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A hybrid algorithm based on artificial bee colony and pigeon inspired optimization for 3D protein structure prediction

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Journal of Bionanoscience 2018年第1期12卷 100-108页

作者： Li, Ting Zhou, Changjun Wang, Bin Xiao, Boxiang Zheng, Xuedong Key Laboratory of Advanced Design and Intelligent Computing Dalian University Ministry of Education Dalian116622 China Beijing Key Laboratory of Digital Plant Beijing100097 China

With the accomplishment of the Human Genome Project, the significance of protein structure research becomes more outstanding. The prediction of protein structure is aimed at the study of amino acid molecules, and belongs to the field of Bio-Nano research. There are two kinds of methods to study protein structure: Experiment and theory. This paper adopts ab-initio prediction method which is one of theoretical methods. Based on the "thermodynamic hypothesis," there are many different models applied to the field. This paper selects 3D AB off-lattice model to solve this problem. ABC-PIO combines the characteristics of the diversity generated by artificial bee colony algorithm and the fast convergence speed of pigeon inspired optimization. At the end of this algorithm, Cauchy perturbation strategy is added to optimize the local optimum. Two functions are introduced to dynamically control two operators of the hybrid algorithm. In order to test the quality of ABC-PIO, ten real protein sequences from the Protein Data Bank have been selected. Compared with other four algorithms, the algorithm gets better result. To calculate the error between the predicted and the true protein structure RMSD is set. Comparisons are made not only in the convergence curves but also in the backbone drawings. © 2018 American Scientific Publishers.

关键词： Optimization

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The polishing surface quality of single crystal diamond with GO green-enhanced diamond hybrid slurry and material removal mechanism analysis

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Wear 2025年 574-575卷

作者： Wang, Zixuan Hou, Xueyan Zhao, Ji Yao, Jie Yu, Tianbiao Qu, Sheng Zhao, Jun School of Mechanical Engineering and Automation Northeastern University Shenyang110819 China Liaoning Provincial Key Laboratory of High-end Equipment Intelligent Design and Manufacturing Technology Shenyang110819 China School of Physics Liaoning University Shenyang110036 China School of Mechanical Engineering Shenyang University of Technology Shenyang110870 China School of Advanced Manufacturing Sun Yat-sen University Shenzhen518107 China

Single crystal diamonds, which have extremely high hardness and brittleness, can provide lower power consumption and higher frequencies for electronic devices compared with other semiconductor materials. The chemical mechanical polishing method is usually used to realize the flattening of single crystal diamond workpiece. However, the conventional oxidants may cause damage to polishing tools and experimental equipment, and even lead to environmental pollution. Therefore, a graphene oxide green-enhanced diamond hybrid slurry was introduced in this study for single crystal diamond polishing with quartz glass as a polishing disk. The effect of graphene oxide on polishing surface quality was analyzed, and the polishing experiments were carried out with different polishing pressures and durations to investigate the influence of varying process parameters. The molecular dynamics method was used to simulate the formation and removal process of graphene oxide-induced degraded layer on single crystal diamond surface. The scratched morphologies on single crystal diamond surfaces were obtained, and the amorphization degree was analyzed to reveal the subsurface damage mechanism. The simulation shows that the oxygen-containing functional groups from graphene oxide chemically react with the carbon atoms on the single crystal diamond surface, removing in the form of CO, CO2, or adhering to the abrasive grains. Also, the chemical adsorption reduced the activation energy of carbon atoms in single crystal diamond, and made it more loosely arranged and easier to be removed by mechanical scratching, which explained the experimental results. © 2025 Elsevier B.V.

关键词： Single crystals

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Deployment strategies of on-orbit service vehicles for multi-objective group and multiple spacecraft

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International Journal of Engineering Systems Modelling and Simulation 2017年第2期9卷 96-102页

作者： Zhang, Jianxin Zhang, Qiang Wei, Xiaopeng Key Lab of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian116622 China

A novel deployment method of on-orbit service vehicles (OSVs) design for multiple-objective and multiple-orbit missions is evaluated in this paper. The given deployment method mainly includes four steps, and respectively are: 1) dividing the predetermined region into unequal and independent servicing spaces;2) calculating parking-orbit for different target areas;3) computing the minimum number of OSVs;4) calculating the position elements of each parking-orbit. The proposed method can cover the service areas by using the fewest OSVs, which can improve the efficiency of the OSV program. Although the present exploration of deployment strategy is based on circular orbital models, this method can be directly extended to other orbital models. The calculation examples based on Glonass and GPS constellation orbits shows the proposed method is effective. © 2017 Inderscience Enterprises Ltd.

