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GWAS identifies candidate genes controlling adventitious rooting in Populus trichocarpa

Horticulture research 2023年第8期10卷 97-108页

作者： Michael F.Nagle Jialin Yuan Damanpreet Kaur Cathleen Ma Ekaterina Peremyslova Yuan Jiang Bahiya Zahl Alexa Niño de Rivera Wellington Muchero Li Fuxin Steven H.Strauss Department of Forest Ecosystems and Society Oregon State University3180 SW Jefferson WayCorvallisOR97331United States Department of Electrical Engineering and Computer Science Oregon State University110 SW Park TerraceCorvallisOR97331United States Statistics Department Oregon State University103 SW Memorial PlaceCorvallisOR97331United States Biosciences Division Oak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830United States Center for Bioenergy Innovation Oak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37830United States Bredesen Center for Interdisciplinary Research University of Tennessee821 Volunteer Blvd.KnoxvilleTN37996United States

Adventitious rooting(AR)is critical to the propagation,breeding,and genetic engineering of *** capacity for plants to undergo this process is highly heritable and of a polygenic nature;however,the basis of its genetic variation is largely *** identify genetic regulators of AR,we performed a genome-wide association study(GWAS)using 1148 genotypes of Populus *** are often limited by the abilities of researchers to collect precise phenotype data on a high-throughput scale;to help overcome this limitation,we developed a computer vision system to measure an array of traits related to adventitious root development in poplar,including temporal measures of lateral and basal root length and *** was performed using multiple methods and significance thresholds to handle non-normal phenotype statistics and to gain statistical *** analyses yielded a total of 277 unique associations,suggesting that genes that control rooting include regulators of hormone signaling,cell division and structure,reactive oxygen species signaling,and other processes with known roles in root *** genes with uncharacterized functions and/or cryptic roles were also *** candidates provide targets for functional analysis,including physiological and epistatic analyses,to better characterize the complex polygenic regulation of AR.

关键词： GWAS breeding overcome

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Organ Segmentation with Recursive Data Augmentation for Deep Models 25th

Organ Segmentation with Recursive Data Augmentation for Deep...

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25th International Conference on Pattern Recognition Workshops, ICPR 2020

作者： Akbar, Muhammad Usman Yamin, Muhammad Abubakar Murino, Vittorio Sona, Diego Pattern Analysis and Computer Vision Istituto Italiano di Tecnologia Genova Italy Department of Electrical Electronics and Telecommunication Engineering Università di Genova Genova Italy Huawei Technologies Ltd. Ireland Research Center Dublin Ireland Department of Computer Science Università di Verona Verona Italy Neuroinformatics Laboratory Fondazione Bruno Kessler Trento Italy

ISBN: (纸本)9783030687625

The precise segmentation of organs from computed tomography is a fundamental and pivotal task for correct diagnosis and proper treatment of diseases. Neural network models are widely explored for their promising performance in the segmentation of medical images. However, the small dimension of available datasets is affecting the biomedical imaging domain significantly and has a huge impact in training of deep learning models. In this paper we try to address this issue by iteratively augmenting the dataset with auxiliary task-based information. This is obtained by introducing a recursive training approach, where a new set of segmented images is generated at each iteration and then concatenated with the original input data as organ attention maps. In the experimental evaluation two different datasets were tested and the results produced from the proposed approach have shown significant improvements in organ segmentation as compared to a standard non-recursive approach. © 2021, Springer Nature Switzerland AG.

关键词： Deep learning

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Screening cognitive impairment in patients with atrial fibrillation: A deep learning model based on retinal fundus photographs

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Heart Rhythm O2 2025年第5期6卷 678.0-686.0页

作者： Wang, Zhen Li, Mingxiao Xia, Peng Jiang, Chao Shen, Ting Ma, Jiaming Bai, Yu Zhang, Suhui Lai, Yiwei Li, Sitong Xu, Hui Xu, Yang Ma, Tong Ju, Lie He, Liu Dong, Li Sang, Caihua Long, Deyong Chen, Yuzhong Du, Xin Ge, Zongyuan Dong, Jianzeng Wei, Wen-Bin Ma, Changsheng Department of Cardiology Beijing Anzhen Hospital Capital Medical University Beijing China Engineering Research Center of Medical Devices for Cardiovascular Diseases Ministry of Education Capital Medical University Beijing China National Clinical Research Center for Cardiovascular Diseases Beijing China Beijing Airdoc Technology Co. Ltd. Beijing China Department of Electrical and Computer Systems Engineering Faculty of Engineering Monash University Clayton Australia Yale School of Medicine New Haven Connecticut United States School of Clinical Medicine Peking Union Medical College and Chinese Academy of Medical Science Beijing China Beijing Tongren Eye Center Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment Beijing Ophthalmology & Visual Sciences Key Lab Medical Artificial Intelligence Research and Verification Key Laboratory of the Ministry of Industry and Information Technology Beijing Tongren Hospital Capital Medical University Beijing China Monash e-Research Center Monash University Clayton Australia

