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The Time-Varying Impact of COVID-19 on the Acute Kidney Disorders:A Historical Matched Cohort Study and Mendelian Randomization Analysis

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Health data science 2024年第1期4卷 215-225页

作者： Chunyang Li Chao Zhang Jie Chen Yilong Chen Zhiye Ying Yao Hu Huan Song Ping Fu Xiaoxi Zeng Division of Nephrology West China Biomedical Big Data CenterWest China HospitalSichuan UniversityChengdu 610041China Med-X Center for Informatics Sichuan UniversityChengdu 610065China Department of Core Laboratory Sichuan Provincial Peopleʼs HospitalUniversity of Electronic Science and Technology of ChinaChengdu 610054China Centre of Public Health Sciences Faculty of MedicineUniversity of IcelandReykjavíkIceland

Background:This study aimed to explore the time-varying impact of COVID-19 on acute kidney disorders,including acute kidney injury and other acute kidney ***:From the UK Biobank,10,121 participants with COVID-19 were matched with up to 3 historically unexposed controls by age,sex,Townsend deprivation index,and the status of hospitalization or receiving critical *** investigated the association between COVID-19 and incidence of acute kidney disorders,within the ffrst 4 weeks after infection,using conditional and time-varying Cox proportional hazard *** addition,one-sample Mendelian randomization,utilizing the polygenic risk score for COVID-19 as an instrumental variable,was conducted to explore the potential causality of the ***:In the matched cohort study,we observed a signiffcant association between COVID-19 and acute kidney disorders predominantly within the ffrst 3 *** impact of COVID-19 was time dependent,peaking in the second week(hazard ratio,12.77;95%conffdence interval,5.93 to 27.70)and decreasing by the fourth week(hazard ratio,2.28;95%conffdence interval,0.75 to 6.93).In subgroup analyses,only moderate to severe COVID-19 cases were associated with acute worsening of renal function in a time-dependent ***-sample Mendelian randomization analyses further showed that COVID-19 might exert a“short-term”causal effect on the risk of acute kidney disorders,primarily conffned to the ffrst week after ***:The risk of acute kidney disorders following COVID-19 demonstrates a time-varying *** effects were observed only in patients with moderate or severe but not mild COVID-19.

关键词： Kidney matched utilizing

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Improving Large Language Models for Clinical Named Entity Recognition via Prompt Engineering

arXiv

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arXiv 2023年

作者： Hu, Yan Chen, Qingyu Du, Jingcheng Peng, Xueqing Keloth, Vipina Kuttichi Zuo, Xu Zhou, Yujia Li, Zehan Jiang, Xiaoqian Lu, Zhiyong Roberts, Kirk Xu, Hua School of Biomedical Informatics University of Texas Health Science at Houston Houston United States Section of Biomedical Informatics and Data Science School of Medicine Yale University New Haven United States National Center for Biotechnology Information National Library of Medicine National Institutes of Health MD United States

Objective: This study quantifies the capabilities of GPT-3.5 and GPT-4 for clinical named entity recognition (NER) tasks and proposes task-specific prompts to improve their performance. Materials and Methods: We evaluated these models on two clinical NER tasks: (1) to extract medical problems, treatments, and tests from clinical notes in the MTSamples corpus, following the 2010 i2b2 concept extraction shared task, and (2) identifying nervous system disorder-related adverse events from safety reports in the vaccine adverse event reporting system (VAERS). To improve the GPT models' performance, we developed a clinical task-specific prompt framework that includes (1) baseline prompts with task description and format specification, (2) annotation guideline-based prompts, (3) error analysis-based instructions, and (4) annotated samples for few-shot learning. We assessed each prompt's effectiveness and compared the models to BioClinicalBERT. Results: Using baseline prompts, GPT-3.5 and GPT-4 achieved relaxed F1 scores of 0.634, 0.804 for MTSamples, and 0.301, 0.593 for VAERS. Additional prompt components consistently improved model performance. When all four components were used, GPT-3.5 and GPT-4 achieved relaxed F1 socres of 0.794, 0.861 for MTSamples and 0.676, 0.736 for VAERS, demonstrating the effectiveness of our prompt framework. Although these results trail BioClinicalBERT (F1 of 0.901 for the MTSamples dataset and 0.802 for the VAERS), it is very promising considering few training samples are needed. Conclusion: While direct application of GPT models to clinical NER tasks falls short of optimal performance, our task-specific prompt framework, incorporating medical knowledge and training samples, significantly enhances GPT models' feasibility for potential clinical applications. Copyright © 2023, The Authors. All rights reserved.