关键词： Orbits

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Adaptive Backdoor Attacks with Reasonable Constraints on Graph Neural Networks

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IEEE Transactions on Dependable and Secure computing 2025年

作者： Dong, Xuewen Li, Jiachen Li, Shujun You, Zhichao Qu, Qiang Kholodov, Yaroslav Shen, Yulong The School of Computer Science and Technology Xidian University The Engineering Research Center of Blockchain Technology Application and Evaluation Ministry of Education China The Shaanxi Key Laboratory of Blockchain and Secure Computing Xi’an710071 China The School of Computing Kent Interdisciplinary Research Centre in Cyber Security University of Kent CanterburyCT2 7NF United Kingdom Shenzhen Institute of Advanced Technology Chinese Academy of Sciences China The Intelligent Transportation Systems Lab Innopolis University Innopolis Russia The School of Computer Science and Technology Xidian University China

Recent studies show that graph neural networks (GNNs) are vulnerable to backdoor attacks. Existing backdoor attacks against GNNs use fixed-pattern triggers and lack reasonable trigger constraints, overlooking individual graph characteristics and rendering insufficient evasiveness. To tackle the above issues, we propose ABARC, the first Adaptive Backdoor Attack with Reasonable Constraints, applying to both graph-level and node-level tasks in GNNs. For graph-level tasks, we propose a subgraph backdoor attack independent of the graph’s topology. It dynamically selects trigger nodes for each target graph and modifies node features with constraints based on graph similarity, feature range, and feature type. For node-level tasks, our attack begins with an analysis of node features, followed by selecting and modifying trigger features, which are then constrained by node similarity, feature range, and feature type. Furthermore, an adaptive edge-pruning mechanism is designed to reduce the impact of neighbors on target nodes, ensuring a high attack success rate (ASR). Experimental results show that even with reasonable constraints for attack evasiveness, our attack achieves a high ASR while incurring a marginal clean accuracy drop (CAD). When combined with the state-of-the-art defense randomized smoothing (RS) method, our attack maintains an ASR over 94%, surpassing existing attacks by more than 7%. © 2004-2012 IEEE. All rights reserved.

关键词： Graph neural networks

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Text-guided Reconstruction Network for Sentiment Analysis with Uncertain Missing Modalities

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IEEE Transactions on Affective computing 2025年

作者： Shi, Piao Hu, Min Nakagawa, Satoshi Zheng, Xiangming Shi, Xuefeng Ren, Fuji Hefei University of Technology Key Laboratory of Knowledge Engineering with Big Data Ministry of Education Anhui Province Key Laboratory of Affective Computing and Advanced Intelligent Machine National Smart Eldercare International Science and Technology Cooperation Base School of Computer Science and Information Engineering Anhui Hefei230601 China Bozhou University School of Electronic and Information Engineering Bozhou236800 China University of Tokyo Graduate School of Information Science and Technology Tokyo113-8656 Japan University of Electronic Science and Technology of China College of Computer Science and Engineering Chengdu611731 China University of Electronic Science and Technology of China Shenzhen Institute for Advanced Study Shenzhen518110 China

Multimodal Sentiment Analysis (MSA) is an attractive research that aims to integrate sentiment expressed in textual, visual, and acoustic signals. There are two main problems in the existing methods: 1) the dominant role of the text is underutilization in unaligned multimodal data, and 2) the modality under uncertain missing feature is not sufficiently explored. This paper proposes a Text-guided Reconstruction Network (TgRN) for MSA with uncertain missing modalities in non-aligned sequences. The TgRN network includes three primary modules: Text-guided Extraction Module (TEM), Reconstruction Module (RM) and Text-guided Fusion Module (TFM). First, the TEM consists of the text-guided cross attention units and self-attention units to capture inter-modal features and intra-modal features, respectively. Second, leveraging enhanced attention units and a three-way squeeze-and-excitation block, the RM is designed to learn semantic information from incomplete data and reconstruct missing modality features. Third, the TFM utilizes a progressive modality-mixing adaptation gate to explore the dynamic correlations between nonverbal and verbal modalities, effectively addressing the modality gap issue. Finally, under the supervision of sentiment prediction loss and reconstruction loss, the TgRN effectively processes both uncertain missing-modality conditions and ideal complete modality conditions. Extensive experiments on CMU-MOSI and CH-SIMS demonstrate that our proposed method outperforms state-of-the-art approaches. © 2010-2012 IEEE.

