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IEEE Transactions on Computational Biology and Bioinformatics 2025年第1期22卷 250-260页

作者： Xiaoxiao Liu Hui Lv Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian China

The application of DNA strand displacement (DSD) for synchronizing chaotic systems has made remarkable progress in recent years. However, uncertainty may exist in the systems, and interference is unavoidable during the synchronization process. This article endeavors to tackle the issue of performance degradation in synchronization caused by disturbances and system uncertainties. Primarily, in order to introduce perturbations in chaotic systems using DSD, the corresponding chemical reaction networks (CRNs) is derived from the ordinary differential equations of the perturbation signal in this paper, leading to the establishment of a composite function that combines trigonometric and exponential functions. Furthermore, combining the design of nonlinear observers with adaptive control methods not only simplifies the derivation process but also allows for the construction of observers using fewer DSD reactions. Through the collaborative efforts of the adaptive law and the observer, it enables the estimation of perturbations and system uncertainties, thereby achieving the synchronization of heterogeneous chaotic systems. Finally, the proposed method successfully synchronizes the Lorenz system and Yang system, even in the presence of system uncertainties and disturbances, demonstrating its effectiveness.

关键词： Observers Synchronization Uncertainty Perturbation methods Computational biology Bioinformatics DNA Chaotic communication Costs Estimation error

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A Dual-Capture and Dual-Output 3D DNA Walker System Integrated with Ligases Enables Ultrasensitive Detection of Single-Nucleotide Polymorphisms

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Analytical Chemistry 2025年第17期97卷 9316-9325页

作者： Zhang, Yunshan Tan, Qianglong Yang, Fang Huang, Tuo Yu, Siyu Ye, Jing Zeng, Jianxian Feng, Xianzhong Zhang, Diming Key Laboratory of Soybean Molecular Design Breeding National Key Laboratory of Black Soils Conservation and Utilization Northeast Institute of Geography and Agroecology Chinese Academy of Sciences Changchun130102 China Research Center for Novel Computing Sensing and Intelligent Processing Zhejiang Laboratory Hangzhou311121 China Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Zhejiang Hangzhou310024 China School of Chemistry and Chemical Engineering Hunan University of Science and Technology Hunan Xiangtan411201 China

DNA walkers, as structurally and functionally programmable signal amplification tools, exhibit great potential for application in the field of biosensing. Traditional DNA walkers often rely on enzymes for operation, posing compatibility challenges, while the handful of existing enzyme-free DNA walkers demonstrate limited performance. To address this, we innovatively developed an efficient enzyme-free 3D DNA walker with dual capture and dual output capabilities. Coupled with ligase chain reaction (LCR), this system facilitates highly sensitive and specific detection of single nucleotide polymorphisms (SNPs). Specifically, LCR precisely identifies single-base mutations, effectively transmitting biological information. The 3D DNA walker system is based on entropy-driven circuit cycling reaction technology. In this system, LCR products serve as the driving strands for the DNA walker, independently binding to track strands and walking legs immobilized on gold nanoparticles, forming a unique dual signal capture mechanism. Each track strand carries two signal chains, significantly enhancing signal amplification efficiency. Benefiting from this novel enzyme-free 3D DNA walker strategy, our biosensing system exhibits exceptional sensitivity to mutant targets (MT), detecting MT at concentrations as low as 30.3 aM and distinguishing heterozygous samples with a 0.01% mutation frequency. Furthermore, this system has been successfully applied to genotyping and mutation abundance assessment of genomes from fresh soybean leaves, demonstrating its vast potential for practical applications. In summary, this research pioneers a novel enzyme-free 3D DNA walker with dual capture and dual output capabilities, and develops an ultrasensitive genotyping tool. This provides strong technical support for the advancement of genetic research. © 2025 American Chemical Society.

关键词： Nucleotides

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MBF-DTI: A Fused Multi-dimensional Biochemical Feature-Based Drug Target Prediction Method Based on Heterogeneous Graph Attention Networks

MBF-DTI: A Fused Multi-dimensional Biochemical Feature-Based...

