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An analysis of reconstruction noise from undersampled 4D flow MRI

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arXiv 2022年

作者： Partin, Lauren Schiavazzi, Daniele E. Long, Carlos A. Sing Department Of Applied And Computational Mathematics And Statistics University Of Notre Dame Notre DameIN United States Institute For Mathematical And Computational Engineering Institute For Biological And Medical Engineering Pontificia Universidad Católica De Chile Santiago Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For The Discovery Of Structures In Complex Data Chile ANID - Millennium Science Initiative Program Millennium Nucleus Center For Cardiovascular Magnetic Resonance Chile

Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction methods from undersampled measurements are routinely used, that leverage representations designed to increase image compressibility. Reconstructed anatomical and hemodynamic images may present visual artifacts. Although some of these artifact are essentially reconstruction errors, and thus a consequence of undersampling, others may be due to measurement noise or the random choice of the sampled frequencies. Said otherwise, a reconstructed image becomes a random variable, and both its bias and its covariance can lead to visual artifacts;the latter leads to spatial correlations that may be misconstrued for visual information. Although the nature of the former has been studied in the literature, the latter has not received as much attention. In this study, we investigate the theoretical properties of the random perturbations arising from the reconstruction process, and perform a number of numerical experiments on simulated and MR aortic flow. Our results show that the correlation length remains limited to two to three pixels when a Gaussian undersampling pattern is combined with recovery algorithms based on 1-norm minimization. However, the correlation length may increase significantly for other undersampling patterns, higher undersampling factors (i.e., 8× or 16× compression), and different reconstruction methods. © 2022, CC BY-NC-ND.

关键词： Magnetic resonance

Gillespie algorithms for stochastic multiagent dynamics in populations and networks

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arXiv 2021年

作者： Masuda, Naoki Vestergaard, Christian L. Department of Mathematics State University of New York at Buffalo NY United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo NY United States Decision and Bayesian Computation Department of Neuroscience Cnrs Umr 3571 Department of Computational Biology Cnrs Usr 3756 Institut Pasteur Paris France

Many multiagent dynamics, including various collective dynamics occurring on networks, can be modeled as a stochastic process in which the agents in the system change their state over time in interaction with each other. The Gillespie algorithms are popular algorithms that exactly simulate such stochastic multiagent dynamics when each state change is driven by a discrete event, the dynamics is defined in continuous time, and the stochastic law of event occurrence is governed by independent Poisson processes. In the first main part of this volume, we provide a tutorial on the Gillespie algorithms focusing on simulation of social multiagent dynamics occurring in populations and networks. We do not assume advanced knowledge of mathematics (or computer science or physics). We clarify why one should use the continuous-time models and the Gillespie algorithms in many cases, instead of easier-to-understand discrete-time models. In the remainder of this volume, we review recent extensions of the Gillespie algorithms aiming to add more reality to the model (i.e., non-Poissonian cases) or to speed up the simulations. © 2021, CC BY.

关键词： Stochastic systems

Estimation of the main air pollutants from different biomasses under combustion atmospheres by artificial neural networks

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Chemosphere 2024年 352卷 141484页

作者： Monteiro, Thalyssa Oliveira Alves, Pedro Augusto Araújo da Silva de Almeida Nava Barradas Filho, Alex Oliveira Villa-Vélez, Harvey Alexander Cruz, Glauber Postgraduate Program in Mechanical Engineering (PPGMEC) Department of Mechanics and Materials Federal Institute of Education Science and Technology of Maranhão (IFMA) Maranhão São Luís Brazil Postgraduate Program in Computer Science and Computational Mathematics (PPG-CCMC) Department of Computer Science University of São Paulo (USP) São Carlos São Paulo Brazil Data Analysis and Artificial Intelligence Laboratory (DARTi) Department of Computational Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Department of Chemical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil Processes and Thermal Systems Laboratory (LPSisTer) Department of Mechanical Engineering Federal University of Maranhão (UFMA) Maranhão São Luís Brazil

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO2, NOx, SOx, and other pollutants), affecting living organisms and requiring careful assessments. H... 详细信息

The production of biofuels to be used as bioenergy under combustion processes generates some gaseous emissions (CO, CO₂, NO_x, SO_x, and other pollutants), affecting living organisms and requiring careful assessments. However, obtaining such information experimentally for data evaluation is costly and time-consuming and its in situ obtaining for regional biomasses (e.g., those from Northeast Brazil (NEB) is still a major challenge. This paper reports on the application of artificial neural networks (ANNs) for the prediction of the main air pollutants (CO, CO₂, NO, and SO₂) produced during the direct biomass combustion (N₂/O₂:80/20%) with the use of ultimate analysis (carbon, hydrogen, nitrogen, sulfur, and oxygen). 116 worldwide biomasses were used as input data, which is a relevant alternative to overcome the lack of experimental resources in NEB and obtain such information. Cross-validation was conducted with k-fold to optimize the ANNs and performance was analyzed with the use of statistical errors for accuracy assessments. The results showed an acceptable statistical performance for all architectures of ANNs, with 0.001–12.41% MAPE, 0.001–5.82 mg Nm⁻³ MAE, and 0.03–52.30 mg Nm⁻³ RMSE, highlighting the high precision of the emissions studied. On average, the differences between predicted and real values for CO, CO₂, NO, and SO₂ emissions from NEB biomasses were approximately 0.01%, 10⁻⁶%, 0.14%, and 0.05%, respectively. Pearson coefficient provided consistent results of concentration of the ultimate analysis in relation to the emissions studied and effectiveness of the test set in the developed models. © 2024 Elsevier Ltd

