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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.

关键词： biomedical data mining biomedical data computer vision artificial intelligence artificial intelligence ai integrating biological knowledge models disease screeningto quantitative biology conference

Regenerative Particle Thompson Sampling

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arXiv 2022年

作者： Zhou, Zeyu Hajek, Bruce Choi, Nakjung Walid, Anwar Department of Radiology Mayo Clinic RochesterMN United States Department of Electrical and Computer Engineering The Coordinated Science Laboratory University of Illinois at Urbana-Champaign United States Network System and Security Research Nokia Bell Labs Murray HillNJ United States Amazon New York United States

This paper proposes regenerative particle Thompson sampling (RPTS), a flexible variation of Thompson sampling. Thompson sampling itself is a Bayesian heuristic for solving stochastic bandit problems, but it is hard to implement in practice due to the intractability of maintaining a continuous posterior distribution. Particle Thompson sampling (PTS) is an approximation of Thompson sampling obtained by simply replacing the continuous distribution by a discrete distribution supported at a set of weighted static particles. We observe that in PTS, the weights of all but a few fit particles converge to zero. RPTS is based on the heuristic: delete the decaying unfit particles and regenerate new particles in the vicinity of fit surviving particles. Empirical evidence shows uniform improvement from PTS to RPTS and flexibility and efficacy of RPTS across a set of representative bandit problems, including an application to 5G network slicing. © 2022, CC BY-SA.

关键词： Stochastic systems

MetaFruit Meets Foundation Models: Leveraging a Comprehensive Multi-Fruit Dataset for Advancing Agricultural Foundation Models

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arXiv 2024年

作者： Li, Jiajia Lammers, Kyle Yin, Xunyuan Yin, Xiang He, Long Lu, Renfu Li, Zhaojian Department of Electrical and Computer Engineering Michigan State University East LansingMI United States School of Chemical and Biomedical Engineering Nanyang Technological University Singapore Department of Automation Key Laboratory of System Control and Information Processing Shanghai Jiao Tong University Shanghai China Department of Agricultural and Biological Engineering Pennsylvania State University United States United States Department of Agriculture Agricultural Research Service East LansingMI United States Department of Mechanical Engineering Michigan State University East LansingMI United States

Fruit harvesting poses a significant labor and financial burden for the industry, highlighting the critical need for advancements in robotic harvesting solutions. Machine vision-based fruit detection has been recognized as a crucial component for robust identification of fruits to guide robotic manipulation. Despite considerable progress in leveraging deep learning and machine learning techniques for fruit detection, a common shortfall is the inability to swiftly extend the developed models across different orchards and/or various fruit species. Additionally, the limited availability of pertinent data further compounds these challenges. In this work, we introduce MetaFruit, the largest publicly available multi-class fruit dataset, comprising 4,248 images and 248,015 manually labeled instances across diverse U.S. orchards. Furthermore, this study proposes an innovative open-set fruit detection system leveraging advanced Vision Foundation Models (VFMs) for fruit detection that can adeptly identify a wide array of fruit types under varying orchard conditions. This system not only demonstrates remarkable adaptability in learning from minimal data through few-shot learning but also shows the ability to interpret human instructions for subtle detection tasks. The performance of the developed foundation model is comprehensively evaluated using several metrics, which outperforms the existing state-of-the-art algorithms in both our MetaFruit dataset and other open-sourced fruit datasets, thereby setting a new benchmark in the field of agricultural technology and robotic harvesting. The MetaFruit dataset (https://***/datasets/jiajiali/metafruit) and detection framework (https://***/JiajiaLi04/FMFruit) are open-sourced to foster future research in vision-based fruit harvesting, marking a significant stride toward addressing the urgent needs of the agricultural sector. © 2024, CC BY-NC-SA.

关键词： Fruits

Broadband and repetition rate tunable frequency comb based on electro-optic time lens with AlGaAsOI waveguide

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Broadband and repetition rate tunable frequency comb based o...

49th European Conference on Optical Communications (ECOC 2023)

作者： C. Ma C. Wang Y. Pi L. Wang Z. He J. E. Bowers L. Chang Z. Cao S. Yu Research Center of Circuits and Systems Peng Cheng Laboratory Shenzhen 518055 Guangdong People's Republic of China Department of Electrical and Computer Engineering University of California Santa Barbara CA 93106 USA State Key Laboratory of Advanced Optical Communications System and Networks Peking University Beijing 100871 People's Republic of China

We present a tunable repetition rate frequency comb realized by cascaded electro-optical modulators with a high nonlinear AlGaAs-on-isolator waveguide. 18-26.5 GHz comb spacing tunability with broadband spectra was achieved. All the devices can be integrated onto a single chip, which makes this work useful for many applications.