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10th China Health Information Processing Conference, CHIP 2024

作者： Zhao, Haixue Yao, Kui Liu, Yunjiong Che, Chao Tang, Lin Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Dalian116622 China School of Software Engineering Dalian University Dalian116622 China

ISBN: (纸本)9789819637515

Drug-target interaction prediction help reduce the cost and time of drug development. However, existing research often overlooks the complexity of biological interactions. To address this issue, this paper proposes a DTI prediction model that integrates multi-dimensional biochemical features. Specifically, the model utilizes a heterogeneous graph attention network to capture the topological relationships among biological entities from diverse data, providing a deep understanding of the interactions among drugs, proteins, diseases, and side effects. A molecular attention Transformer network and a CBiNet module are used to extract the key structural features of drugs and targets. By automatically optimizing the weight distribution between drugs and targets, the model enhances the information transfer during network training, significantly improving model performance. Experimental results on real-world datasets demonstrate that the proposed model outperforms the current state-of-the-art methods in the field. Among the top 50 novel COVID-19 therapeutic drugs predicted by our model, 30 have been supported by clinical trials or scientific literature, further demonstrating the effectiveness of our proposed method in drug repurposing. Experimental data and supplementary materials are available online at: https://***/Eadog/MBF-DTI. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： COVID-19

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A Flexible Knowledge Graph Error Detection Framework Combined with Semantic Information 12th

A Flexible Knowledge Graph Error Detection Framework Combine...

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12th CCF Conference on BigData, BigData 2024

作者： Zhao, Yangwu Liu, Yang Ao, Xiang He, Qing Henan Institute of Advanced Technology Zhengzhou University Zhengzhou China Beijing China Key Lab of Intelligent Information Processing Institute of Computing Technology CAS Beijing China

ISBN: (纸本)9789819610235

Knowledge graphs (KGs) are extensively utilized in numerous applications, including question-answering systems and recommender systems. However, knowledge graphs are often constructed through web crawling or crowdsourcing, leading to errors in the data. The task of knowledge graph error detection aims to identify inaccurate triplets in KGs and has received substantial attention in recent years. However, the majority of current error detection methods overlook the semantic information of the triplets, which can be vital for accurate error detection. In this paper, we introduce a Flexible Knowledge Graph Error Detection Framework that integrates Semantic Information (FKED), which combines both structural and semantic information to detect errors within the knowledge graph. FKED first extracts the structural information of KGs using a graph embedding model. Next, FKED employs a pre-trained language model (PLM) to extract semantic information from the triplets. Then the structural and semantic information are combined to detect errors within the knowledge graph. FKED can be flexibly added to other structure-based error detection models, enhancing their capabilities in downstream tasks of knowledge graphs. We assess FKED using two benchmark datasets: FB15k-237 and WN18RR. Experimental results indicate that our method is both superior and effective, substantially improving the performance of the base models. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： Knowledge graph

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Rsta: A Reversible Signal Transmission Architecture for Breaking the Limitation of Unidirectional Transmission

SSRN

引用

SSRN 2025年

作者： Liu, Xin Cui, Shuang Zhang, Xun Zhou, Fuxing Sheng, Kaikai Wang, Bin Zhang, Qiang School of Computer Science and Technology Dalian University of Technology Dalian116024 China Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian University Dalian116622 China

Molecular circuits are essential tools for biosensing and molecular information processing. However, the long-distance and reversible transmission of orthogonal signals remains a significant challenge in molecular circuits, preventing molecular signals from achieving reversible transmission similar to that of electrical signals in wires. To overcome the limitations of unidirectional signal transmission and facilitate the integration of antagonistic circuits. We propose a reversible signal transmission architecture (RSTA) with wire-like characteristics to achieve reversible signal transmission based on fundamental molecular devices known as reversible signal fan-out devices (RSFDs). The polarity of the input signal dictates the transmission direction, establishing the initial condition for the output signals. Cascaded RSFDs within RSTA offer two key advantages. First, the temporal response to signals. Second, the reversible transformation of opposite circuit types without structural modification. We experimentally validated the principles and functionality of RSTA using temporal logic device and integrated molecular circuits. This work advances the field of reversible molecular signal transmission, enabling the rational design of complex molecular circuits and molecular information processing systems. We envision applications of this technology in nanomachines, molecular computing, and biosensing. © 2025, The Authors. All rights reserved.

