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Profiling Adaptive Immunity: A Quantitative Framework for Immune Repertoire Dynamics and Clinical Diagnostics

Fundamental Research 2025年

作者： Yexing Chen Haiwen Ni Yongjie Li Jin Ma Chen Huang Sixian Yang Xiangfei Xie Haitao Lv Min Li Peng Cao State Key Laboratory of Technologies for Chinese Medicine Pharmaceutical Process Control and Intelligent Manufacture Nanjing University of Chinese Medicine Nanjing 210000 China Jiangsu Provincial Medical Innovation Center Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine Nanjing 210000 China Department of Hematology Affiliated Hospital of Nanjing University of Chinese Medicine The First Clinical College of Nanjing University of Chinese Medicine Nanjing 210000 China Children’s Hospital of Soochow University Suzhou 215000 China Key Laboratory of Quantum Information University of Science and Technology of China Hefei 230000 China Department of Computer Science College of Engineering and Applied Science University of Cincinnati Cincinnati 45221 USA Department of Oncology Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine Nanjing 210000 China

While immune repertoire(IR) dynamics encode critical disease signatures, existing models fail to capture the non-equilibrium processes that governing clonal selection and somatic hypermutation (SHM). We develop a biophysical framework that mathematically reconstructs IR evolution through energy landscape optimization, where 1) clonal emergence probabilities map to metastable states, 2) repertoire transitions obey non-equilibrium dynamics, and 3) inter-IR distances quantify the distribution transformation costs via optimal transport theory. This model enables macroscopic immune state detection from 10k cells by resolving critical fluctuations in sparse sampling regimes. Experimental validation across murine/human cohorts demonstrates precise unsupervised stratification of immune stages and disease states without prior clinical annotations. By bridging stochastic SHM kinetics with deterministic repertoire shifts, our approach establishes quantitative metrics for tracking immunological trajectories and pathological progression. This paradigm shift from static pattern recognition to dynamic process decoding empowers sensitive immunomonitoring and personalized therapeutic design through ultra-low-input clinical sampling.

关键词： Deductive reasoning Immune repertoire analysis Repertoire shift quantification Early disease screening Systemic immunity inference Kawasaki disease Colorectal cancer

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Hyperspectral image classification with attention aided CNNs

arXiv

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arXiv 2020年

作者： Hang, Renlong Li, Zhu Liu, Qingshan Ghamisi, Pedram Bhattacharyya, Shuvra S. School of Automation Nanjing University of Information Science and Technology Nanjing210044 China Department of Computer Science and Electrical Engineering University of Missouri Kansas CityMO64110 United States Jiangsu Key Laboratory of Big Data Analysis Technology School of Automation Nanjing University of Information Science and Technology Nanjing210044 China Exploration FreibergD-09599 Germany Department of Electrical and Computer Engineering University of Maryland College ParkMD20742 United States

Convolutional neural networks (CNNs) have been widely used for hyperspectral image classification. As a common process, small cubes are firstly cropped from the hyperspectral image and then fed into CNNs to extract spectral and spatial features. It is well known that different spectral bands and spatial positions in the cubes have different discriminative abilities. If fully explored, this prior information will help improve the learning capacity of CNNs. Along this direction, we propose an attention aided CNN model for spectral-spatial classification of hyperspectral images. Specifically, a spectral attention sub-network and a spatial attention sub-network are proposed for spectral and spatial classification, respectively. Both of them are based on the traditional CNN model, and incorporate attention modules to aid networks focus on more discriminative channels or positions. In the final classification phase, the spectral classification result and the spatial classification result are combined together via an adaptively weighted summation method. To evaluate the effectiveness of the proposed model, we conduct experiments on three standard hyperspectral datasets. The experimental results show that the proposed model can achieve superior performance compared to several state-of-the-art CNN-related models. Copyright © 2020, The Authors. All rights reserved.

关键词： Convolutional neural networks

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Sequential 3D Human Pose and Shape Estimation From Point Clouds

Sequential 3D Human Pose and Shape Estimation From Point Clo...

