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arXiv 2022年

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 ArborMI United States Department of Internal Medicine University of Michigan Ann ArborMI United States Department of Pediatrics University of Michigan Ann ArborMI United States Department of Computational Medicine and Bioinformatics University of Michigan Ann ArborMI United States Michigan Institute for Data Science University of Michigan Ann ArborMI United States Department of Emergency Medicine University of Michigan Ann ArborMI United States Department of Computer Science and Engineering University of Michigan Ann ArborMI United States Max Harry Weil Institute for Critical Care Research and Innovation University of Michigan Ann ArborMI United States Mary H. Weiser Food Allergy Center University of Michigan Ann ArborMI United States Department of Computer Science Queens College City University of New York New YorkNY 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. Copyright © 2022, The Authors. All rights reserved.

关键词： Machine learning

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SATVAM: Toward an iot cyber-infrastructure for low-cost urban air quality monitoring 15

SATVAM: Toward an iot cyber-infrastructure for low-cost urba...

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15th IEEE International Conference on escience, escience 2019

作者： Simmhan, Yogesh Nair, Srijith Monga, Sumit Sahu, Ravi Dixit, Kuldeep Sutaria, Ronak Mishra, Brijesh Sharma, Anamika Anand, S.V.R. Hegde, Malati Zele, Rajesh Tripathi, Sachchida N. Department of Computational and Data Sciences Indian Institute of Science Bangalore India Department of Electrical Communication Engineering Indian Institute of Science Bangalore India Departments of Civil Engineering and Earth Sciences Indian Institute of Technology Kanpur India Centre for Urban Science and Engineering Indian Institute of Technology Bombay India Department of Electrical Engineering Indian Institute of Technology Bombay India

ISBN: (纸本)9781728124513

Air pollution is a public health emergency in large cities. The availability of commodity sensors and the advent of Internet of Things (IoT) enable the deployment of a city-wide network of 1000's of low-cost real-Time air quality monitors to help manage this challenge. This needs to be supported by an IoT cyber-infrastructure for reliable and scalable data acquisition from the edge to the Cloud. The low accuracy of such sensors also motivates the need for data-driven calibration models that can accurately predict the science variables from the raw sensor signals. Here, we offer our experiences with designing and deploying such an IoT software platform and calibration models, and validate it through a pilot field deployment at two mega-cities, Delhi and Mumbai. Our edge data service is able to even-out the differential bandwidths from the sensing devices and to the Cloud repository, and recover from transient failures. Our analytical models reduce the errors of the sensors from a best-case of 63% using the factory baseline to as low as 21%, and substantially advances the state-of-The-Art in this domain. © 2019 IEEE.

关键词： Internet of things

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Accelerated MRI reconstruction with separable and enhanced low-rank Hankel regularization

arXiv

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arXiv 2021年

作者： Zhang, Xinlin Lu, Hengfa Guo, Di Lai, Zongying Ye, Huihui Peng, Xi Zhao, Bo Qu, Xiaobo Biomedical Intelligent Cloud R&D Center Department of Electronic Science National Institute for Data Science in Health and Medicine Xiamen University Xiamen361105 China The Department of Biomedical Engineering University of Texas at Austin AustinTX78712 United States The School of Computer and Information Engineering Xiamen University of Technology Xiamen361021 China The School of Information Engineering Jimei University Xiamen361024 China The State of Key Laboratory of Modern Optical Instrumentation College of Optical Science and Engineering Zhejiang University Hangzhou310058 China The Department of Radiology Mayo Clinic RochesterMN55902 United States The Department of Biomedical Engineering Oden Institute for Computational Engineering and Sciences University of Texas at Austin AustinTX78712 United States