关键词： Medical problems

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CANCERLLM: A LARGE LANGUAGE MODEL IN CANCER DOMAIN

arXiv

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arXiv 2024年

作者： Li, Mingchen Blaes, Anne Johnson, Steven Liu, Hongfang Xu, Hua Zhang, Rui Division of Computational Health Sciences University of Minnesota Twin Cities United States Division of Hematology Oncology and Transplantation University of Minnesota Twin Cities United States Institute for Health Informatics University of Minnesota Twin Cities United States McWilliams School of Biomedical Informatics UTHealth Houston United States Department of Biomedical Informatics and Data Science Yale School of Medicine United States

Medical Large Language Models (LLMs) such as ClinicalCamel 70B, Llama3- OpenBioLLM 70B have demonstrated impressive performance on a wide variety of medical NLP task. However, there still lacks a large language model (LLM) specifically designed for cancer domain. Moreover, these LLMs typically have billions of parameters, making them computationally expensive for healthcare systems. Thus, in this study, we propose CancerLLM, a model with 7 billion parameters and a Mistral-style architecture, pre-trained on 2,676,642 clinical notes and 515,524 pathology reports covering 17 cancer types, followed by fine-tuning on three cancer-relevant tasks, including cancer phenotypes extraction, cancer diagnosis generation, and cancer treatment plan generation. Our evaluation demonstrated that CancerLLM achieves state-of-the-art results compared to other existing LLMs, with an average F1 score improvement of 8.1%. Additionally, CancerLLM outperforms other models on two proposed robustness testbeds. This illustrates that CancerLLM can be effectively applied to clinical AI systems, enhancing clinical research and healthcare delivery in the field of cancer. © 2024, CC BY.

关键词： Clinical research

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rmlnomogram: An R package to construct an explainable nomogram for any machine learning algorithms

arXiv

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arXiv 2025年

作者： Sufriyana, Herdiantri Su, Emily Chia-Yu Institute of Biomedical Informatics College of Medicine National Yang Ming Chiao Tung University Taipei Taiwan Graduate Institute of Biomedical Informatics College of Medical Science and Technology Taipei Medical University Taipei Taiwan Clinical Big Data Research Center Taipei Medical University Hospital Taipei Taiwan Institute of Biomedical Informatics College of Medicine National Yang Ming Chiao Tung University 155 Section 2 Linong Street Beitou District Taipei112304 Taiwan

Background: Current nomogram can only be created for regression algorithm. Providing nomogram for any machine learning (ML) algorithms may accelerate model deployment in clinical settings or improve model availability. We developed an R package and web application to construct nomogram with model explainability of any ML algorithms. Methods: We formulated a function to transform an ML prediction model into a nomogram, requiring datasets with: (1) all possible combinations of predictor values;(2) the corresponding outputs of the model;and (3) the corresponding explainability values for each predictor (optional). Web application was also created. Results: Our R package could create 5 types of nomograms for categorical predictors and binary outcome without probability (1), categorical predictors and binary outcome with probability (2) or continuous outcome (3), and categorical with single numerical predictors and binary outcome with probability (4) or continuous outcome (5). Respectively, the first and remaining types optimally allowed maximum 15 and 5 predictors with maximum 3,200 combinations. Web application is provided with such limits. The explainability values were possible for types 2 to 5. Conclusions: Our R package and web application could construct nomogram with model explainability of any ML algorithms using a fair number of predictors. © 2025, CC BY-NC-SA.

关键词： Adversarial machine learning

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Stroke Prediction Using Machine Learning

Stroke Prediction Using Machine Learning

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International Conference on Advances in Electronics, Computers and Communications (ICAECC)

作者： Abinandhini D M Aman Kumar Gudi Vishnu Teja Mandava Sukesh Divya S Naman Chauhan I R Oviya Kalpana Raja Department of Computer Science and Engineering (Artificial Intelligence) Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350305449

ISBN: (纸本)9798350305456

A stroke is a serious medical emergency that happens when bleeding or blood clots cut off the blood flow to a part of the brain. With a mortality rate of 5.5 million per year, it ranks as the second leading cause of death globally. Over 15 million individuals experience a stroke each year, and one person dies from one every four minutes. According to the World Health Organization, stroke is the main cause of death and disability worldwide (WHO). Identifying the many stroke warning signs helps lessen the severity of the stroke. A stroke can be avoided in up to 80% of instances because it is typically the result of a poor lifestyle. As a result, stroke prediction becomes important and should be employed to stop it from causing long-term harm. The current study uses a variety of machine learning models, including Gaussian Naive Bayes, Logistic Regression, Support Vector Machine (SVM), KNN and Random Forest to predict stroke. The paper presents the comparison among all machine learning algorithms. Analysis of results revealed that KNN had the least accuracy of 76.32% and Random Forest had the highest accuracy of 94.81%.

