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arXiv 2022年

作者： Benisty, Hadas Song, Alexander Mishne, Gal Charles, Adam S. Yale Neuroscience New HavenCT06510 United States Max Planck Institute for Intelligent Systems Stuttgart Germany Halıcıoğlu Data Science Institute Department of Electrical and Computer Engineering Neurosciences Graduate Program UC San Diego 9500 Gilman Drive La Jolla CA92093 United States Department of Biomedical Engineering Kavli Neuroscience Discovery Institute Center for Imaging Science Department of Neuroscience Mathematical Institute for Data Science Johns Hopkins University BaltimoreMD21287 United States

Functional optical imaging in neuroscience is rapidly growing with the development of new optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. In this review, we cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges. © 2022, CC BY-NC-ND.

关键词： Fluorescence microscopy

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Accelerating Real-Time Imaging for Radiotherapy: Leveraging Multi-GPU Training with PyTorch

Accelerating Real-Time Imaging for Radiotherapy: Leveraging ...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Ruth Obe Brandt Kaufmann Kaelen Baird Sam Kadel Yasmin Soltani Mostafa Cham Matthias K. Gobbert Carlos A. Barajas Zhuoran Jiang Vijay R. Sharma Lei Ren Stephen W. Peterson Jerimy C. PoIf Dept. of Computer Science and of Software Engineering U. of Houston-Clear Lake USA Dept. of Mathematics and Statistics U. of San Francisco USA Dept. of Computer Science and of Mathematics Skidmore College USA Dept. of Computer Science and of Psychology Mount Holyoke College USA Dept. of Biomedical Engineering U. of Houston USA Dept. of Information Systems U. of Maryland Baltimore County Dept. of Mathematics and Statistics U. of Maryland Baltimore County Medical Physics Graduate Program Duke University USA Dept. of Radiation Oncology U. of Maryland School of Medicine USA Department of Radiation Oncology U. of Maryland School of Medicine USA Dept. of Physics U. of Cape Town South Africa H3D Inc. USA

Proton beam therapy is an advanced form of cancer radiotherapy that uses high-energy proton beams to deliver precise and targeted radiation to tumors. This helps to mit-igate unnecessary radiation exposure in healthy tissues. Real-time imaging of prompt gamma rays with Compton cameras has been suggested to improve therapy efficacy. However, the camera's non-zero time resolution leads to incorrect interaction classifications and noisy images that are insufficient for accurately assessing proton delivery in patients. To address the challenges posed by the Compton camera's image quality, machine learning techniques are employed to classify and refine the generated data. These machine-learning techniques include recurrent and feedforward neural networks. A PyTorch model was designed to improve the data captured by the Compton camera. This decision was driven by PyTorch's flexibility, powerful capabilities in handling sequential data, and enhanced G PU usage. This accelerates the model's computations on large-scale radiotherapy data. Through hyperparameter tuning, the validation accuracy of our PyTorch model has been improved from an initial 7 % to over 60 %. Moreover, the PyTorch Distributed Data Parallelism strategy was used to train the RNN models on multiple G PU s, which significantly reduced the training time with a minor impact on model accuracy.

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A Normal Distribution Transform-Based Radar Odometry Designed For Scanning and Automotive Radars

arXiv

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arXiv 2021年

作者： Kung, Pou-Chun Wang, Chieh-Chih Lin, Wen-Chieh Graduate Degree Program of Robotics National Chiao Tung University Hsinchu Taiwan Department of Electrical and Computer Engineering National Chiao Tung University The Mechanical and Mechatronics Systems Research Laboratories Industrial Technology Research Institute Hsinchu Taiwan Department of Computer Science National Chiao Tung University Hsinchu Taiwan

Existing radar sensors can be classified into automotive and scanning radars. While most radar odometry (RO) methods are only designed for a specific type of radar, our RO method adapts to both scanning and automotive radars. Our RO is simple yet effective, where the pipeline consists of thresholding, probabilistic submap building, and an NDT-based radar scan matching. The proposed RO has been tested on two public radar datasets: the Oxford Radar RobotCar dataset and the nuScenes dataset, which provide scanning and automotive radar data respectively. The results show that our approach surpasses state-of-the-art RO using either automotive or scanning radar by reducing translational error by 51% and 30%, respectively, and rotational error by 17% and 29%, respectively. Besides, we show that our RO achieves centimeter-level accuracy as lidar odometry, and automotive and scanning RO have similar accuracy. Copyright © 2021, The Authors. All rights reserved.

