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Prediction of oral food challenge outcomes via ensemble learning

Informatics in Medicine Unlocked 2023年 36卷

作者： Zhang, Justin Lee, Deborah Jungles, Kylie Shaltis, Diane Najarian, Kayvan Ravikumar, Rajan Sanders, Georgiana Gryak, Jonathan Department of Electrical and Computer Engineering University of Michigan Ann Arbor MI United States Department of Internal Medicine University of Michigan Ann Arbor MI United States Department of Pediatrics University of Michigan Ann Arbor MI United States Department of Computational Medicine and Bioinformatics University of Michigan Ann Arbor MI United States Michigan Institute for Data Science University of Michigan Ann Arbor MI United States Department of Emergency Medicine University of Michigan Ann Arbor MI United States Department of Computer Science and Engineering University of Michigan Ann Arbor MI United States Max Harry Weil Institute for Critical Care Research and Innovation University of Michigan Ann Arbor MI United States Mary H. Weiser Food Allergy Center University of Michigan Ann Arbor MI United States Department of Computer Science Queens College City University of New York New York NY United States

Oral Food Challenges (OFCs) are essential to accurately diagnosing food allergy due to the limitations of existing clinical testing. However, some patients are hesitant to undergo OFCs, while those willing suffer from limited access to allergists in rural/community healthcare settings. Despite its success in predicting patient outcomes in other clinical settings, few applications of machine learning to food allergy have been developed. Thus, in this study, we seek to leverage machine learning methodologies for OFC outcome prediction. Retrospective data was gathered from 1,112 patients who collectively underwent a total of 1,284 OFCs, and consisted of clinical factors including serum-specific Immunoglobulin E (IgE), total IgE, skin prick tests (SPTs), comorbidities, sex, and age. Using these features, multiple machine learning models were constructed to predict OFC outcomes for three common allergens: peanut, egg, and milk. The best performing model for each allergen was an ensemble of random forest (egg) or Learning Using Concave and Convex Kernels (LUCCK) (peanut, milk) models, which achieved an Area under the Curve (AUC) of 0.91, 0.96, and 0.94, in predicting OFC outcomes for peanut, egg, and milk, respectively. Moreover, all such models had sensitivity and specificity values ≥89%. Model interpretation via SHapley Additive exPlanations (SHAP) indicates that specific IgE, along with wheal and flare values from SPTs, are highly predictive of OFC outcomes. The results of this analysis suggest that ensemble learning has the potential to predict OFC outcomes and reveal relevant clinical factors for further study. © 2022 The Author(s)

关键词： Ensemble learning Learning Using Concave and Convex Kernels Machine learning Oral food challenges SHAP

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Corrigendum to “Molecular subtypes classification of breast cancer in DCE-MRI using deep features” [Expert Syst. Appl. 236 (2024) 121371]

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Expert Systems with applications 2025年 270卷

作者： Ali M. Hasan Noor K.N. Al-Waely Hadeel K. Aljobouri Hamid A. Jalab Rabha W. Ibrahim Farid Meziane College of Medicine Al-Nahrain University Baghdad Iraq Biomedical Engineering Department College of Engineering Al-Nahrain University Iraq Faculty of Computer Science and Information Technology University of Malaya 50603 Kuala Lumpur Malaysia Information and Communication Technology Research Group Scientific Research Center Al-Ayen University Nile Street 64001 Thi-Qar Iraq Department of Computer Science and Mathematics Lebanese American University Beirut 1102 2801 Lebanon Near East University Mathematics Research Center Department of Mathematics Near East Boulevard PC: 99138 Nicosia/Mersin 10 Turkey Data Science Research Centre School of Computing and Engineering University of Derby United Kingdom

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Blockchain-Based Participant Selection for Federated Learning 2nd

Blockchain-Based Participant Selection for Federated Learnin...

