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IEEE International Conference on Big Data

作者： Hongryul Ahn Inuk Jung Heejoon Chae Minsik Oh Inyoung Kim Sun Kim Division of Data Science DS&ML Center The University of Suwon Hwaseong Republic of Korea School of Computer Science and Engineering Kyungpook National University Daegu Republic of Korea Division of Computer Science Sookmyung Women's University Seoul Republic of Korea BK21 Four Intelligence Computing Seoul National University Seoul Republic of Korea Artificial Intelligence Institute Seoul National University Seoul Republic of Korea Interdisciplinary Program in Bioinformatics and Bioinformatics Institute Seoul National University Seoul Republic of Korea

ISBN: (纸本)9781665445993

Hierarchical clustering, a traditional clustering method, has been getting attention again. Among several reasons, a credit goes to a recent paper by Dasgupta in 2016 that proposed a cost function that quantitatively evaluates hierarchical clustering trees. An important question is how to combine this recent advance with existing successful clustering methods. In this paper, we propose a hierarchical clustering method to minimize the cost function of clustering tree by incorporating existing clustering techniques. First, we developed an ensemble tree-search method that finds an integrated tree with reduced cost by integrating multiple existing hierarchical clustering methods. Second, to operate on large and arbitrary shape data, we designed an efficient hierarchical clustering framework, called integrating divisive and ensemble-agglomerate (IDEA) by combining it with advanced clustering techniques such as nearest neighbor graph construction, divisive-agglomerate hybridization, and dynamic cut tree. The IDEA clustering method showed better performance in minimizing Dasgupta's cost and improving accuracy (adjusted rand index) over existing cost-minimization-based, and density-based hierarchical clustering methods in experiments using arbitrary shape datasets and complex biology-domain datasets.

关键词： Costs Shape Clustering methods Conferences Big Data Cost function Minimization

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Research on E-book Security Tracking Schemes

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International Journal of Network Security 2021年第4期23卷 549-557页

作者： Lin, Cheng-Ying Wu, Chia-Chun Hwang, Min-Shiang Department of Computer Science & Information Engineering Asia University 500 Lioufeng Rd. Wufeng TaichungTaichung41354 Taiwan The Ph.D. Program in Artificial Intelligence Asia University 500 Lioufeng Rd. Wufeng TaichungTaichung41354 Taiwan Department of Industrial Engineering and Management National Quemoy University No. 1 University Rd. Jinning Township Kinmen County892 Taiwan Department of Medical Research China Medical University Hospital China Medical University Taiwan

There are many business models for e-books, such as billing by time, billing by the hour, and database authorization. Copyright authorization and pricing methods are also different. How to assist the industry in formulating appropriate authorization and pricing mechanisms under different operating models is the key to the overall development of e-book services in the future. This research will be divided into two parts. The first one will start with the E-book authorization tracking mechanism. The purpose of this research is to solve the current problem of unauthorized and illegal distribution of e-books. The content consists of three parts. The first is privacy protection technology for legitimate users. Even sellers cannot obtain the personal information of legitimate users. The second part is the tracking mechanism for illegally authorized users. When the user performs illegal authorization, the e-book provider can use the tracking mechanism to find the illegal person. The third part is to build an e-book authorization management mechanism for different business models to achieve authorization tracking. The second topic will research the "e-book pricing tracking mechanism." The purpose is to design appropriate securities pricing mechanisms for different operating models. The project’s content is divided into three sub-topics: E-book pricing and tracking mechanism, E-book time-limited pricing management mechanism and building an E-book payment transaction server. The research will understand users’ browsing habits and compare them with industry interests. To develop a win-win pricing system, we will formulate an appropriate charging pricing system for different browsing methods and adopt the system according to the situation. © 2021

关键词： Crime

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artificial intelligence for modelling infectious disease epidemics

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Nature 2025年第8051期638卷 623-635页