关键词： Brazilian northeastern Environmental statistics Evaluation metrics Gaseous emissions Predictive models Thermoconversion

Temporal motifs in patent opposition and collaboration networks

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arXiv 2021年

作者： Liu, Penghang Masuda, Naoki Kito, Tomomi Sarıyüce, Ahmet Erdem Department of Computer Science and Engineering State University of New York at Buffalo BuffaloNY United States Department of Mathematics State University of New York at Buffalo BuffaloNY United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY United States Faculty of Science and Engineering Waseda University Tokyo Japan

Patents are intellectual properties that reflect innovative activities of companies and organizations. The literature is rich with the studies that analyze the citations among the patents and the collaboration relations among companies that own the patents. However, the adversarial relations between the patent owners are not as well investigated. One proxy to model such relations is the patent opposition, which is a legal activity in which a company challenges the validity of a patent. Characterizing the patent oppositions, collaborations, and the interplay between them can help better understand the companies’ business strategies. Temporality matters in this context as the order and frequency of oppositions and collaborations characterize their interplay. In this study, we construct a two-layer temporal network to model the patent oppositions and collaborations among the companies. We utilize temporal motifs to analyze the oppositions and collaborations from structural and temporal perspectives. We first characterize the frequent motifs in patent oppositions and investigate how often the companies of different sizes attack other companies. We show that large companies tend to engage in opposition with multiple companies. Then we analyze the temporal interplay between collaborations and oppositions. We find that two adversarial companies are more likely to collaborate in the future than two collaborating companies oppose each other in the future. © 2021, CC BY.

关键词： Patents and inventions

Network Intrusion Detection System Using Principal Component Analysis Algorithm and Decision Tree Classifier

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Network Intrusion Detection System Using Principal Component...

International Conference on computational science and computational Intelligence (CSCI)

作者： Oyeyemi Osho Sungbum Hong Tor A. Kwembe Department of Computational Data-Enabled Science and Engineering(CDS&#x0026 E) Jackson State University Jackson MS USA Department of Electrical &#x0026 Computer Engineering and Computer Science Jackson State University Jackson MS USA Department of Mathematics &#x0026 Statistical Sciences Jackson State University Jackson MS USA

ISBN: (纸本)9781665458429

Network Intrusion Detection Systems (IDS) have become expedient for network security and ensures the safety of all connected devices. Network Intrusion Detection System (IDS) alludes to observing network data information swiftly, detecting any intrusion pattern and preventing any harmful effect of anomaly intrusion that will cost the network. To combat this issue, we present in this concept paper an IDS based on the Principal Component Analysis (PCA) and Decision Tree Classifier algorithm, a supervised machine learning model to detect intrusion in the Network.

关键词： Machine learning algorithms Costs Scientific computing Network intrusion detection Network security Classification algorithms Safety

Biomedical data and AI

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science China Life sciences 2025年第5期68卷 1536-1540页

作者： Hao Xu Shibo Zhou Zefeng Zhu Vincenzo Vitelli Liangyi Chen Ziwei Dai Ning Yang Luhua Lai Shengyong Yang Sergey Ovchinnikov Zhuoran Qiao Sirui Liu Chen Song Jianfeng Pei Han Wen Jianfeng Feng Yaoyao Zhang Zhengwei Xie Yang-Yu Liu Zhiyuan Li Fulai Jin Hao Li Mohammad Lotfollahi Xuegong Zhang Ge Yang Shihua Zhang Ge Gao Pulin Li Qi Liu Jing-Dong Jackie Han Peking-Tsinghua Center for Life Sciences (CLS) Academy for Advanced Interdisciplinary StudiesPeking University Center for Quantitative Biology (CQB) Academy for Advanced Interdisciplinary StudiesPeking University Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program Academy for Advanced Interdisciplinary StudiesPeking University Department of Physics University of Chicago School of Life Sciences Southern University of Science and Technology Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies College of Chemistry and Molecular Engineering Peking University Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan University Department of Biology Massachusetts Institute of Technology Lambic Therapeutics Inc. Changping Laboratory Al for Science Institute Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence Fudan University Department of Obstetrics and Gynecology West China Second University HospitalSichuan University Peking University International Cancer Institute and Peking University-Yunnan Baiyao International Medical Institute and State Key Laboratory of Natural and Biomimetic Drugs Department of Molecular and Cellular PharmacologySchool of Pharmaceutical SciencesPeking University Health Science CenterPeking University Channing Division of Network Medicine Department of MedicineBrigham and Women's Hospital and Harvard Medical School Center for Artificial Intelligence and Modeling the Carl R.Woese Institute for Genomic BiologyUniversity of Illinois Urbana-Champaign Department of Genetics and Genome Sciences School of Medicine and Department of Computer and Data Sciences and Department of Population and Quantitative Health SciencesCase Western Reserve University Department of Biochemistry and Biophysics University of California Sanger Institute Department of Automation Tsinghua University State Key Laboratory of Multimodal Artificial Intelligence Systems I