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2nd International Conference on Blockchain and Trustworthy Systems, Blocksys 2020

作者： Zhang, Keshan Huang, Huawei Guo, Song Zhou, Xiaocong School of Data and Computer Science Sun Yat-Sen University Guangzhou China National Engineering Research Center of Digital Life Sun Yat-Sen University Guangzhou China Department of Computing The Hong Kong Polytechnic University Kowloon Hong Kong Shenzhen Research Institute The Hong Kong Polytechnic University Kowloon Hong Kong

ISBN: (纸本)9789811592126

Federated Learning (FL) advocates training a global model using a large-scale of distributed devices such that the collaborative model training can be benefited from the rich local datasets, while preserving the privacy of local training dataset in each participant. This is because only the training results, i.e., the updated model parameters and model weights are needed to report to the FL server for aggregation in each round of FL-training. However, during the model transmission of the original FL protocol, there is no security guarantee towards the training results. Thus, every step during model uploading phase can be attacked by malicious attackers. To address such threat, we propose a new federated learning architecture by taking the advantages of blockchain into account. The proposed architecture includes two-phase design. The first phase is a numerical evaluation, which can prevent the malicious devices from being selected. For the second phase, we devise a participant-selection algorithm that enables the FL server to select the appropriate group of devices for each round of FL-training. We believe that our study can shed new light on the joint research of blockchain and federated learning. © 2020, Springer Nature Singapore Pte Ltd.

关键词： Blockchain

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The Multi-modality Cell Segmentation Challenge: Towards Universal Solutions

arXiv

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arXiv 2023年

作者： Ma, Jun Xie, Ronald Ayyadhury, Shamini Ge, Cheng Gupta, Anubha Gupta, Ritu Gu, Song Zhang, Yao Lee, Gihun Kim, Joonkee Lou, Wei Li, Haofeng Upschulte, Eric Dickscheid, Timo de Almeida, José Guilherme Wang, Yixin Han, Lin Yang, Xin Labagnara, Marco Gligorovski, Vojislav Scheder, Maxime Rahi, Sahand Jamal Kempster, Carly Pollitt, Alice Espinosa, Leon Mignot, Tâm Middeke, Jan Moritz Eckardt, Jan-Niklas Li, Wangkai Li, Zhaoyang Cai, Xiaochen Bai, Bizhe Greenwald, Noah F. Van Valen, David Weisbart, Erin Cimini, Beth A. Cheung, Trevor Brück, Oscar Bader, Gary D. Wang, Bo Peter Munk Cardiac Centre University Health Network TorontoON Canada Department of Laboratory Medicine and Pathobiology University of Toronto TorontoON Canada Vector Institute TorontoON Canada Department of Molecular Genetics University of Toronto TorontoON Canada Donnelly Centre University of Toronto TorontoON Canada Princess Margaret Cancer Centre University Health Network TorontoON Canada School of Medicine and Pharmacy Ocean University of China Qingdao China New Delhi India Laboratory Oncology Dr. BRA-IRCH All India Institute of Medical Sciences New Delhi India Department of Image Reconstruction Nanjing Anke Medical Technology Co. Ltd. Nanjing China Shanghai Artificial Intelligence Laboratory Shanghai China Graduate School of AI KAIST Seoul Korea Republic of Shenzhen Research Institute of Big Data Shenzhen China Shenzhen China Helmholtz AI Research Center Jülich Jülich Germany Faculty of Mathematics and Natural Sciences Institute of Computer Science Heinrich Heine University Düsseldorf Düsseldorf Germany Hinxton United Kingdom Champalimaud Foundation - Centre for the Unknown Lisbon Portugal Department of Bioengineering Stanford University Palo AltoCA United States Tandon School of Engineering New York University New YorkNY United States School of Biomedical Engineering Health Science Center Shenzhen University Shenzhen China Lausanne Switzerland School of Biological Sciences University of Reading Reading United Kingdom Laboratoire de Chimie Bactérienne CNRS Université Aix Marseille UMR Institut de Microbiologie de la Méditerranée Marseille France Department of Internal Medicine I University Hospital Dresden Technical University Dresden Dresden Germany Else Kroener Fresenius Center for Digital Health Technical University Dresden Dresden Germany Department of Automation University of Science and Technology of China Hefei China Institute of Advanced Technology University of Science and Technology of China Hefei Chi