作者： Kraemer, Moritz U. G. Tsui, Joseph L.-H. Chang, Serina Y. Lytras, Spyros Khurana, Mark P. Vanderslott, Samantha Bajaj, Sumali Scheidwasser, Neil Curran-Sebastian, Jacob Liam Semenova, Elizaveta Zhang, Mengyan Unwin, H. Juliette T. Watson, Oliver J. Mills, Cathal Dasgupta, Abhishek Ferretti, Luca Scarpino, Samuel V. Koua, Etien Morgan, Oliver Tegally, Houriiyah Paquet, Ulrich Moutsianas, Loukas Fraser, Christophe Ferguson, Neil M. Topol, Eric J. Duchêne, David A. Stadler, Tanja Kingori, Patricia Parker, Michael J. Dominici, Francesca Shadbolt, Nigel Suchard, Marc A. Ratmann, Oliver Flaxman, Seth Holmes, Edward C. Gomez-Rodriguez, Manuel Schölkopf, Bernhard Donnelly, Christl A. Pybus, Oliver G. Cauchemez, Simon Bhatt, Samir Pandemic Sciences Institute University of Oxford Oxford United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Electrical Engineering and Computer Science University of California Berkeley Berkeley CA United States UCSF UC Berkeley Joint Program in Computational Precision Health Berkeley CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Section of Epidemiology Department of Public Health University of Copenhagen Copenhagen Denmark Oxford Vaccine Group University of Oxford and NIHR Oxford Biomedical Research Centre Oxford United Kingdom Department of Epidemiology and Biostatistics Imperial College London London United Kingdom Department of Computer Science University of Oxford Oxford United Kingdom School of Mathematics University of Bristol Bristol United Kingdom MRC Centre for Global Infectious Disease Analysis School of Public Health Imperial College London London United Kingdom Department of Statistics University of Oxford Oxford United Kingdom Doctoral Training Centre University of Oxford Oxford United Kingdom Institute for Experiential AI Northeastern University MA Boston Thailand Santa Fe Institute Santa Fe NM United States World Health Organization Regional Office for Africa Brazzaville Congo WHO Hub for Pandemic and Epidemic Intelligence Health Emergencies Programme World Health Organization Berlin Germany Centre for Epidemic Response and Innovation (CERI) School for Data Science and Computational Thinking Stellenbosch University Stellenbosch South Africa African Institute for Mathematical Sciences (AIMS) South Africa Muizenberg Cape Town South Africa Genomics England London United Kingdom Scripps Research La Jolla CA United States Department of Biosystems Science and Engineering ETH Zürich Basel Switzerland Swiss Institute of Bioinformatics Lausanne Switzerland The Ethox Centre Nuffield

Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI. © Springer Nature Limited 2025.

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Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

arXiv

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arXiv 2022年

作者： Jivanjee, Tasneem Ibrahim, Samira Nyquist, Sarah K. James Gatter, G. Bromley, Joshua D. Jaiswal, Swati Berger, Bonnie Behar, Samuel M. Christopher Love, J. Shalek, Alex K. Institute for Medical Engineering & Science Department of Chemistry Massachusetts Institute of Technology CambridgeMA United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology CambridgeMA United States Ragon Institute of MGH MIT and Harvard CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Massachusetts Institute of Technology CambridgeMA United States Program in Computational and Systems Biology Massachusetts Institute of Technology CambridgeMA United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA United States Microbiology Graduate Program Massachusetts Institute of Technology CambridgeMA02139 United States Department of Microbiology and Physiological Systems University of Massachusetts Medical School WorcesterMA United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA United States Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA United States

Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process;however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods. Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes, and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer results in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq

关键词： RNA

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Mitigating errors in mobile-based dietary assessments: Effects of a data modification process on the validity of an image-assisted food and nutrition app

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Nutrition 2023年 116卷 112212-112212页