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Perceptual Attacks of No-Reference Image Quality Models with Human-in-the-Loop

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arXiv 2022年

作者： Zhang, Weixia Li, Dingquan Min, Xiongkuo Zhai, Guangtao Guo, Guodong Yang, Xiaokang Ma, Kede MoE Key Lab of Artificial Intelligence AI Institute Shanghai Jiao Tong University China Network Intelligence Research Department Peng Cheng Laboratory China Department of Computer Science and Electrical Engineering West Virginia University United States Department of Computer Science City University of Hong Kong Hong Kong

No-reference image quality assessment (NR-IQA) aims to quantify how humans perceive visual distortions of digital images without access to their undistorted references. NR-IQA models are extensively studied in computational vision, and are widely used for performance evaluation and perceptual optimization of man-made vision systems. Here we make one of the first attempts to examine the perceptual robustness of NR-IQA models. Under a Lagrangian formulation, we identify insightful connections of the proposed perceptual attack to previous beautiful ideas in computer vision and machine learning. We test one knowledge-driven and three data-driven NR-IQA methods under four full-reference IQA models (as approximations to human perception of just-noticeable differences). Through carefully designed psychophysical experiments, we find that all four NR-IQA models are vulnerable to the proposed perceptual attack. More interestingly, we observe that the generated counterexamples are not transferable, manifesting themselves as distinct design flows of respective NR-IQA methods. © 2022, CC BY.

关键词： Image quality

Metafruit Meets Foundation Models: Leveraging a Comprehensive Multi-Fruit Dataset for Advancing Agricultural Foundation Models

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SSRN

SSRN 2024年

Fruit harvesting poses a significant labor and financial burden for the industry, highlighting the critical need for advancements in robotic harvesting solutions. Machine vision-based fruit detection has been recognized as a crucial component for robust identification of fruits to guide robotic manipulation. Despite considerable progress in leveraging deep learning and machine learning techniques for fruit detection, a common shortfall is the inability to swiftly extend the developed models across different orchards and/or various fruit species. Additionally, the limited availability of pertinent data further compounds these challenges. In this work, we introduce MetaFruit, the largest publicly available multi-class fruit dataset, comprising 4,248 images and 248,015 manually labeled instances across diverse U.S. orchards. Furthermore, this study proposes an innovative open-set fruit detection system leveraging advanced Vision Foundation Models (VFMs) for fruit detection that can adeptly identify a wide array of fruit types under varying orchard conditions. This system not only demonstrates remarkable adaptability in learning from minimal data through few-shot learning but also shows the ability to interpret human instructions for subtle detection tasks. The performance of the developed foundation model is comprehensively evaluated using several metrics, which outperforms the existing state-of-the-art algorithms in both our MetaFruit dataset and other open-sourced fruit datasets, thereby setting a new benchmark in the field of agricultural technology and robotic harvesting. The MetaFruit dataset and detection framework are open-sourced to foster future research in vision-based fruit harvesting, marking a significant stride toward addressing the urgent needs of the agricultural sector. © 2024, The Authors. All rights reserved.

关键词： Fruits

Coalition Formation for Heterogeneous Federated Learning Enabled Channel Estimation in RIS-assisted Cell-free MIMO

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arXiv 2025年

作者： Qi, Nan Liu, Haoxuan Tsiftsis, Theodoros A. Boulogeorgos, Alexandros-Apostolos A. Zhou, Fuhui Jin, Shi Wu, Qihui Key Laboratory of Dynamic Cognitive System of Electromagnetic Spectrum Space Ministry of Industry and Information Technology Nanjing University of Aeronautics and Astronautics Nanjing210016 China Department of Informatics and Telecommunications University of Thessaly Lamia35100 Greece Department of Electrical and Computer Engineering University of Western Macedonia Kozani50100 Greece National Mobile Communications Research Laboratory Frontiers Science Center for Mobile Information Communication and Security Southeast University Nanjing210096 China