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimental settings. Here, we present a multi-modality cell segmentation benchmark, comprising over 1500 labeled images derived from more than 50 diverse biological experiments. The top participants developed a Transformer-based deep-learning algorithm that not only exceeds existing methods but can also be applied to diverse microscopy images across imaging platforms and tissue types without manual parameter adjustments. This benchmark and the improved algorithm offer promising avenues for more accurate and versatile cell analysis in microscopy imaging. © 2023, CC BY-NC-ND.

关键词： Deep learning

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A systematic collection of medical image datasets for deep learning

arXiv

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arXiv 2021年

作者： Li, Johann Zhu, Guangming Hua, Cong Feng, Mingtao Bennamoun, Basheer Li, Ping Lu, Xiaoyuan Song, Juan Shen, Peiyi Xu, Xu Mei, Lin Zhang, Liang Shah, Syed Afaq Ali Bennamoun, Mohammed School of Computer Science and Technology Xidian University China School of Medicine University of Notre Dame Australia Data and Virtual Research Room Shanghai Broadband Network Center China Third Research Institute of The Ministry of Public Security China Discipline of Information Technology Media and Communications Murdoch University Australia Department of Computer Science and Software Engineering University of Western Australia Australia

The astounding success made by artificial intelligence (ai) in healthcare and other fields proves that ai can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and "others". Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods’ performance and robustness on relevant datasets, 3) to provide a "route" to relevant algorithms for the relevant medical topics, and challenge leaderboards. © 2021, CC BY-NC-SA.

关键词： Deep learning

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A Geometric Strategy Algorithm for Orthogonal Pro jection onto a Parametric Surface

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Journal of computer science & Technology 2019年第6期34卷 1279-1293页

作者： Xiaowu Li Zhinan Wu Feng Pan Juan Liang Jiafeng Zhang Linke Hou College of Data Science and Information Engineering Guizhou Minzu UniversityGuiyang 550025China School of Mathematics and Computer Science Yichun UniversityYichun 336000China School of Software Engineering South China University of TechnologyGuangzhou 510006China Department of Science Taiyuan Institute of TechnologyTaiyuan 030008China Center for Economic Research Shandong UniversityJinan 250100China

In this paper, we investigate how to compute the minimum distance between a point and a parametric surface, and then to return the nearest point (foot point) on the surface as well as its corresponding parameter, which is also called the point projection problem of a parametric surface. The geometric strategy algorithm (hereafter GSA) presented consists of two parts as follows. The normal curvature to a given parametric surface is used to find the corresponding foot point firstly, and then the Taylor's expansion of the parametric surface is employed to compute parameter increments and to get the iteration formula to calculate the orthogonal projection point of test point to the parametric surface. Our geometric strategy algorithm is essentially dependent on the geometric property of the normal curvature, and performs better than existing methods in two ways. Firstly, GSA converges faster than existing methods, such as the method to turn the problem into a root-finding of nonlinear system, subdividing methods, clipping methods, geometric methods (tangent vector and geometric curvature) and hybrid second-order method, etc. Specially, it converges faster than the classical Newton's iterative method. Secondly, GSA is independent of the initial iterative value, which we prove in Theorem 1. Many numerical examples confirm GSA's robustness and efficiency.

