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An Early Stage Researcher's Primer on Systems Medicine Terminology

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Network and Systems Medicine

Network and Systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

A Novel Experience-Based Exploration Method for Q-Learning

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A Novel Experience-Based Exploration Method for Q-Learning

2018国际计算机前沿大会（原国际青年计算机大会）

作者： Bohong Yang Hong Lu Baogen Li Zheng Zhang Wenqiang Zhang Shanghai Key Laboratory of Intelligent Information Processing School of Computer ScienceFudan University Shanghai Engineering Research Center for Video Technology and System School of Computer ScienceFudan University School of Computer Science New York University Shanghai

Reinforcement learning algorithms are used to deal with a lot of sequential problems, such as playing games, mechanical control,and so on. Q-Learning is a model-free reinforcement learning *** traditional Q-learning algorithms, the agent stops immediately after it has reached the goal. We propose in this paper a new method—Experience-based Exploration method—in order to sample more efficient state-action pairs for Q-learning updating. In the Experience-based Exploration method, the agent does not stop and continues to search the states with high bellman-error inversely. In this setting, the agent will set the terminal state as a new start point, and generate pairs of action and state which could be useful. The efficacy of the method is proved analytically. And the experimental results verify the hypothesis on Gridworld.

关键词： Inverse exploration Reinforcement learning Q-learning Deep learning Deep Q-learning Network

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

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Nature methods 2023年第6期20卷 824-835页

作者： Linus Manubens-Gil Zhi Zhou Hanbo Chen Arvind Ramanathan Xiaoxiao Liu Yufeng Liu Alessandro Bria Todd Gillette Zongcai Ruan Jian Yang Miroslav Radojević Ting Zhao Li Cheng Lei Qu Siqi Liu Kristofer E Bouchard Lin Gu Weidong Cai Shuiwang Ji Badrinath Roysam Ching-Wei Wang Hongchuan Yu Amos Sironi Daniel Maxim Iascone Jie Zhou Erhan Bas Eduardo Conde-Sousa Paulo Aguiar Xiang Li Yujie Li Sumit Nanda Yuan Wang Leila Muresan Pascal Fua Bing Ye Hai-Yan He Jochen F Staiger Manuel Peter Daniel N Cox Michel Simonneau Marcel Oberlaender Gregory Jefferis Kei Ito Paloma Gonzalez-Bellido Jinhyun Kim Edwin Rubel Hollis T Cline Hongkui Zeng Aljoscha Nern Ann-Shyn Chiang Jianhua Yao Jane Roskams Rick Livesey Janine Stevens Tianming Liu Chinh Dang Yike Guo Ning Zhong Georgia Tourassi Sean Hill Michael Hawrylycz Christof Koch Erik Meijering Giorgio A Ascoli Hanchuan Peng Institute for Brain and Intelligence Southeast University Nanjing China. Microsoft Corporation Redmond WA USA. Tencent AI Lab Bellevue WA USA. Computing Environment and Life Sciences Directorate Argonne National Laboratory Lemont IL USA. Kaya Medical Seattle WA USA. University of Cassino and Southern Lazio Cassino Italy. Center for Neural Informatics Structures and Plasticity Krasnow Institute for Advanced Study George Mason University Fairfax VA USA. Faculty of Information Technology Beijing University of Technology Beijing China. Beijing International Collaboration Base on Brain Informatics and Wisdom Services Beijing China. Nuctech Netherlands Rotterdam the Netherlands. Janelia Research Campus Howard Hughes Medical Institute Ashburn VA USA. Department of Electrical and Computer Engineering University of Alberta Edmonton Alberta Canada. Ministry of Education Key Laboratory of Intelligent Computation and Signal Processing Anhui University Hefei China. Paige AI New York NY USA. Scientific Data Division and Biological Systems and Engineering Division Lawrence Berkeley National Lab Berkeley CA USA. Helen Wills Neuroscience Institute and Redwood Center for Theoretical Neuroscience UC Berkeley Berkeley CA USA. RIKEN AIP Tokyo Japan. Research Center for Advanced Science and Technology (RCAST) The University of Tokyo Tokyo Japan. School of Computer Science University of Sydney Sydney New South Wales Australia. Texas A&M University College Station TX USA. Cullen College of Engineering University of Houston Houston TX USA. Graduate Institute of Biomedical Engineering National Taiwan University of Science and Technology Taipei Taiwan. National Centre for Computer Animation Bournemouth University Poole UK. PROPHESEE Paris France. Department of Neuroscience Columbia University New York NY USA. Mortimer B. Zuckerman Mind Brain Behavior Institute Columbia University New York NY USA. Department of Computer Science Northern Illinois Universit

