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Pan-omics-based characterization and prediction of highly multidrugadapted strains from an outbreak fungal species complex

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The Innovation 2024年第5期5卷 101-109,100页

作者： Xin Fan Lei Chen Min Chen Na Zhang Hong Chang Mingjie He Zhenghao Shen Lanyue Zhang Hao Ding Yuyan Xie Yemei Huang Weixin Ke Meng Xiao Xuelei Zang Heping Xu Wenxia Fang Shaojie Li Cunwei Cao Yingchun Xu Shiguang Shan Wenjuan Wu Changbin Chen Xinying Xue Linqi Wang Department of Infectious Diseases and Clinical Microbiology Beijing Institute of Respiratory Medicine and Beijing Chao-Yang HospitalCapital Medical UniversityBeijing 100020China Beijing Research Center for Respiratory Infectious Diseases Beijing 100020China State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Department of Dermatology Shanghai Key Laboratory of Molecular Medical MycologyChangzheng HospitalShanghai 200003China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Department of Respiratory and Critical Care Emergency and Critical Care Medical CenterBeijing Shijitan HospitalCapital Medical UniversityBeijing 100038China Department of Laboratory Medicine State Key Laboratory of Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical SciencesBeijing 100730China Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases Beijing 100730China Department of Clinical Laboratory First Affiliated Hospital of Xiamen UniversityXiamen 361003China Institute of Biological Science and Technology Guangxi Academy of SciencesNanning 530007China Department of Dermatology The First Affiliated Hospital of Guangxi Medical UniversityNanning 530021China Guangxi Key Laboratory of Mycosis Prevention and Treatment Nanning 530021China Department of Laboratory Medicine Shanghai East HospitalTongji University School of MedicineShanghai 200120China The Unit of Pathogenic Fungal Infection&Host Immunity Shanghai Institute of Immunity and InfectionChinese Academy of SciencesShanghai 200031China Nanjing Advanced Academy of Life and Health Nanjing 211135China Department of Respiratory and Critical Care Shandong Second Medical UniversityWeifang 261035China

Strains from the Cryptococcus gattii species complex(CGSC)have caused the Pacific Northwest cryptococcosis outbreak,the largest cluster of lifethreatening fungal infections in otherwise healthy human hosts known to *** this study,we utilized a pan-phenome-based method to assess the fitness outcomes of CGSC strains under 31 stress conditions,providing a comprehensive overview of 2,821 phenotype-strain associations within this pathogenic *** clustering analysis revealed a strong correlation between distinct types of stress phenotypes in a subset of CGSC strains,suggesting that shared determinants coordinate their adaptations to various ***,a specific group of strains,including the outbreak isolates,exhibited a remarkable ability to adapt to all three of the most commonly used antifungal drugs for treating cryptococcosis(amphotericin B,5-fluorocytosine,and fluconazole).By integrating pan-genomic and pan-transcriptomic analyses,we identified previously unrecognized genes that play crucial roles in conferring multidrug resistance in an outbreak strain with high multidrug *** these genes,we identified biomarkers that enable the accurate prediction of highly multidrug-adapted CGSC strains,achieving maximum accuracy and area under the curve(AUC)of 0.79 and 0.86,respectively,using machine learning ***,we developed a pan-omic approach to identify cryptococcal multidrug resistance determinants and predict highly multidrug-adapted CGSC strains that may pose significant clinical concern.

关键词： multidrug adapted prediction

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Visual Alignment Constraint for Continuous Sign Language Recognition

Visual Alignment Constraint for Continuous Sign Language Rec...

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International Conference on Computer Vision (ICCV)

作者： Yuecong Min Aiming Hao Xiujuan Chai Xilin Chen Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS) Institute of Computing Technology CAS Beijing China University of Chinese Academy of Sciences Beijing China Agricultural Information Institute Chinese Academy of Agricultural Sciences Beijing China

ISBN: (纸本)9781665428132

Vision-based Continuous Sign Language Recognition (CSLR) aims to recognize unsegmented signs from image streams. Overfitting is one of the most critical problems in CSLR training, and previous works show that the iterative training scheme can partially solve this problem while also costing more training time. In this study, we revisit the iterative training scheme in recent CSLR works and realize that sufficient training of the feature extractor is critical to solving the overfitting problem. Therefore, we propose a Visual Alignment Constraint (VAC) to enhance the feature extractor with alignment supervision. Specifically, the proposed VAC comprises two auxiliary losses: one focuses on visual features only, and the other enforces prediction alignment between the feature extractor and the alignment module. Moreover, we propose two metrics to reflect overfitting by measuring the prediction inconsistency between the feature extractor and the alignment module. Experimental results on two challenging CSLR datasets show that the proposed VAC makes CSLR networks end-to-end trainable and achieves competitive performance.