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Conference on computer Vision and Pattern Recognition (CVPR)

作者： Kangkan Wang Jin Xie Guofeng Zhang Lei Liu Jian Yang Key Lab of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education Jiangsu Key Lab of Image and Video Understanding for Social Security School of Computer Science and Engineering Nanjing University of Science and Technology China State Key Laboratory of CAD&CG Zhejiang University China ZJU-SenseTime Joint Lab of 3D Vision

ISBN: (数字)9781728171685

ISBN: (纸本)9781728171692

This work addresses the problem of 3D human pose and shape estimation from a sequence of point clouds. Existing sequential 3D human shape estimation methods mainly focus on the template model fitting from a sequence of depth images or the parametric model regression from a sequence of RGB images. In this paper, we propose a novel sequential 3D human pose and shape estimation framework from a sequence of point clouds. Specifically, the proposed framework can regress 3D coordinates of mesh vertices at different resolutions from the latent features of point clouds. Based on the estimated 3D coordinates and features at the low resolution, we develop a spatial-temporal mesh attention convolution (MAC) to predict the 3D coordinates of mesh vertices at the high resolution. By assigning specific attentional weights to different neighboring points in the spatial and temporal domains, our spatial-temporal MAC can capture structured spatial and temporal features of point clouds. We further generalize our framework to the real data of human bodies with a weakly supervised fine-tuning method. The experimental results on SURREAL, Human3.6M, DFAUST and the real detailed data demonstrate that the proposed approach can accurately recover the 3D body model sequence from a sequence of point clouds.

关键词： Three-dimensional displays Solid modeling Shape Biological system modeling Estimation Spatial resolution Feature extraction

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Simulation optimization of AOA estimation algorithm based on MIMO UWB communication system 2

Simulation optimization of AOA estimation algorithm based on...

引用

2nd International Conference on information Technologies and Electrical Engineering, ICITEE 2019

作者： Zhang, Kun Shen, Chong Aslam, Bhatti Uzair Long, Keliu Chen, Xiaoyan Li, Nan Education Center of MTA Hainan Tropical Ocean University Hainan Sanya China State Key Laboratory of Marine Resources Utilization in South China Sea Hainan University Hainan Haikou China College of Computer Science and Information Technology Nanjing Normal University Jiangsu Nanjing China College of Computer Science and Technology Hainan Tropical Ocean University Hainan Sanya China

ISBN: (纸本)9781450372930

The application of UWB technology is mainly used for positioning systems both at home and abroad. Compared with conventional wireless communication technologies, UWB also has outstanding advantages such as large capacity, high speed, and low power [1]. UWB signals also have great advantages in data transmission performance. This paper proposes a method of combining AOA estimation in UWB MIMO system. Firstly, the tag position is located, and then the position information is packaged and sent to the base station along with other detection data, which is beneficial to the data transmission process. Position for real-time precise positioning. The adoption of MIMO technology can improve the spectrum efficiency and improve the system performance for the system. The AOA estimation can achieve accurate positioning accuracy by using multiple antennas. © 2019 ACM.

关键词： MIMO systems

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Dexterous Manipulation through Imitation Learning: A Survey

arXiv

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arXiv 2025年

作者： An, Shan Meng, Ziyu Tang, Chao Zhou, Yuning Liu, Tengyu Ding, Fangqiang Zhang, Shufang Mu, Yao Song, Ran Zhang, Wei Hou, Zeng-Guang Zhang, Hong School of Electrical and Information Engineering Tianjin University Tianjin300072 China School of Control Science and Engineering Shandong University Jinan250061 China State Key Laboratory of General Artificial Intelligence Beijing100086 China Department of Mechanical and Process Engineering ETH Zurich Zurich8092 Switzerland Department of Electronic and Electrical Engineering Southern University of Science and Technology Shenzhen518055 China School of Informatics University of Edinburgh EH8 9AB United Kingdom Department of Computer Science University of Hong Kong 999077 Hong Kong State Key Laboratory of Multimodal Artificial Intelligence Systems Institute of Automation Chinese Academy of Sciences Beijing100190 China School of Artificial Intelligence University of Chinese Academy of Sciences Beijing100049 China CASIA-MUST Joint Laboratory of Intelligence Science and Technology Institute of Systems Engineering Macau University of Science and Technology 999078 China