关键词： point projection problem point inversion problem normal curvature normal curvature sphere convergence analysis

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Paddy rice methane emissions across Monsoon Asia

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Remote Sensing of Environment 2023年 284卷

作者： Ouyang, Zutao Jackson, Robert B. McNicol, Gavin Fluet-Chouinard, Etienne Runkle, Benjamin R.K. Papale, Dario Knox, Sara H. Cooley, Sarah Delwiche, Kyle B. Feron, Sarah Irvin, Jeremy Andrew Malhotra, Avni Muddasir, Muhammad Sabbatini, Simone Alberto, Ma. Carmelita R. Cescatti, Alessandro Chen, Chi-Ling Dong, Jinwei Fong, Bryant N. Guo, Haiqiang Hao, Lu Iwata, Hiroki Jia, Qingyu Ju, Weimin Kang, Minseok Li, Hong Kim, Joon Reba, Michele L. Nayak, Amaresh Kumar Roberti, Debora Regina Ryu, Youngryel Swain, Chinmaya Kumar Tsuang, Benjei Xiao, Xiangming Yuan, Wenping Zhang, Geli Zhang, Yongguang Department of Earth System Science Stanford University StanfordCA United States Woods Institute for the Environment Stanford University StanfordCA United States Precourt Institute for Energy Stanford University StanfordCA United States Department of Earth and Environmental Sciences University of Illinois Chicago ChicagoIL United States Department of Biological and Agricultural Engineering University of Arkansas FayettevilleAR United States University of Tuscia Viterbo Italy IAFES division Viterbo Italy Department of Geography The University of British Columbia VancouverBC Canada Department of Geography University of Oregon EugeneOR United States Department of Environmental Science Policy And Management UC Berkeley BerkeleyCA United States Campus Fryslan University of Groningen Groningen Netherlands Department of Computer Science Stanford University StanfordCA United States Department of Geography University of Zurich Zurich Switzerland International Rice Research Institute Laguna Philippines Ispra Italy Taiwan Agricultural Research Institute Taichung Wufeng Taiwan Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China USDA ARS Delta Water Management Research Unit JonesboroAR United States Fudan University Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and Coastal Ecosystems Research Station of the Yangtze River Estuary Shanghai China / Jiangsu Key Laboratory of Agricultural Meteorology Nanjing University of Information Science and Technology Nanjing China Department of Environmental Science Shinshu University Matsumoto Japan China Meteorological Administration Institute of Atmospheric Environment Shenyang China International Institute for Earth System Sciences Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application Nanjing University Jiangsu Nanjing210023 China National Center for AgroM

Although rice cultivation is one of the most important agricultural sources of methane (CH4) and contributes ∼8% of total global anthropogenic emissions, large discrepancies remain among estimates of global CH4 emissions from rice cultivation (ranging from 18 to 115 Tg CH4 yr−1) due to a lack of observational constraints. The spatial distribution of paddy-rice emissions has been assessed at regional-to-global scales by bottom-up inventories and land surface models over coarse spatial resolution (e.g., > 0.5°) or spatial units (e.g., agro-ecological zones). However, high-resolution CH4 flux estimates capable of capturing the effects of local climate and management practices on emissions, as well as replicating in situ data, remain challenging to produce because of the scarcity of high-resolution maps of paddy-rice and insufficient understanding of CH4 predictors. Here, we combine paddy-rice methane-flux data from 23 global eddy covariance sites and MODIS remote sensing data with machine learning to 1) evaluate data-driven model performance and variable importance for predicting rice CH4 fluxes;and 2) produce gridded up-scaling estimates of rice CH4 emissions at 5000-m resolution across Monsoon Asia, where ∼87% of global rice area is cultivated and ∼ 90% of global rice production occurs. Our random-forest model achieved Nash-Sutcliffe Efficiency values of 0.59 and 0.69 for 8-day CH4 fluxes and site mean CH4 fluxes respectively, with land surface temperature, biomass and water-availability-related indices as the most important predictors. We estimate the average annual (winter fallow season excluded) paddy rice CH4 emissions throughout Monsoon Asia to be 20.6 ± 1.1 Tg yr−1 for 2001–2015, which is at the lower range of previous inventory-based estimates (20–32 CH4 Tg yr−1). Our estimates also suggest that CH4 emissions from paddy rice in this region have been declining from 2007 through 2015 following declines in both paddy-rice growing area and emission rates per unit

关键词： Climate change

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SPRSound: Open-Source SJTU Paediatric Respiratory Sound database