关键词： Training Measurement Visualization Image recognition Costing Gesture recognition Assistive technologies

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CRSOT: Cross-Resolution Object Tracking using Unaligned Frame and Event Cameras

arXiv

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arXiv 2024年

作者： Zhu, Yabin Wang, Xiao Li, Chenglong Jiang, Bo Zhu, Lin Huang, Zhixiang Tian, Yonghong Tang, Jin Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui University China School of Computer Science and Technology Anhui University China School of Artificial Intelligence Anhui University China Beijing Institute of Technology Beijing China School of Electronic and Information Engineering Anhui University China Peng Cheng Laboratory Shenzhen China School of Computer Science Peking University Beijing China School of Electronic and Computer Engineering Peking University Shenzhen China

Existing datasets for RGB-DVS tracking are collected with DVS346 camera and their resolution (346 × 260) is low for practical applications. Actually, only visible cameras are deployed in many practical systems, and the newly designed neuromorphic cameras may have different resolutions. The latest neuromorphic sensors can output high-definition event streams, but it is very difficult to achieve strict alignment between events and frames on both spatial and temporal views. Therefore, how to achieve accurate tracking with unaligned neuromorphic and visible sensors is a valuable but unresearched problem. In this work, we formally propose the task of object tracking using unaligned neuromorphic and visible cameras. We build the first unaligned frame-event dataset CRSOT collected with a specially built data acquisition system, which contains 1,030 high-definition RGB-Event video pairs, 304,974 video frames. In addition, we propose a novel unaligned object tracking framework that can realize robust tracking even using the loosely aligned RGB-Event data. Specifically, we extract the template and search regions of RGB and Event data and feed them into a unified ViT backbone for feature embedding. Then, we propose uncertainty perception modules to encode the RGB and Event features, respectively, then, we propose a modality uncertainty fusion module to aggregate the two modalities. These three branches are jointly optimized in the training phase. Extensive experiments demonstrate that our tracker can collab.rate the dual modalities for high-performance track- Copyright © 2024, The Authors. All rights reserved.

关键词： Cameras

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Subspace Aggregation Query and Index Generation for Multidimensional Resource Space Model

arXiv

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arXiv 2025年

作者： Sun, Xiaoping Zhuge, Hai Lab of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China Great Bay University Great Bay Institute for Advanced Study Guangdong Dongguan China

Organizing resources in a multidimensional classification space is an approach to efficiently managing and querying large-scale resources. This paper defines an aggregation query on subspace defined by a range on the partial order on coordinate tree at each dimension, where each point contains resources aggregated along the paths of partial order relations on the points so that aggregated resources at each point within the subspace can be measured, ranked and selected. To efficiently locate non-empty points in a large subspace, an approach to generating graph index is proposed to build inclusion links with partial order relations on coordinates of dimensions to enable a subspace query to reach non-empty points by following indexing links and aggregate resources along indexing paths back to their super points. Generating such an index is costly as the number of children of an index node can be very large so that the total number of indexing nodes is unbounded. The proposed approach adopts the following strategies to reduce the cost: (1) adding intersection links between two indexing nodes, which can better reduce query processing costs while controlling the number of nodes of the graph index;(2) intersection links are added between two nodes according to the probabilistic distribution calculated for estimating the costs of adding intersection between two nodes;(3) coordinates at one dimension having more resources are split by coordinates at another dimension to balance the number of resources hold by indexing nodes;and, (4) short-cut links are added between sibling coordinates of coordinate trees to make an efficient query on linear order coordinates. Analysis and experiments verified the effectiveness of the generated index in supporting subspace aggregation query. This work makes significant contributions to the development of data model based on multi-dimensional classification. © 2025, CC BY.

关键词： Indexing (materials working)

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Iterative network pruning with uncertainty regularization for lifelong sentiment classification

arXiv

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arXiv 2021年

作者： Geng, Binzong Yang, Min Yuan, Fajie Wang, Shupeng Ao, Xiang Xu, Ruifeng University of Science and Technology of China China Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Westlake University Key Lab of Intelligent Information Processing Chinese Academy of Sciences Institute of Computing Technology CAS Harbin Institute of Technology Shenzhen China Tencent

