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MEFFGRN: Matrix enhancement and feature fusion-based method for reconstructing the gene regulatory network of epithelioma papulosum cyprini cells by spring viremia of carp virus infection

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Computers in Biology and Medicine 2024年 179卷 108835-108835页

作者： Wei, Pi-Jing Bao, Jin-Jin Gao, Zhen Tan, Jing-Yun Cao, Rui-Fen Su, Yansen Zheng, Chun-Hou Deng, Li Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education Institutes of Physical Science and Information Technology Anhui University 111 Jiulong Road HefeiAnhui230601 China Key Laboratory of Intelligent Computing & Signal Processing of Ministry of Education School of Computer Science and Technology Anhui University 111 Jiulong Road HefeiAnhui230601 China Shenzhen Key Laboratory of Microbial Genetic Engineering College of Life Sciences and Oceanology Shenzhen University Guangdong Shenzhen518055 China School of Artificial Intelligence Anhui University 111 Jiulong Road HefeiAnhui230601 China

Gene regulatory networks (GRNs) are crucial for understanding organismal molecular mechanisms and processes. Construction of GRN in the epithelioma papulosum cyprini (EPC) cells of cyprinid fish by spring viremia of carp virus (SVCV) infection helps understand the immune regulatory mechanisms that enhance the survival capabilities of cyprinid fish. Although many computational methods have been used to infer GRNs, specialized approaches for predicting the GRN of EPC cells following SVCV infection are lacking. In addition, most existing methods focus primarily on gene expression features, neglecting the valuable network structural information in known GRNs. In this study, we propose a novel supervised deep neural network, named MEFFGRN (Matrix Enhancement- and Feature Fusion-based method for Gene Regulatory Network inference), to accurately predict the GRN of EPC cells following SVCV infection. MEFFGRN considers both gene expression data and network structure information of known GRN and introduces a matrix enhancement method to address the sparsity issue of known GRN, extracting richer network structure information. To optimize the benefits of CNN (Convolutional Neural Network) in image processing, gene expression and enhanced GRN data were transformed into histogram images for each gene pair respectively. Subsequently, these histograms were separately fed into CNNs for training to obtain the corresponding gene expression and network structural features. Furthermore, a feature fusion mechanism was introduced to comprehensively integrate the gene expression and network structural features. This integration considers the specificity of each feature and their interactive information, resulting in a more comprehensive and precise feature representation during the fusion process. Experimental results from both real-world and benchmark datasets demonstrate that MEFFGRN achieves competitive performance compared with state-of-the-art computational methods. Furthermore, study

关键词： Gene expression

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Alignment-Free RGB-T Salient Object Detection: A Large-scale Dataset and Progressive Correlation Network

arXiv

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arXiv 2024年

作者： Wang, Kunpeng Chen, Keke Li, Chenglong Tu, Zhengzheng Luo, Bin Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Anhui Provincial Key Laboratory of Multimodal Cognitive Computation School of Computer Science and Technology Anhui University China Anhui Provincial Key Laboratory of Security Artificial Intelligence School of Artificial Intelligence Anhui University China

Alignment-free RGB-Thermal (RGB-T) salient object detection (SOD) aims to achieve robust performance in complex scenes by directly leveraging the complementary information from unaligned visible-thermal image pairs, without requiring manual alignment. However, the labor-intensive process of collecting and annotating image pairs limits the scale of existing benchmarks, hindering the advancement of alignment-free RGB-T SOD. In this paper, we construct a large-scale and high-diversity unaligned RGB-T SOD dataset named UVT20K, comprising 20,000 image pairs, 407 scenes, and 1256 object categories. All samples are collected from real-world scenarios with various challenges, such as low illumination, image clutter, complex salient objects, and so on. To support the exploration for further research, each sample in UVT20K is annotated with a comprehensive set of ground truths, including saliency masks, scribbles, boundaries, and challenge attributes. In addition, we propose a Progressive Correlation Network (PCNet), which models inter- and intra-modal correlations on the basis of explicit alignment to achieve accurate predictions in unaligned image pairs. Extensive experiments conducted on unaligned and aligned datasets demonstrate the effectiveness of our method. Copyright © 2024, The Authors. All rights reserved.

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Optimized Statistical Model for Complex Chemical Processes Monitoring

Optimized Statistical Model for Complex Chemical Processes M...