Dexterous manipulation, which refers to the ability of a robotic hand or multi-fingered end-effector to skillfully control, reorient, and manipulate objects through precise, coordinated finger movements and adaptive force modulation, enables complex interactions similar to human hand dexterity. With recent advances in robotics and machine learning, there is a growing demand for these systems to operate in complex and unstructured environments. Traditional model-based approaches struggle to generalize across tasks and object variations due to the high-dimensionality and complex contact dynamics of dexterous manipulation. Although model-free methods such as reinforcement learning (RL) show promise, they require extensive training, large-scale interaction data, and carefully designed rewards for stability and effectiveness. Imitation learning (IL) offers an alternative by allowing robots to acquire dexterous manipulation skills directly from expert demonstrations, capturing fine-grained coordination and contact dynamics while bypassing the need for explicit modeling and large-scale trial-and-error. This survey provides an overview of dexterous manipulation methods based on imitation learning (IL), details recent advances, and addresses key challenges in the field. Additionally, it explores potential research directions to enhance IL-driven dexterous manipulation. Our goal is to offer researchers and practitioners a comprehensive introduction to this rapidly evolving domain. Copyright © 2025, The Authors. All rights reserved.

关键词： Grippers

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Dynamic Optimization of Chemical processes using Symbiotic Organisms Search Algorithm

Dynamic Optimization of Chemical Processes using Symbiotic O...

引用

Chinese Automation Congress (CAC)

作者： Peng Tian Xu Chen Wenxiang Zhao Wenli Du School of Electrical and Information Engineering Jiangsu University Zhenjiang Jiangsu China Key Laboratory of Advanced Control and Optimization for Chemical Process Ministry of Education East China University of Science and Technology Shanghai China

Chemical process optimization problems are often modeled as dynamic optimization problems (DOPs). Due to the nonlinear, multimodal and multi-dimensional nature of DOPs, efficient solution of DOPs is a very challenging task. In this paper, a new intelligent search algorithm called symbiotic organisms search (SOS) is proposed for tackling the chemical DOPs. SOS mainly mimics three symbiotic relationships in ecosystem, namely mutualism, commensalism and parasitism, to perform global search. In addition, compared with previous intelligent search algorithms, SOS has the advantages of no tuning parameters, easy to implement and high performance. Combined with control vector parameterization, the proposed SOS is applied to solve five chemical DOPs with different levels of complexity. Simulation results show that SOS can achieve solutions with accuracy comparable to those methods in the literature, and thus can be regarded as an effective tool for the chemical DOPs.

关键词： Optimization Heuristic algorithms Chemicals Symbiosis Sociology Statistics Organisms

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Building an efficient intrusion detection system based on feature selection and ensemble classifier

arXiv

引用

arXiv 2019年

作者： Zhou, Yuyang Cheng, Guang Jiang, Shanqing Dai, Mian School of Cyber Science and Engineering Southeast University Nanjing China Key Laboratory of Computer Network and Information Integration Ministry of Education Nanjing China Jiangsu Provincial Key Laboratory of Computer Network Technology Southeast University Nanjing China National Key Laboratory of Science and Technology on Information System Security Beijing China

Intrusion detection system (IDS) is one of extensively used techniques in a network topology to safeguard the integrity and availability of sensitive assets in the protected systems. Although many supervised and unsupervised learning approaches from the field of machine learning have been used to increase the efficacy of IDSs, it is still a problem for existing intrusion detection algorithms to achieve good performance. First, lots of redundant and irrelevant data in high-dimensional datasets interfere with the classification process of an IDS. Second, an individual classifier may not perform well in the detection of each type of attacks. Third, many models are built for stale datasets, making them less adaptable for novel attacks. Thus, we propose a new intrusion detection framework in this paper, and this framework is based on the feature selection and ensemble learning techniques. In the first step, a heuristic algorithm called CFS-BA is proposed for dimensionality reduction, which selects the optimal subset based on the correlation between features. Then, we introduce an ensemble approach that combines C4.5, Random Forest (RF), and Forest by Penalizing Attributes (Forest PA) algorithms. Finally, voting technique is used to combine the probability distributions of the base learners for attack recognition. The experimental results, using NSL-KDD, AWID, and CIC-IDS2017 datasets, reveal that the proposed CFS-BA-Ensemble method is able to exhibit better performance than other related and state of the art approaches under several metrics. Copyright © 2019, The Authors. All rights reserved.

