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Protein Structure Prediction:Challenges,Advances,and the Shift of Research Paradigms

Genomics, Proteomics & Bioinformatics 2023年第5期21卷 913-925页

作者： Bin Huang Lupeng Kong Chao Wang Fusong Ju Qi Zhang Jianwei Zhu Tiansu Gong Haicang Zhang Chungong Yu Wei-Mou Zheng Dongbo Bu Key Laboratory of Intelligent Information Processing Institute of Computing TechnologyChinese Academy of SciencesBeijing 100190China University of Chinese Academy of Sciences Beijing 100049China Changping Laboratory Beijing 102206China Microsoft Research AI4Science Beijing 100080China Huawei Noah’s Ark Lab Wuhan 430206China Zhongke Big Data Academy Zhengzhou 450046China Institute of Theoretical Physics Chinese Academy of SciencesBeijing 100190China

Protein structure prediction is an interdisciplinary research topic that has attracted researchers from multiple fields,including biochemistry,medicine,physics,mathematics,and computer *** researchers adopt various research paradigms to attack the same structure prediction problem:biochemists and physicists attempt to reveal the principles governing protein folding;mathematicians,especially statisticians,usually start from assuming a probability distribution of protein structures given a target sequence and then find the most likely structure,while computer scientists formulate protein structure prediction as an optimization problem-finding the structural conformation with the lowest energy or minimizing the difference between predicted structure and native *** research paradigms fall into the two statistical modeling cultures proposed by Leo Breiman,namely,data modeling and algorithmic ***,we have also witnessed the great success of deep learning in protein structure *** this review,we present a survey of the efforts for protein structure *** compare the research paradigms adopted by researchers from different fields,with an emphasis on the shift of research paradigms in the era of deep *** short,the algorithmic modeling techniques,especially deep neural networks,have considerably improved the accuracy of protein structure prediction;however,theories interpreting the neural networks and knowledge on protein folding are still highly desired.

关键词： Protein folding Protein structure prediction Deep learning Transformer Language model

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TFGDA: Exploring Topology and Feature Alignment in Semi-supervised Graph Domain Adaptation through Robust Clustering 38

TFGDA: Exploring Topology and Feature Alignment in Semi-supe...

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38th Conference on Neural information processing Systems, NeurIPS 2024

作者： Dan, Jun Liu, Weiming Xie, Chunfeng Yu, Hua Dong, Shunjie Tan, Yanchao Zhejiang University China Queen Mary University of London United Kingdom Dalian University of Technology China Shanghai Jiao Tong University China Fuzhou University China Engineering Research Center of Big Data Intelligence Ministry of Education China Fujian Key Laboratory of Network Computing and Intelligent Information Processing China

Semi-supervised graph domain adaptation, as a branch of graph transfer learning, aims to annotate unlabeled target graph nodes by utilizing transferable knowledge learned from a label-scarce source graph. However, most existing studies primarily concentrate on aligning feature distributions directly to extract domain-invariant features, while ignoring the utilization of the intrinsic structure information in graphs. Inspired by the significance of data structure information in enhancing models' generalization performance, this paper aims to investigate how to leverage the structure information to assist graph transfer learning. To this end, we propose an innovative framework called TFGDA. Specially, TFGDA employs a structure alignment strategy named STSA to encode graphs' topological structure information into the latent space, greatly facilitating the learning of transferable features. To achieve a stable alignment of feature distributions, we also introduce a SDA strategy to mitigate domain discrepancy on the sphere. Moreover, to address the overfitting issue caused by label scarcity, a simple but effective RNC strategy is devised to guide the discriminative clustering of unlabeled nodes. Experiments on various benchmarks demonstrate the superiority of TFGDA over SOTA methods. © 2024 Neural information processing systems foundation. All rights reserved.