The combination of the sparse sampling and the low-rank structured matrix reconstruction has shown promising performance, enabling a significant reduction of the magnetic resonance imaging data acquisition time. However, the low-rank structured approaches demand considerable memory consumption and are time-consuming due to a noticeable number of matrix operations performed on the huge-size block Hankel-like matrix. In this work, we proposed a novel framework to utilize the low-rank property but meanwhile to achieve faster reconstructions and promising results. The framework allows us to enforce the low-rankness of Hankel matrices constructing from 1D vectors instead of 2D matrices from 1D vectors and thus avoid the construction of huge block Hankel matrix for 2D k-space matrices. Moreover, under this framework, we can easily incorporate other information, such as the smooth phase of the image and the low-rankness in the parameter dimension, to further improve the image quality. We built and validated two models for parallel and parameter magnetic resonance imaging experiments, respectively. Our retrospective in-vivo results indicate that the proposed approaches enable faster reconstructions than the state-of-the-art approaches, e.g., about 8× faster than STDLR-SPIRiT, and faithful removal of undersampling artifacts. Copyright © 2021, The Authors. All rights reserved.

关键词： Image reconstruction

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Completely self-supervised crowd counting via distribution matching

arXiv

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arXiv 2020年

作者： Sam, Deepak Babu Agarwalla, Abhinav Joseph, Jimmy Sindagi, Vishwanath A. Babu, R. Venkatesh Patel, Vishal M. Video Analytics Lab Department of Computational and Data Sciences Indian Institute of Science Bangalore India Vision & Image Understanding Lab Department of Electrical and Computer Engineering Johns Hopkins University Baltimore United States

Dense crowd counting is a challenging task that demands millions of head annotations for training models. Though existing self-supervised approaches could learn good representations, they require some labeled data to map these features to the end task of density estimation. We mitigate this issue with the proposed paradigm of complete self-supervision, which does not need even a single labeled image. The only input required to train, apart from a large set of unlabeled crowd images, is the approximate upper limit of the crowd count for the given dataset. Our method dwells on the idea that natural crowds follow a power law distribution, which could be leveraged to yield error signals for backpropagation. A density regressor is first pretrained with self-supervision and then the distribution of predictions is matched to the prior by optimizing Sinkhorn distance between the two. Experiments show that this results in effective learning of crowd features and delivers significant counting performance. Furthermore, we establish the superiority of our method in less data setting as well. The code and models for our approach is available at https://***/val-iisc/css-ccnn. Copyright © 2020, The Authors. All rights reserved.

关键词： Deep learning

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Batch reverse osmosis:a new research direction in water desalination

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science Bulletin 2020年第20期65卷 1705-1708页

作者： Mingheng Li Yi Heng Jiu Luo Department of Chemical and Materials Engineering California State Polytechnic UniversityPomonaCA 91768USA School of Data and Computer Science Sun Yat-sen UniversityGuangzhou 510006China Guangdong Province Key Laboratory of Computational Science Guangzhou 510006China National Supercomputing Center in Guangzhou(NSCC-GZ) Guangzhou 510006China School of Materials Science and Engineering Sun Yat-sen UniversityGuangzhou 510275China

Water scarcity is one of the grand challenges across the world[1].Spiral wound reverse osmosis(RO)desalination is the most popular industrial technology to produce portable water from saline water *** terms of flow pattern,it falls into the category of cross-flow filtration where feed flows tangentially along the membrane surface while filtrate permeates across the membrane.

关键词： flow tangential category

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An overview of deep learning techniques for epileptic seizures detection and prediction based on neuroimaging modalities: Methods, challenges, and future works

arXiv

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arXiv 2021年

作者： Shoeibi, Afshin Moridian, Parisa Khodatars, Marjane Ghassemi, Navid Jafari, Mahboobeh Alizadehsani, Roohallah Kong, Yinan Gorriz, Juan Manuel Ramírez, Javier Khosravi, Abbas Nahavandi, Saeid Acharya, U. Rajendra Data Science and Computational Intelligence Institute University of Granada Spain Faculty of Engineering Science and Research Branch Islamic Azad University Tehran Iran Department of Medical Engineering Mashhad Branch Islamic Azad University Mashhad Iran Computer Engineering department Ferdowsi University of Mashhad Mashhad Iran Electrical and Computer Engineering Faculty Semnan University Semnan Iran Deakin University VIC3217 Australia School of Engineering Macquarie University Sydney2109 Australia Department of Signal Theory Networking and Communications Universidad de Granada Spain Ngee Ann Polytechnic Singapore599489 Singapore Dept. of Biomedical Informatics and Medical Engineering Asia University Taichung Taiwan Dept. of Biomedical Engineering School of Science and Technology Singapore University of Social Sciences Singapore