关键词： Data mining

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Geographic information science in the era of geospatial big data: A cyberspace perspective

引用

The Innovation 2022年第5期3卷 21-22页

作者： Xintao Liu Min Chen Christophe Claramunt Michael Batty Mei-Po Kwan Ahmad MSenousi Tao Cheng Josef Strobl Arzu Cöltekin John Wilson Temenoujka Bandrova Milan Konecny Paul MTorrens Fengyuan Zhang Li He Jinfeng Wang Carlo Ratti Olaf Kolditz Alexander Klippel Songnian Li Hui Lin Guonian Lu Department of Land Surveying and Geo-Informatics Hong Kong Polytechnic UniversityHong Kong SARKowloonChina Key Laboratory of Virtual Geographic Environment(Ministry of Education of PRC) Nanjing Normal UniversityNanjing 210023China The French Naval Academy Research Institute 29240 Lanveoc-PoulmicFrance The Bartlett Centre for Advanced Spatial Analysis(CASA) University College London(UCL)WC1E 6BT LondonUK Institute of Space and Earth Information Science The Chinese University of Hong KongHong Kong SARShatin 999077China Department of Civil Engineering Cairo University12613 CairoEgypt SpaceTimeLab Department of CivilEnvironmental and Geomatic EngineeringUniversity College London(UCL)WC1E 6BT LondonUK Department of Geoinformatics University of Salzburg5020 SalzburgAustria Institute of Interactive Technologies(IIT) University of Applied Sciences and Arts Northwestern Switzerland FHNW5210 WindischSwitzerland Spatial Sciences Institute University of Southern CaliforniaLos AngelesCA 90007USA Laboratory on Cartography Department of Photogrammetry and CartographyUniversity of ArchitectureCivil Engineering and Geodesy1164 SofiaBulgaria Laboratory on Geoinformatics and Cartography Department of GeographyMasaryk University61137 BrnoCeskáRepublika Computer Science and Engineering Tandon School&Center for Urban Science+ProgressNew York UniversityNew YorkNY 10012USA School of Humanities and Social Science Xi’an Jiaotong UniversityXi’an 710049China Institute of Geographic Sciences and Natural Resources Research Chinese Academy of SciencesBeijing 100101China Department of Urban Studies and Planning Massachusetts Institute of TechnologyCambridgeMA 02139USA Centre for Environmental Research Helmholtz Centre for Environmental Research-UFZ04318 LeipzigGermany Laboratory of Geo-information Science and Remote Sensing Wageningen University&ResearchWageningen 6708the Netherlands Department of Civil Engineering Toronto Metropolitan UniversityTorontoON M5B 2K3Canada School of Geography and Env

The advent of information and communication technology and the Internet of Things have led our society toward a digital *** proliferation of personal computers,smartphones,intelligent autonomous sensors,and pervasive network interactions with individuals have gradually shifted human activities from offline to online and from in person to *** transformation has brought a series of challenges in a variety of fields,such as the dilemma of placelessness,some aspects of timelessness(no time relevance),and the changing relevance of distance in the field of geographic information science(GIScience).In the last two decades,“cyber thinking”in GIScience has received significant attention from different *** instance,human activities in“cyberspace”need to be reconsidered when coupled with the geographic space to observe the first law of geography.

关键词： computer cyber instance

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Machine learning for modelling unstructured grid data in computational physics: a review

arXiv

引用

arXiv 2025年

作者： Cheng, Sibo Bocquet, Marc Ding, Weiping Finn, Tobias Sebastian Fu, Rui Fu, Jinlong Guo, Yike Johnson, Eleda Li, Siyi Liu, Che Moro, Eric Newton Pan, Jie Piggott, Matthew Quilodran, Cesar Sharma, Prakhar Wang, Kun Xiao, Dunhui Xue, Xiao Zeng, Yong Zhang, Mingrui Zhou, Hao Zhu, Kewei Arcucci, Rossella CEREA ENPC EDF R&D Institut Polytechnique de Paris Île-de-France France School of Artificial Intelligence and Computer Science Nantong University Jiangsu Nantong226019 China School of Mathematical Sciences Key Laboratory of Intelligent Computing and Applications Tongji University Shanghai200092 China School of Engineering and Materials Science Faculty of Science and Engineering Queen Mary University of London LondonE1 4NS United Kingdom Zienkiewicz Centre for Modelling Data and AI Faculty of Science and Engineering Swansea University SwanseaSA1 8EN United Kingdom Department of Computer Science and Engineering Hong Kong university of science and technology Hong Kong Department of Earth Science & Engineering Imperial College London LondonSW7 2AZ United Kingdom Tianjin Key Laboratory of Imaging and Sensing Microelectronics Technology School of Microelectronics Tianjin University Tianjin300072 China Centre for Health Informatics Cumming School of Medicine University of Calgary CalgaryABT2N 1N4 Canada Department of Community Health Sciences Cumming School of Medicine University of Calgary CalgaryABT2N 1N4 Canada Undaunted Grantham Institute for Climate Change and the Environment Imperial College London LondonSW7 2AZ United Kingdom Culham Campus AbingdonOX14 3DB United Kingdom Centre for Computational Science Department of Chemistry University College London LondonWC1E 6BT United Kingdom Concordia Institute for Information Systems Engineering Concordia University MontrealQCH3G 1M8 Canada School of Mechanical Medical and Process Engineering Faculty of Engineering Queensland University of Technology BrisbaneQLD Australia Department of Chemical Engineering University College London LondonWC1E 6BT United Kingdom