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MEFA-Net: A mask enhanced feature aggregation network for polyp segmentation

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Computers in Biology and Medicine 2025年 186卷 109601-109601页

作者： Ke, Xiao Chen, Guanhong Liu, Hao Guo, Wenzhong Fujian Provincial Key Laboratory of Networking Computing and Intelligent Information Processing College of Computer and Data Science Fuzhou University Fuzhou350116 China Engineering Research Center of Big Data Intelligence Ministry of Education Fuzhou350116 China

Accurate polyp segmentation is crucial for early diagnosis and treatment of colorectal cancer. This is a challenging task for three main reasons: (i) the problem of model overfitting and weak generalization due to the multi-center distribution of data;(ii) the problem of interclass ambiguity caused by motion blur and overexposure to endoscopic light;and (iii) the problem of intraclass inconsistency caused by the variety of morphologies and sizes of the same type of polyps. To address these challenges, we propose a new high-precision polyp segmentation framework, MEFA-Net, which consists of three modules, including the plug-and-play Mask Enhancement Module (MEG), Separable Path Attention Enhancement Module (SPAE), and Dynamic Global Attention Pool Module (DGAP). Specifically, firstly, the MEG module regionally masks the high-energy regions of the environment and polyps through a mask, which guides the model to rely on only a small amount of information to distinguish between polyps and background features, avoiding the model from overfitting the environmental information, and improving the robustness of the model. At the same time, this module can effectively counteract the "dark corner phenomenon" in the dataset and further improve the generalization performance of the model. Next, the SPAE module can effectively alleviate the inter-class fuzzy problem by strengthening the feature expression. Then, the DGAP module solves the intra-class inconsistency problem by extracting the invariance of scale, shape and position. Finally, we propose a new evaluation metric, MultiColoScore, for comprehensively evaluating the segmentation performance of the model on five datasets with different domains. We evaluated the new method quantitatively and qualitatively on five datasets using four metrics. Experimental results show that MEFA-Net significantly improves the accuracy of polyp segmentation and outperforms current state-of-the-art algorithms. Code posted on https://***/

关键词： Endoscopy

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A Fine-Grained Anomaly Detection Method Fusing Isolation Forest and Knowledge Graph Reasoning 19th

A Fine-Grained Anomaly Detection Method Fusing Isolation For...

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19th International Conference on Web information Systems and Applications, WISA 2022

作者： Xu, Jie Zhou, Jiantao College of Computer Science Engineering Research Center of Ecological Big Data Ministry of Education National and Local Joint Engineering Research Center of Mongolian Intelligent Information Processing Technology Inner Mongolia Cloud Computing and Service Software Engineering Laboratory Inner Mongolia Social Computing and Data Processing Key Laboratory Inner Mongolia Discipline Inspection and Supervision Big Data Key Laboratory Inner Mongolia Big Data Analysis Technology Engineering Laboratory Inner Mongolia University Hohhot China

ISBN: (纸本)9783031203084

Anomaly detection aims to find outliers data that do not conform to expected behaviors in a specific scenario, which is indispensable and critical in current safety environments related studies. However, when performing outlier detection on a large-scale multidimensional dataset, most of the traditional methods make no distinctions between classes of outliers and lack the reasoning ability and the explainability of the analysis results, which leads to the low accuracy of global outlier detection and the inability to effectively identify local outliers. In this paper, we propose a fine-grained anomaly detection method which well utilizes isolation forest and knowledge graph reasoning tactics. First, a better extracting data feature method and a more reasonable weighted strategy are used to find global outliers based on the traditional isolation forest algorithm, and then we construct a custom rule base according to the in-depth research and analysis of global abnormal data, and at last the ontology knowledge is reasoned based on such rule base to achieve the detection of local outliers. Through analysis of extensive experiment results, our method could effectively discover more abnormal data without big loss of time costs, has strong generalization, and correspondingly improves the performance for abnormal detection. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Anomaly detection

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ReconBoost: Boosting Can Achieve Modality Reconcilement 41

ReconBoost: Boosting Can Achieve Modality Reconcilement

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41st International Conference on Machine Learning, ICML 2024

作者： Hua, Cong Xu, Qianqian Bao, Shilong Yang, Zhiyong Huang, Qingming Key Laboratory of Intelligent Information Processing Institute of Computing Technology Chinese Academy of Sciences Beijing China School of Computer Science and Technology University of Chinese Academy of Sciences Beijing China Institute of Information Engineering Chinese Academy of Sciences Beijing China School of Cyber Security University of Chinese Academy of Sciences Beijing China Key Laboratory of Big Data Mining and Knowledge Management Chinese Academy of Sciences Beijing China