Epilepsy is a disorder of the brain denoted by frequent seizures. The symptoms of seizure include confusion, abnormal staring, and rapid, sudden, and uncontrollable hand movements. Epileptic seizure detection methods involve neurological exams, blood tests, neuropsychological tests, and neuroimaging modalities. Among these, neuroimaging modalities have received considerable attention from specialist physicians. One method to facilitate the accurate and fast diagnosis of epileptic seizures is to employ computer-aided diagnosis systems (CADS) based on deep learning (DL) and neuroimaging modalities. This paper has studied a comprehensive overview of DL methods employed for epileptic seizures detection and prediction using neuroimaging modalities. First, DL-based CADS for epileptic seizures detection and prediction using neuroimaging modalities are discussed. Also, descriptions of various datasets, preprocessing algorithms, and DL models which have been used for epileptic seizures detection and prediction have been included. Then, research on rehabilitation tools has been presented, which contains brain-computer interface (BCI), cloud computing, internet of things (IoT), hardware implementation of DL techniques on field-programmable gate array (FPGA), etc. In the discussion section, a comparison has been carried out between research on epileptic seizure detection and prediction. The challenges in epileptic seizures detection and prediction using neuroimaging modalities and DL models have been described. In addition, possible directions for future works in this field, specifically for solving challenges in datasets, DL, rehabilitation, and hardware models, have been proposed. The final section is dedicated to the conclusion which summarizes the significant findings of the paper. © 2021, CC BY-NC-ND.

关键词： Forecasting

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Adaptive gradient methods with dynamic bound of learning rate 7

Adaptive gradient methods with dynamic bound of learning rat...

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7th International Conference on Learning Representations, ICLR 2019

作者： Luo, Liangchen Xiong, Yuanhao Liu, Yan Sun, Xu MOE Key Lab of Computational Linguistics School of EECS Peking University China College of Information Science and Electronic Engineering Zhejiang University China Department of Computer Science University of Southern California United States Center for Data Science Beijing Institute of Big Data Research Peking University China

Adaptive optimization methods such as ADAGRAD, RMSPROP and ADAM have been proposed to achieve a rapid training process with an element-wise scaling term on learning rates. Though prevailing, they are observed to generalize poorly compared with SGD or even fail to converge due to unstable and extreme learning rates. Recent work has put forward some algorithms such as AMSGRAD to tackle this issue but they failed to achieve considerable improvement over existing methods. In our paper, we demonstrate that extreme learning rates can lead to poor performance. We provide new variants of ADAM and AMSGRAD, called ADABOUND and AMSBOUND respectively, which employ dynamic bounds on learning rates to achieve a gradual and smooth transition from adaptive methods to SGD and give a theoretical proof of convergence. We further conduct experiments on various popular tasks and models, which is often insufficient in previous work. Experimental results show that new variants can eliminate the generalization gap between adaptive methods and SGD and maintain higher learning speed early in training at the same time. Moreover, they can bring significant improvement over their prototypes, especially on complex deep networks. The implementation of the algorithm can be found at https://***/Luolc/AdaBound. © 7th International Conference on Learning Representations, ICLR 2019. All Rights Reserved.

关键词： Gradient methods

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Translation dysregulation in cancer as a source for targetable antigens

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Cancer Cell 2025年第5期43卷 823-840.e18,20页

