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A conceptual framework of cognitive-affective theory of mind: towards a precision identification of mental disorders

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Npj mental health research 2023年第1期2卷 12页

作者： Peng Zhou Huimin Ma Bochao Zou Xiaowen Zhang Shuyan Zhao Yuxin Lin Yidong Wang Lei Feng Gang Wang School of International Studies Zhejiang University Hangzhou China. School of Computer and Communication Engineering University of Science and Technology Beijing Beijing China. mhmpub@***. School of Computer and Communication Engineering University of Science and Technology Beijing Beijing China. Department of Foreign Languages and Literatures Tsinghua University Beijing China. Department of Electronic Engineering Tsinghua University Beijing China. National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders Beijing Anding Hospital Capital Medical University Beijing China. Advanced Innovation Center for Human Brain Protection Capital Medical University Beijing China.

To explore the minds of others, which is traditionally referred to as Theory of Mind (ToM), is perhaps the most fundamental ability of humans as social beings. Impairments in ToM could lead to difficulties or even deficits in social interaction. The present study focuses on two core components of ToM, the ability to infer others' beliefs and the ability to infer others' emotions, which we refer to as cognitive and affective ToM respectively. Charting both typical and atypical trajectories underlying the cognitive-affective ToM promises to shed light on the precision identification of mental disorders, such as depressive disorders (DD) and autism spectrum disorder (ASD). However, most prior studies failed to capture the underlying processes involved in the cognitive-affective ToM in a fine-grained manner. To address this problem, we propose an innovative conceptual framework, referred to as visual theory of mind (V-ToM), by constructing visual scenes with emotional and cognitive meanings and by depicting explicitly a four-stage process of how humans make inferences about the beliefs and emotions of others. Through recording individuals' eye movements while looking at the visual scenes, our model enables us to accurately measure each stage involved in the computation of cognitive-affective ToM, thereby allowing us to infer about potential difficulties that might occur in each stage. Our model is based on a large sample size (n > 700) and a novel audio-visual paradigm using visual scenes containing cognitive-emotional meanings. Here we report the obtained differential features among healthy controls, DD and ASD individuals that overcome the subjectivity of conventional questionnaire-based assessment, and therefore could serve as valuable references for mental health applications based on AI-aided digital medicine.

关键词： human behaviour Diagnostic markers Psychiatric disorders

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A Scalable Deep Attention Mechanism of Instance Segmentation for the Investigation of Chromosome

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SLAS technology 2025年 33卷 100306页

作者： Neelam Umbreen Sara Ali Hasan Sajid Yasar Ayaz Shrooq Alsenan Yunyoung Nam So Yeon Kim Muhammad Baber Sial National University of Sciences and Technology (NUST) Islamabad Pakistan. Electronic address: neelamumbreen.phd@smme.edu.pk. National University of Sciences and Technology (NUST) Islamabad Pakistan Suzhou Industrial Park (SIP) Monash Research Institute of Science and Technology Monash University 8Q9C+R6W Suzhou Jiangsu China. School of Mechanical and Manufacturing Engineering (SMME) National University of Sciences and Technology (NUST) Islamabad NUST-COVENTRY Human-Robot Interaction (NC-HRI) Laboratory Pakistan Intelligent Field Robotics Laboratory (IFRL) National Center for Artificial Intelligence (NCAI) National University of Sciences and Technology (NUST) Islamabad Pakistan. Electronic address: sarababer@smme.nust.edu.pk. National University of Sciences and Technology (NUST) Islamabad Pakistan. Electronic address: hasan.sajid@smme.nust.edu.pk. Intelligent Field Robotics Laboratory (IFRL) National Center for Artificial Intelligence (NCAI) National University of Sciences and Technology (NUST) Islamabad Pakistan. Electronic address: yasar@smme.nust.edu.pk. Information Systems Department College of Computer and Information Sciences Princess Nourah bint Abdulrahman University P.O. Box 84428 Riyadh 11671 Saudi Arabia. Electronic address: shalsenan@pnu.edu.sa. Emotional and Intelligent Child Care Convergence Research Center Soonchunhyang University Asan 31538 Korea. Electronic address: ynam@sch.ac.kr. Department of Artificial Intelligence Department of Software and Computer Engineering Ajou University. Electronic address: jebi1771@ajou.ac.kr. School of Automation Science and Electrical Engineering Beihang University Beijing 100191 China. Electronic address: babersial@***.

