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Prediction of piRNA-mRNA interactions based on an interactive inference network

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Prediction of piRNA-mRNA interactions based on an interactiv...

IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yajun Liu Ru Li Aimin Li Rong Fei Xie Guo Fang-Xiang Wu Shaanxi Key Laboratory for Network Computing and Security Technology Xi'an University of Technology Xi'an China Shaanxi Key Laboratory of Complex System Control and Intelligent Information Processing Xi'an University of Technology Xi'an China Department of Computer Science Department of Mechanical Engineering Division of Biomedical Engineering University of Saskatchewan Saskatoon Canada

As the largest class of small non-coding RNAs, piRNAs primarily present in the reproductive cells of mammals, which influence post-transcriptional processes of mRNAs in multiple ways. Effective methods for predicting piRNA and mRNA target relationships can help identify piRNA functions, investigate the possibility of piRNAs as biomarkers and therapeutic targets. In this study, we propose a computational approach for classifying the relationships of piRNA-mRNA pairs based on an interactive inference network (IIN). First, we gather piRNA-mRNA target data, collect sequence data by position alignment, and construct a benchmark dataset. Furthermore, a reliable negative set is constructed by positive-unlabeled learning. Finally, we view a piRNA and a mRNA sequence as a premise and hypothesis sentence, respectively, and IIN model is used to predict the relationship between them. The experiments demonstrate that our method effectively characterizes piRNA-mRNA interaction and could be beneficial for researchers to investigate piRNA functions.

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BMDP:Blockchain-Based Multi-Cloud Storage Data Provenance

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BMDP:Blockchain-Based Multi-Cloud Storage Data Provenance

International Conference on Computer Supported Cooperative Work in Design

作者： Feiyu Wang Jian-Tao Zhou Xu Guo College of Computer Science Inner Mongolia University Hohhot Inner Mongolia China Inner Mongolia Engineering Laboratory for Cloud Computing and Service Software Engineering Research Center of Ecological Big Data Ministry of Education National & Local Joint Engineering Research Center of Intelligent Information Processing Technology for Mongolian Inner Mongolia Key Laboratory of Social Computing and Data Processing Inner Mongolia Engineering Laboratory for Big Data Analysis Technology China

In a multi-cloud storage system, provenance data records all operations and ownership during its lifecycle, which is critical for data security and audibility. However, recording provenance data also poses some challenging security and storage issues. In this paper, we present a secure and efficient multi-cloud storage data source scheme, BMDP. We use blockchain technology to ensure the secure storage of provenance data and design a smart contract to utilize the provenance data to ensure the proper operation of the multi-cloud storage system. Finally, we analyze the scheme’s safety and do simulation experiments to show that the scheme has practicality.

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PFS3F: Probabilistic Fusion of Superpixel-wise and Semantic-aware Structural Features for Hyperspectral Image Classification

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IEEE Transactions on Circuits and Systems for Video technology 2025年

作者： Zhang, Ying Duan, Puhong Liang, Lianhui Kang, Xudong Li, Jun Plaza, Antonio Hunan University of Technology College of Railway Transportation Zhuzhou412007 China Hunan University School of Robotics Changsha410082 China Guangxi University School of Electrical Engineering Nanning530004 China China University of Geosciences Hubei Key Laboratory of Intelligent Geo-Information Processing the School of Computer Science Wuhan430078 China Hyperspectral Computing Laboratory Department of Technology of Computers and Communications Escuela Politecnica University of Extremadura CaceresE-10071 Spain

processing high-dimensional data cubes and developing high-performance classifiers are core objectives in the field of hyperspectral image classification (HSIC). Superpixel-based methods are widely used in HSIC due to their efficacy in reducing redundant information and enhancing local features. However, imprecise segmentation, especially in complex structures and textures of hyperspectral images (HSIs), may lead to inconsistencies in the regions extracted by superpixels and the boundaries between different ground objects. Such inconsistencies significantly degrade the classification performance of HSIs. Alternatively, when parameter settings are inaccurate, edge-aware feature extraction methods often introduce sharpening artifacts at the image boundaries, resulting in a decrease in classification accuracy. To effectively address these challenges, we propose a novel probabilistic fusion method for HSIC. This method consists of the following stages. First, spatial information is extracted by a multiscale superpixel segmentation method and then probabilistically optimized by the extended random walk (ERW) method. Next, semantic-aware structural features (S2Fs) are extracted along with edge information of different objects. Lastly, a probabilistic framework is proposed to fuse the class probabilities of superpixel-based spatial information and semantic-aware structural features. Experimental results on three real datasets show state-of-the-art classification performance, even with limited training sets. ©1991-2012 IEEE.

