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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Kuo Guo Yifan Li Hao Chen Hong-Bin Shen Yang Yang Department of Computer Science and Engineering Shanghai Jiao Tong University and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China Computational Biology Department School of Computer Science Carnegie Mellon University Pittsburgh PA USA

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function.

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Spectrum Sensing Based on Deep Learning Classification for Cognitive Radios

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China Communications 2020年第2期17卷 138-148页

作者： Shilian Zheng Shichuan Chen Peihan Qi Huaji Zhou Xiaoniu Yang Science and Technology on Communication Information Security Control Laboratory Jiaxing 314033China State Key Laboratory of Integrated Service Networks Xidian UniversityXi’an 710071China Key Laboratory of Intelligent Perception and Image Understanding Ministry of Education of ChinaXidian UniversityXi’an 710071China

Spectrum sensing is a key technology for cognitive *** present spectrum sensing as a classification problem and propose a sensing method based on deep learning *** normalize the received signal power to overcome the effects of noise power *** train the model with as many types of signals as possible as well as noise data to enable the trained network model to adapt to untrained new *** also use transfer learning strategies to improve the performance for real-world *** experiments are conducted to evaluate the performance of this *** simulation results show that the proposed method performs better than two traditional spectrum sensing methods,i.e.,maximum-minimum eigenvalue ratio-based method and frequency domain entropy-based *** addition,the experimental results of the new untrained signal types show that our method can adapt to the detection of these new ***,the real-world signal detection experiment results show that the detection performance can be further improved by transfer ***,experiments under colored noise show that our proposed method has superior detection performance under colored noise,while the traditional methods have a significant performance degradation,which further validate the superiority of our method.

关键词： spectrum sensing deep learning convolutional neural network cognitive radio spectrum management

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Adversarial attacks and defenses in physiological computing:a systematic review

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National Science Open 2023年第1期2卷 62-90页

作者： Dongrui Wu Jiaxin Xu Weili Fang Yi Zhang Liuqing Yang Xiaodong Xu Hanbin Luo Xiang Yu Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and AutomationHuazhong University of Science and TechnologyWuhan 430074China Zhejiang Lab Hangzhou 311121China School of Civil and Hydraulic Engineering Huazhong University of Science and TechnologyWuhan 430074China College of Public Administration Huazhong University of Science and TechnologyWuhan 430074China Electrical Engineering and Computer Science Department University of MichiganAnn Arbor MI 48109USA School of Management and Sino-European Institute for Intellectual Property Huazhong University of Science and TechnologyWuhan 430074China

Physiological computing uses human physiological data as system inputs in real *** includes,or significantly overlaps with,brain-computer interfaces,affective computing,adaptive automation,health informatics,and physiological signal based *** computing increases the communication bandwidth from the user to the computer,but is also subject to various types of adversarial attacks,in which the attacker deliberately manipulates the training and/or test examples to hijack the machine learning algorithm output,leading to possible user confusion,frustration,injury,or even ***,the vulnerability of physiological computing systems has not been paid enough attention to,and there does not exist a comprehensive review on adversarial attacks to *** study fills this gap,by providing a systematic review on the main research areas of physiological computing,different types of adversarial attacks and their applications to physiological computing,and the corresponding defense *** hope this review will attract more research interests on the vulnerability of physiological computing systems,and more importantly,defense strategies to make them more secure.

关键词： physiological computing brain-computer interfaces health informatics biometrics machine learning adversarial attack

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EMPIRICAL STUDIES ON THE PROPERTIES OF LINEAR REGIONS IN DEEP NEURAL NETWORKS 8

EMPIRICAL STUDIES ON THE PROPERTIES OF LINEAR REGIONS IN DEE...

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8th International Conference on Learning Representations, ICLR 2020

作者： Zhang, Xiao Wu, Dongrui Ministry of Education Key Laboratory of Image Processing and Intelligent Control School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan China

A deep neural network (DNN) with piecewise linear activations can partition the input space into numerous small linear regions, where different linear functions are fitted. It is believed that the number of these regions represents the expressivity of the DNN. This paper provides a novel and meticulous perspective to look into DNNs: Instead of just counting the number of the linear regions, we study their local properties, such as the inspheres, the directions of the corresponding hyperplanes, the decision boundaries, and the relevance of the surrounding regions. We empirically observed that different optimization techniques lead to completely different linear regions, even though they result in similar classification accuracies. We hope our study can inspire the design of novel optimization techniques, and help discover and analyze the behaviors of DNNs. © 2020 8th International Conference on Learning Representations, ICLR 2020. All rights reserved.