作者： Weller, Chen Bartok, Osnat McGinnis, Christopher S. Palashati, Heyilimu Chang, Tian-Gen Malko, Dmitry Shmueli, Merav D. Nagao, Asuteka Hayoun, Deborah Murayama, Ayaka Sakaguchi, Yuriko Poulis, Panagiotis Khatib, Aseel Erlanger Avigdor, Bracha Gordon, Sagi Cohen Shvefel, Sapir Zemanek, Marie J. Nielsen, Morten M. Boura-Halfon, Sigalit Sagie, Shira Gumpert, Nofar Yang, Weiwen Alexeev, Dmitry Kyriakidou, Pelgia Yao, Winnie Zerbib, Mirie Greenberg, Polina Benedek, Gil Litchfield, Kevin Petrovich-Kopitman, Ekaterina Nagler, Adi Oren, Roni Ben-Dor, Shifra Levin, Yishai Pilpel, Yitzhak Rodnina, Marina Cox, Jürgen Merbl, Yifat Satpathy, Ansuman T. Carmi, Yaron Erhard, Florian Suzuki, Tsutomu Buskirk, Allen R. Olweus, Johanna Ruppin, Eytan Schlosser, Andreas Samuels, Yardena Department of Molecular Cell Biology Weizmann Institute of Science Rehovot 7610001 Israel Department of Pathology Stanford University Stanford 94305 CA United States Parker Institute for Cancer Immunotherapy San Francisco 94129 CA United States Department of Cancer Immunology Institute for Cancer Research Oslo University Hospital Oslo 0379 Norway Precision Immunotherapy Alliance University of Oslo Oslo Norway Cancer Data Science Laboratory Center for Cancer Research National Cancer Institute National Institutes of Health Bethesda 20892 MD United States Department of Systems Immunology Weizmann Institute of Science Rehovot 7610001 Israel Department of Chemistry and Biotechnology of Engineering The University of Tokyo Tokyo 113-8656 Japan Department of Physical Biochemistry Max Planck Institute for Multidisciplinary Sciences Göttingen 37077 Germany Department of Pathology Sackler School of Medicine Tel Aviv University Tel Aviv 69978 Israel Department of Immunology and Regenerative Biology Weizmann Institute of Science Rehovot 7610001 Israel Computational Systems Biochemistry Research Group Max-Planck Institute of Biochemistry Martinsried 82152 Germany Department of Veterinary Resources Weizmann Institute of Science Rehovot 7610001 Israel Tissue Typing and Immunogenetics Unit Hadassah Hebrew University Hospital Jerusalem 9112102 Israel CRUK Lung Cancer Centre of Excellence University College London Cancer Institute London WC1E 6DD United Kingdom Tumour Immunogenomics and Immunosurveillance Laboratory University College London Cancer Institute London WC1E 6DD United Kingdom Department of Life Science Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel Bioinformatics Unit Department of Life Sciences Core Facilities Weizmann Institute of Science Rehovot 7610001 Israel de Botton Institute for Protein Profiling the Nancy and Stephen Grand Israel National Center for Personalized Medicine Weizmann Institute of Science Rehovot

Aberrant peptides presented by major histocompatibility complex (MHC) molecules are targets for tumor eradication, as these peptides can be recognized as foreign by T cells. Protein synthesis in malignant cells is dysregulated, which may result in the generation and presentation of aberrant peptides that can be exploited for T cell-based therapies. To investigate the role of translational dysregulation in immunological tumor control, we disrupt translation fidelity by deleting tRNA wybutosine (yW)-synthesizing protein 2 (TYW2) in tumor cells and characterize the downstream impact on translation fidelity and immunogenicity using immunopeptidomics, genomics, and functional assays. These analyses reveal that TYW2 knockout (KO) cells generate immunogenic out-of-frame peptides. Furthermore, Tyw2 loss increases tumor immunogenicity and leads to anti-programmed cell death 1 (PD-1) checkpoint blockade sensitivity in vivo. Importantly, reduced TYW2 expression is associated with increased response to checkpoint blockade in patients. Together, we demonstrate that defects in translation fidelity drive tumor immunogenicity and may be leveraged for cancer immunotherapy. © 2025 The Author(s)

关键词： cancer immunopeptidome immune checkpoint blockade neoantigens non-canonical peptides translation fidelity

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Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies

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Cell Genomics 2025年第5期5卷 100845-100845页