关键词： Superpixels

Application of graph-curvature features in computer-aided diagnosis for histopathological image identification of gastric cancer

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intelligent Medicine 2024年第3期4卷 141-152页

作者： Ruilin He Chen Li Xinyi Yang Jinzhu Yang Tao Jiang Marcin Grzegorzek Hongzan Sun Microscopic Image and Medical Image Analysis Group College of Medicine and Biological Information EngineeringNortheastern UniversityShenyangLiaoning 110016China Key Laboratory of Intelligent Computing in Medical Image Ministry of EducationNortheastern UniversityShenyangLiaoning 110016China School of Intelligent Medicine Chengdu University of Traditional Chinese MedicineChengduSichuan 610075China International Joint Institute of Robotics and Intelligent Systems Chengdu University of Information TechnologyChengduSichuan 610225China Institute for Medical Informatics University of LuebeckLuebeckGermany Department of Knowledge Engineering University of Economics in KatowiceKatowicePoland Shengjing Hospital of China Medical University ShenyangLiaoning 110136China

Background Histopathology diagnosis is often regarded as the final diagnostic method for malignant tumors;however,it has some *** study explored a computer-aided diagnostic method that can be used to identify benign and malignant gastric cancer using histopathological *** The most suitable process was selected through multiple experiments by comparing multiple meth-ods and features for ***,the U-net was applied to segment the ***,the nucleus was extracted from the segmented image,and the minimum spanning tree(MST)diagram structure that can cap-ture the topological information was *** third step was to extract the graph-curvature features of the histopathological image according to the MST ***,by inputting the graph-curvature features into the classifier,the recognition results for benign or malignant cancer can be *** During the experiment,we used various methods for *** the image segmentation stage,U-net,watershed algorithm,and Otsu threshold segmentation methods were *** found that the U-net method,combined with multiple indicators,was the most suitable for segmentation of histopathological *** the feature extraction stage,in addition to extracting graph-edge and graph-curvature features,several basic im-age features were extracted,including the red,green and blue feature,gray-level co-occurrence matrix feature,histogram of oriented gradient feature,and local binary pattern *** the classifier design stage,we exper-imented with various methods,such as support vector machine(SVM),random forest,artificial neural network,K nearest neighbors,VGG-16,and *** comparison and analysis,it was found that classifica-tion results with an accuracy of 98.57%can be obtained by inputting the graph-curvature feature into the SVM classifier.

关键词： Gastric cancer Graph-curvature feature Image identification

Artificial Intelligence-Generated Terahertz Multi-Resonant Metasurfaces via Improved Transformer and CGAN Neural Networks

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arXiv 2023年

作者： Huang, Yangpeng Feng, Naixing Cai, Yijun Smart Sensing Integrated Circuit Engineering Research Center of Universities in Fujian Province Xiamen University of Technology Xiamen361000 China The Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Anhui University Hefei230601 China Information Materials and Intelligent Sensing Laboratory of Anhui Province Anhui University Hefei230601 China

It is well known that the inverse design of terahertz (THz) multi-resonant graphene metasurfaces by using traditional deep neural networks (DNNs) has limited generalization ability. In this paper, we propose improved Transformer and conditional generative adversarial neural networks (CGAN) for the inverse design of graphene metasurfaces based upon THz multi-resonant absorption spectra. The improved Transformer can obtain higher accuracy and generalization performance in the StoV (Spectrum to Vector) design compared to traditional multilayer perceptron (MLP) neural networks, while the StoI (Spectrum to Image) design achieved through CGAN can provide more comprehensive information and higher accuracy than the StoV design obtained by MLP. Moreover, the improved CGAN can achieve the inverse design of graphene metasurface images directly from the desired multi-resonant absorption spectra. It is turned out that this work can finish facilitating the design process of artificial intelligence-generated metasurfaces (AIGM), and even provide a useful guide for developing complex THz metasurfaces based on 2D materials using generative neural networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Graphene

Not All Diffusion Model Activations Have Been Evaluated as Discriminative Features

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arXiv 2024年

作者： Meng, Benyuan Xu, Qianqian Wang, Zitai Cao, Xiaochun Huang, Qingming Institute of Information Engineering CAS China School of Cyber Security University of Chinese Academy of Sciences China Key Lab. of Intelligent Information Processing Institute of Computing Technology CAS China Peng Cheng Laboratory China School of Cyber Science and Tech. Shenzhen Campus of Sun Yat-sen University China School of Computer Science and Tech. University of Chinese Academy of Sciences China Key Laboratory of Big Data Mining and Knowledge Management CAS China

Diffusion models are initially designed for image generation. Recent research shows that the internal signals within their backbones, named activations, can also serve as dense features for various discriminative tasks such as semantic segmentation. Given numerous activations, selecting a small yet effective subset poses a fundamental problem. To this end, the early study of this field performs a large-scale quantitative comparison of the discriminative ability of the activations. However, we find that many potential activations have not been evaluated, such as the queries and keys used to compute attention scores. Moreover, recent advancements in diffusion architectures bring many new activations, such as those within embedded ViT modules. Both combined, activation selection remains unresolved but overlooked. To tackle this issue, this paper takes a further step with a much broader range of activations evaluated. Considering the significant increase in activations, a full-scale quantitative comparison is no longer operational. Instead, we seek to understand the properties of these activations, such that the activations that are clearly inferior can be filtered out in advance via simple qualitative evaluation. After careful analysis, we discover three properties universal among diffusion models, enabling this study to go beyond specific models. On top of this, we present effective feature selection solutions for several popular diffusion models. Finally, the experiments across multiple discriminative tasks validate the superiority of our method over the SOTA competitors. Our code is available at this url. © 2024, CC BY.

