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DMFVAE:miRNA-disease associations prediction based on deep matrix factorization method with variational autoencoder

Frontiers of computer Science 2024年第6期18卷 259-270页

作者： Pijing WEI Qianqian WANG Zhen GAO Ruifen CAO Chunhou ZHENG Information Materials and Intelligent Sensing Laboratory of Anhui Province Institutes of Physical Science and Information TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and TechnologyAnhui UniversityHefei 230601China Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Artificial IntelligenceAnhui UniversityHefei 230601China

MicroRNAs(miRNAs)are closely related to numerous complex human diseases,therefore,exploring miRNA-disease associations(MDAs)can help people gain a better understanding of complex disease *** increasing number of computational methods have been developed to predict ***,the sparsity of the MDAs may hinder the performance of many *** addition,many methods fail to capture the nonlinear relationships of miRNA-disease network and inadequately leverage the features of network and neighbor *** this study,we propose a deep matrix factorization model with variational autoencoder(DMFVAE)to predict potential *** first decomposes the original association matrix and the enhanced association matrix,in which the enhanced association matrix is enhanced by self-adjusting the nearest neighbor method,to obtain sparse vectors and dense vectors,***,the variational encoder is employed to obtain the nonlinear latent vectors of miRNA and disease for the sparse vectors,and meanwhile,node2vec is used to obtain the network structure embedding vectors of miRNA and disease for the dense ***,sample features are acquired by combining the latent vectors and network structure embedding vectors,and the final prediction is implemented by convolutional neural network with channel *** evaluate the performance of DMFVAE,we conduct five-fold cross validation on the HMDD v2.0 and HMDD v3.2 datasets and the results show that DMFVAE performs ***,case studies on lung neoplasms,colon neoplasms,and esophageal neoplasms confirm the ability of DMFVAE in identifying potential miRNAs for human diseases.

关键词： miRNA-disease association deep matrix factorization self-adjusted nearest neighbor variational encoder network structure

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ϵ-π: A Nonparametric Model for Neural Power Spectra Decomposition

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IEEE Journal of Biomedical and Health Informatics 2024年第5期28卷 2624-2635页

作者： Hu, Shiang Zhang, Zhihao Zhang, Xiaochu Wu, Xiaopei Valdes-Sosa, Pedro A. Anhui University Anhui Provincial Key Lab of Multimodal Cognitive Computation Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Hefei230601 China University of Science and Technology of China School of Humanities and Social Science Department of Psychology Hefei230026 China University of Electronic Science and Technology of China MOE Key Lab for Neuroinformation School of Life Science and Technology Chengdu611731 China

The power spectra estimated from the brain recordings are the mixed representation of aperiodic transient activity and periodic oscillations, i.e., aperiodic component (AC) and periodic component (PC). Quantitative neurophysiology requires precise decomposition preceding parameterizing each component. However, the shape, statistical distribution, scale, and mixing mechanism of AC and PCs are unclear, challenging the effectiveness of current popular parametric models such as FOOOF, IRASA, BOSC, etc. Here, was proposed to decompose the neural spectra by embedding the nonparametric spectra estimation with penalized Whittle likelihood and the shape language modeling into the expectation maximization framework. was validated on the synthesized spectra with loss statistics and on the sleep EEG and the large sample iEEG with evaluation metrics and neurophysiological evidence. Compared to FOOOF, both the simulation presenting shape irregularities and the batch simulation with multiple isolated peaks indicated that improved the fit of AC and PCs with less loss and higher F1-score in recognizing the centering frequencies and the number of peaks;the sleep EEG revealed that produced more distinguishable AC exponents and improved the sleep state classification accuracy;the iEEG showed that approached the clinical findings in peak discovery. Overall, offered good performance in the spectra decomposition, which allows flexible parameterization using descriptive statistics or kernel functions. is a seminal tool for brain signal decoding in fields such as cognitive neuroscience, brain-computer interface, neurofeedback, and brain diseases. © 2013 IEEE.

关键词： Electroencephalography

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Improving Transferability Reversible Adversarial Examples Based on Flipping Transformation 9th

Improving Transferability Reversible Adversarial Examples Ba...