TechRxiv

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TechRxiv 2022年

作者： Li, Yongfu Zhang, Qing Zhang, Jing Yuan, Jiajun Huang, Huajie Zhang, Yuhang Zhang, Baoqin Lv, Gaomei Lin, Shuzhu Wang, Na Liu, Xin Tang, Mingyu Wang, Yahua Ma, Hui Liu, Lu Yuan, Shuhua Zhou, Hongyuan Zhao, Jian Yin, Yong Zhao, Liebin Wang, Guoxing Lian, Yong Department of Micro-Nano Electronics and MoE Key Lab of Artificial Intelligence Shanghai Jiao Tong University Shanghai200240 China Pediatric AI Clinical Application and Research Center Shanghai Children’s Medical Center Shanghai Jiao Tong University School of Medicine China Department of Respiratory Medicine Shanghai Children’s Medical Center Shanghai Jiao Tong University School of Medicine China China School of Computer Engineering and Science Shanghai University China Sanya Maternity and Child Care Hospital China Department of Paediatrics Taicang Affiliated Hospital of Soochow University The First People’s Hospital of Taicang China Linyi City People Hospital China Department of Paediatrics Fengcheng Hospital China Department of Pediatrics Fifth Affiliated Hospital of Harbin Medical University China Shanghai Tuoxiao Intelligent Technology Co. Ltd China

It has proved that the auscultation of respiratory sound has advantage in early respiratory diagnosis. Various methods have been raised to perform automatic respiratory sound analysis to reduce subjective diagnosis and physicians’ workload. However, these methods highly rely on the quality of respiratory sound database. In this work, we have developed the first open-access paediatric respiratory sound database, SPRSound. The database consists of 2,683 records and 9,089 respiratory sound events from 292 participants. Accurate label is important to achieve a good prediction for adventitious respiratory sound classification problem. A custom-made sound label annotation software (SoundAnn) has been developed to perform sound editing, sound annotation, and quality assurance evaluation. A team of 11 experienced paediatric physicians is involved in the entire process to establish golden standard reference for the dataset. To verify the robustness and accuracy of the classification model, we have investigated the effects of different feature extraction methods and machine learning classifiers on the classification performance of our dataset. As such, we have achieved a score of 75.22%, 61.57%, 56.71%, and © 2022, CC BY.

关键词： Pediatrics

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Volumetric measurement of manually drawn segmentations in cone beam computed tomography images of newly formed bone after sinus floor augmentation with bovine-derived bone substitutes

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Journal of Stomatology, Oral and Maxillofacial Surgery 2025年 102221页

作者： Grün, Pascal Hatamikia, Sepideh Lakes, Tim Schneider, Benedikt Pfaffeneder-Mantai, Florian Fitzek, Sebastian von See, Constantin Turhani, Dritan Center for Oral and Maxillofacial Surgery Department of Dentistry Faculty of Medicine and Dentistry Danube Private University Steiner Landstraße 124 3500 Krems an der Donau Austria Clinical Application of Artificial Intelligence in Dentistry (CAAID) Group Department of Dentistry Faculty of Medicine and Dentistry Danube Private University Steiner Landstraße 124 Krems an der Donau 3500 Austria Research Center for Clinical AI-Research in Omics and Medical Data Science (CAROM) Department of Medicine Faculty of Medicine and Dentistry Danube Private University Steiner Landstraße 124 Krems an der Donau 3500 Austria Austrian Center for Medical Innovation and Technology Viktor Kaplan-Straße 2/1 Wiener Neustadt 2700 Austria Division for Chemistry and Physics of Materials Department of Medicine Faculty of Medicine and Dentistry Danube Private University Steiner Landstraße 124 Krems an der Donau 3500 Austria Health Services Research Group Medical Images Analysis and Artificial Intelligence (MIAAI) Department of Medicine Faculty of Medicine and Dentistry Danube Private University Steiner Landstraße 124 Krems an der Donau 3500 Austria Center for Digital Technologies in Dentistry and CAD/CAM Department of Dentistry Faculty of Medicine and Dentistry Danube Private University Krems an der Donau Steiner Landstraße 124 3500 Austria