Chromosome segmentation in metaphase images is a critical yet challenging task in cytogenetics and genomics due to the inherent complexity, variability in chromosome shapes, and the scarcity of high-quality annotated datasets. This study proposes a robust instance segmentation framework that integrates an automated annotation pipeline with an enhanced deep learning architecture to address these challenges. A novel dataset is introduced, comprising metaphase images and corresponding karyograms, annotated with precise instance segmentation information across 24 chromosome classes in COCO format. To overcome the labor-intensive manual annotation process, a feature-based image registration technique leveraging SIFT and homography is employed, enabling the accurate mapping of chromosomes from karyograms to metaphase images and significantly improving annotation quality and segmentation performance. The proposed framework includes a custom Mask R-CNN model enhanced with an Attention-based Feature Pyramid Network (AttFPN), spatial attention mechanisms, and a LastLevelMaxPool block for superior multi-scale feature extraction and focused attention on critical regions of the image. Experimental evaluations demonstrate the model's efficacy, achieving a mean average precision (mAP) of 0.579 at IoU = 0.50:0.95, surpassing the baseline Mask R-CNN and Mask R-CNN with AttFPN by 3.94% and 5.97% improvements in mAP and AP50, respectively. Notably, the proposed architecture excels in segmenting small and medium-sized chromosomes, addressing key limitations of existing methods. This research not only introduces a state-of-the-art segmentation framework but also provides a benchmark dataset, setting a new standard for chromosome instance segmentation in biomedical imaging. The integration of automated dataset creation with advanced model design offers a scalable and transferable solution, paving the way for tackling similar challenges in other domains of biomedical and cytogenetic imagi

关键词： Chromosome segmentation Instance segmentation, cytogenetics Mask R-CNN attention mechanism biomedical imaging multi-scale feature fusion

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White Matter Abnormalities in Major Depression Biotypes Identified by Diffusion Tensor Imaging

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Neuroscience Bulletin 2019年第5期35卷 867-876页

作者： Sugai Liang Qiang Wang Xiangzhen Kong Wei Deng Xiao Yang Xiaojing Li Zhong Zhang Jian Zhang Chengcheng Zhang Xin-min Li Xiaohong Ma Junming Shao Andrew J. Greenshaw Tao Li Mental Health Centre West China Hospital Sichuan University Chengdu 610041 China Huaxi Brain Research Centre West China Hospital Sichuan University Chengdu 610041 China Language and Genetics Department Max Planck Institute for Psycholinguistics 6525 XD Nijmegen Netherlands Big Data Research Center School of Computer Science and Engineering University of Electronic Science and Technology of China Chengdu 611731 China Department of Psychiatry University of Alberta Edmonton T6G 2B7 Canada

Identifying data-driven biotypes of major depressive disorder(MDD) has promise for the clarification of diagnostic heterogeneity. However, few studies have focused on white-matter abnormalities for MDD subtyping. This study included 116 patients with MDD and118 demographically-matched healthy controls assessed by diffusion tensor imaging and neurocognitive *** clustering was applied to the major fiber tracts, in conjunction with tract-based spatial statistics, to reveal white-matter alterations associated with *** and neurocognitive differences were compared between identified subgroups and healthy controls. With fractional anisotropy extracted from 20 fiber tracts, cluster analysis revealed 3 subgroups based on the patterns of abnormalities. Patients in each subgroup versus healthy controls showed a stepwise pattern of white-matter alterations as follows: subgroup 1(25.9% of patient sample),widespread white-matter disruption;subgroup 2(43.1% of patient sample), intermediate and more localized abnormalities in aspects of the corpus callosum and left cingulate;and subgroup 3(31.0% of patient sample),possible mild alterations, but no statistically significant tract disruption after controlling for family-wise error. The neurocognitive impairment in each subgroup accompanied the white-matter alterations: subgroup 1, deficits in sustained attention and delayed memory;subgroup 2, dysfunction in delayed memory;and subgroup 3, no significant deficits. Three subtypes of white-matter abnormality exist in individuals with major depression, those having widespread abnormalities suffering more neurocognitive impairments, which may provide evidence for parsing the heterogeneity of the disorder and help optimize typespecific treatment approaches.