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9th International Conference of Pioneering computer Scientists, Engineers and Educators, ICPCSEE 2023

作者： Fang, Youqing Jia, Jingwen Yang, Yuhai Lyu, Wanli Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei230601 China

ISBN: (纸本)9789819959679

Adding subtle perturbations to an image can cause the classification model to misclassify, and such images are called adversarial examples. Adversarial examples threaten the safe use of deep neural networks, but when combined with reversible data hiding (RDH) technology, they can protect images from being correctly identified by unauthorized models and recover the image lossless under authorized models. Based on this, the reversible adversarial example (RAE) is rising. However, existing RAE technology focuses on feasibility, attack success rate and image quality, but ignores transferability and time complexity. In this paper, we optimize the data hiding structure and combine data augmentation technology, which flips the input image in probability to avoid overfitting phenomenon on the dataset. On the premise of maintaining a high success rate of white-box attacks and the image’s visual quality, the proposed method improves the transferability of reversible adversarial examples by approximately 16% and reduces the computational cost by approximately 43% compared to the state-of-the-art method. In addition, the appropriate flip probability can be selected for different application scenarios. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

关键词： Deep neural networks

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Adversarial Example Generation Method Based on Probability Histogram Equalization 42

Adversarial Example Generation Method Based on Probability H...

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42nd Chinese Control Conference, CCC 2023

作者： Fang, Youqing Jia, Jingwen Yang, Yuhai Lyu, Wan-Li School of Computer Science and Technology Key Lab of Intelligent Computing and Signal Processing of Ministry of Education Anhui University Hefei230601 China

ISBN: (纸本)9789887581543

CNNs (Convolutional Neural Networks) have a good performance on most classification tasks, but they are vulnerable when meeting adversarial examples. Research and design of highly aggressive adversarial examples can help enhance the security and robustness of CNNs. The transferability of adversarial examples is still low in black-box settings. Therefore, an adversarial example method based on probability histogram equalization, namely HE-MI-FGSM (Histogram Equalization Momentum Iterative Fast Gradient Sign Method) is proposed. In each iteration of the adversarial example generation process, the original input image is randomly histogram equalized, and then the gradient is calculated to generate adversarial perturbations to mitigate overfitting in the adversarial example. The effectiveness of the method is verified on the ImageNet dataset. Compared with the advanced method I-FGSM (Iterative Fast Gradient Sign Method) and MI-FGSM (Momentum I-FGSM), the attack success rate in the adversarial training network increased by 27.9% and 7.7% on average, respectively. © 2023 Technical Committee on Control Theory, Chinese Association of Automation.

关键词： Iterative methods

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Adaptively feature matching via joint transformational-spatial clustering

Adaptively feature matching via joint transformational-spati...

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作者： Wang, Linbo Tan, Li Fang, Xianyong Guo, Yanwen Wan, Shaohua MOE Key Laboratory of Intelligent Computing and Signal Processing School of Computer Science and Technology Anhui University Hefei China National Key Lab for Novel Software Technology Nanjing University Nanjing China School of Information and Safety Engineering Zhongnan University of Economics and Law Wuhan China

The transformational and spatial proximities are important cues for identifying inliers from an appearance based match set because correct matches generally stay close in input images and share similar local transformations. However, most existing approaches only check one type of them or both types consecutively with manually set thresholds, and thus their matching accuracy and flexibility in handling large-scale images are limited. In this paper, we present an efficient clustering based approach to identify match inliers with both proximities simultaneously. It first projects the putative matches into a joint transformational-spatial space, where mismatches tend to scatter all around while correct matches gather together. A mode-seeking process based on joint kernel density estimation is then proposed to obtain significant clusters in the joint space, where each cluster contains matches mapping the same object across images with high accuracy. Moreover, kernel bandwidths for measuring match proximities are adaptively set during density estimation, which enhances its applicability for matching different images. Experiments on three standard datasets show that the proposed approach delivers superior performance on a variety of feature matching tasks, including multi-object matching, duplicate object matching and object retrieval. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

关键词： Clustering Density estimation Feature matching Mode-seeking

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Exploring Trial-and-Error in Deep Learning:Initial Application to Isotope Detection in Mass Spectrometry

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Big Data Mining and Analytics 2024年第4期7卷 1251-1261页

作者： Qihong Jiao Yuxiao Wang Yongshuai Wang Shiwei Sun Xuefeng Cui School of Computer Science and Technology Shandong UniversityQingdao 266237China Key Lab of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China

Mass spectrometry plays a crucial role in biomedicine by detecting isotopes,contributing significantly to research,diagnostics,and therapy *** study introduces IsoFusion,a deep learning model designed to address isotope detection in raw mass *** than directly applying convolutional layers to all signal and noise peaks,IsoFusion employs a trial-and-error ***,it investigates all potential charge states(trials)and collects signal peaks around expected m/z values for each ***,convolutional layers extract features from each trial,which are fused to identify the correct ***,the reparameterization trick predicts isotope features based on this correct trial.A key advantage of IsoFusion is shared model parameters across all trials,enhancing feature learning for less common charge states using data from prevalent *** results show a significant accuracy improvement for charge state 5,reaching 99.42%,compared to DeepIso’s 43.36%.Moreover,IsoFusion achieves a 97.33%detection accuracy for isotopes,with 2.4%of detected isotopes previously unidentified by four commonly used methods.