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

关键词：

A Multiscale Superpixel-Level Salient Object Detection Model Using Local-Global Contrast Cue

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Journal of shanghai Jiaotong university(science) 2017年第1期22卷 121-128页

作者：穆楠徐新王英林张晓龙 School of Computer Science and Technology Wuhan University of Science and Technology Hubei Province Key Laboratory of Intelligent Information Processing and Real-Time Industrial System Wuhan University of Science and Technology School of Information Management and Engineering Shanghai University of Finance and Economics

The goal of salient object detection is to estimate the regions which are most likely to attract human's visual attention. As an important image preprocessing procedure to reduce the computational complexity, salient object detection is still a challenging problem in computer vision. In this paper, we proposed a salient object detection model by integrating local and global superpixel contrast at multiple scales. Three features are computed to estimate the saliency of superpixel. Two optimization measures are utilized to refine the resulting saliency map. Extensive experiments with the state-of-the-art saliency models on four public datasets demonstrate the effectiveness of the proposed model.

关键词： salient object detection superpixel multiple scales local contrast global contrast TP 391.4 A

NTIRE 2020 Challenge on Real-World Image Super-Resolution: Methods and Results

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arXiv 2020年

作者： Lugmayr, Andreas Danelljan, Martin Timofte, Radu Ahn, Namhyuk Bai, Dongwoon Cai, Jie Cao, Yun Chen, Junyang Cheng, Kaihua Chun, SeYoung Deng, Wei El-Khamy, Mostafa Man Ho, Chiu Ji, Xiaozhong Kheradmand, Amin Kim, Gwantae Ko, Hanseok Lee, Kanghyu Lee, Jungwon Li, Hao Liu, Ziluan Liu, Zhi-Song Liu, Shuai Lu, Yunhua Meng, Zibo Navarrete Michelini, Pablo Micheloni, Christian Prajapati, Kalpesh Ren, Haoyu Hyeok Seo, Yong Siu, Wan-Chi Sohn, Kyung-Ah Tai, Ying Muhammad Umer, Rao Wang, Shuangquan Wang, Huibing Haoning Wu, Timothy Wu, Haoning Yang, Biao Yang, Fuzhi Yoo, Jaejun Zhao, Tongtong Zhou, Yuanbo Zhuo, Haijie Zong, Ziyao Zou, Xueyi Wang, Li-Wen Cani, Marie-Paule Siu, Wan-Chi Yang, Huan Fu, Jianlong Shi, Yukai Chen, Junyang Lee, Kanghyu Park, Jaihyun Lee, Junyeop Min, Jeongki Lee, Bokyeung Ko, Hanseok Yoo, Jaejun Sohn, Kyung-Ah Micheloni, Christian Hu, Fengshuo Wang, Yanhong Lu, Yunhua Peng, Jinjia Wang, Huibing Zhuo, Haijie Lee, Junyeop Min, Jeongki Lee, Bokyeung Park, Jaihyun Ko, Hanseok Tai, lab Ying Jilin Li, Youtu lab Liu, Shuai Yang, Biao Liu, Xing Chen, Shuaijun Zhao, Lei Wang, Zhan Lin, Yuxuan Jia, Xu Gao, Qinquan Deng, Wei Kheradmand, Amin El-Khamy, Mostafa Wang, Shuangquan Bai, Dongwoon Lee, Jungwon Patel, Heena Chudasama, Vishal Upla, Kishor Ramachandra, Raghavendra Raja, Kiran Busch, Christoph Meng, Zibo Ho, Chiu Man Computer Vision Lab ETH Zurich Switzerland LIX - Computer science laboratory at the cole polytechnique Palaiseau France Center of Multimedia Signal Processing Hong Kong Polytechnic University Hong Kong Shanghai Jiao Tong University China Microsoft Research Beijing China Guangdong University of Technology China Intelligent Signal Processing Laboratory Korea University Korea Republic of Ajou University Korea Republic of EPFL University of Udine Italy BOE Technology Group Co. Ltd Dalian Maritime University China Guangdong OPPO Mobile Telecommunications Corp. Ltd Department of Video Information Processing Korea University Korea Republic of School of Electrical Engineering Korea University Korea Republic of Tencent Youtu Lab Yun Cao Tencent Youtu Tencent Youtu Lab Chengjie Wang Tencent Tencent Youtu Lab Feiyue Huang Tencent Youtu Lab Peking University China North China University of Technology China Huawei Technologies Co. Ltd China Fuzhou University Tong Tong Fuzhou University Imperial Vision Technology China Fuzhou University Imperial Vision Technology China Imperial Vision Technology SOC R&D Samsung Semiconductor Inc. United States Ulsan national institute of science and technology Korea Republic of Sardar Vallabhbhai National Institute Of Technology Surat India Norwegian University of Science and Technology Gjøvik Norway InnoPeak Technology