关键词： Support vector machines Accuracy Organizations Stroke (medical condition) Predictive models Vectors Physiology

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ML Based Phenotype Analysis Using Differential Gene Expression data in Schizophrenia

ML Based Phenotype Analysis Using Differential Gene Expressi...

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Smart Technologies in Computing, Electrical and Electronics (ICSTCEE), International Conference on

作者： Aadhithyan D Shabarirajan KJ Varun Maniappan Shivanesh B Divya S Praghaadeesh R Kalpana Raja I R Oviya Department of Computer Science and Engineering (Artificial Intelligence) Amrita Vishwa Vidyapeetham Chennai India Section for Biomedical Informatics and Data Science School of Medicine Yale University New Haven Connecticut USA

ISBN: (数字)9798350384628

ISBN: (纸本)9798350384635

In this paper, differential gene expression (DGE) data in schizophrenia is analysed using machine learning approaches with the objective of predicting cell phenotypes related to the condition. The dataset contains information on cis eQTNs, gene orientation, probe information, gene expression profiles, and SNP information. When first investigating well-known machine learning methods, a hybrid model combining Random Forests and XGBoost is suggested, however it only offers a little increase. Increases in predicted accuracy of more than 99.12% are made possible by the H2O AutoML package. The results demonstrate the capability of ML-based analysis to unravel the underlying biological mechanisms of schizophrenia and contribute to the design of individualised therapeutic approaches. The paper represents the capability of machine learning to comprehend the relationship between gene expression patterns and complicated illnesses like schizophrenia.

关键词： Water Training Accuracy Phenotypes Mental disorders Predictive models data models

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Development of Automated Detection Methods for Calculating Blood Vessel Width and Stenosis Rate in Cardiac Catheterization Imaging 24

Development of Automated Detection Methods for Calculating B...

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8th International Conference on Medical and Health informatics, ICMHI 2024

作者： Huang, Hsien-Cheng Chang, Hsiao-Huang Ke, Xiang-Wei Chien, Ting-Ying Department of Computer Science and Engineering Yuan Ze University Taoyuan City Taiwan Cardiovascular Surgery Department Taipei Veterans General Hospital Taipei City Taiwan Taipei Medical University Taipei City Taiwan Graduate Program in Biomedical Informatics Yuan Ze University Taoyuan City Taiwan Innovation Center for Big Data and Digital Convergence Yuan Ze University Taoyuan City Taiwan

ISBN: (纸本)9798400716874

Coronary artery disease is the most prevalent type of heart disease and has a considerable mortality rate. In diagnosing and assessing coronary artery disease, physicians must integrate a variety of clinical information and test results to evaluate the degree of coronary artery obstruction and continually learn and improve their skills in clinical practice to ensure the most accurate assessment of patients. Currently, the use of information technology to assist medical staff allows more effective and accurate analysis of symptoms. This approach not only serves as an auxiliary standard for physician diagnosis, thereby reducing the possibility of misdiagnosis, but also significantly improves patient treatment outcomes and medical quality while reducing the time burden on physicians for diagnosing patients. This study utilized image processing techniques and thinning algorithms to automate the detection of coronary artery width and, following the recommended methods of physicians in related fields, used specific vessel widths to calculate the degree of coronary artery narrowing. This provides a more accurate and efficient assessment method for evaluating the degree of vascular constriction in patients with coronary artery disease. © 2024 Copyright ACM.

关键词： Patient treatment

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TransXNet: Learning Both Global and Local Dynamics With a Dual Dynamic Token Mixer for Visual Recognition

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IEEE Transactions on Neural Networks and Learning Systems 2025年第6期36卷 11534-11547页

作者： Meng Lou Shu Zhang Hong-Yu Zhou Sibei Yang Chuan Wu Yizhou Yu School of Computing and Data Science The University of Hong Kong Hong Kong SAR China Artificial Intelligence Laboratory Deepwise Healthcare Beijing China Department of Biomedical Informatics Harvard Medical School Boston CA USA Department of Computer Science The University of Hong Kong Hong Kong SAR China School of Information Science and Technology ShanghaiTech University Shanghai China