Background: Patients with atrial fibrillation (AF) have a higher risk of cognitive impairment (CI). However, complexity of CI diagnosis and lack of simple screening approaches limited early screening and intervention of CI in AF patients. Objective: Our study aimed to develop deep learning models based on fundus photographs for easy screening of CI in AF patients. Methods: From May 2021 to April 2023, patients who completed fundus examination and cognitive function evaluation in the Chinese Atrial Fibrillation Registry Study were included. The training and validation sets were randomly split at an 8:2 ratio. Participants from the Beijing Eye Study served as the external validation set. Different deep learning models were trained, and their CI detection ability was validated. Results: A total of 899 patients in the Chinese Atrial Fibrillation Registry Study were included. In the validation set, the vision-ensemble model based on fundus images alone had an area under the receiver-operating characteristic curve (AUROC) of 0.855 (95% confidence interval 0.816–0.894) for CI screening. The multimodal model (AUROC 0.861, 95% confidence interval 0.823–0.898), based on fundus photographs and 4 clinical variables, performed comparably to the vision-ensemble model. The AUROC of the vision-ensemble model for CI screening achieved 0.773 (95% confidence interval 0.709–0.837) in the external test set. In the saliency map, the vision-ensemble model focused on areas around retinal vessels and the optic disc. Conclusion: A vision-ensemble model based on fundus images might be practical for preliminary screening of CI in AF patients. © 2025 Heart Rhythm Society

关键词： Artificial intelligence Atrial fibrillation Cognitive impairment Deep learning Fundus photography

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Imitating dolphins: Nature-inspired boundary modulation to reduce frictional drag

Imitating dolphins: Nature-inspired boundary modulation to r...

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International Symposium on Underwater Technology

作者： Silvia Matt Hongyang Shi Xiaobo Tan Austin Thombs Weilin Hou Ocean Sciences Division US Naval Research Laboratory Stennis Space Center USA Department of Electrical & Computer Engineering Michigan State University East Lansing USA Asia Pacific Office of Naval Research Global Singapore

In recent years, there has been a renewed interest in mechanisms of flow and turbulence control inspired by aquatic animals. This includes passive mechanisms such as the boundary roughness changes found on shark skin, as well as active boundary modulation, inspired by the viscoelastic properties of dolphin skin. In this work, we present a novel device to control boundary morphology and impact near-boundary flow. We developed this device as a 5-by-5 actuator array, using voice coil motors, and implemented it in the wall of a laminar-to-turbulent flow channel. The actuators are overlaid by a flexible membrane and embedded in the wall of the channel. Each actuator can be controlled individually, and the system can generate wave patterns on the boundary along or across the flow direction. The boundary deformation patterns were quantified using a computer vision approach. The system was tested to assess its impact on near-boundary velocity and turbulence. A DPIV (Digital Particle Image Velocimetry) system was used to quantify velocity fields. Velocity decomposition showed that boundary actuation impacts the mean boundary layer velocity profile. The impact on near-boundary velocity was found to be consistent with a reduction in frictional drag. A numerical tank was set up using Computational Fluid Dynamics, and the results from the model support the laboratory findings. To our knowledge, this is the first such device allowing boundary modulation using individual actuator control that has been implemented and tested in direct contact with water with the impact on flow assessed. A successful implementation of such a device in a natural underwater environment could lead to wide-ranging benefits including increased platform energy-efficiency and reduction of flow-induced noise.

关键词： Actuators Deformation Drag Modulation Morphology Skin Energy efficiency

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CLASSIFICATION OF LUNG CANCER SUBTYPES ON CT IMAGES WITH SYNTHETIC PATHOLOGICAL PRIORS

arXiv

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arXiv 2023年

作者： Zhu, Wentao Jin, Yuan Ma, Gege Chen, Geng Egger, Jan Zhang, Shaoting Metaxas, Dimitris N. Research Center for Healthcare Data Science Zhejiang Lab Hangzhou311121 China School of Computer Science and Engineering Northwestern Polytechnical University Shaanxi Xi’an710072 China Institute of Computer Graphics and Vision Graz University of Technology Graz8010 Austria Shanghai Artificial Intelligence Laboratory Shanghai200120 China Department of Computer Science Rutgers University PiscatawayNJ08854 United States