关键词： Semantics

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Acoustic scene classification by enhanced high- frequency weak signal characteristic spectrum 8

Acoustic scene classification by enhanced high- frequency we...

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8th International Conference on computing and Pattern Recognition, ICCPR 2019

作者： Hao, Wenjie Zhao, Lasheng Zhang, Qiang Key Laboratory of Advanced Design Intelligent Computing Ministry of Education Dalian University China

ISBN: (纸本)9781450376570

In the acoustic scene classification task, the method of using melspectrogram to express the acoustic scene information is widely applied. However, mel-spectrogram has defects and it ignores important information about some acoustic scenes. The paper improves the mel-spectrogram and its generation algorithm. Including: I. For the sensitivity of the acoustic scene to highfrequency acoustic signals, the paper changes the filter design method of Mel Frequency Cepstrum Coefficient (MFCC). This method preserves more high frequency information by applying the equal-height triangular filter banks and increasing the number of the filters. II. Based on the previous step, an enhancement algorithm is proposed for the problem of the lack of highfrequency weak signals in the characteristic spectrum. The algorithm performs nonlinear mapping on the mel-spectrogram, which makes the transformed high-frequency weak signal feature information more obvious. The algorithm is verified by DCASE 2018 acoustic scene classification dataset and LITIS ROUEN dataset. The experimental results demonstrate the effectiveness of the proposed algorithm. © 2019 Association for computing Machinery.

关键词： Spectrographs

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Effects of Woody Plant Roots on Migration of Ciprofloxacin and Tylosin in Soil

SSRN

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SSRN 2025年

作者： Li, Jingfang Ma, Huiting Hu, Xiaoming Chen, Liang Fallgren, Paul H. State Key Laboratory of Hydraulic Engineering Intelligent Construction and Operation Tianjin University Tianjin300350 China School of Civil Engineering Tianjin University Tianjin300350 China Shandong Province Traffic Planning and Design Institute Group Co. Ltd. Jinan Shandong250101 China Advanced Environmental Technologies LLC Fort CollinsCO80525 United States

Antibiotics are an emerging environmental concern that may impact water sources via transport through soil. Woody plants with well-developed root systems and longer root lengths change soil properties that may influence the migration of antibiotics. This study investigated the migration of ciprofloxacin (CIP) and tylosin (TYL) through soil with woody plant roots. Experiments were conducted with soil columns with three different woody plants with different root types, which included Sophora japonica (taproot), Malus baccata (fibrous root), and Malus pumila Mill. (characteristically both taproot and fibrous root). The woody plant roots increased the infiltration capacity by 39.53–56.29%, which was a factor in increasing antibiotic mass in the soil column discharge. The CIP discharge mass increased by 0.05–0.52 times and the TYL discharge mass increased by 1.36–2.59 times, where higher discharge mass was observed from the taproot system of S. japonica compared to the other root system types. The woody plant roots promoted CIP adsorption (increase of 30.41–101.22%) and inhibited TYL adsorption (decrease of 62.41–86.49%). The woody plant roots promoted antibiotic migration to the middle and lower root layers in the soil column. The correlation between CIP adsorption to soil and soil organic matter (SOM) was insignificant (p > 0.05, r = 0.41), while there was a negative correlation between TYL adsorption and SOM content (p © 2025, The Authors. All rights reserved.

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Stfi: Structure-Aware and Time-Frequency Domain Interaction Network for Deformable Medical Image Registration

SSRN

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SSRN 2025年

作者： Hu, Rui Wang, Nian Zhang, Yuxin Li, Teng Key Laboratory of Intelligent Computing and Signal Processing Ministry of Education School of Electrical Engineering and Automation Anhui University Hefei230601 China Advanced Imaging Research Center University of Texas Southwestern Medical Center 5323 Harry Hines Blvd Dallas75390 United States School of Cyber Science and Engineering Southeast University No.2 Southeast University Road Nanjing211189 China

Deformable image registration is crucial in medical image analysis. Recently, unsupervised methods using intensity matching have shown promising results without labeled data. However, these methods still face challenges: (1) They often encounter local optima when handling anatomical structures with significant variations in intensity distribution;(2) Time domain convolution in decoders leads to loss of high-frequency fine features, limiting the effectiveness of generating fine deformation vector fields. To address these issues, we propose a novel structure-aware and time-frequency domain interaction (STFI) network. STFI integrates a structure-aware frequency domain loss and a time-frequency domain interaction module. The former leverages principal structural information from the weighted phase spectrum to guide the registration process, thereby reducing the risk of local optima. The latter processes and amalgamates information from both the time and frequency domains, effectively preserving high-frequency details. The efficacy and adaptability of our approach have been demonstrated on two types of data, offering a new perspective on exploiting time-frequency domain information for medical image registration. © 2025, The Authors. All rights reserved.