The development of artificial intelligence(AI) and the mining of biomedical data complement each other. From the direct use of computer vision results to analyze medical images for disease screening, to now integrating biological knowledge into models and even accelerating the development of new AI based on biological discoveries, the boundaries of both are constantly expanding, and their connections are becoming closer.

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Empowering Precision Medicine: AI-Driven Schizophrenia Diagnosis via EEG Signals: A Comprehensive Review from 2002-2023

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arXiv 2023年

作者： Jafari, Mahboobeh Sadeghi, Delaram Shoeibi, Afshin Alinejad-Rokny, Hamid Beheshti, Amin García, David López Chen, Zhaolin Acharya, U. Rajendra Gorriz, Juan M. Internship in BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia Data Science and Computational Intelligence Institute University of Granada Spain BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering UNSW Sydney SydneyNSW2052 Australia UNSW Data Science Hub The University of New South Wales SydneyNSW2052 Australia Health Data Analytics Program Centre for Applied Artificial Intelligence Macquarie University Sydney2109 Australia Data Science Lab School of Computing Macquarie University SydneyNSW2109 Australia Monash University Melbourne Australia School of Mathematics Physics and Computing University of Southern Queensland Springfield Australia Department of Psychiatry University of Cambridge United Kingdom

Schizophrenia (SZ) is a prevalent mental disorder characterized by cognitive, emotional, and behavioral changes. Symptoms of SZ include hallucinations, illusions, delusions, lack of motivation, and difficulties in concentration. While the exact causes of SZ remain unproven, factors such as brain injuries, stress, and psychotropic drugs have been implicated in its development. SZ can be classified into different types, including paranoid, disorganized, catatonic, undifferentiated, and residual. Diagnosing SZ involves employing various tools, including clinical interviews, physical examinations, psychological evaluations, the Diagnostic and Statistical Manual of Mental Disorders (DSM), and neuroimaging techniques. Electroencephalography (EEG) recording is a significant functional neuroimaging modality that provides valuable insights into brain function during SZ. However, EEG signal analysis poses challenges for neurologists and scientists due to the presence of artifacts, long-term recordings, and the utilization of multiple channels. To address these challenges, researchers have introduced artificial intelligence (AI) techniques, encompassing conventional machine learning (ML) and deep learning (DL) methods, to aid in SZ diagnosis. This study reviews papers focused on SZ diagnosis utilizing EEG signals and AI methods. The introduction section provides a comprehensive explanation of SZ diagnosis methods and intervention techniques. Subsequently, review papers in this field are discussed, followed by an introduction to the AI methods employed for SZ diagnosis and a summary of relevant papers presented in tabular form. Additionally, this study reports on the most significant challenges encountered in SZ diagnosis, as identified through a review of papers in this field. Future directions to overcome these challenges are also addressed. The discussion section examines the specific details of each paper, culminating in the presentation of conclusions and findings. © 2023,

关键词： Electroencephalography

Biases in Inverse Ising Estimates of Near-Critical Behaviour

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arXiv 2023年

作者： Kloucek, Maximilian B. Machon, Thomas Kajimura, Shogo Royall, C. Patrick Masuda, Naoki Turci, Francesco H.H. Wills Laboratory School of Physics University of Bristol Bristol United Kingdom Bristol Centre for Functional Nanomaterials University of Bristol Bristol United Kingdom Faculty of Information and Human Sciences Kyoto Institute of Technology Kyoto606-8585 Japan Gulliver UMR CNRS 7083 ESPCI Paris Université PSL Paris75005 France Department of Mathematics State University of New York BuffaloNY14260-2900 United States Computational and Data-Enabled Science and Engineering Program State University of New York at Buffalo BuffaloNY14260-5030 United States

Inverse Ising inference allows pairwise interactions of complex binary systems to be reconstructed from empirical correlations. Typical estimators used for this inference, such as Pseudo-likelihood maximization (PLM), are biased. Using the Sherrington-Kirkpatrick (SK) model as a benchmark, we show that these biases are large in critical regimes close to phase boundaries, and may alter the qualitative interpretation of the inferred model. In particular, we show that the small-sample bias causes models inferred through PLM to appear closer-to-criticality than one would expect from the data. data-driven methods to correct this bias are explored and applied to a functional magnetic resonance imaging (fMRI) dataset from neuroscience. Our results indicate that additional care should be taken when attributing criticality to real-world datasets. Copyright © 2023, The Authors. All rights reserved.

关键词： Criticality (nuclear fission)

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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