关键词： Major depressive disorder Hierarchal clustering Diffusion tensor imaging Biotype Heterogeneity

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Using ASR Methods for OCR

Using ASR Methods for OCR

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International Conference on Document Analysis and Recognition

作者： Ashish Arora Chun Chieh Chang Babak Rekabdar Bagher BabaAli Daniel Povey David Etter Desh Raj Hossein Hadian Jan Trmal Paola Garcia Shinji Watanabe Vimal Manohar Yiwen Shao Sanjeev Khudanpur Center for Language and Speech Processing Johns Hopkins University Baltimore USA Human Language Technology Center of Excellence Johns Hopkins University Baltimore USA School of Mathematics Statistics and Computer Sciences University of Tehran Iran Department of Computer Engineering Sharif University of Technology Iran

Hybrid deep neural network hidden Markov models (DNN-HMM) have achieved impressive results on large vocabulary continuous speech recognition (LVCSR) tasks. However, the recent approaches using DNN-HMM models are not explored much for text recognition. Inspired by the current work in automatic speech recognition (ASR) and machine translation, we present an open vocabulary sub-word text recognition system. The sub-word lexicon and sub-word language model (LM) helps in overcoming the challenge of recognizing out of vocabulary (OOV) words, and a time delay neural network (TDNN) and convolution neural network (CNN) based DNN-HMM optical model (OM) efficiently models the sequence dependency in the line image. We present results on 12 datasets with training data varying from 6k lines to 600k lines. The system is built for 8 languages, i.e., English, French, Arabic, Chinese, Farsi, Tamil, Russian, and Korean. We report competitive results on several commonly used handwritten and printed text datasets.

关键词： Hidden Markov models Text recognition Vocabulary Training Optical imaging Training data Feature extraction

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Eye tracking: empirical foundations for a minimal reporting guideline

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Behavior research methods 2023年第1期55卷 364-416页

作者： Kenneth Holmqvist Saga Lee Örbom Ignace T C Hooge Diederick C Niehorster Robert G Alexander Richard Andersson Jeroen S Benjamins Pieter Blignaut Anne-Marie Brouwer Lewis L Chuang Kirsten A Dalrymple Denis Drieghe Matt J Dunn Ulrich Ettinger Susann Fiedler Tom Foulsham Jos N van der Geest Dan Witzner Hansen Samuel B Hutton Enkelejda Kasneci Alan Kingstone Paul C Knox Ellen M Kok Helena Lee Joy Yeonjoo Lee Jukka M Leppänen Stephen Macknik Päivi Majaranta Susana Martinez-Conde Antje Nuthmann Marcus Nyström Jacob L Orquin Jorge Otero-Millan Soon Young Park Stanislav Popelka Frank Proudlock Frank Renkewitz Austin Roorda Michael Schulte-Mecklenbeck Bonita Sharif Frederick Shic Mark Shovman Mervyn G Thomas Ward Venrooij Raimondas Zemblys Roy S Hessels Department of Psychology Nicolaus Copernicus University Torun Poland. kenneth.holmqvist@ur.de. Department of Computer Science and Informatics University of the Free State Bloemfontein South Africa. kenneth.holmqvist@ur.de. Department of Psychology Regensburg University Regensburg Germany. kenneth.holmqvist@ur.de. Department of Psychology Regensburg University Regensburg Germany. Experimental Psychology Helmholtz Institute Utrecht University Utrecht The Netherlands. Lund University Humanities Lab and Department of Psychology Lund University Lund Sweden. Department of Ophthalmology SUNY Downstate Health Sciences University Brooklyn NY USA. Tobii Pro AB Danderyd Sweden. Social Health and Organizational Psychology Utrecht University Utrecht The Netherlands. Department of Computer Science and Informatics University of the Free State Bloemfontein South Africa. TNO Soesterberg The Netherlands. Department of Ergonomics Leibniz Institute for Working Environments and Human Factors Dortmund Germany. Institute of Informatics LMU Munich Munich Germany. Institute of Child Development University of Minnesota Minneapolis USA. School of Psychology University of Southampton Southampton UK. School of Optometry and Vision Sciences Cardiff University Cardiff UK. Department of Psychology University of Bonn Bonn Germany. Vienna University of Economics and Business Vienna Austria. Department of Psychology University of Essex Essex UK. Department of Neuroscience Erasmus MC Rotterdam The Netherlands. Machine Learning Group Department of Computer Science IT University of Copenhagen Copenhagen Denmark. SR Research Ltd Ottawa Canada. Human-Computer Interaction University of Tübingen Tübingen Germany. University of British Columbia Columbia Canada. Department of Eye and Vision Science Institute of Life Course and Medical Sciences University of Liverpool Liverpool UK. Department of Education and Pedagogy Division Education Faculty of Social and Behavioral Sciences Ut