关键词： Image registration

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Hybrid Matching Teacher Framework for Cross-Domain Visual Detection Transformer

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IEEE Transactions on intelligent Transportation Systems 2025年

作者： Wang, Xiaowei Suo, Jinhui Li, Yang Gao, Ming Jiang, Peiwen Dai, Pengwen Hunan University State Key Laboratory of Advanced Design and Manufacturing Technology for Vehicle College of Mechanical and Vehicle Engineering Changsha 410082 China Hunan University Wuxi Intelligent Control Research Institute Wuxi 214115 China Sun Yat-sen University School of Cyber Science and Technology Shenzhen Campus Shenzhen 518107 China

Object detection is a critical component of autonomous vehicle perception systems. However, domain shifts between training environments and real-world scenarios often degrade detector performance. Cross-domain object detection aims to adapt detectors to unlabeled target domains utilizing only labeled source data. Recent popular cross-domain object detection methods employ the mean teacher framework, which uses pseudo-labels generated by the teacher model to guide training on unlabeled real-world data. Despite its effectiveness, continuous training with noisy pseudo-labels leads to abnormal performance degradation in the later stages of training. To address this issue, we propose a novel Hybrid Matching Teacher (HMT) framework for cross-domain visual detection transformers, which enhances cross-domain knowledge transfer across pseudo-label generation, filtering, and training processes. Specifically, we design a Feature Sparse Alignment (FSA) module to adapt DETR tokens and queries, generate domain-adaptive weights to initialize the teacher-student models, and mitigate the inherent initial source bias in the teacher model. Next, a Localization-aware Pseudo-label Filtering (LPF) module ensures high-quality pseudo-labels by considering the consistency between localization and classification tasks. Furthermore, to improve the efficiency of pseudo-label training, the Cross-view Hybrid Matching (CHM) module introduces an auxiliary matching branch to increase the number of positive queries that match with pseudo-labels. Extensive experiments demonstrate that our approach achieves state-of-the-art performance, outperforming previous benchmarks by 3.1%, 8.5%, and 4.4% in adverse weather, diverse scenes, and synthetic-to-real, respectively. © 2000-2011 IEEE.

关键词： Autonomous vehicles cross-domain object detection detection transformer domain adaptation mean teacher

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Non-reciprocity of energy transfer derived from cubic stiffness-induced nonlinear phenomena

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Results in Physics 2025年 73卷

作者： Kong, Na Sun, Min Chen, Jianen Tianjin Key Laboratory for Advanced Mechatronic System Design and Intelligent Control School of Mechanical Engineering Tianjin University of Technology Tianjin 300384 China National Demonstration Center for Experimental Mechanical and Electrical Engineering Education Tianjin University of Technology Tianjin 300384 China School of Science Tianjin Chengjian University Tianjin 300384 China

Introducing purely nonlinear elastic elements can induce rich dynamic behaviors, such as bifurcations, jumps and isolated resonance curves, to linear systems. Therefore, these elements are suitable for constructing strong non-reciprocity of vibration energy transfer. First, the energy transfer along reciprocal directions in a three-degree-of-freedom system is investigated, where three oscillators are connected by cubic springs. The semi-analytical solutions of the system are obtained using the complexification-averaging method and the least squares method. The results are compared against numerical solutions obtained by the Runge-Kutta method. The excitation amplitude range that produces strong non-reciprocity of vibration energy is analyzed. The jump phenomenon under combined excitation is investigated, and a trigger method for constructing non-reciprocity using an impulse is proposed. Then, an oscillator chain with cubic stiffness and scaling parameters is embedded into a multi-degree-of-freedom linear oscillator system to further explore the effect of cubic stiffness. Energy transfer along two directions is compared by exciting the leftmost oscillator and the rightmost oscillator. Moreover, the trigger effect of the impulse on non-reciprocity is demonstrated. The results show significant differences in vibration energy transfer within three distinct frequency bands. The critical points between reciprocal and non-reciprocal states are obtained, and the three stages of reciprocity related to excitation amplitude are analyzed. Lastly, the modulation effect of the cubic stiffness on non-reciprocity is conducted by comparing the energy of the output oscillator. © 2025 The Authors

关键词： Cubic stiffness Energy transfer Jump phenomenon Non-reciprocity

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