关键词： Deep neural networks

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Large, Complex, and Realistic Safety Clothing and Helmet Detection: Dataset and Method

arXiv

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arXiv 2023年

作者： Yu, Fusheng Li, Jiang Wang, Xiaoping Wu, Shaojin Zhang, Junjie Zeng, Zhigang The School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China The Institute of Artificial Intelligence Huazhong University of Science and Technology Wuhan430074 China The Hubei Key Laboratory of Brain-Inspired Intelligent Systems Huazhong University of Science and Technology Wuhan430074 China The Key Laboratory of Image Processing and Intelligent Control Huazhong University of Science and Technology Ministry of Education Wuhan430074 China

Detecting safety clothing and helmets is paramount for ensuring the safety of construction workers. However, the development of deep learning models in this domain has been impeded by the scarcity of high-quality datasets. In this study, we construct a large, complex, and realistic safety clothing and helmet detection (SFCHD) dataset. SFCHD is derived from two authentic chemical plants, comprising 12,373 images, 7 categories, and 50,552 annotations. We partition the SFCHD dataset into training and testing sets with a ratio of 4:1 and validate its utility by applying several classic object detection algorithms. Furthermore, drawing inspiration from spatial and channel attention mechanisms, we design a spatial and channel attention-based low-light enhancement (SCALE) module. SCALE is a plug-and-play component with a high degree of flexibility. Extensive evaluations of the SCALE module on both the ExDark and SFCHD datasets have empirically demonstrated its efficacy in enhancing the performance of detectors under low-light conditions. The dataset and code are publicly available at https://***/lijfrankopen/SFCHD-SCALE. Copyright © 2023, The Authors. All rights reserved.

关键词： Chemical plants

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A Single-Cell Clustering Algorithm Based on Structure Perturbation Non-Negative Matrix Factorization

A Single-Cell Clustering Algorithm Based on Structure Pertur...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Jiang, Hanjing Wang, Meineng Zhang, Luping Huang, Yu-An Li, Yangyuan Huang, Yabing Huazhong University of Science and Technology Key Laboratory of Image Information Processing and Intelligent Control Education Ministry of China Institute of Artificial Intelligence School of Artificial Intelligence and Automation Hubei Wuhan430074 China China University of Mining and Technology School of Computer Science and Technology Xuzhou221116 China Yichun University School of Mathematics and Computer Science Yichun336000 China East China University of Technology School of Information Engineering Nanchang330013 China Northwestern Polytechnical University School of Computer Science Xi'an710129 China Renmin Hospital Wuhan University Department of Pathology Wuhan430060 China

ISBN: (纸本)9798350386226

The advent of single-cell RNA sequencing (scRNA-seq) has facilitated the acquisition of high-resolution data regarding cell heterogeneity across various tissues. A fundamental and critical step in the analysis of scRNA-seq data is cell type identification. An appropriate graph construction strategy can reflect the topological structure between cells and allows for detailed exploration of the relationships between cells and genes. Given the sparsity of scRNA-seq data and the pronounced noise generated by shallow sequencing, choosing an appropriate graph construction strategy has become a significant challenge. In this paper, we propose a single-cell clustering method, named Sc-PNNMF, based on structural perturbation of nonnegative matrix factorization. Sc-PNNMF employs a structural perturbation algorithm to optimize the gene expression matrix. The optimized matrix guides the matrix factorization process, effectively overcoming the impact of data sparsity and significant noise in gene expression data on the graph construction strategy. We compared the clustering abilities of Sc-PNNMF with five other methods on ten real datasets. © 2024 IEEE.

关键词： Non-negative matrix factorization

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Learning from Noisy Labels with Coarse-to-Fine Sample Credibility Modeling

arXiv

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arXiv 2022年

作者： Zhang, Boshen Li, Yuxi Tu, Yuanpeng Peng, Jinlong Wang, Yabiao Wu, Cunlin Xiao, Yang Zhao, Cairong YouTu Lab Tencent Shanghai China Tongji University Shanghai China Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology China

Training deep neural network (DNN) with noisy labels is practically challenging since inaccurate labels severely degrade the generalization ability of DNN. Previous efforts tend to handle part or full data in a unified denoising flow via identifying noisy data with a coarse small-loss criterion to mitigate the interference from noisy labels, ignoring the fact that the difficulties of noisy samples are different, thus a rigid and unified data selection pipeline cannot tackle this problem well . In this paper, we first propose a coarse-to-fine robust learning method called CREMA, to handle noisy data in a divide-and-conquer manner. In coarse-level, clean and noisy sets are firstly separated in terms of credibility in a statistical sense. Since it is practically impossible to categorize all noisy samples correctly, we further process them in a fine-grained manner via modeling the credibility of each sample. Specifically, for the clean set, we deliberately design a memory-based modulation scheme to dynamically adjust the contribution of each sample in terms of its historical credibility sequence during training, thus alleviating the effect from noisy samples incorrectly grouped into the clean set. Meanwhile, for samples categorized into the noisy set, a selective label update strategy is proposed to correct noisy labels while mitigating the problem of correction error. Extensive experiments are conducted on benchmarks of different modality, including image classification (CIFAR, Clothing1M etc) and text recognition (IMDB), with either synthetic or natural semantic noises, demonstrating the superiority and generality of CREMA. © 2022, CC BY.