In this paper, we present a review of how the various aspects of any study using an eye tracker (such as the instrument, methodology, environment, participant, etc.) affect the quality of the recorded eye-tracking data and the obtained eye-movement and gaze measures. We take this review to represent the empirical foundation for reporting guidelines of any study involving an eye tracker. We compare this empirical foundation to five existing reporting guidelines and to a database of 207 published eye-tracking studies. We find that reporting guidelines vary substantially and do not match with actual reporting practices. We end by deriving a minimal, flexible reporting guideline based on empirical research (Section "An empirically based minimal reporting guideline").

关键词： Data quality Eye movements Eye tracking Replicability Reporting guidelines Reporting practices Reporting standards Reproducibility

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End-to-end speech recognition using lattice-free MMI 19

End-to-end speech recognition using lattice-free MMI

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19th Annual Conference of the International Speech Communication, INTERSPEECH 2018

作者： Hadian, Hossein Sameti, Hossein Povey, Daniel Khudanpur, Sanjeev Department of Computer Engineering Sharif University of Technology Tehran Iran Center for Language and Speech Processing Johns Hopkins University BaltimoreMD United States Human Language Technology Center of Excellence Johns Hopkins University Baltimore United States

We present our work on end-to-end training of acoustic models using the lattice-free maximum mutual information (LF-MMI) objective function in the context of hidden Markov models. By end-to-end training, we mean flat-start training of a single DNN in one stage without using any previously trained models, forced alignments, or building state-tying decision trees. We use full biphones to enable context-dependent modeling without trees, and show that our end-to-end LF-MMI approach can achieve comparable results to regular LF-MMI on well-known large vocabulary tasks. We also compare with other end-to-end methods such as CTC in character-based and lexicon-free settings and show 5 to 25 percent relative reduction in word error rates on different large vocabulary tasks while using significantly smaller models. © 2018 International Speech Communication Association. All rights reserved.

关键词： Hidden Markov models

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Large language models surpass human experts in predicting neuroscience results