关键词： Optical radar

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Applying mobility business intelligence concept in analyzing oil palm plantation productivity

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AIP Conference Proceedings 2024年第1期3026卷

作者： Andreas Wahyu Krisdiarto Irya Wisnubhadra Anzaludin Samsinga Perbangsa Teddy Suparyanto Bens Pardamean Faculty of Agricultural Technology STIPER Institute of Agriculture Yogyakarta Indonesia Informatics Engineering Department Atma Jaya Yogyakarta University Yogyakarta Indonesia Information Systems Department School of Information Systems Bina Nusantara University Jakarta Indonesia BDSRC Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia

The palm oil business employs almost 20 million people, generates USD 21 billion in revenue, and plays a vital role in Indonesia’s social economy. The Fresh Fruit Bunches (FFB) to Palm Oil Mills (POM) distribution system is one important aspect of fruit quality. Three steps are involved in getting Oil Palm FFB from the plantation to the POM. The first part of the procedure involves cutting FFB from the tree, the second stage involves gathering the fruit at a fruit collection point (FCP), and the third stage involves transporting the fruit to the palm oil mill (POM). As of now, the cost of the FFB transportation is still considerable, accounting for roughly 15% to 20% of the FFB pricing. The use of the Business Intelligence (BI) idea in the oil palm harvesting system is presented in this study as a foundation for creating web-based applications.

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Drum-aware ensemble architecture for improved joint musical beat and downbeat tracking

arXiv

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arXiv 2021年

作者： Chiu, Ching-Yu Su, Alvin Wen-Yu Yang, Yi-Hsuan The Graduate Program of Multimedia Systems and Intelligent Computing National Cheng Kung University Academia Sinica Taiwan The Department of Computer Science and Information Engineering National Cheng Kung University Taiwan Yating Music Team Taiwan AI Labs Taiwan Research Center for IT Innovation Academia Sinica Taiwan

This paper presents a novel system architecture that integrates blind source separation with joint beat and downbeat tracking in musical audio signals. The source separation module segregates the percussive and non-percussive components of the input signal, over which beat and downbeat tracking are performed separately and then the results are aggregated with a learnable fusion mechanism. This way, the system can adaptively determine how much the tracking result for an input signal should depend on the input's percussive or non-percussive components. Evaluation on four testing sets that feature different levels of presence of drum sounds shows that the new architecture consistently outperforms the widely-adopted baseline architecture that does not employ source separation. Copyright © 2021, The Authors. All rights reserved.

关键词： Blind source separation

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cytoNet: Spatiotemporal network analysis of cell communities (vol 18, e1009846, 2022)

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PLOS COMPUTATIONAL BIOLOGY 2022年第11期18卷 e1009846页

作者： Mahadevan, A. S. Long, B. L. Hu, C. W. Ryan, D. T. Grandel, N. E. Department of Bioengineering University of Pennsylvania Philadelphia Pennsylvania United States of America. Department of Bioengineering Rice University Houston Texas United States of America. Systems Synthetic and Physical Biology Program Rice University Houston Texas United States of America. Department of Biomedical Engineering University of Texas at San Antonio San Antonio Texas United States of America. Biophysics Graduate Program University of California Berkeley California United States of America. Department of Oral & Maxillofacial Surgery University of Texas Health Science Center at San Antonio San Antonio Texas United States of America. Department of Electrical and Computer Engineering Rice University Houston Texas United States of America.

We introduce cytoNet, a cloud-based tool to characterize cell populations from microscopy images. cytoNet quantifies spatial topology and functional relationships in cell communities using principles of network science. Capturing multicellular dynamics through graph features, cytoNet also evaluates the effect of cell-cell interactions on individual cell phenotypes. We demonstrate cytoNet's capabilities in four case studies: 1) characterizing the temporal dynamics of neural progenitor cell communities during neural differentiation, 2) identifying communities of pain-sensing neurons in vivo, 3) capturing the effect of cell community on endothelial cell morphology, and 4) investigating the effect of laminin α4 on perivascular niches in adipose tissue. The analytical framework introduced here can be used to study the dynamics of complex cell communities in a quantitative manner, leading to a deeper understanding of environmental effects on cellular behavior. The versatile, cloud-based format of cytoNet makes the image analysis framework accessible to researchers across domains.

关键词： Calcium imaging Fluorescence imaging Growth factors Centrality Cell cycle and cell division Endothelial cells Network analysis Stem cells

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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.

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programmable threshold sensing in wireless devices using Ising dynamics

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Nature Electronics 2025年 1-8页

作者： Nicolas Casilli Hussein M. E. Hussein Ryan Tetro Luca Colombo Matteo Rinaldi Cristian Cassella Seunghwi Kim Andrea Alù Philip X.-L. Feng Institute for Nano Systems Innovation (NanoSI) Department of Electrical and Computer Engineering Northeastern University Boston MA USA Photonics Initiative Advanced Science Research Center City University of New York New York City NY USA Physics Program Graduate Center City University of New York New York City NY USA Department of Electrical and Computer Engineering University of Florida Gainesville FL USA

Ising machines—comprising dissipatively coupled nodes capable of emulating the behaviour of ferromagnetic spins—can form analogue computing engines that surpass the sequential processing constraints of von Neumann architectures. However, the incorporation of Ising dynamics into radio-frequency wireless technologies remains limited, especially in terms of their potential to enhance wireless sensing capabilities. Here we report a passive wireless sensor that uses Ising dynamics to accurately implement threshold sensing. The device correlates the occurrence of violations in a sensed parameter with transitions in the coupling state of two parametric oscillators acting as Ising spins. As a result, the accuracy of the device is unaffected by distortions in its input and output signals due to multipath and is less prone to clutter caused by co-site interference. We illustrate the potential of the approach in temperature threshold sensing using a microfabricated lithium niobate microelectromechanical temperature sensor to couple two radio-frequency parametric oscillators, and show that such a system allows the sensor threshold to be wirelessly reprogrammed.