关键词： Temporal logic

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Improving Event-Level Financial Sentiment Analysis with Retrieval-Augmented Multipath Chain-of-Thought Prompting 12th

Improving Event-Level Financial Sentiment Analysis with Ret...

引用

12th CCF Conference on BigData, BigData 2024

作者： Zhang, Yiming Ao, Xiang Yu, Guoxin He, Qing Henan Institute of Advanced Technology Zhengzhou University Zhengzhou450002 China Beijing100190 China Key Lab of Intelligent Information Processing Institute of Computing Technology CAS Beijing100190 China

ISBN: (纸本)9789819610235

Event-level Financial Sentiment Analysis (EFSA) aims to extract all the quintuples containing five sentiment elements from a given financial news text, which has gained prominence as an emerging domain recently. The present study utilizes a 4-hop Chain-of-Thought (CoT) prompting based on LLMs to predict sentiment elements in a fixed order, which neglects the interdependencies among the sentiment elements within a quintuple. Inspired by recent multi-view prompting (MvP) and CoT ideas, we propose a novel framework termed Retrieval-Augmented Multipath Chain-of-Thought (RMP-CoT) that aggregates quintuples generated by LLMs through different reasoning paths, leveraging a retrieval-augmented mechanism. Specifically, RMP-CoT integrates different element orders into CoT prompting to guide LLMs in generating multiple sentiment quintuples through the utilization of retrieval-augmented mechanism, and then selects the most plausible quintuples by voting. To investigate the effectiveness of our framework, we conduct extensive experiments on four benchmark tasks of EFSA. RMP-CoT pushes the state-of-the-art by over 6% F1 on the EFSA task and also performs quite effectively on the other sub-tasks of EFSA. © The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd. 2025.

关键词： Chain-of-Thought Event-level Sentiment Analysis Financial Sentiment Analysis

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Family of Mutually Uncorrelated Codes for DNA Storage Address design

IEEE Transactions on Nanobioscience

引用

IEEE Transactions on Nanobioscience 2025年 PP卷 PP页

作者： Liu, Zhenlu Cao, Ben Shao, Qi Zheng, Yanfen Wang, Bin Zhou, Shihua Zheng, Pan Dalian University Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education School of Software Engineering Dalian116622 China Dalian University of Technology School of Computer Science and Technology Dalian116024 China University of Canterbury Upper Riccarton Department of Accounting and Information Systems Christchurch8140 New Zealand

Deoxyribonucleic acid (DNA) has become an ideal medium for long-term storage and retrieval due to its extremely high storage density and long-term stability. But access efficiency is an existing bottleneck in DNA storage, especially the lack of high-quality random access address sequences. Therefore, in this paper, we report a series of approaches based on k-weakly mutually uncorrelated (k-WMU) codes to design the address sequence to improve the access efficiency of DNA storage. To address the problem of DNA sequences that are poorly scalable at the base level, we propose a 0-m-ruling coding scheme combined with k-WMU codes that can make address sequences avoid generating secondary structure with stem lengths ranging from 3 to 9. Based on the decoupled structure, We further extend the k-WMU codes with error correction function while satisfying combinatorial biological constraints. In order to investigate the performance of the designed address sequences for real-world applications, we perform simulation experiments based on thermodynamic properties and error correction capability as well as compared the minimum free energy (MFE), melting temperature (TM), and average decoding success rate (ADSR) with previous work. The results show that designed address sequences have a high MFE value and ADSR and a substantial reduction in TM-variance while satisfying the combinatorial biological constraints. As the quality of address sequences improves, this will help to achieve accurate random access as well as enhance the robustness of the DNA storage system. © 2002-2011 IEEE.