The accurate diagnosis on pathological subtypes for lung cancer is of significant importance for the follow-up treatments and prognosis managements. In this paper, we propose self-generating hybrid feature network (SGHF-Net) for accurately classifying lung cancer subtypes on computed tomography (CT) images. Inspired by studies stating that cross-scale associations exist in the image patterns between the same case’s CT images and its pathological images, we innovatively developed a pathological feature synthetic module (PFSM), which quantitatively maps cross-modality associations through deep neural networks, to derive the "gold standard" information contained in the corresponding pathological images from CT images. Additionally, we designed a radiological feature extraction module (RFEM) to directly acquire CT image information and integrated it with the pathological priors under an effective feature fusion framework, enabling the entire classification model to generate more indicative and specific pathologically related features and eventually output more accurate predictions. The superiority of the proposed model lies in its ability to self-generate hybrid features that contain multi-modality image information based on a single-modality input. To evaluate the effectiveness, adaptability, and generalization ability of our model, we performed extensive experiments on a large-scale multi-center dataset (i.e., 829 cases from three hospitals) to compare our model and a series of state-of-the-art (SOTA) classification models. The experimental results demonstrated the superiority of our model for lung cancer subtypes classification with significant accuracy improvements in terms of accuracy (ACC), area under the curve (AUC), and F1 score. © 2023, CC0.

关键词： Classification (of information)

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Robin: A Novel Method to Produce Robust Interpreters for Deep Learning-Based Code Classifiers

Robin: A Novel Method to Produce Robust Interpreters for Dee...

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IEEE International Conference on Automated Software engineering (ASE)

作者： Zhen Li Ruqian Zhang Deqing Zou Ning Wang Yating Li Shouhuai Xu Chen Chen Hai Jin School of Cyber Science and Engineering Huazhong University of Science and Technology Wuhan China Services Computing Technology and System Lab Hubei Key Laboratory of Distributed System Security Cluster and Grid Computing Lab National Engineering Research Center for Big Data Technology and System Hubei Engineering Research Center on Big Data Security Department of Computer Science University of Colorado Colorado Springs USA Center for Research in Computer Vision University of Central Florida USA School of Computer Science and Technology Huazhong University of Science and Technology Wuhan China

Deep learning has been widely used in source code classification tasks, such as code classification according to their functionalities, code authorship attribution, and vulnerability detection. Unfortunately, the black-box nature of deep learning makes it hard to interpret and understand why a classifier (i.e., classification model) makes a particular prediction on a given example. This lack of interpretability (or explainability) might have hindered their adoption by practitioners because it is not clear when they should or should not trust a classifier's prediction. The lack of interpretability has motivated a number of studies in recent years. However, existing methods are neither robust nor able to cope with out-of-distribution examples. In this paper, we propose a novel method to produce Robust interpreters for a given deep learning-based code classifier; the method is dubbed Robin. The key idea behind Robin is a novel hybrid structure combining an interpreter and two approximators, while leveraging the ideas of adversarial training and data augmentation. Experimental results show that on average the interpreter produced by Robin achieves a 6.11% higher fidelity (evaluated on the classifier), 67.22% higher fidelity (evaluated on the approximator), and 15.87x higher robustness than that of the three existing interpreters we evaluated. Moreover, the interpreter is 47.31% less affected by out-of-distribution examples than that of LEMNA.

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An Effective Scheme for Maize Disease Recognition based on Deep Networks

arXiv

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arXiv 2022年

作者： Osouli, Saeedeh Haghighi, Behrouz Bolourian Sadrossadat, Ehsan Electrical Engineering Department Ferdowsi University of Mashhad Mashhad Iran Computer Engineering Department Ferdowsi University of Mashhad Mashhad Iran Machine Vision Laboratory Ferdowsi University of Mashhad Mashhad Iran School of Engineering University of Western Australia Perth Australia

In the last decades, the area under cultivation of maize products has increased because of its essential role in the food cycle for humans, livestock, and poultry. Moreover, the diseases of plants impact food safety and can significantly reduce both the quality and quantity of agricultural products. There are many challenges to accurate and timely diagnosis of the disease. This research presents a novel scheme based on a deep neural network to overcome the mentioned challenges. Due to the limited number of data, the transfer learning technique is employed with the help of two well-known architectures. In this way, a new effective model is adopted by a combination of pre-trained MobileNetV2 and Inception Networks due to their effective performance on object detection problems. The convolution layers of MoblieNetV2 and Inception modules are parallelly arranged as earlier layers to extract crucial features. In addition, the imbalance problem of classes has been solved by an augmentation strategy. The proposed scheme has a superior performance compared to other state-of-the-art models published in recent years. The accuracy of the model reaches 97%, approximately. In summary, experimental results prove the method's validity and significant performance in diagnosing disease in plant leaves. Copyright © 2022, The Authors. All rights reserved.