This paper reviews the NTIRE 2020 challenge on real world super-resolution. It focuses on the participating methods and final results. The challenge addresses the real world setting, where paired true high and low-resolution images are unavailable. For training, only one set of source input images is therefore provided along with a set of unpaired high-quality target images. In Track 1: Image processing artifacts, the aim is to super-resolve images with synthetically generated image processing artifacts. This allows for quantitative benchmarking of the approaches w.r.t. a ground-truth image. In Track 2: Smartphone Images, real low-quality smart phone images have to be super-resolved. In both tracks, the ultimate goal is to achieve the best perceptual quality, evaluated using a human study. This is the second challenge on the subject, following AIM 2019, targeting to advance the state-of-the-art in super-resolution. To measure the performance we use the benchmark protocol from AIM 2019. In total 22 teams competed in the final testing phase, demonstrating new and innovative solutions to the problem. Copyright © 2020, The Authors. All rights reserved.

关键词： Optical resolving power

Deep Learning in Digital Breast Tomosynthesis: Current Status, Challenges, and Future Trends

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MedComm

MedComm 2025年第6期6卷 e70247页

作者： Wang, Ruoyun Chen, Fanxuan Chen, Haoman Lin, Chenxing Shuai, Jincen Wu, Yutong Ma, Lixiang Hu, Xiaoqu Wu, Min Wang, Jin Zhao, Qi Shuai, Jianwei Pan, Jingye Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine Vision and Brain Health) Wenzhou Institute University of Chinese Academy of Sciences Wenzhou China Wenzhou Medical University Wenzhou China UCSC Baskin School of Engineering University of California Santa Cruz CA United States Key Laboratory of Intelligent Treatment and Life Support for Critical Diseases of Zhejiang Province Wenzhou China Department of Anatomy Histology & Embryology School of Basic Medical Sciences Fudan University Shanghai China Department of Medicine Harvard Medical School and Brigham and Women's Hospital Boston MA United States Joint Research Centre on Medicine The Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China Stony Brook University Stony Brook NY United States School of Computer Science and Software Engineering University of Science and Technology Liaoning Anshan China Department of Big Data in Health Science The First Affiliated Hospital of Wenzhou Medical University Wenzhou China Zhejiang Engineering Research Center for Hospital Emergency and Process Digitization Wenzhou China

The high-resolution three-dimensional (3D) images generated with digital breast tomosynthesis (DBT) in the screening of breast cancer offer new possibilities for early disease diagnosis. Early detection is especially important as the incidence of breast cancer increases. However, DBT also presents challenges in terms of poorer results for dense breasts, increased false positive rates, slightly higher radiation doses, and increased reading times. Deep learning (DL) has been shown to effectively increase the processing efficiency and diagnostic accuracy of DBT images. This article reviews the application and outlook of DL in DBT-based breast cancer screening. First, the fundamentals and challenges of DBT technology are introduced. The applications of DL in DBT are then grouped into three categories: diagnostic classification of breast diseases, lesion segmentation and detection, and medical image generation. Additionally, the current public databases for mammography are summarized in detail. Finally, this paper analyzes the main challenges in the application of DL techniques in DBT, such as the lack of public datasets and model training issues, and proposes possible directions for future research, including large language models, multisource domain transfer, and data augmentation, to encourage innovative applications of DL in medical imaging. © 2025 The Author(s). MedComm published by Sichuan International Medical Exchange & Promotion Association (SCIMEA) and John Wiley & Sons Australia, Ltd.