This paper explores a novel multi-modal alternating learning paradigm pursuing a reconciliation between the exploitation of uni-modal features and the exploration of cross-modal interactions. This is motivated by the fact that current paradigms of multi-modal learning tend to explore multi-modal features simultaneously. The resulting gradient prohibits further exploitation of the features in the weak modality, leading to modality competition, where the dominant modality overpowers the learning process. To address this issue, we study the modality-alternating learning paradigm to achieve reconcilement. Specifically, we propose a new method called ReconBoost to update a fixed modality each time. Herein, the learning objective is dynamically adjusted with a reconcilement regularization against competition with the historical models. By choosing a KL-based reconcilement, we show that the proposed method resembles Friedman's Gradient-Boosting (GB) algorithm, where the updated learner can correct errors made by others and help enhance the overall performance. The major difference with the classic GB is that we only preserve the newest model for each modality to avoid overfitting caused by ensembling strong learners. Furthermore, we propose a memory consolidation scheme and a global rectification scheme to make this strategy more effective. Experiments over six multi-modal benchmarks speak to the efficacy of the method. We release the code at https://***/huacong/ReconBoost. Copyright 2024 by the author(s)

关键词： Contrastive Learning

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Polyp Segmentation Neural Network with Simple Encoding Structure and Reverse Attention Module 13

Polyp Segmentation Neural Network with Simple Encoding Struc...

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13th International Conference on information Technology in Medicine and Education, ITME 2023

作者： Wang, Jie Li, Zuoyong Xu, Haiping Cheng, Xuesong Teng, Shenghua College of Electronic and Information Engineering Shandong University of Science and Technology Qingdao266590 China Fujian Provincial Key Laboratory of Information Processing and Intelligent Control College of Computer and Control Engineering Minjiang University Fuzhou350121 China Fujian Key Laboratory of Medical Big Data Engineering Fujian Provincial Hospital Fuzhou350001 China College of Mathematics and Data Science Minjiang University Fuzhou350121 China

ISBN: (纸本)9798350319156

Colorectal cancer is a common malignancy. In colonoscopy images, computer-assisted polyp segmentation helps doctors diagnose and treat disorders more precisely. In recent years, some methods based on deep convolutional neural networks have made significant breakthroughs in this task. However, only a few algorithms explicitly consider the effect of light intensity on segmentation performance, which results in algorithms needing to be more robust for complex samples. This paper proposes a neural network combining a simple encoding structure with a reverse attention module. Specifically, the model uses HarDNet68 as the backbone network, adds a camouflage identification module (CIM) to enhance the capture of polyp details on the underlying features, and finally utilizes adaptive feature fusion with the reverse attention module (RAM). The proposed model effectively addresses the challenge of poor segmentation quality in colonoscopy images caused by inconsistent illumination. Extensive experiments on five datasets show that the proposed model performs well in polyp segmentation. © 2023 IEEE.

关键词： Diseases

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Research on Enhanced Perception and Attention-Driven Person Re-Identification 20

Research on Enhanced Perception and Attention-Driven Person ...

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20th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2024

作者： Wu, Cancan Li, Dong Zhang, Zhi College of Computer Science and Technology Wuhan University of Science and Technology Hubei Wuhan430065 China Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System Hubei Wuhan430065 China Big Data Science and Engineering Research Institute Wuhan University of Science and Technology Hubei Wuhan430065 China

ISBN: (纸本)9798350356328

When matching similarity among pedestrians in images, pedestrian re-identification algorithms are often disturbed by occlusions. A typical tactic is to improve the robustness of occlusion features in the model. However, this approach neglects the noise introduced by other pedestrians in the image, leading to limited learning of relevant information between images. To address these issues, this paper introduces a pedestrian re-identification model that leverages perception-enhanced and attention mechanisms. By enhancing the perception of non-pedestrian noise and erasing non-pedestrian features, we then employ a cross-attention mechanism to subtly embed global and local features for finer feature recognition. Finally, through context attention, we learn the interaction between pedestrian images to improve re-identification accuracy. Results from studies performed on the Market-1501, CUHK03-D, and Duke-ReID datasets indicate that the suggested model surpasses leading contemporary models regarding Rank-1 scores and mean Average Precision (mAP), while maintaining good robustness. © 2024 IEEE.