作者： Ho, Dang Khanh Ngan Chiu, Wan-Chun Kao, Jing-Wen Tseng, Hsiang-Tung Yao, Chih-Yuan Su, Hsiu-Yueh Wei, Pin-Hui Le, Nguyen Quoc Khanh Nguyen, Hung Trong Chang, Jung-Su School of Nutrition and Health Sciences College of Nutrition Taipei Medical University Taipei Taiwan Department of Nutrition Wan Fang Hospital Taipei Medical University Taipei Taiwan Department of Computer Science and Information Engineering National Taiwan University of Science and Technology Taipei Taiwan Department of Dietetics Taipei Medical University Hospital Taipei Taiwan Professional Master Program in Artificial Intelligence in Medicine College of Medicine Taipei Medical University Taipei Taiwan Research Center for Artificial Intelligence in Medicine Taipei Medical University Taipei Taiwan Translational Imaging Research Center Taipei Medical University Hospital Taipei Taiwan Department of Adult Nutrition Counselling National Institute of Nutrition Hanoi Viet Nam Department of Clinical Nutrition and Dietetics National Hospital of Endocrinology Hanoi Viet Nam Graduate Institute of Metabolism and Obesity Sciences College of Nutrition Taipei Medical University Taipei Taiwan Nutrition Research Center Taipei Medical University Hospital Taipei Taiwan Chinese Taipei Society for the Study of Obesity (CTSSO) Taipei Taiwan TMU Research Center for Digestive Medicine Taipei Medical University Taipei Taiwan

Objective: Mobile nutrition applications (apps) provide a simple way for individuals to record their diet, but the validity and inherent errors need to be carefully evaluated. The aim of this study was to assess the validity and clarify the sources of measurement errors of image-assisted mobile nutrition apps. Methods: This was a cross-sectional study with 98 students recruited from School of Nutrition and Health Sciences, Taipei Medical University. A 3-d nutrient intake record by Formosa Food and Nutrient Recording App (FoodApp) was compared with a 24-h dietary recall (24-HDR). A two-stage data modification process, manual data cleaning, and reanalyzing of prepackaged foods were employed to address inherent errors. Nutrient intake levels obtained by the two methods were compared with the recommended daily intake (DRI), Taiwan. Paired t test, Spearman's correlation coefficients, and Bland–Altman plots were used to assess agreement between the FoodApp and 24-HDR. Results: Manual data cleaning identified 166 food coding errors (12%;stage 1), and 426 food codes with missing micronutrients (32%) were reanalyzed (stage 2). Positive linear trends were observed for total energy and micronutrient intake (all P_trend < 0.05) after the two stages of data modification, but not for dietary fat, carbohydrates, or vitamin D. There were no statistical differences in mean energy and macronutrient intake between the FoodApp and 24-HDR, and this agreement was confirmed by Bland–Altman plots. Spearman's correlation analyses showed strong to moderate correlations (r = 0.834 ∼ 0.386) between the two methods. Participants’ nutrient intake tended to be lower than the DRI, but no differences in proportions of adequacy/inadequacy for DRI values were observed between the two methods. Conclusions: Mitigating errors significantly improved the accuracy of the Formosa FoodApp, indicating its validity and reliability as a self-reporting mobile-based dietary assessment tool. Dietitians a

关键词： Food records Mobile application Mobile health Smartphone application

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Scientific discovery in the age of artificial intelligence

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NATURE 2023年第7978期621卷 E33-E33页

作者： Wang, Hanchen Fu, Tianfan Du, Yuanqi Gao, Wenhao Huang, Kexin Liu, Ziming Chandak, Payal Liu, Shengchao Van Katwyk, Peter Deac, Andreea Anandkumar, Anima Bergen, Karianne Gomes, Carla P. Ho, Shirley Kohli, Pushmeet Lasenby, Joan Leskovec, Jure Liu, Tie-Yan Manrai, Arjun Marks, Debora Ramsundar, Bharath Song, Le Sun, Jimeng Tang, Jian Velickovic, Petar Welling, Max Zhang, Linfeng Coley, Connor W. Bengio, Yoshua Zitnik, Marinka Department of Engineering University of Cambridge Cambridge UK Department of Computing and Mathematical Sciences California Institute of Technology Pasadena CA USA NVIDIA Santa Clara CA USA Department of Computational Science and Engineering Georgia Institute of Technology Atlanta GA USA Department of Computer Science Cornell University Ithaca NY USA Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Computer Science Stanford University Stanford CA USA Department of Physics Massachusetts Institute of Technology Cambridge MA USA Harvard-MIT Program in Health Sciences and Technology Cambridge MA USA Mila – Quebec AI Institute Montreal Quebec Canada Université de Montréal Montreal Quebec Canada HEC Montréal Montreal Quebec Canada CIFAR AI Chair Toronto Ontario Canada Department of Earth Environmental and Planetary Sciences Brown University Providence RI USA Data Science Institute Brown University Providence RI USA Center for Computational Astrophysics Flatiron Institute New York NY USA Department of Astrophysical Sciences Princeton University Princeton NJ USA Department of Physics Carnegie Mellon University Pittsburgh PA USA Department of Physics and Center for Data Science New York University New York NY USA Google DeepMind London UK Department of Computer Science and Technology University of Cambridge Cambridge UK Microsoft Research Beijing China Department of Biomedical Informatics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Harvard Data Science Initiative Cambridge MA USA Kempner Institute for the Study of Natural and Artificial Intelligence Harvard University Cambridge MA USA Department of Systems Biology Harvard Medical School Boston MA USA Deep Forest Sciences Palo Alto CA USA BioMap Beijing China Mo

