识别生理信号中存在的复杂模式。针对这一局限性,我们的研究引入了深度学习技术的创新应用,利用以 XResNet 为基础的复杂端到端架构。通过整合对比学习和价值注意机制,这一架构得到了进一步增强,专门用于分析动脉血压(ABP)波形信号。与现有的先进 ABP 模型相比,我们的方法提高了低血压预测的性能[7]。这项研究向优化患者护理迈出了一步,体现了下一代人工智能驱动的医疗解决方案。通过我们的研究成果,我们展示了深度学习在克服传统预测模型局限性方面的前景,从而为提高临床环境中患者的治疗效果提供了一条途径。
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引用次数: 0
Sentence-Aligned Simplification of Biomedical Abstracts. 生物医学摘要的句子对齐简化。
Pub Date : 2024-01-01 Epub Date: 2024-07-25 DOI: 10.1007/978-3-031-66538-7_32
Brian Ondov, Dina Demner-Fushman

The availability of biomedical abstracts in online databases could improve health literacy and drive more informed choices. However, the technical language of these documents makes them inaccessible to healthcare consumers, causing disengagement, frustration and potential misuse. In this work we explore adapting foundation language models to the Plain Language Adaptation of Biomedical Abstracts benchmark. This task is challenging because it requires sentence-by-sentence simplifications, but entire abstracts must also be simplified cohesively. We present a sentence-wise autoregressive approach and report experiments with this technique in both zero-shot and fine-tuned settings, using both proprietary and open-source models. We also introduce a stochastic regularization technique to encourage recovery from source-copying during autoregressive inference. Our best-performing model achieves a 32 point increase in SARI and 6 point increase in BERTscore over the reported state-of-the-art. This also surpasses performance of recent open-domain and biomedical sentence simplification models on this task. Further, in manual evaluation, models achieve factual accuracy comparable to human-level, with simplicity close to that of humans. Abstracts simplified by these models could unlock a massive source of health information while retaining clear provenance for each statement to enhance trustworthiness.

在线数据库中生物医学摘要的可用性可以提高健康素养并推动更明智的选择。然而,这些文档的技术语言使医疗保健消费者无法访问它们,从而导致脱离、沮丧和潜在的误用。在这项工作中,我们探索了将基础语言模型适应为生物医学摘要的普通语言适应基准。这项任务具有挑战性,因为它需要逐句简化,但整个摘要也必须连贯地简化。我们提出了一种句子智能自回归方法,并报告了在零射击和微调设置下使用该技术的实验,使用专有和开源模型。我们还引入了一种随机正则化技术,以鼓励在自回归推理期间从源复制中恢复。我们表现最好的模型在SARI中增加了32分,在BERTscore中增加了6分。这也超过了最近的开放领域和生物医学句子简化模型在这个任务上的表现。此外,在人工评估中,模型达到了与人类水平相当的事实准确性,简单性接近人类。通过这些模型简化的摘要可以解锁大量的健康信息来源,同时为每个陈述保留明确的来源,以提高可信度。
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引用次数: 0
Uncovering hidden therapeutic indications through drug repurposing with graph neural networks and heterogeneous data. 利用图神经网络和异构数据,通过药物再利用发现隐藏的治疗适应症。
Adrián Ayuso-Muñoz, Lucía Prieto-Santamaría, Esther Ugarte-Carro, E. Serrano, A. Rodríguez-González
Drug repurposing has gained the attention of many in the recent years. The practice of repurposing existing drugs for new therapeutic uses helps to simplify the drug discovery process, which in turn reduces the costs and risks that are associated with de novo development. Representing biomedical data in the form of a graph is a simple and effective method to depict the underlying structure of the information. Using deep neural networks in combination with this data represents a promising approach to address drug repurposing. This paper presents BEHOR a more comprehensive version of the REDIRECTION model, which was previously presented. Both versions utilize the DISNET biomedical graph as the primary source of information, providing the model with extensive and intricate data to tackle the drug repurposing challenge. This new version's results for the reported metrics in the RepoDB test are 0.9604 for AUROC and 0.9518 for AUPRC. Additionally, a discussion is provided regarding some of the novel predictions to demonstrate the reliability of the model. The authors believe that BEHOR holds promise for generating drug repurposing hypotheses and could greatly benefit the field.
近年来,药物再利用已经引起了许多人的注意。将现有药物重新用于新的治疗用途的做法有助于简化药物发现过程,从而降低与从头开发相关的成本和风险。以图的形式表示生物医学数据是描述信息底层结构的一种简单有效的方法。将深度神经网络与这些数据相结合,是解决药物再利用问题的一种很有前途的方法。本文提出了BEHOR,这是先前提出的重定向模型的一个更全面的版本。这两个版本都利用DISNET生物医学图作为信息的主要来源,为模型提供广泛而复杂的数据,以解决药物再利用的挑战。对于RepoDB测试中报告的指标,这个新版本的结果是AUROC的0.9604和AUPRC的0.9518。此外,还对一些新的预测进行了讨论,以证明模型的可靠性。作者认为,BEHOR有望产生药物再利用假设,并可能极大地造福该领域。
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引用次数: 0
Learning EKG Diagnostic Models with Hierarchical Class Label Dependencies. 学习具有分层类标签依赖关系的心电图诊断模型。
Junheng Wang, Milos Hauskrecht