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Data Driven Control and Learning Systems (DDCLS)

作者： Jian Zhang Xiaohe Qu Zhiwei Lei Haifeng Zhang Kai Zhong Datang East China Electric Power Test and Research Institute Hefei China Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education School of Mathematical Science Anhui University Hefei China Key Laboratory of Intelligent Computing and Signal Processing of the Ministry of Education Institutes of Physical Science and Information Technology Anhui University Hefei Anhui China

The traditional kernel principal components analysis (KPCA) and linear discriminant analysis (LDA) have been verified to be two effective approaches for fault detection and diagnosis in recent years. Nevertheless, the conventional method and corresponding improved ones still exposed their deficiencies in some ways. Facing this dilemma, this paper presents a combination of optimized KPCA and modified LDA (OKPCA-MLDA), in which the OKPCA avoids the loss of original features after centralizing data in the eigenspace by adjusting covariance matrix's eigenvalue and transforming the distribution of variables thus providing representative and abundant principal components for the classifier. In addition, the MLDA maximizes a brand new objective function in feature space which achieves better classification performance than the conventional LDA, then utilizing diagnostic thresholds and similarity coefficients to identify the fault types. Based on the combined model, not only the fault detection and diagnosis can be realized simultaneously but also the accuracy of detection and diagnosis can be guaranteed. Furthermore, the simulation experiments on Tennessee Eastman (TE) benchmark process clearly illustrated the superiority of our proposed strategy.

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Investigation on a quantum algorithm for linear differential equations

arXiv

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arXiv 2024年

作者： Dong, Xiaojing Peng, Yizhe Tang, Qili Yang, Yin Yu, Yue Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education National Center for Applied Mathematics in Hunan School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China

Ref. [BCOW17] introduced a pioneering quantum approach (coined BCOW algorithm) for solving linear differential equations with optimal error tolerance. Originally designed for a specific class of diagonalizable linear differential equations, the algorithm was extended by Krovi in [Kro23] to encompass broader classes, including non-diagonalizable and even singular matrices. Despite the common misconception, the original algorithm is indeed applicable to non-diagonalizable matrices, with diagonalisation primarily serving for theoretical analyses to establish bounds on condition number and solution error. By leveraging basic estimates from [Kro23], we derive bounds comparable to those outlined in the Krovi algorithm, thereby reinstating the advantages of the BCOW approach. Furthermore, we extend the BCOW algorithm to address time-dependent linear differential equations by transforming non-autonomous systems into higher-dimensional autonomous ones, a technique also applicable for the Krovi algorithm. © 2024, CC BY-NC-ND.

关键词： Consensus algorithm

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Conditional Video-Text Reconstruction Network with Cauchy Mask for Weakly Supervised Temporal Sentence Grounding

Conditional Video-Text Reconstruction Network with Cauchy Ma...

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IEEE International Conference on Multimedia and Expo (ICME)

作者： Jueqi Wei Yuanwu Xu Mohan Chen Yuejie Zhang Rui Feng Shang Gao School of Computer Science Shanghai Key Laboratory of Intelligent Information Processing Shanghai Collaborative Innovation Center of Intelligent Visual Computing Fudan University School of Information Technology Deakin University

Temporal sentence grounding aims to detect the target segment most related to a given query in an untrimmed video. To alleviate the expensive annotation cost for temporal labels, researchers paid more attention to weakly supervised setting. Prior studies neglected the utilization of video representation reconstruction, which led to an unbalanced alignment learning. Moreover, they used different strategies to generate proposals which ignored the temporal structure in a query. In this paper, we propose a novel Conditional Video-Text Reconstruction Network (CVTRN). It supports conditional reconstruction of video and text representation. Specifically, video and text features are fused to compute semantic alignment, which is the condition of reconstruction. A new mask strategy for mask conditioned sentence reconstruction is also devised. This strategy focuses more on boundary regions than the widely used Gaussian mask in previous methods. Experimental results on two public benchmark datasets show that our CVTRN outperforms the state-of-the-art methods.

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Investigation of double-gyroid grain boundaries beyond twinning

arXiv

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arXiv 2024年

作者： Chen, Jing Sun, Zhangpeng Jiang, Kai Xu, Jie Hunan Key Laboratory for Computation and Simulation in Science and Engineering Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education School of Mathematics and Computational Science Xiangtan University Hunan Xiangtan411105 China Chinese Academy of Sciences Beijing China

We study four double-gyroid (DG) grain boundaries (GBs) with different orientations numerically using the Landau–Brazovskii free energy, including the (422) twin boundary studied recently, a network switching GB, and two tilt GBs. Topological variations and geometric deformations are investigated. It is found that deviations in strut lengths and dihedral angles from the bulk DG substantially exceed changes in strut angles and nodal coplanarity. We also examine the spectra along the contact plane of two grains and utilize them to evaluate the GB widths. Of the four GBs we study, the network switching GB changes to the least extent topologically and geometrically, meanwhile has the lowest energy and the smallest GB width. Copyright © 2024, The Authors. All rights reserved.