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Robust joint registration of multiple stains and MRI for multimodal 3D histology reconstruction: Application to the Allen human brain atlas

arXiv

引用

arXiv 2021年

作者： Casamitjana Díaz, Adrià Lorenzi, Marco Ferraris, Sebastiano Peter, Loïc Modat, Marc Stevens, Allison Fischl, Bruce Vercauteren, Tom Iglesias, Juan Eugenio Center for Medical Image Computing University College London United Kingdom Université Côte dÁzur Inria Epione Team Sophia Antipolis06902 France School of Biomedical Engineering & Imaging Sciences King’s College London United Kingdom Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology United States Program in Health Sciences and Technology Massachusetts Institute of Technology United States

Joint registration of a stack of 2D histological sections to recover 3D structure ("3D histology reconstruction") finds application in areas such as atlas building and validation of in vivo imaging. Straightforward pairwise registration of neighbouring sections yields smooth reconstructions but has well-known problems such as "banana effect" (straightening of curved structures) and "z-shift" (drift). While these problems can be alleviated with an external, linearly aligned reference (e.g., Magnetic Resonance (MR) images), registration is often inaccurate due to contrast differences and the strong nonlinear distortion of the tissue, including artefacts such as folds and tears. In this paper, we present a probabilistic model of spatial deformation that yields reconstructions for multiple histological stains that that are jointly smooth, robust to outliers, and follow the reference shape. The model relies on a spanning tree of latent transforms connecting all the sections and slices of the reference volume, and assumes that the registration between any pair of images can be see as a noisy version of the composition of (possibly inverted) latent transforms connecting the two images. Bayesian inference is used to compute the most likely latent transforms given a set of pairwise registrations between image pairs within and across modalities. We consider two likelihood models: Gaussian (`2 norm, which can be minimised in closed form) and Laplacian (`1 norm, minimised with linear programming). Results on synthetic deformations on multiple MR modalities, show that our method can accurately and robustly register multiple contrasts even in the presence of outliers. The framework is used for accurate 3D reconstruction of two stains (Nissl and parvalbumin) from the Allen human brain atlas, showing its benefits on real data with severe distortions. Moreover, we also provide the registration of the reconstructed volume to MNI space, bridging the gaps between two of the most widely

关键词： Brain

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Corrections to "iPhantom: A Framework for Automated Creation of Individualized Computational Phantoms and its Application to CT Organ Dosimetry"

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IEEE journal of biomedical and health informatics 2022年第1期26卷 478页

作者： Wanyi Fu Shobhit Sharma Ehsan Abadi Alexandros-Stavros Iliopoulos Qi Wang Joseph Y Lo Xiaobai Sun William P Segars Ehsan Samei Department of Electrical and Computer Engineering and Carl E. Ravin Advanced Imaging Laboratories Duke University Durham NC USA Department of Physics and Carl E. Ravin Advanced Imaging Laboratories Duke University Durham NC USA Department of Computer Science Duke University Durham NC USA Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology Cambridge MA USA Department of Radiology the Fourth Clinical Hospital of Hebei Medical University Heibei China Departments of Electrical and Computer Engineering Biomedical Engineering Medical Physics Graduate Program and Carl E. Ravin Advanced Imaging Laboratories Duke University Durham NC USA Medical Physics Graduate Program and Radiology and the Carl E. Ravin Advanced Imaging Laboratories Departments of Biomedical Engineering Duke University Durham NC USA Carl E. Ravin Advanced Imaging Laboratories Medical Physics Graduate Program Department of Radiology Electrical and Computer Engineering Biomedical Engineering and Physics Duke University Durham NC USA

In [1], the dose estimation accuracy using the alternative baseline method under modulated tube current was not correctly calculated due to an unintentional simulation error.