Electrocardiogram (EKG/ECG) is a key diagnostic tool to assess patient's cardiac condition and is widely used in clinical applications such as patient monitoring, surgery support, and heart medicine research. With recent advances in machine learning (ML) technology there has been a growing interest in the development of models supporting automatic EKG interpretation and diagnosis based on past EKG data. The problem can be modeled as multi-label classification (MLC), where the objective is to learn a function that maps each EKG reading to a vector of diagnostic class labels reflecting the underlying patient condition at different levels of abstraction. In this paper, we propose and investigate an ML model that considers class-label dependency embedded in the hierarchical organization of EKG diagnoses to improve the EKG classification performance. Our model first transforms the EKG signals into a low-dimensional vector, and after that uses the vector to predict different class labels with the help of the conditional tree structured Bayesian network (CTBN) that is able to capture hierarchical dependencies among class variables. We evaluate our model on the publicly available PTB-XL dataset. Our experiments demonstrate that modeling of hierarchical dependencies among class variables improves the diagnostic model performance under multiple classification performance metrics as compared to classification models that predict each class label independently.

心电图(EKG/ECG)是评估患者心脏状况的重要诊断工具,在患者监护、手术支持、心脏医学研究等临床应用中有着广泛的应用。随着机器学习(ML)技术的最新进展,人们对基于过去的心电图数据开发支持自动心电图解释和诊断的模型越来越感兴趣。该问题可以建模为多标签分类(MLC),其目标是学习一个函数,该函数将每个心电图读数映射到反映不同抽象级别的潜在患者状况的诊断类标签向量。在本文中,我们提出并研究了一种ML模型,该模型考虑了嵌入在EKG诊断层次组织中的类标签依赖关系,以提高EKG分类性能。我们的模型首先将心电图信号转换为低维向量,然后在能够捕获类变量之间的层次依赖关系的条件树结构贝叶斯网络(CTBN)的帮助下,使用该向量来预测不同的类标签。我们在公开可用的PTB-XL数据集上评估我们的模型。我们的实验表明,与独立预测每个类标签的分类模型相比,在多个分类性能指标下,类变量之间的分层依赖关系建模提高了诊断模型的性能。
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引用次数: 0
Predicting Kidney Transplant Survival using Multiple Feature Representations for HLAs. 利用hla的多特征表示预测肾移植生存。
Mohammadreza Nemati, Haonan Zhang, Michael Sloma, Dulat Bekbolsynov, Hong Wang, Stanislaw Stepkowski, Kevin S Xu

Kidney transplantation can significantly enhance living standards for people suffering from end-stage renal disease. A significant factor that affects graft survival time (the time until the transplant fails and the patient requires another transplant) for kidney transplantation is the compatibility of the Human Leukocyte Antigens (HLAs) between the donor and recipient. In this paper, we propose new biologically-relevant feature representations for incorporating HLA information into machine learning-based survival analysis algorithms. We evaluate our proposed HLA feature representations on a database of over 100,000 transplants and find that they improve prediction accuracy by about 1%, modest at the patient level but potentially significant at a societal level. Accurate prediction of survival times can improve transplant survival outcomes, enabling better allocation of donors to recipients and reducing the number of re-transplants due to graft failure with poorly matched donors.

肾移植可以显著提高终末期肾病患者的生活水平。肾移植中影响移植物存活时间(移植失败和患者需要另一次移植的时间)的一个重要因素是供体和受体之间的人类白细胞抗原(hla)的相容性。在本文中,我们提出了将HLA信息纳入基于机器学习的生存分析算法的新的生物学相关特征表示。我们在超过100,000例移植的数据库中评估了我们提出的HLA特征表示,发现它们将预测准确性提高了约1%,在患者水平上是适度的,但在社会水平上可能具有重要意义。准确预测存活时间可以改善移植存活结果,使供体更好地分配给受者,并减少由于供体匹配不良导致移植失败而再次移植的数量。
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引用次数: 0
Identifying Symptom Clusters Through Association Rule Mining. 通过关联规则挖掘识别症状聚类。
Pub Date : 2021-06-01 Epub Date: 2021-06-08 DOI: 10.1007/978-3-030-77211-6_58
Mikayla Biggs, Carla Floricel, Lisanne Van Dijk, Abdallah S R Mohamed, C David Fuller, G Elisabeta Marai, Xinhua Zhang, Guadalupe Canahuate

Cancer patients experience many symptoms throughout their cancer treatment and sometimes suffer from lasting effects post-treatment. Patient-Reported Outcome (PRO) surveys provide a means for monitoring the patient's symptoms during and after treatment. Symptom cluster (SC) research seeks to understand these symptoms and their relationships to define new treatment and disease management methods to improve patient's quality of life. This paper introduces association rule mining (ARM) as a novel alternative for identifying symptom clusters. We compare the results to prior research and find that while some of the SCs are similar, ARM uncovers more nuanced relationships between symptoms such as anchor symptoms that serve as connections between interference and cancer-specific symptoms.

癌症患者在整个癌症治疗过程中会经历许多症状,有时会在治疗后遭受持久的影响。患者报告的结果(PRO)调查提供了一种在治疗期间和治疗后监测患者症状的方法。症状群(SC)研究旨在了解这些症状及其关系,以确定新的治疗和疾病管理方法,以改善患者的生活质量。本文介绍了关联规则挖掘(ARM)作为识别症状聚类的一种新方法。我们将结果与先前的研究进行了比较,发现虽然一些SCs是相似的,但ARM揭示了症状之间更微妙的关系,例如锚定症状,它作为干扰和癌症特异性症状之间的联系。
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引用次数: 1
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Artificial intelligence in medicine. Conference on Artificial Intelligence in Medicine (2005- )
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