Downlink channel estimation remains a significant bottleneck in reconfigurable intelligent surface-assisted cell-free multiple-input multiple-output communication systems. Conventional approaches primarily rely on centralized deep learning methods to estimate the high-dimensional and complex cascaded channels. These methods require data aggregation from all users for centralized model training, leading to excessive communication overhead and significant data privacy concerns. Additionally, the large size of local learning models imposes heavy computational demands on end users, necessitating strong computational capabilities that most commercial devices lack. To address the aforementioned challenges, a coalition-formation-guided heterogeneous federated learning (FL) framework is proposed. This framework leverages coalition formation to guide the formation of heterogeneous FL user groups for efficient channel estimation. Specifically, by utilizing a distributed deep reinforcement learning (DRL) approach, each FL user intelligently and independently decides whether to join or leave a coalition, aiming at improving channel estimation accuracy, while reducing local model size and computational costs for end users. Moreover, to accelerate the DRL-FL convergence process and reduce computational burdens on end users, a transfer learning method is introduced. This method incorporates both received reference signal power and distance similarity metrics, by considering that nodes with similar distances to the base station and comparable received signal power have a strong likelihood of experiencing similar channel fading. Massive experiments performed that reveal that, compared with the benchmarks, the proposed framework significantly reduces the computational overhead of end users by 16%, improves data privacy, and improves channel estimation accuracy by 20%. © 2025, CC BY.

关键词： Federated learning

TomoSAR-ALISTA: Efficient TomoSAR Imaging via Deep Unfolded network

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TomoSAR-ALISTA: Efficient TomoSAR Imaging via Deep Unfolded ...

2022 International Conference on Radar systems, RADAR 2022

作者： Wang, Muhan Zhang, Zhe Wang, Yue Gao, Silin Qiu, Xiaolan Key Laboratory of Technology in Geo-spatial Information Processing and Application System Chinese Academy of Sciences Beijing100190 China Key Laboratory of Intelligent Aerospace Big Data Application Technology Suzhou215123 China Suzhou Aerospace Information Research Institute Suzhou215123 China School of Electronic Electrical and Communication Engineering University of Chinese Academy of Sciences Beijing100049 China Aerospace Information Research Institute Chinese Academy of Sciences Beijing100094 China Electrical and Computer Engineering Department George Mason University FairfaxVA22030 United States

ISBN: (纸本)9781839537776

Synthetic aperture radar (SAR) tomography (TomoSAR) has attracted remarkable interest for its ability in achieving three-dimensional reconstruction along the elevation direction from multiple observations. In recent years, compressed sensing (CS) technique has been introduced into TomoSAR considering for its super-resolution ability with limited samples. Whereas, the CS-based methods suffer from several drawbacks, including weak noise resistance, high computational complexity and complex parameter fine-tuning. Among the different CS algorithms, iterative soft-thresholding algorithm (ISTA) is widely used as a robust reconstruction approach, however, the parameters in the ISTA are manually chosen, which usually requires a time-consuming fine-tuning process to achieve the best performance. Aiming at efficient TomoSAR imaging, a novel sparse unfolding network named analytic learned ISTA (ALISTA) is proposed towards the TomoSAR imaging problem in this paper, and the key parameters of ISTA are learned from training data via deep learning to avoid complex parameter fine-tuning and significantly relieves the training burden. In addition, experiments verify that it is feasible to use traditional CS algorithms as training labels, which provides a tangible supervised training method to achieve better 3D reconstruction performance even in the absence of labeled data in real applications. © 2022 IET Conference Proceedings. All rights reserved.

关键词： Compressed sensing

AOCC-FL: Federated Learning with Aligned Overlapping via Calibrated Compensation

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AOCC-FL: Federated Learning with Aligned Overlapping via Cal...

IEEE Annual Joint Conference: INFOCOM, IEEE computer and Communications Societies

作者： Haozhao Wang Wenchao Xu Yunfeng Fan Ruixuan Li Pan Zhou School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China Department of Computing The Hong Kong Polytechnic University Hong Kong Hubei Key Laboratory of Distributed System Security Hubei Engineering Research Center on Big Data Security School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan China

Federated Learning enables collaboratively model training among a number of distributed devices with the coordination of a centralized server, where each device alternatively performs local gradient computation and communication to the server. FL suffers from significant performance degradation due to the excessive communication delay between the server and devices, especially when the network bandwidth of these devices is limited, which is common in edge environments. Existing methods overlap the gradient computation and communication to hide the communication latency to accelerate the FL training. However, the overlapping can also lead to an inevitable gap between the local model in each device and the global model in the server that seriously restricts the convergence rate of learning process. To address this problem, we propose a new overlapping method for FL, AOCC-FL, which aligns the local model with the global model via calibrated compensation such that the communication delay can be hidden without deteriorating the convergence performance. Theoretically, we prove that AOCC-FL admits the same convergence rate as the non-overlapping method. On both simulated and testbed experiments, we show that AOCC-FL achieves a comparable convergence rate relative to the non-overlapping method while outperforming the state-of-the-art overlapping methods.

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