关键词： Semantics

The interior penalty virtual element method for fourth-order singular perturbation problems

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arXiv 2023年

作者： Feng, Fang Yu, Yue School of Mathematics and Statistics Nanjing University of Science and Technology Nanjing China School of Mathematics and Computational Science Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing Ministry of Education Xiangtan University Hunan Xiangtan411105 China

This paper is dedicated to the numerical solution of a fourth-order singular perturbation problem using the interior penalty virtual element method (IPVEM) proposed in [42]. The study introduces modifications to the jumps and averages in the penalty term, as well as presents an automated mesh-dependent selection of the penalty parameter. Drawing inspiration from the modified Morley finite element methods, we leverage the conforming interpolation technique to handle the lower part of the bilinear form. Through our analysis, we establish optimal convergence in the energy norm and provide a rigorous proof of uniform convergence concerning the perturbation parameter in the lowest-order case. © 2023, CC BY-NC-ND.

关键词： Numerical methods

Unified-modal Salient Object Detection via Adaptive Prompt Learning

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arXiv 2023年

作者： Wang, Kunpeng Li, Chenglong Tu, Zhengzheng Liu, Zhengyi Luo, Bin Information Materials and Intelligent Sensing Laboratory of Anhui Province Anhui Provincial Key Laboratory of Multimodal Cognitive Computation School of Computer Science and Technology Anhui University Hefei230601 China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University Hefei China Anhui Provincial Key Laboratory of Multimodal Cognitive Computation School of Artificial Intelligence Anhui University Hefei230601 China The Institute of Physical Science and Information Technology Anhui University Hefei230601 China

Existing single-modal and multi-modal salient object detection (SOD) methods focus on designing specific architectures tailored for their respective tasks. However, developing completely different models for different tasks leads to labor and time consumption, as well as high computational and practical deployment costs. In this paper, we attempt to address both single-modal and multi-modal SOD in a unified framework called UniSOD, which fully exploits the overlapping prior knowledge between different tasks. Nevertheless, assigning appropriate strategies to modality variable inputs is challenging. To this end, UniSOD learns modality-aware prompts with task-specific hints through adaptive prompt learning, which are plugged into the proposed pre-trained baseline SOD model to handle corresponding tasks, while only requiring few learnable parameters compared to training the entire model. Each modality-aware prompt is generated from a switchable prompt generation block, which adaptively performs structural switching based on single-modal and multi-modal inputs without human intervention. Through end-to-end joint training, UniSOD achieves overall performance improvement on 14 benchmark datasets for RGB, RGB-D, and RGB-T SOD, which demonstrates that our method effectively and efficiently unifies single-modal and multi-modal SOD tasks. The code and results are available at https://***/Angknpng/UniSOD. Copyright © 2023, The Authors. All rights reserved.

关键词： Object detection

Understanding the Robustness of 3D Object Detection with Bird'View Representations in Autonomous Driving

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Understanding the Robustness of 3D Object Detection with Bir...

Conference on Computer Vision and Pattern Recognition (CVPR)

作者： Zijian Zhu Yichi Zhang Hai Chen Yinpeng Dong Shu Zhao Wenbo Ding Jiachen Zhong Shibao Zheng Institute of Image Communication and Network Engineering Shanghai Jiao Tong University Dept. of Comp. Sci. and Tech. THBI Lab Institute for AI Tsinghua University BNRist Center Zhongguancun Laboratory Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education Information Materials and Intelligent Sensing Laboratory of Anhui Province School of Computer Science and Technology Anhui University SAIC Motor AI Lab

3D object detection is an essential perception task in autonomous driving to understand the environments. The Bird's-Eye-View (BEV) representations have significantly improved the performance of 3D detectors with camera inputs on popular benchmarks. However, there still lacks a systematic understanding of the robustness of these vision-dependent BEV models, which is closely related to the safety of autonomous driving systems. In this paper, we evaluate the natural and adversarial robustness of various representative models under extensive settings, to fully understand their behaviors influenced by explicit BEV features compared with those without BEV. In addition to the classic settings, we propose a 3D consistent patch attack by applying adversarial patches in the 3D space to guarantee the spatiotemporal consistency, which is more realistic for the scenario of autonomous driving. With substantial experiments, we draw several findings: 1) BEV models tend to be more stable than previous methods under different natural conditions and common corruptions due to the expressive spatial representations; 2) BEV models are more vulnerable to adversarial noises, mainly caused by the redundant BEV features; 3) Camera-LiDARfusion models have superior performance under different settings with multi-modal inputs, but BEV fusion model is still vulnerable to adversarial noises of both point cloud and image. These findings alert the safety issue in the applications of BEV detectors and could facilitate the development of more robust models.

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