关键词： Image classification

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Lightweight Deep Learning for Resource-Constrained Environments: A Survey

arXiv

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arXiv 2024年

作者： Liu, Hou-I Galindo, Marco Xie, Hongxia Wong, Lai-Kuan Shuai, Hong-Han Li, Yung-Yui Cheng, Wen-Huang Department of Electronics and Electrical Engineering National Yang Ming Chiao Tung University Hsinchu300 Taiwan College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun130000 China Faculty of Computing and Informatics Multimedia University Cyberjaya63100 Malaysia Hon Hai Research Institute Taipei114 Taiwan Department of Computer Science and Information Engineering National Taiwan University Taipei106 Taiwan

Over the past decade, the dominance of deep learning has prevailed across various domains of artificial intelligence, including natural language processing, computer vision, and biomedical signal processing. While there have been remarkable improvements in model accuracy, deploying these models on lightweight devices, such as mobile phones and microcontrollers, is constrained by limited resources. In this survey, we provide comprehensive design guidance tailored for these devices, detailing the meticulous design of lightweight models, compression methods, and hardware acceleration strategies. The principal goal of this work is to explore methods and concepts for getting around hardware constraints without compromising the model's accuracy. Additionally, we explore two notable paths for lightweight deep learning in the future: deployment techniques for TinyML and Large Language Models. Although these paths undoubtedly have potential, they also present significant challenges, encouraging research into unexplored areas. Copyright © 2024, The Authors. All rights reserved.

关键词： computer hardware

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Open-Vocabulary Audio-Visual Semantic Segmentation

arXiv

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arXiv 2024年

作者： Guo, Ruohao Qu, Liao Niu, Dantong Qi, Yanyu Yue, Wenzhen Shi, Ji Xing, Bowei Ying, Xianghua National Key Laboratory of General Artificial Intelligence School of Intelligence Science and Technology Peking University Beijing China Department of Electrical and Computer Engineering Carnegie Mellon University PittsburghPA United States Berkeley AI Research University of California Berkeley BerkeleyCA United States College of Information and Electrical Engineering China Agricultural University Beijing China

Audio-visual semantic segmentation (AVSS) aims to segment and classify sounding objects in videos with acoustic cues. However, most approaches operate on the close-set assumption and only identify pre-defined categories from training data, lacking the generalization ability to detect novel categories in practical applications. In this paper, we introduce a new task: open-vocabulary audio-visual semantic segmentation, extending AVSS task to open-world scenarios beyond the annotated label space. This is a more challenging task that requires recognizing all categories, even those that have never been seen nor heard during training. Moreover, we propose the first open-vocabulary AVSS framework, OV-AVSS, which mainly consists of two parts: 1) a universal sound source localization module to perform audio-visual fusion and locate all potential sounding objects and 2) an open-vocabulary classification module to predict categories with the help of the prior knowledge from large-scale pre-trained vision-language models. To properly evaluate the open-vocabulary AVSS, we split zero-shot training and testing subsets based on the AVSBench-semantic benchmark, namely AVSBench-OV. Extensive experiments demonstrate the strong segmentation and zero-shot generalization ability of our model on all categories. On the AVSBench-OV dataset, OV-AVSS achieves 55.43% mIoU on base categories and 29.14% mIoU on novel categories, exceeding the state-of-the-art zero-shot method by 41.88%/20.61% and open-vocabulary method by 10.2%/11.6%. The code is available at https://***/ruohaoguo/ovavss. © 2024, CC BY-NC-SA.

关键词： Semantic Segmentation

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Tunable unidirectional surface plasmon-polaritons at the interface between gyrotropic and isotropic conductors 22

Tunable unidirectional surface plasmon-polaritons at the int...

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22nd International Conference on Electromagnetics in Advanced Applications, ICEAA 2021

作者： Liang, Y. Pakniyat, S. Xiang, Y. Chen, J. Shi, F. Hanson, G.W. Cen, C. West Virginia University Department of Physics and Astronomy MorgantownWV26506 United States University of Wisconsin-Milwaukee Department of Electrical Engineering MilwaukeeWI53211 United States University of Pittsburgh Peterson Institute of Nano Science and Engineering Department of Electrical and Computer Engineering PittsburghPA15261 United States Guangxi Key Lab for Relativistic Astrophysics Center on Nanoenergy Research School of Physical Science and Technology Guangxi University Nanning Guangxi530004 China Key Laboratory of Computer Vision and System of Ministry of Education Tianjin University of Technology Tianjin300384 China

ISBN: (纸本)9781665413862

The propagation of SPPs in solid state systems is usually reciprocal, which means that a forward-traveling SPP wave can be easily backscattered by disorders. Since such backscattering is detrimental for SPP-based information processing applications, the development of nonreciprocal plasmonic platforms that enforce unidirectional SPP propagations is of great importance. © 2021 IEEE.

关键词： Electromagnetic wave polarization

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