Lifelong learning capabilities are crucial for sentiment classifiers to process continuous streams of opinioned information on the Web. However, performing lifelong learning is non-trivial for deep neural networks as continually training of incrementally availab.e information inevitably results in catastrophic forgetting or interference. In this paper, we propose a novel iterative network pruning with uncertainty regularization method for lifelong sentiment classification (IPRLS), which leverages the principles of network pruning and weight regularization. By performing network pruning with uncertainty regularization in an iterative manner, IPRLS can adapt a single BERT model to work with continuously arriving data from multiple domains while avoiding catastrophic forgetting and interference. Specifically, we leverage an iterative pruning method to remove redundant parameters in large deep networks so that the freed-up space can then be employed to learn new tasks, tackling the catastrophic forgetting problem. Instead of keeping the old-tasks fixed when learning new tasks, we also use an uncertainty regularization based on the Bayesian online learning framework to constrain the update of old tasks weights in BERT, which enables positive backward transfer, i.e. learning new tasks improves performance on past tasks while protecting old knowledge from being lost. In addition, we propose a task-specific low-dimensional residual function in parallel to each layer of BERT, which makes IPRLS less prone to losing the knowledge saved in the base BERT network when learning a new task. Extensive experiments on 16 popular review corpora demonstrate that the proposed IPRLS method significantly outperforms the strong baselines for lifelong sentiment classification. For reproducibility, we submit the code and data at: https://***/siat-nlp/IPRLS. Copyright © 2021, The Authors. All rights reserved.

关键词： Deep neural networks

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ER: Equivariance Regularizer for Knowledge Graph Completion

arXiv

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arXiv 2022年

作者： Cao, Zongsheng Xu, Qianqian Yang, Zhiyong Huang, Qingming State Key Laboratory of Information Security Institute of Information Engineering CAS Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Intelligent Information Processing Institute of Computing Technology CAS Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China Peng Cheng Laboratory Shenzhen China

Tensor factorization and distanced based models play important roles in knowledge graph completion (KGC). However, the relational matrices in KGC methods often induce a high model complexity, bearing a high risk of overfitting. As a remedy, researchers propose a variety of different regularizers such as the tensor nuclear norm regularizer. Our motivation is based on the observation that the previous work only focuses on the "size" of the parametric space, while leaving the implicit semantic information widely untouched. To address this issue, we propose a new regularizer, namely, Equivariance Regularizer (ER), which can suppress overfitting by leveraging the implicit semantic information. Specifically, ER can enhance the generalization ability of the model by employing the semantic equivariance between the head and tail entities. Moreover, it is a generic solution for both distance based models and tensor factorization based models. The experimental results indicate a clear and substantial improvement over the state-of-the-art relation prediction methods. © 2022, CC BY.

关键词： Knowledge graph

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Geometry Interaction Knowledge Graph Embeddings

arXiv

引用

arXiv 2022年

作者： Cao, Zongsheng Xu, Qianqian Yang, Zhiyong Cao, Xiaochun Huang, Qingming State Key Laboratory of Information Security Institute of Information Engineering CAS Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Intelligent Information Processing Institute of Computing Technology CAS Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China Peng Cheng Laboratory Shenzhen China

Knowledge graph (KG) embeddings have shown great power in learning representations of entities and relations for link prediction tasks. Previous work usually embeds KGs into a single geometric space such as Euclidean space (zero curved), hyperbolic space (negatively curved) or hyperspherical space (positively curved) to maintain their specific geometric structures (e.g., chain, hierarchy and ring structures). However, the topological structure of KGs appears to be complicated, since it may contain multiple types of geometric structures simultaneously. Therefore, embedding KGs in a single space, no matter the Euclidean space, hyperbolic space or hyperspheric space, cannot capture the complex structures of KGs accurately. To overcome this challenge, we propose Geometry Interaction knowledge graph Embeddings (GIE), which learns spatial structures interactively between the Euclidean, hyperbolic and hyperspherical spaces. Theoretically, our proposed GIE can capture a richer set of relational information, model key inference patterns, and enable expressive semantic matching across entities. Experimental results on three well-established knowledge graph completion benchmarks show that our GIE achieves the state-of-the-art performance with fewer parameters. © 2022, CC BY.