关键词： Phantoms Image segmentation Computed tomography Image registration

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Meta-control of social learning strategies

arXiv

引用

arXiv 2021年

作者： Yaman, Anil Bredeche, Nicolas Çaylak, Onur Leibo, Joel Z. Lee, Sang Wan Computer Science Department Vrije Universiteit Amsterdam Amsterdam Netherlands Institut des Systèmes Intelligents et de Robotique Sorbonne Université CNRS Paris France Department of Mathematics and Computer Science Eindhoven University of Technology Eindhoven Netherlands DeepMind London United Kingdom Department of Bio and Brain Engineering Korea Advanced Institute of Science and Technology Daejeon Korea Republic of Center for Neuroscience-Inspired AI Korea Advanced Institute of Science and Technology Daejeon Korea Republic of Program of Brain and Cognitive Engineering Korea Advanced Institute of Science and Technology Daejeon Korea Republic of KI for Health Science and Technology Korea Advanced Institute of Science and Technology Daejeon Korea Republic of KI for Artificial Intelligence Korea Advanced Institute of Science and Technology Daejeon Korea Republic of Computer Science Department Vrije Universiteit Amsterdam Amsterdam Netherlands

Social learning, copying other's behavior without actual experience, offers a cost-effective means of knowledge acquisition. However, it raises the fundamental question of which individuals have reliable information: successful individuals versus the majority. The former and the latter are known respectively as success-based and conformist social learning strategies. We show here that while the success-based strategy fully exploits the benign environment of low uncertainly, it fails in uncertain environments. On the other hand, the conformist strategy can effectively mitigate this adverse effect. Based on these findings, we hypothesized that meta-control of individual and social learning strategies provides effective and sample-efficient learning in volatile and uncertain environments. Simulations on a set of environments with various levels of volatility and uncertainty confirmed our hypothesis. The results imply that meta-control of social learning affords agents the leverage to resolve environmental uncertainty with minimal exploration cost, by exploiting others' learning as an external knowledge base. Copyright © 2021, The Authors. All rights reserved.

关键词： Learning systems

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An overview of facial micro-expression analysis: Data, methodology and challenge

arXiv

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arXiv 2020年

作者： Xie, Hong-Xia Lo, Ling Shuai, Hong-Han Cheng, Wen-Huang The Institute of of Electronics National Chiao Tung Univresity Hsinchu300 Taiwan The Department of Electrical and Computer Engineering National Chiao Tung Univresity Hsinchu300 Taiwan The Institute of Electronics National Chiao Tung Univresity Hsinchu300 Taiwan The Artificial Intelligence and Data Science Program National Chung Hsing University Taichung400 Taiwan

Facial micro-expressions indicate brief and subtle facial movements that appear during emotional communication. In comparison to macro-expressions, micro-expressions are more challenging to be analyzed due to the short span of time and the fine-grained changes. In recent years, micro-expression recognition (MER) has drawn much attention because it can benefit a wide range of applications, e.g. police interrogation, clinical diagnosis, depression analysis, and business negotiation. In this survey, we offer a fresh overview to discuss new research directions and challenges these days for MER tasks. For example, we review MER approaches from three novel aspects: macro-to-micro adaptation, recognition based on key apex frames, and recognition based on facial action units. Moreover, to mitigate the problem of limited and biased ME data, synthetic data generation is surveyed for the diversity enrichment of micro-expression data. Since micro-expression spotting can boost micro-expression analysis, the state-of-the-art spotting works are also introduced in this paper. At last, we discuss the challenges in MER research and provide potential solutions as well as possible directions for further investigation. Copyright © 2020, The Authors. All rights reserved.

关键词： Surveys

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