arXiv

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arXiv 2024年

作者： Luo, Xiaoliang Rechardt, Akilles Sun, Guangzhi Nejad, Kevin K. Yáñez, Felipe Yilmaz, Bati Lee, Kangjoo Cohen, Alexandra O. Borghesani, Valentina Pashkov, Anton Marinazzo, Daniele Nicholas, Jonathan Salatiello, Alessandro Sucholutsky, Ilia Minervini, Pasquale Razavi, Sepehr Rocca, Roberta Yusifov, Elkhan Okalova, Tereza Gu, Nianlong Ferianc, Martin Khona, Mikail Patil, Kaustubh R. Lee, Pui-Shee Mata, Rui Myers, Nicholas E. Bizley, Jennifer K. Musslick, Sebastian Bilgin, Isil Poyraz Niso, Guiomar Ales, Justin M. Gaebler, Michael Murty, N. Apurva Ratan Loued-Khenissi, Leyla Behler, Anna Hall, Chloe M. Dafflon, Jessica Bao, Sherry Dongqi Love, Bradley C. Department of Experimental Psychology University College London London United Kingdom Department of Engineering University of Cambridge Cambridge United Kingdom Department of Physiology Anatomy & Genetics University of Oxford Oxford United Kingdom Max Planck Institute for Neurobiology of Behavior – caesar Bonn Germany Bilkent University Ankara Turkey Department of Computer Science University of Bristol Bristol United Kingdom The Alan Turing Institute London United Kingdom Department of Psychiatry Yale University New Haven United States Psychology Emory University Atlanta United States Faculty of Psychology and Educational Sciences Université de Genève Genève Switzerland Neurosurgery Novosibirsk State Medical University Novosibirsk Russia Federal Center of Neurosurgery FSBI Novosibirsk Russia Department of Data Collection and Processing Systems Novosibirsk State Technical University Novosibirsk Russia Department of Data Analysis Ghent University Ghent Belgium Psychology New York University New York United States Department of Cognitive Neurology University of Tübingen Tübingen Germany Computer Science Princeton University Princeton United States ILCC University of Edinburgh Edinburgh United Kingdom Philosophy Psychology and Language Sciences The University of Edinburgh Edinburgh United Kingdom Department of Culture Cognition and Computation Aarhus University Aarhus Denmark Department of Molecular Life Sciences University of Zurich Zurich Switzerland Bioengineering University of Pennsylvania Philadelphia United States Linguistic Research Infrastructure University of Zurich Zurich Switzerland Electronic and Electrical Engineering University College London London United Kingdom Brain and Cognitive Sciences Massachusetts Institute of Technology CambridgeMA United States Institute of Neuroscience and Medicine INM-7: Brain and Behaviour Research Centre Jülich Jülich Germany Medical Faculty Institute of Systems Neuroscience Heinrich Hein

Scientific discoveries often hinge on synthesizing decades of research, a task that potentially outstrips human information processing capacities. Large language models (LLMs) offer a solution. LLMs trained on the vast scientific literature could potentially integrate noisy yet interrelated findings to forecast novel results better than human experts. To evaluate this possibility, we created BrainBench, a forward-looking benchmark for predicting neuroscience results. We find that LLMs surpass experts in predicting experimental outcomes. BrainGPT, an LLM we tuned on the neuroscience literature, performed better yet. Like human experts, when LLMs were confident in their predictions, they were more likely to be correct, which presages a future where humans and LLMs team together to make discoveries. Our approach is not neuroscience-specific and is transferable to other knowledge-intensive endeavors. © 2024, CC BY.

关键词： Prediction models

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Explainable AI: Definition and attributes of a good explanation for health AI