关键词： Reamers

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FELSDiff: Image Super-Resolution Based on Diffusion Model Fusing Feature Extraction with Latent Space 20

FELSDiff: Image Super-Resolution Based on Diffusion Model Fu...

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20th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2024

作者： Wu, Cancan Zhang, Zhi Wuhan University of Science and Technology College of Computer Science and Technology Hubei Wuhan430065 China Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System Wuhan430065 China Big Data Science and Engineering Research Institute Wuhan University of Science and Technology Hubei Wuhan430065 China

ISBN: (纸本)9798350356328

In addressing issues like an excessive number of network parameters and the loss of fine texture details in image super-resolution reconstruction approaches based on diffusion models, this passage introduces a novel image super-resolution model (FELSDiff). This model relies on the fusion of diffusion models, feature extraction, and latent space. FELSDiff utilizes a Pre-trained CNN for initial super-resolution to extract the primary low-band features and part high-band features of the image. The preliminary super-resolved image is then concatenated as a condition to this model. We introduce a cross-attention mechanism guided by the high-band features of the preliminary super-resolved image to enhance the network's feature extraction capability and obtain more effective features. In the U-Net structure, we incorporate a latent space strategy, enabling the model's training and inference processes to be conducted in the latent space, thereby reducing the number of network parameters. Experimental results on multiple standard datasets indicate that this method outperforms other advanced methods overall. © 2024 IEEE.

关键词： Convolutional neural networks

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Steel Surface Defect Detection Based on Improved YOLOv8 20

Steel Surface Defect Detection Based on Improved YOLOv8

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20th International Conference on Natural Computation, Fuzzy Systems and Knowledge Discovery, ICNC-FSKD 2024

作者： Zhang, Jichen Zhang, Zhi College of Computer Science and Technology Wuhan University of Science and Technology Hubei Wuhan430065 China Hubei Province Key Laboratory of Intelligent Information Processing and Real-time Industrial System Hubei Wuhan430065 China Big Data Science and Engineering Research Institute Wuhan University of Science and Technology Hubei Wuhan430065 China

ISBN: (纸本)9798350356328

There are some defects on the surface of steel that are difficult to detect, so we propose an improved algorithm based on YOLOv8 for detecting defects that are difficult to be detected. This improvement includes the introduction of an SPD module to minimize the problem of information loss due to downsampling;the addition of a small object detection head combined with EMA attention to further enhance the detection capabilities for small targets;the use of BiFPN to replace the original PANet, applying different weights to different features to strengthen feature fusion. Experiments were conducted on the NEU-DET dataset, and the algorithm improved mAP to 80.2%, an improvement of 3.9% over the baseline model. © 2024 IEEE.

关键词： Change detection

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A Unified Framework Integrating Knowledge and data for Collaborative Root Cause Identification

A Unified Framework Integrating Knowledge and Data for Colla...

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Sensing, Measurement & data Analytics in the era of Artificial Intelligence (ICSMD), International Conference on

作者： Jiefei Yu Zicheng Cao Siyi He Zuyi Gu Yingcheng Xu Kai Zhong Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education Institutes of Physical Science and Information Technology Anhui University Anhui China Data Science and Big Data Technology School of Big Data and Statistics Anhui University Anhui China

ISBN: (数字)9798331529192

ISBN: (纸本)9798331529208

Capturing the root cause and propagation path of the fault is critical to ensuring the safety and efficiency of industrial processes, especially those that inadequately utilize process knowledge and data. To address this issue, a unified framework integrating knowledge and data for collaborative root cause identification is proposed. First, the knowledge causal graph (KCG) is constructed using expert knowledge and industrial flow charts, providing a preliminary reference for subsequent causality analysis. Next, by replacing the traditional vector autoregression (VAR) model in Granger Causality (GC) with the gated recurrent unit (GRU), a more reliable causal relationship between variables is obtained. Additionally, a causality fusion propagation path identification method (CF-PPI) is designed to identify the root cause and propagation path of the fault, so that the obtained fault propagation path has less redundancy and higher accuracy. Finally, the method is validated using data from the ASHRAE RP-1043 centrifugal chiller.

关键词： Fault diagnosis Knowledge engineering Reactive power Analytical models Delay effects Redundancy Collaboration Cause effect analysis Vectors Safety

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