关键词： Grain boundaries

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SPTNET: Span-based Prompt Tuning for Video Grounding

SPTNET: Span-based Prompt Tuning for Video Grounding

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IEEE International Conference on Multimedia and Expo (ICME)

作者： Yiren Zhang Yuanwu Xu Mohan Chen Yuejie Zhang Rui Feng Shang Gao School of Computer Science Shanghai Key Laboratory of Intelligent Information Processing Shanghai Collaborative Innovation Center of Intelligent Visual Computing Fudan University School of Information Technology Deakin University

When a Pre-trained Language Model (PLM) is adopted in video grounding task, it usually acts as a text encoder without having its knowledge fully utilized. Also, there exists an inconsistency problem between the pre-training and downstream objectives. To solve the issues, we propose a new paradigm, named Span-based Prompt Tuning (SPTNet). It can convert the video grounding task into a cloze form. Specifically, a query is first changed into a form with mask token by a template, then the video and the query embeddings are integrated through a cross-modal transformer. The start and end points of the query matching time span are predicted with the embedding of the mask token. Experimental results on two public benchmarks ActivityNet Captions and Charades-STA show that our SPTNet achieves surpassing performance compared with state-of-the-art methods.

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

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

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2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, CVPR 2023

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

ISBN: (纸本)9798350301298

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. © 2023 IEEE.

关键词： Autonomous driving

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Efficient Finite-Difference Time-Domain Method for Solving Electromagnetic Scattering in Layered Anisotropies

Efficient Finite-Difference Time-Domain Method for Solving E...

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International Symposium on Antennas, Propagation and EM Theory (ISAPE)

作者： Yilin Kang Yuxian Zhang Xiaoli Feng Lixia Yang Zhixiang Huang Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education and with the Information Materials and Intelligent Sensing Laboratory of Anhui Province Industry-Education-Research Institute of Advanced Materials and Technology for Integrated Circuits and with School of Electronic and Information Engineering Anhui University Hefei China

ISBN: (数字)9798350353129

ISBN: (纸本)9798350353136

In this article, we propose an efficient numerical method for layered models based on the conventional finite difference time-domain (FDTD) method. The three-dimensional (3-D) layered model is compressed into one-dimensional (1-D) calculation, which improves the problem of large space memory and long running time for 3-D modeling while ensuring the accuracy and feasibility of the algorithm. On the one hand, by employing the transformation relationship between the transverse wave vector and the field in space, the expanded Maxwell's rotation equations are simplified, so that the equation system only retains the spatial transformation in the propagation direction. This processing allows for the calculation of the propagation characteristics of layered media without requiring more computational resources. On the other hand, to ensure the universality of the algorithm, a fully tensor anisotropic medium is selected for detecting the propagation data. At the same time, we design the layered structure and conduct the consistent 3-D modeling in the simulation software COMSOL. The results showed that our proposed efficient numerical algorithm greatly reduced the loss of computing resources while ensuring accuracy.

关键词： Solid modeling Three-dimensional displays Accuracy Tensors Software algorithms Vectors Mathematical models Numerical models Time-domain analysis Finite difference methods

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OpenViewer: Openness-Aware Multi-View Learning 39

OpenViewer: Openness-Aware Multi-View Learning

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39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Du, Shide Fang, Zihan Tan, Yanchao Wang, Changwei Wang, Shiping Guo, Wenzhong College of Computer and Data Science Fuzhou University Fuzhou China Fujian Provincial Key Laboratory of Network Computing and Intelligent Information Processing Fuzhou University Fuzhou China Key Laboratory of Computing Power Network and Information Security Ministry of Education Shandong Computer Science Center Qilu University of Technology Jinan China

ISBN: (纸本)157735897X

Multi-view learning methods leverage multiple data sources to enhance perception by mining correlations across views, typically relying on predefined categories. However, deploying these models in real-world scenarios presents two primary openness challenges. 1) Lack of Interpretability: The integration mechanisms of multi-view data in existing black-box models remain poorly explained;2) Insufficient Generalization: Most models are not adapted to multi-view scenarios involving unknown categories. To address these challenges, we propose OpenViewer, an openness-aware multi-view learning framework with theoretical support. This framework begins with a Pseudo-Unknown Sample Generation Mechanism to efficiently simulate open multi-view environments and previously adapt to potential unknown samples. Subsequently, we introduce an Expression-Enhanced Deep Unfolding Network to intuitively promote interpretability by systematically constructing functional prior-mapping modules and effectively providing a more transparent integration mechanism for multi-view data. Additionally, we establish a Perception-Augmented Open-Set Training Regime to significantly enhance generalization by precisely boosting confidences for known categories and carefully suppressing inappropriate confidences for unknown ones. Experimental results demonstrate that OpenViewer effectively addresses openness challenges while ensuring recognition performance for both known and unknown samples. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Multi-task learning

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