关键词： Deep neural networks

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Memory Analysis for Memristors and Memristive Recurrent Neural Networks

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IEEE/CAA Journal of Automatica Sinica 2020年第1期7卷 96-105页

作者： Gang Bao Yide Zhang Zhigang Zeng Key Laboratory of Cascaded Hydropower Stations Operation and Control Electrical Engineering and New EnergyChina Three Gorges UniversityYichang 443002and Hubei Key Laboratory of Applied Mathematics(Hubei University)Wuhan 430074China Department of Medical Engineering California Institute of TechnologyPasadenaCalifornia 91125 USA School of Artificial Intelligence and Automation Huazhong University of Science and Technologyand also with the Key Laboratory of Image Processing and Intelligent Control of Education Ministry of ChinaWuhan 430074China

Traditional recurrent neural networks are composed of capacitors, inductors, resistors, and operational *** neural networks are constructed by replacing resistors with memristors. This paper focuses on the memory analysis,i.e. the initial value computation, of memristors. Firstly, we present the memory analysis for a single memristor based on memristors’ mathematical models with linear and nonlinear ***, we present the memory analysis for two memristors in series and parallel. Thirdly, we point out the difference between traditional neural networks and those that are memristive. Based on the current and voltage relationship of memristors, we use mathematical analysis and SPICE simulations to demonstrate the validity of our methods.

关键词： Dopant drift memory memristive neural networks memristor

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Thymine-Hg2+-Thymine Strategy in Mof-Based Electrochemical Aptamer Sensor for Paes Detection

SSRN

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SSRN 2024年

作者： Liu, Xiaofang Diao, Zhan Liu, Huan Wang, Qun Lei, Jincan Huo, Danqun Hou, Jingzhou Hou, Changjun Key Laboratory for Biorheological Science and Technology Ministry of Education Bioengineering College Chongqing University Chongqing400044 China Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare Chongqing City Management College Chongqing401331 China Key Laboratory of Condiment Supervision Technology for State Market Regulation Chongqing Institute for Food and Drug Control Chongqing401121 China Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing School of Microelectronics and Communication Engineering Chongqing University Chongqing400044 China

Phthalate acid esters (PAEs), known food contaminants, can lead to reproductive problems, respiratory diseases, childhood obesity, and neuropsychological disorders. This work aims to develop an electrochemical aptamer sensor for the detection of DAP and its analogs. To achieve specific recognition ability for PAEs, We have introduced the thymidine-Hg2+-thymidine strategy for the first time in an electrochemical aptamer sensor, incorporating metal-organic frameworks (MOFs) as the carrier for the aptamer. Additionally, nanoamplification technology was applied by immobilizing MXene on the electrode to intensify the sensor's current signal. In the presence of PAEs, these molecules specifically bound to the aptamers, resulting in competitive release of Hg2+ and aptamers connected to Hg2+, subsequently reducing current signaling. Under optimal experimental conditions, the designed sensor achieved a linear range from 1.65×10-5 mg/mL to 3×10-2 mg/ml and an extremely low detection limit of 8.94×10-6 mg/mL. Furthermore, it exhibited good reliability and practicality in detecting actual samples. © 2024, The Authors. All rights reserved.

关键词： Esters

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CrossGLG: LLM Guides One-shot Skeleton-based 3D Action Recognition in a Cross-level Manner

arXiv

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arXiv 2024年

作者： Yan, Tingbing Zeng, Wenzheng Xiao, Yang Tong, Xingyu Tan, Bo Fang, Zhiwen Cao, Zhiguo Zhou, Joey Tianyi Key Laboratory of Image Processing and Intelligent Control Ministry of Education School of Artificial Intelligence and Automation Huazhong University of Science and Technology Wuhan430074 China School of Biomedical Engineering Southern Medical University Guangzhou510515 China Department of Rehabilitation Medicine Zhujiang Hospital Southern Medical University Guangzhou510280 China Singapore Singapore Singapore Singapore

Most existing one-shot skeleton-based action recognition focuses on raw low-level information (e.g., joint location), and may suffer from local information loss and low generalization ability. To alleviate these, we propose to leverage text description generated from large language models (LLM) that contain high-level human knowledge, to guide feature learning, in a global-local-global way. Particularly, during training, we design 2 prompts to gain global and local text descriptions of each action from an LLM. We first utilize the global text description to guide the skeleton encoder focus on informative joints (i.e.,global-tolocal). Then we build non-local interaction between local text and joint features, to form the final global representation (i.e., local-to-global). To mitigate the asymmetry issue between the training and inference phases, we further design a dual-branch architecture that allows the model to perform novel class inference without any text input, also making the additional inference cost neglectable compared with the base skeleton encoder. Extensive experiments on three different benchmarks show that CrossGLG consistently outperforms the existing SOTA methods with large margins, and the inference cost (model size) is only 2.8% than the previous SOTA. CrossGLG can also serve as a plug-and-play module that can substantially enhance the performance of different SOTA skeleton encoders with a neglectable cost during inference. The source code will be released soon. © 2024, CC BY.

关键词： Signal encoding

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