Unstructured grid data are essential for modelling complex geometries and dynamics in computational physics. Yet, their inherent irregularity presents significant challenges for conventional machine learning (ML) techniques. This paper provides a comprehensive review of advanced ML methodologies designed to handle unstructured grid data in high-dimensional dynamical systems. key approaches discussed include graph neural networks, transformer models with spatial attention mechanisms, interpolation-integrated ML methods, and meshless techniques such as physics-informed neural networks. These methodologies have proven effective across diverse fields, including fluid dynamics and environmental simulations. This review is intended as a guidebook for computational scientists seeking to apply ML approaches to unstructured grid data in their domains, as well as for ML researchers looking to address challenges in computational physics. It places special focus on how ML methods can overcome the inherent limitations of traditional numerical techniques and, conversely, how insights from computational physics can inform ML development. To support benchmarking, this review also provides a summary of open-access datasets of unstructured grid data in computational physics. Finally, emerging directions such as generative models with unstructured data, reinforcement learning for mesh generation, and hybrid physics-data-driven paradigms are discussed to inspire future advancements in this evolving field. © 2025, CC BY-NC-SA.

关键词： Mesh generation

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ThreeF-Net: Fine-grained feature fusion network for breast ultrasound image segmentation

引用

computers in biology and medicine 2025年 194卷 110527页

作者： Xuesheng Bian Jia Liu Sen Xu Weiquan Liu Leyi Mei Chaoshen Xiao Fan Yang School Of Information Engineering Yancheng Institute Of Technology Hope Avenue Middle Road Yancheng 224051 Jiangsu China. Electronic address: xsbian@***. School Of Information Engineering Yancheng Institute Of Technology Hope Avenue Middle Road Yancheng 224051 Jiangsu China. College of Computer Engineering Jimei University Yinjiang Road No. 183 Xiamen 361005 Fujian China. National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility) Key Laboratory of Genetic Evolution & Animal Models and National Resource Center for Nonhuman Primates Kunming Institute of Zoology Chinese Academy of Sciences East Jiaochang Road No. 32 Kunming 650221 Yunnan China. National Key Laboratory of Radar Signal Processing Xidian university No. 2 South Taibai Road Xian 710071 Shaanxi China. School of Resources and Environmental Engineering Wuhan University of Science and Technology 947 Heping Avenue Qingshan District Xian 430081 Wuhan China.

Convolutional Neural Networks (CNNs) have achieved remarkable success in breast ultrasound image segmentation, but they still face several challenges when dealing with breast lesions. Due to the limitations of CNNs in modeling long-range dependencies, they often perform poorly in handling issues such as similar intensity distributions, irregular lesion shapes, and blurry boundaries, leading to low segmentation accuracy. To address these issues, we propose the ThreeF-Net, a fine-grained feature fusion network. This network combines the advantages of CNNs and Transformers, aiming to simultaneously capture local features and model long-range dependencies, thereby improving the accuracy and stability of segmentation tasks. Specifically, we designed a Transformer-assisted Dual Encoder Architecture (TDE), which integrates convolutional modules and self-attention modules to achieve collaborative learning of local and global features. Additionally, we designed a Global Group Feature Extraction (GGFE) module, which effectively fuses the features learned by CNNs and Transformers, enhancing feature representation ability. To further improve model performance, we also introduced a Dynamic Fine-grained Convolution (DFC) module, which significantly improves lesion boundary segmentation accuracy by dynamically adjusting convolution kernels and capturing multi-scale features. Comparative experiments with state-of-the-art segmentation methods on three public breast ultrasound datasets demonstrate that ThreeF-Net outperforms existing methods across multiple key evaluation metrics.

关键词： Attention mechanism Breast lesion segmentation Deep learning Feature fusion Ultrasound images

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