作者： Huang, Yu-Ning Munteanu, Viorel Love, Michael I. Ronkowski, Cynthia Flaire Deshpande, Dhrithi Wong-Beringer, Annie Corbett-Detig, Russell Dimian, Mihai Moore, Jason H. Garmire, Lana X. Reddy, T.B.K. Butte, Atul J. Robinson, Mark D. Eskin, Eleazar Abedalthagafi, Malak S. Mangul, Serghei Department of Clinical Pharmacy Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences University of Southern California Los Angeles 90089 CA United States Department of Computers Informatics and Microelectronics Technical University of Moldova Chisinau 2045 Moldova Department of Biological and Morphofunctional Sciences College of Medicine and Biological Sciences Stefan cel Mare University of Suceava Suceava 720229 Romania Department of Genetics University of North Carolina at Chapel Hill Chapel Hill 27514 NC United States Department of Biostatistics University of North Carolina at Chapel Hill Chapel Hill 27514 NC United States Department of Biomolecular Engineering University of California Santa Cruz Santa Cruz 95064 CA United States Genomics Institute University of California Santa Cruz Santa Cruz 95064 CA United States Department of Computers Electronics and Automation Stefan cel Mare University of Suceava Suceava 720229 Romania Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles 90069 CA United States Department of Computational Medicine and Bioinformatics University of Michigan Medical School Ann Arbor 48105 MI United States US Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Berkeley 94720 CA United States Bakar Computational Health Sciences Institute University of California San Francisco (UCSF) San Francisco 94143 CA United States Center for Data-Driven Insights and Innovation University of California Oakland Oakland 94607 CA United States SIB Swiss Institute of Bioinformatics and Department of Molecular Life Sciences University of Zurich Zurich 8057 Switzerland Department of Computer Science University of California Los Angeles Los Angeles CA United States Department of Computational Medicine University of California Los Angeles Los Angeles CA United States Department of Human Genetics University of California Los Angeles Los Angeles CA United Stat

Metadata, or “data about data,” is essential for organizing, understanding, and managing large-scale omics datasets. It enhances data discovery, integration, and interpretation, enabling reproducibility, reusability, and secondary analysis. However, metadata sharing remains hindered by perceptual and technical barriers, including the lack of uniform standards, privacy concerns, study design limitations, insufficient incentives, inadequate infrastructure, and a shortage of trained personnel. These challenges compromise data reliability and obstruct integrative meta-analyses. Addressing these issues requires standardization, education, stronger roles for journals and funding agencies, and improved incentives and infrastructure. Looking ahead, emerging technologies such as artificial intelligence and machine learning may offer promising solutions to automate metadata processes, increasing accuracy and scalability. Fostering a collaborative culture of metadata sharing will maximize the value of omics data, accelerating innovation and scientific discovery. © 2025 The Authors

关键词： barriers in metadata sharing practices data metadata metadata completeness

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One-dimensional deep low-rank and sparse network for accelerated MRI

arXiv

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arXiv 2021年

作者： Wang, Zi Qian, Chen Guo, Di Sun, Hongwei Li, Rushuai Zhao, Bo Qu, Xiaobo Department of Electronic Science Biomedical Intelligent Cloud R&D Center Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Xiamen University China School of Computer and Information Engineering Xiamen University of Technology Xiamen China United Imaging Research Institute of Intelligent Imaging Beijing China Department of Nuclear Medicine Nanjing First Hospital Nanjing Medical University Nanjing China Department of Biomedical Engineering Oden Institute for Computational Engineering and Sciences University of Texas at Austin Austin United States

Deep learning has shown astonishing performance in accelerated magnetic resonance imaging (MRI). Most state-of-the-art deep learning reconstructions adopt the powerful convolutional neural network and perform 2D convolution since many magnetic resonance images or their corresponding k-space are in 2D. In this work, we present a new approach that explores the 1D convolution, making the deep network much easier to be trained and generalized. We further integrate the 1D convolution into the proposed deep network, named as One-dimensional Deep Low-rank and Sparse network (ODLS), which unrolls the iteration procedure of a low-rank and sparse reconstruction model. Extensive results on in vivo knee and brain datasets demonstrate that, the proposed ODLS is very suitable for the case of limited training subjects and provides improved reconstruction performance than state-of-the-art methods both visually and quantitatively. Additionally, ODLS also shows nice robustness to different undersampling scenarios and some mismatches between the training and test data. In summary, our work demonstrates that the 1D deep learning scheme is memory-efficient and robust in fast MRI. Copyright © 2021, The Authors. All rights reserved.

关键词： Magnetic resonance imaging

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