arXiv

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arXiv 2024年

作者： Kyrimi, Evangelia McLachlan, Scott Wohlgemut, Jared M. Perkins, Zane B. Lagnado, David A. Marsh, William Gimson, Alexander Shafti, Ali Ercole, Ari Banerjee, Amitava Glocker, Ben Schafer, Burkhard Gatsonis, Constantine Grosan, Crina Sent, Danielle Berman, David S. Glass, David O'Regan, Declan P. Letsios, Dimitrios Morrissey, Dylan Pisirir, Erhan Leofante, Francesco Soyel, Hamit Williamson, Jon Grieman, Keri Dube, Kudakwashe Mardsen, Max Nagendran, Myura Tai, Nigel Kostopoulou, Olga Jones, Owain Curzon, Paul Stoner, Rebecca S. Tandle, Sankalp Joshi, Shalmali Mossadegh, Somayyeh Buijsman, Stefan Miller, Tim Madai, Vince Istvan School of Electronic Engineering and Computer Science Queen Mary University of London London United Kingdom School of Nursing Midwifery and Palliative Care King's College London London United Kingdom Centre for Trauma Sciences Blizard Institute Queen Mary University of London London United Kingdom Royal London Hospital Barts Health NHS Trust London United Kingdom Department of Experiment Psychology University College London London United Kingdom Cambridge Liver Unit Addenbrooke's Hospital Cambridge University Hospitals Hills Road Box 210 Cambridge United Kingdom University of Cambridge United Kingdom Cambridge Consultants Ltd. United Kingdom Division of Anaesthesia Cambridge Centre for AI in Medicine University of Cambridge Cambridge United Kingdom Magdelene College University of Cambridge United Kingdom Institute of Health Informatics University College London London United Kingdom Department of Computing Imperial College London London United Kingdom SCRIPT Centre for IT and IP Law School of Law University of Edinburgh United Kingdom Center for Statistical Sciences School of Public Health Brown University Providence United States Research Group Artificial Intelligence HU University of Applied Sciences Utrecht Netherlands Jheronimus Academy of Data Science Tilburg University Eindhoven University of Technology s-Hertogenbosch Netherlands Centre for Theoretical Physics Queen Mary University of London London United Kingdom School of Computing Ulster University Belfast United Kingdom MRC Laboratory of Medical Sciences Imperial College London London United Kingdom Department of Informatics King's College London United Kingdom Physiotherapy Department Barts Health NHS Trust London United Kingdom Sport and Exercise Medicine Queen Mary University of London London United Kingdom School of Electronic Engineering and Computer Science Queen Mary University of London United Kingdom Department of Computing Imperial College London United Kingdom Departmen

Proposals of artificial intelligence (AI) solutions based on increasingly complex and accurate predictive models are becoming ubiquitous across many disciplines. As the complexity of these models grows, transparency and users' understanding often diminish. This suggests that accurate prediction alone is insufficient for making an AI-based solution truly useful. In the development of healthcare systems, this introduces new issues related to accountability and safety. Understanding how and why an AI system makes a recommendation may require complex explanations of its inner workings and reasoning processes. Although research on explainable AI (XAI) has significantly increased in recent years and there is high demand for XAI in medicine, defining what constitutes a good explanation remains ad hoc, and providing adequate explanations continues to be challenging. To fully realize the potential of AI, it is critical to address two fundamental questions about explanations for safety-critical AI applications, such as health-AI: (1) What is an explanation in health-AI? and (2) What are the attributes of a good explanation in health-AI? In this study, we examined published literature and gathered expert opinions through a two-round Delphi study. The research outputs include (1) a definition of what constitutes an explanation in health-AI and (2) a comprehensive list of attributes that characterize a good explanation in health-AI. © 2024, CC BY.

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The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

arXiv

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arXiv 2024年

作者： Lyu, Jun Qin, Chen Wang, Shuo Wang, Fanwen Li, Yan Wang, Zi Guo, Kunyuan Ouyang, Cheng Tänzer, Michael Liu, Meng Sun, Longyu Sun, Mengting Li, Qin Shi, Zhang Hua, Sha Li, Hao Chen, Zhensen Zhang, Zhenlin Xin, Bingyu Metaxas, Dimitris N. Yiasemis, George Teuwen, Jonas Zhang, Liping Chen, Weitian Pang, Yanwei Liu, Xiaohan Razumov, Artem Dylov, Dmitry V. Dou, Quan Yan, Kang Xue, Yuyang Du, Yuning Dietlmeier, Julia Garcia-Cabrera, Carles Hemidi, Ziad Al-Haj Vogt, Nora Xu, Ziqiang Zhang, Yajing Chu, Ying-Hua Chen, Weibo Bai, Wenjia Zhuang, Xiahai Qin, Jing Wu, Lianmin Yang, Guang Qu, Xiaobo Wang, He Wang, Chengyan Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School 399 Revolution Drive BostonMA02215 United States Department of Electrical and Electronic Engineering & I-X Imperial College London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Bioengineering & I-X Imperial College London LondonW12 7SL United Kingdom Cardiovascular Magnetic Resonance Unit Royal Brompton Hospital Guy’s and St Thomas’ NHS Foundation Trust LondonSW3 6NP United Kingdom Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Institute of Artificial Intelligence Xiamen University Xiamen361102 China Department of Computing Department of Brain Sciences Imperial College London LondonSW7 2AZ United Kingdom Human Phenome Institute Fudan University 825 Zhangheng Road Pudong New District Shanghai201203 China Department of Radiology Zhongshan Hospital Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai200433 China Department of Computer Science Rutgers University PiscatawayNJ08854 United States AI for Oncology Netherlands Cancer Institute Plesmanlaan 121 Amsterdam1066 CX Netherlands Department of Imaging and Interventional Radiology The Chinese University of Hong Kong Hong Kong TJK-BIIT Lab School of Electrical and Information Engineering Tianjin University Tianjin300072 China Skolkovo Institute Of Science And Technology Center for Artificial Intelligence Technology 30/1 Bolshoy blvd. Moscow121205 Russia Department of Biomedical Engineering University of Virginia