Recent studies have integrated convolutions into transformers to introduce inductive bias and improve generalization performance. However, the static nature of conventional convolution prevents it from dynamically adapting to input variations, resulting in a representation discrepancy between convolution and self-attention as self-attention calculates attention matrices dynamically. Furthermore, when stacking token mixers that consist of convolution and self-attention to form a deep network, the static nature of convolution hinders the fusion of features previously generated by self-attention into convolution kernels. These two limitations result in a suboptimal representation capacity of the constructed networks. To find a solution, we propose a lightweight dual dynamic token mixer (D-Mixer) to simultaneously learn global and local dynamics, that is, mechanisms that compute weights for aggregating global contexts and local details in an input-dependent manner. D-Mixer works by applying an efficient global attention module and an input-dependent depthwise convolution separately on evenly split feature segments, endowing the network with strong inductive bias and an enlarged effective receptive field. We use D-Mixer as the basic building block to design TransXNet, a novel hybrid CNN–transformer vision backbone network that delivers compelling performance. In the ImageNet-1K image classification task, TransXNet-T surpasses Swin-T by 0.3% in top-1 accuracy while requiring less than half of the computational cost. Furthermore, TransXNet-S and TransXNet-B exhibit excellent model scalability, achieving top-1 accuracy of 83.8% and 84.6%, respectively, with reasonable computational costs. In addition, our proposed network architecture demonstrates strong generalization capabilities in various dense prediction tasks, outperforming other state-of-the-art networks while having lower computational costs. Code is publicly available at https://***/LMMMEng/TransXNet .

关键词： Mixers Transformers Computational modeling Kernel Computational efficiency Feature extraction Convolutional codes Computer vision Accuracy Stacking

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Captions Speak Louder than Images (CASLIE): Generalizing Foundation Models for E-commerce from High-quality Multimodal Instruction data

arXiv

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arXiv 2024年

作者： Ling, Xinyi Peng, Bo Du, Hanwen Zhu, Zhihui Ning, Xia Department of Computer Science and Engineering The Ohio State University United States Translational Data Analytics Institute The Ohio State University United States Department of Biomedical Informatics The Ohio State University United States

Leveraging multimodal data to drive breakthroughs in e-commerce applications through Multimodal Foundation Models (MFMs) is gaining increasing attention from the research community. However, there are significant challenges that hinder the optimal use of multimodal e-commerce data by foundation models: (1) the scarcity of large-scale, high-quality multimodal benchmark datasets;and (2) the lack of effective multimodal information integration methods. To address these challenges, in this paper, we introduce MMECInstruct, the first-ever, large-scale, and high-quality multimodal instruction dataset for e-commerce. We also develop CASLIE, a simple, lightweight, yet effective framework for integrating multimodal information for e-commerce. Leveraging MMECInstruct, we fine-tune a series of e-commerce MFMs within CASLIE, denoted as CASLIE models. Our comprehensive evaluation demonstrates that CASLIE models substantially outperform 5 categories of advanced baseline models in the in-domain evaluation. Moreover, CASLIE models show strong generalizability to out-of-domain settings. MMECInstruct and CASLIE models are publicly accessible through https://***/CASLIE/. © 2024, CC BY.

关键词： Large datasets

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Dual Prompting for Diverse Count-Level Pet Denoising

Dual Prompting for Diverse Count-Level Pet Denoising

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IEEE International Symposium on biomedical Imaging

作者： Xiaofeng Liu Yongsong Huang Thibault Marin Yanis Chemli Samira Vafay Eslahi Amal Tiss Keith A. Johnson Georges El Fakhri Jinsong Ouyang Dept. of Radiology and Biomedical Imaging Yale University New Haven CT USA Dept. of Biomedical Informatics and Data Science Yale University New Haven CT USA Dept. of Radiology Massachusetts General Hospital and Harvard Medical School Boston MA USA

ISBN: (数字)9798331520526

ISBN: (纸本)9798331520533

The to-be-denoised positron emission tomography (PET) volumes are inherent with diverse count levels, which imposes challenges for a unified model to tackle varied cases. In this work, we resort to the recently flourished prompt learning to achieve generalizable PET denoising with different count levels. Specifically, we propose dual prompts to guide the PET denoising in a divide-and-conquer manner, i.e., an explicitly count-level prompt to provide the specific prior information and an implicitly general denoising prompt to encode the essential PET denoising knowledge. Then, a novel prompt fusion module is developed to unify the heterogeneous prompts, followed by a prompt-feature interaction module to inject prompts into the features. The prompts are able to dynamically guide the noise-conditioned denoising process. Therefore, we are able to efficiently train a unified denoising model for various count levels, and deploy it to different cases with personalized prompts. We evaluated on 1940 low-count PET 3D volumes with uniformly randomly selected 13-22% fractions of events from 97 18F-MK6240 tau PET studies. It shows our dual prompting can largely improve the performance with informed count-level and outperform the count-conditional model.

关键词： Degradation Three-dimensional displays Biological system modeling Noise reduction Image restoration Positron emission tomography Image denoising biomedical imaging

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