关键词： Liquid Chromatography-Mass Spectrometry(LC-MS) isotope detection retention time prediction charge state prediction deep learning

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Reversible Data Hiding for 3D Mesh Model Based on Block Modulus Encryption and Multi-MSB Prediction 10th

Reversible Data Hiding for 3D Mesh Model Based on Block Modu...

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10th International Conference of Pioneering computer Scientists, Engineers and Educators, ICPCSEE 2024

作者： Fu, Zihao Gao, Yang Lyu, Wanli Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei230601 China

ISBN: (纸本)9789819787456

Reversible data hiding in encrypted domain (RDH-ED) fortifies data security and privacy safeguards while upholding the original data’s integrity and accessibility. Current research on RDH-ED focuses on 2D images, while research on 3D mesh models is still immature. This paper introduces an RDH-ED method using block modulus encryption and multi-MSB prediction. Initially, the original mesh model is partitioned into non-overlapping subblocks of equal size, and then the vertices in each subblock are encrypted with the same key for additive modulus encryption, ensuring that the spatial correlation present in the original mesh subblocks remains preserved within the encrypted subblocks. Subsequently, the subblocks are disrupted one by one using the 3D Arnold Transform to enhance security. The vertices in each embeddable subblock are divided into a reference vertex and several embeddable vertices, where the multi-MSB prediction strategy is employed to allocate embedding room for each embeddable vertex. Finally, the secret information is embedded into the allocated room. Since the proposed method almost completely preserves the spatial correlation within each subblock, the achieved embedding rate surpasses that of all previous outstanding methods that rely on vacating room after encryption (VRAE). The experimental findings demonstrate that the proposed approach achieves an average embedding rate of 45.55 bits per vertex (bpv), surpassing the state-of-the-art method that achieves 25.63 bpv. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2024.

关键词： Mesh generation

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Adversarial Example Generation Method Based on Probability Histogram Equalization

Adversarial Example Generation Method Based on Probability H...

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第42届中国控制会议

作者： Youqing Fang Jingwen Jia Yuhai Yang Wan-Li Lyu Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and TechnologyAnhui University

CNNs(Convolutional Neural Networks) have a good performance on most classification tasks,but they are vulnerable when meeting adversarial *** and design of highly aggressive adversarial examples can help enhance the security and robustness of *** transferability of adversarial examples is still low in black-box ***,an adversarial example method based on probability histogram equalization,namely HE-MI-FGSM(Histogram Equalization Momentum Iterative Fast Gradient Sign Method) is *** each iteration of the adversarial example generation process,the original input image is randomly histogram equalized,and then the gradient is calculated to generate adversarial perturbations to mitigate overfitting in the adversarial *** effectiveness of the method is verified on the ImageNet *** with the advanced method I-FGSM(Iterative Fast Gradient Sign Method) and MI-FGSM(Momentum I-FGSM),the attack success rate in the adversarial training network increased by 27.9% and 7.7% on average,respectively.

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Improving Transferability Reversible Adversarial Examples Based on Flipping Transformation

Improving Transferability Reversible Adversarial Examples Ba...

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作者： Youqing Fang Jingwen Jia Yuhai Yang Wanli Lyu Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University

Adding subtle perturbations to an image can cause the classification model to misclassify, and such images are called adversarial examples. Adversarial examples threaten the safe use of deep neural networks, but when combined with reversible data hiding(RDH) technology, they can protect images from being correctly identified by unauthorized models and recover the image lossless under authorized models. Based on this, the reversible adversarial example(RAE) is rising. However, existing RAE technology focuses on feasibility, attack success rate and image quality, but ignores transferability and time complexity. In this paper,we optimize the data hiding structure and combine data augmentation technology,which flips the input image in probability to avoid overfitting phenomenon on the dataset. On the premise of maintaining a high success rate of white-box attacks and the image's visual quality, the proposed method improves the transferability of reversible adversarial examples by approximately 16% and reduces the computational cost by approximately 43% compared to the state-of-the-art method. In addition, the appropriate flip probability can be selected for different application scenarios.

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Adversarial Example Generation Method Based on Probability Histogram Equalization

Adversarial Example Generation Method Based on Probability H...

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Chinese Control Conference (CCC)

作者： Youqing Fang Jingwen Jia Yuhai Yang Wan-Li Lyu Key Lab of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China

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