Cardiac magnetic resonance imaging (MRI) provides detailed and quantitative evaluation of the heart’s structure, function, and tissue characteristics with high-resolution spatial-temporal imaging. However, its slow imaging speed and motion artifacts are notable limitations. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on Medical Image Computing and computer-Assisted Intervention (MICCAI). CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techn

关键词： Mapping

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Genomic Surveillance of SARS-CoV-2 in Taiwan: A Perspective on Evolutionary Data Interpretation and Sequencing Issues

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Biomedical journal 2024年 100820页

作者： Yu-Nong Gong Nai-Yu Kuo Ting-Syuan Yeh Shin-Ru Shih Guang-Wu Chen Research Center for Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan International Master Degree Program for Molecular Medicine in Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan Department of Laboratory Medicine Linkou Chang Gung Memorial Hospital Taoyuan Taiwan. Medical Education Department Linkou Chang Gung Memorial Hospital Taoyuan Taiwan. National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan. Department of Laboratory Medicine Linkou Chang Gung Memorial Hospital Taoyuan Taiwan Department of Medical Biotechnology and Laboratory Science College of Medicine Chang Gung University Taoyuan Taiwan Research Center for Chinese Herbal Medicine Research Center for Food and Cosmetic Safety and Graduate Institute of Health Industry Technology College of Human Ecology Chang Gung University of Science and Technology Taoyuan Taiwan. Department of Computer Science and Information Engineering College of Engineering Chang Gung University Taoyuan Taiwan. Electronic address: gwchen@mail.cgu.edu.tw.

This review presents a comprehensive perspective on the genomic surveillance of SARS-CoV-2 in Taiwan, with a focus on next-generation sequencing and phylogenetic interpretation. This article aimed to explore how Taiwan has utilized genomic sequencing technologies and surveillance to monitor and mitigate the spread of COVID-19. We examined databases and sources of genomic sequences and highlighted the role of data science methodologies in the explanation and analyses of evolutionary data. This review addressed the challenges and limitations inherent in genomic surveillance, such as concerns regarding data quality and the necessity for interdisciplinary expertise for accurate data interpretation. Special attention was given to the unique challenges faced by Taiwan, including its high population density and major transit destination for international travelers. We underscored the far-reaching implications of genomic surveillance data for public health policy, particularly in influencing decisions regarding travel restrictions, vaccine administration, and public health decision-making. Studies were examined to demonstrate the effectiveness of using genomic data to implement public health measures. Future research should prioritize the integration of methodologies and technologies in evolutionary data science, particularly focusing on phylodynamic analytics. This integration is crucial to enhance the precision and applicability of genomic data. Overall, we have provided an overview of the significance of genomic surveillance in tracking SARS-CoV-2 variants globally and the pivotal role of data science methodologies in interpreting these data for effective public health interventions.

关键词： SARS-CoV-2 data science genomic surveillance next-generation sequencing phylodynamics

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