关键词： Knowledge graph

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LIMOT: A Tightly-Coupled System for LiDAR-Inertial Odometry and Multi-Object Tracking

arXiv

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arXiv 2023年

作者： Zhu, Zhongyang Zhao, Junqiao Huang, Kai Tian, Xuebo Lin, Jiaye Ye, Chen Department of Computer Science and Technology School of Electronics and Information Engineering Tongji University Shanghai China The MOE Key Lab of Embedded System and Service Computing Tongji University Shanghai China Institute of Intelligent Vehicles Tongji University Shanghai China The School of Surveying and Geo-Informatics Tongji University Shanghai China

Simultaneous localization and mapping (SLAM) is critical to the implementation of autonomous driving. Most LiDAR-inertial SLAM algorithms assume a static environment, leading to unreliable localization in dynamic environments. Moreover, the accurate tracking of moving objects is of great significance for the control and planning of autonomous vehicles. This study proposes LIMOT, a tightly-coupled multi-object tracking and LiDAR-inertial odometry system that is capable of accurately estimating the poses of both ego-vehicle and objects. We propose a trajectory-based dynamic feature filtering method, which filters out features belonging to moving objects by leveraging tracking results before scan-matching. Factor graph-based optimization is then conducted to optimize the bias of the IMU and the poses of both the ego-vehicle and surrounding objects in a sliding window. Experiments conducted on the KITTI tracking dataset and self-collected dataset show that our method achieves better pose and tracking accuracy than our previous work DL-SLOT and other baseline methods. Our open-source implementation is availab.e at https://***/tiev-tongji/LIMOT. Copyright © 2023, The Authors. All rights reserved.

关键词： Autonomous vehicles

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Static Gesture Recognition and Distance Estimation Using a Capacitive Proximity Sensor Array

SSRN

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SSRN 2023年

作者： Ye, Yong Liu, Yuting Du, Chunhui Deng, Jiahao Qiu, Chenguang School of Electronics and Information Engineering The Information Materials and Intelligent Sensing Laboratory of Anhui Province The Key Laboratory of Intelligent Computing & Signal Processing Ministry of Education The Key Laboratory of Electromagnetic Environmental Sensing of Anhui Higher Education Institutes Anhui University No. 111 Jiulong Road Anhui Province Hefei230601 China Institute of high energy physics Chinese academy of sciences The School of Mechatronical Engineering Beijing Institute of Technology Beijing100081 China Tai Yuan institute Co. Ltd. of China coal technology and engineering group Shanxi Province Taiyuan030006 China East China Institute of Photo-Electronic IC Jiangsu Province Suzhou215163 China

In this paper, we present a capacitive proximity sensor (CPS) array for static gesture recognition and distance estimation. A 4×4 electrode matrix is employed as the sensing element that is configured to 14 electrode operation patterns to obtain 14 capacitive sensors to percept objects within their sensing region. These 14 capacitances are fused into one feature vector which is used as the input of machine learning (ML) classifier for gesture recognition and neural network or regression model for distance estimation. In our experiments, we selected 10 static gestures to verify the proposed method. We compared the performance of 8 ML classifiers and their variations with training data size. The results show that the Bagging achieves the highest average accuracy of 93.2% and the KNN shows a good performance even with a small training data size. The results in distance estimation experiment demonstrate that the RBF network performs a high accuracy. © 2023, The Authors. All rights reserved.

关键词： Machine learning

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LOG-LIO: A LiDAR-Inertial Odometry with Efficient Local Geometric information Estimation

arXiv

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arXiv 2023年

作者： Huang, Kai Zhao, Junqiao Zhu, Zhongyang Ye, Chen Feng, Tiantian The School of Surveying and Geo-Informatics Tongji University Shanghai China Department of Computer Science and Technology School of Electronics and Information Engineering Tongji University Shanghai China The MOE Key Lab of Embedded System and Service Computing Tongji University Shanghai China Institute of Intelligent Vehicles Tongji University Shanghai China

Local geometric information, i.e., normal and distribution of points, is crucial for LiDAR-based simultaneous localization and mapping (SLAM) because it provides constraints for data association, which further determines the direction of optimization and ultimately affects the accuracy of localization. However, estimating normal and distribution of points are time-consuming tasks even with the assistance of kdtree or volumetric maps. To achieve fast normal estimation, we look into the structure of LiDAR scan and propose a ring-based fast approximate least squares (Ring FALS) method. With the Ring structural information, estimating the normal requires only the range information of the points when a new scan arrives. To efficiently estimate the distribution of points, we extend the ikd-tree to manage the map in voxels and update the distribution of points in each voxel incrementally while maintaining its consistency with the normal estimation. We further fix the distribution after its convergence to balance the time consumption and the correctness of representation. Based on the extracted and maintained local geometric information, we devise a robust and accurate hierarchical data association scheme where point-to-surfel association is prioritized over point-to-plane. Extensive experiments on diverse public datasets demonstrate the advantages of our system compared to other state-of-the-art methods. Our open source implementation is availab.e at https://***/tiev-tongji/LOG-LIO. Copyright © 2023, The Authors. All rights reserved.

关键词： Optical radar

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