关键词： deep learning digital breast tomosynthesis early breast cancer screening medical image analysis public database

U-Net: Machine reading comprehension with unanswerable questions

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arXiv 2018年

作者： Sun, Fu Li, Linyang Qiu, Xipeng Liu, Yang Shanghai Key Laboratory of Intelligent Information Processing Fudan University School of Computer Science Fudan University Liulishuo Silicon Valley AI Lab

Machine reading comprehension with unanswerable questions is a new challenging task for natural language processing. A key subtask is to reliably predict whether the question is unanswerable. In this paper, we propose a unified model, called U-Net, with three important components: answer pointer, no-answer pointer, and answer verifier. We introduce a universal node and thus process the question and its context passage as a single contiguous sequence of tokens. The universal node encodes the fused information from both the question and passage, and plays an important role to predict whether the question is answerable and also greatly improves the conciseness of the U-Net. Different from the state-of-art pipeline models, U-Net can be learned in an end-to-end fashion. The experimental results on the SQuAD 2.0 dataset show that U-Net can effectively predict the unanswerability of questions and achieves an F1 score of 71.7 on SQuAD 2.0. Copyright © 2018, The Authors. All rights reserved.

关键词： Forecasting

Pixel2Mesh: Generating 3D mesh models from single RGB images

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arXiv 2018年

作者： Wang, Nanyang Zhang, Yinda Li, Zhuwen Fu, Yanwei Liu, Wei Jiang, Yu-Gang Shanghai Key Lab of Intelligent Information Processing School of Computer Science Fudan University Princeton University Intel Labs School of Data Science Fudan University Tencent AI Lab

We propose an end-to-end deep learning architecture that produces a 3D shape in triangular mesh from a single color image. Limited by the nature of deep neural network, previous methods usually represent a 3D shape in volume or point cloud, and it is non-trivial to convert them to the more ready-to-use mesh model. Unlike the existing methods, our network represents 3D mesh in a graph-based convolutional neural network and produces correct geometry by progressively deforming an ellipsoid, leveraging perceptual features extracted from the input image. We adopt a coarse-to-fine strategy to make the whole deformation procedure stable, and define various of mesh related losses to capture properties of different levels to guarantee visually appealing and physically accurate 3D geometry. Extensive experiments show that our method not only qualitatively produces mesh model with better details, but also achieves higher 3D shape estimation accuracy compared to the state-of-the-art. Copyright © 2018, The Authors. All rights reserved.

关键词： Deep neural networks

Facial aging and rejuvenation by conditional multi-adversarial autoencoder with ordinal regression

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arXiv 2018年

作者： Zhu, Haiping Zhou, Qi Zhang, Junping Wang, James Z. Shanghai Key Lab of Intelligent Information Processing School of Computer Science Fudan University Shanghai200433 China College of Information Sciences and Technology Pennsylvania State University University ParkPA16802 United States

Facial aging and facial rejuvenation analyze a given face photograph to predict a future look or estimate a past look of the person. To achieve this, it is critical to preserve human identity and the corresponding aging progression and regression with high accuracy. However, existing methods cannot simultaneously handle these two objectives well. We propose a novel generative adversarial network based approach, named the Conditional Multi-Adversarial AutoEncoder with Ordinal Regression (CMAAE-OR). It utilizes an age estimation technique to control the aging accuracy and takes a high-level feature representation to preserve personalized identity. Specifically, the face is first mapped to a latent vector through a convolutional encoder. The latent vector is then projected onto the face manifold conditional on the age through a deconvolutional generator. The latent vector preserves personalized face features and the age controls facial aging and rejuvenation. A discriminator and an ordinal regression are imposed on the encoder and the generator in tandem, making the generated face images to be more photorealistic while simultaneously exhibiting desirable aging effects. Besides, a high-level feature representation is utilized to preserve personalized identity of the generated face. Experiments on two benchmark datasets demonstrate appealing performance of the proposed method over the state-of-the-art. Copyright © 2018, The Authors. All rights reserved.

关键词： Benchmarking