Introduction: Precise volumetric measurement of newly formed bone after maxillary sinus floor augmentation (MSFA) can help clinicians in planning for dental implants. This study aimed to introduce a novel modular framework to facilitate volumetric calculations based on manually drawn segmentations of user-defined areas of interest on cone-beam computed tomography (CBCT) images Material & Methods: Two interconnected networks for manual segmentation of a defined volume of interest and dental implant volume calculation, respectively, were used in parallel. The volume data of dental implant manufacturers were used for reference. The efficacy of this framework was demonstrated through practical applications for collecting CBCT data from patients after MSFA with the same quantity of two different bovine-derived bone substitutes: xenohybrid composite bone (Group I, n = 10) and hydroxyapatite (Group II, n = 10). The study was approved by the central Ethical Review Board of the federal state of Lower Austria (approval number: GS4-EK-4/451–2021). The volumes were measured immediately (T1) and 6 months (T2) after MSFA and before insertion of the dental implant. All measurements were analyzed for inter- and intravariability. P-values of >0.05 were obtained from the t-test analysis Results: The manual delineation of Group II (n = 10) was easier than that of Group I (n = 10) due to the visual contrast of the CBCT scan. The mean volume was 861.65 ± 290.02 mm³ at T1 and 875.9 ± 288.96 mm³ at T2. This shows a moderate dispersion around the mean value, which indicates variability of the analyzed data Discussion: The proposed network may be useful for the development of computer-based diagnostic systems for assessing the success of MSFA with bone replacement materials. The volumetric stability achieved with the two bone replacement materials were comparable. © 2025 The Author(s)

关键词： Augmentation Cone-beam computed tomography Hydroxyapatite

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data Partition Optimization for High Energy Efficiency by Decoupling Local Dependence in Holographic Video Decoder

Data Partition Optimization for High Energy Efficiency by De...

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IEEE International Conference on Electronics, Circuits and Systems (ICECS)

作者： Xinzhe Liu Jianwen Luo David Blinder Fupeng Chen Heng Yu Peter Schelkens Francky Catthoor Yajun Ha School of Information Science and Technology ShanghaiTech University Shanghai China Shanghai Institute of Microsystem and Information Technology Chinese Academy of Sciences China University of Chinese Academy of Sciences China Department of Electronics and Informatics (ETRO) Vrije Universiteit Brussel (VUB) Belgium Interuniversity Microelectronics Centre (IMEC) Leuven Belgium Silicon Realization Group Synopsys Shanghai China School of Computer Science University of Nottingham Ningbo China Ningbo China Catholic University of Leuven (K.U.Leuven) Leuven Belgium Shanghai Engineering Research Center of Energy Efficient and Custom AI IC Shanghai China

Holography has attracted considerable attention from researchers due to its ability to store and recreate the wavefront emanating from a three-dimensional object. However, holographic video requires enormous resolution $(128 k \times 128 k)$ at the same frame rates(60fps) as normal video to achieve acceptable visual effects. data compression is thus essential for its storage/transmission. When implementing its decompression pipeline on hardware for mobile scenarios, data dependency and energy consumption must be handled carefully. In this work, we present a novel design framework and a data partition optimization approach to optimize the overall energy consumption by tackling local dependence in the motion compensation module for holographic video codec, and exploring the design space of data partition layout. First, we propose a local data dependency propagation (LDDP) method that transforms one holographic frame with strong local dependence into multiple mutually independent virtual blocks without local dependence at all. Second, we formulate a model for the data partitioning problem, allowing us to analyze and optimize energy consumption by adjusting the layout of data partitions. Third, we provide a heuristic and efficient solution to the formulated model taking advantage of the target application scenarios. Experiment results in various scenarios show that our proposed optimization method achieves 2.94 ~ 3.91 $\times$ energy efficiency and 46.37% ~ 63.63% area efficiency compared to baseline approaches.

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