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Radar Occupancy Prediction with Lidar Supervision while Preserving Long-Range Sensing and Penetrating Capabilities

arXiv

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arXiv 2021年

作者： Kung, Pou-Chun Wang, Chieh-Chih Lin, Wen-Chieh The Graduate Degree Program of Robotics National Yang Ming Chiao Tung University Hsinchu Taiwan The Department of Electrical and Computer Engineering National Yang Ming Chiao Tung University Taiwan The Mechanical and Mechatronics Systems Research Laboratories Industrial Technology Research Institute Hsinchu Taiwan The Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan

Radar shows great potential for autonomous driving by accomplishing long-range sensing under diverse weather conditions. But radar is also a particularly challenging sensing modality due to the radar noises. Recent works have made enormous progress in classifying free and occupied spaces in radar images by leveraging lidar label supervision. However, there are still several unsolved issues. Firstly, the sensing distance of the results is limited by the sensing range of lidar. Secondly, the performance of the results is degenerated by lidar due to the physical sensing discrepancies between the two sensors. For example, some objects visible to lidar are invisible to radar, and some objects occluded in lidar scans are visible in radar images because of the radar's penetrating capability. These sensing differences cause false positive and penetrating capability degeneration, respectively. In this paper, we propose training data preprocessing and polar sliding window inference to solve the issues. The data preprocessing aims to reduce the effect caused by radar-invisible measurements in lidar scans. The polar sliding window inference aims to solve the limited sensing range issue by applying a near-range trained network to the long-range region. Instead of using common Cartesian representation, we propose to use polar representation to reduce the shape dissimilarity between long-range and near-range data. We find that extending a near-range trained network to long-range region inference in the polar space has 4.2 times better IoU than in Cartesian space. Besides, the polar sliding window inference can preserve the radar penetrating capability by changing the viewpoint of the inference region, which makes some occluded measurements seem non-occluded for a pretrained network. Copyright © 2021, The Authors. All rights reserved.

关键词： Optical radar

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Accurately predicting anticancer peptide using an ensemble of heterogeneously trained classifiers

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Informatics in Medicine Unlocked 2023年 42卷

作者： Azim, Sayed Mehedi Sabab, Noor Hossain Nuri Noshadi, Iman Alinejad-Rokny, Hamid Sharma, Alok Shatabda, Swakkhar Dehzangi, Iman Center for Computational and Integrative Biology Rutgers University Camden 08102 NJ United States Department of Computer Science and Engineering United International University Plot 2 United City Madani Avenue BaddaDhaka 1212 Bangladesh Department of Bioengineering University of California Riverside 92507 CA United States BioMedical Machine Learning Lab The Graduate School of Biomedical Engineering The University of New South Wales (UNSW Sydney) Sydney NSW 2052 Australia UNSW Data Science Hub UNSW Sydney Sydney NSW 2052 Australia Health Data Analytics Program AI-enabled Processes Research Centre Macquarie University Sydney 2109 Australia Institute for Integrated and Intelligent Systems Griffith University Brisbane Australia Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama 230-0045 Japan Department of Computer Science Rutgers University Camden 08102 NJ United States

The use of therapeutic peptides for the treatment of cancer has received tremendous attention in recent years. Anticancer peptides (ACPs) are considered new anticancer drugs which have several advantages over chemistry-based drugs including high specificity, strong tumor penetration capacity, and low toxicity level for normal cells. Due to the rise of experimentally verified bioactive peptides, several in silico approaches became imperative for the investigation of the characteristics of ACPs. In this paper, we proposed a new machine learning tool named iACP-RF that uses a combination of several sequence-based features and an ensemble of three heterogeneously trained Random Forest classifiers to accurately predict anticancer peptides. Experimental results show that our proposed model achieves an accuracy of 75.9% which outperforms other state-of-the-art methods by a significant margin. We also achieve 0.52, 75.6%, and 76.2% in terms of Matthews Correlation Coefficient (MCC), Sensitivity, and Specificity, respectively. iACP-RF as a standalone tool and its source code are publicly available at: https://***/MLBC-lab/iACP-RF. © 2023 The Authors

关键词： Anticancer peptides Ensemble learning Feature extraction Heterogeneous classifiers Machine learning Random Forest

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