关键词： DNA sequences

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NavG: Risk-Aware Navigation in Crowded Environments Based on Reinforcement Learning with Guidance Points

arXiv

引用

arXiv 2025年

作者： Zhang, Qianyi Luo, Wentao Liu, Boyi Zhang, Ziyang Wang, Yaoyuan Liu, Jingtai Institute of Robotics and Automatic Information System Nankai University Tianjin Key Laboratory of Intelligent Robotics Tianjin China Advanced Computing and Storage Lab Huawei 2012 Lab China Department of Electronic and Computer Engineering The Kong Kong University of Science and Technology Hong Kong

Motion planning in navigation systems is highly susceptible to upstream perceptual errors, particularly in human detection and tracking. To mitigate this issue, the concept of guidance points—a novel directional cue within a reinforcement learning-based framework—is introduced. A structured method for identifying guidance points is developed, consisting of obstacle boundary extraction, potential guidance point detection, and redundancy elimination. To integrate guidance points into the navigation pipeline, a perception-to-planning mapping strategy is proposed, unifying guidance points with other perceptual inputs and enabling the RL agent to effectively leverage the complementary relationships among raw laser data, human detection and tracking, and guidance points. Qualitative and quantitative simulations demonstrate that the proposed approach achieves the highest success rate and near-optimal travel times, greatly improving both safety and efficiency. Furthermore, real-world experiments in dynamic corridors and lobbies validate the robot’s ability to confidently navigate around obstacles and robustly avoid pedestrians. © 2025, CC BY.

关键词： Travel time

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A novel ECT image reconstruction method based on the deblurring diffusion model

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Flow Measurement and Instrumentation 2025年 104卷

作者： Liu, Yan-Dong Wu, Xin-Jie Liu, Shi-Xing Wang, Yi-Fan Key Laboratory of Advanced Design and Intelligent Computing Ministry of Education Dalian University Liaoning Dalian116622 China School of Software Engineering Dalian University Liaoning Dalian116622 China College of Physics Liaoning University Liaoning Shenyang110036 China School of Information Science and Engineering Shenyang University of Technology Liaoning Shenyang110870 China

To address the challenge of low reconstruction accuracy in Electrical Capacitance Tomography (ECT) images, we propose an imaging method based on a deblurring diffusion model, transforming the image reconstruction into image generation. In cases where the noise type affecting the ECT image reconstruction cannot be determined, inspired by the cold diffusion model, we use an alpha kernel instead of Gaussian noise to perform the image blurring process. During the deblurring process, we utilize the U-Net as the backbone network and incorporated the Linear Attention module to improve imaging accuracy. Additionally, recognizing the similarity between image error metrics and the Dice function, we integrate the Dice function into the loss. Simulation experiments demonstrate that the image errors and correlation coefficients using the proposed method outperform those achieved with the LBP, Tikhonov, Landweber, and classic CNNs. Finally, we deploy the proposed algorithm to the actual ECT system. © 2025 Elsevier Ltd

关键词： Image denoising

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AN EMPIRICAL ANALYSIS OF UNCERTAINTY IN LARGE LANGUAGE MODEL EVALUATIONS

arXiv

引用

arXiv 2025年

作者： Xie, Qiujie Li, Qingqiu Yu, Zhuohao Zhang, Yuejie Zhang, Yue Yang, Linyi Zhejiang University China School of Engineering Westlake University China School of Computer Science Shanghai Key Lab of Intelligent Information Processing Shanghai Collaborative Innovation Center of Intelligent Visual Computing Fudan University China Peking University China Westlake Institute for Advanced Study China University College London United Kingdom Huawei Noah’s Ark Lab Hong Kong

As LLM-as-a-Judge emerges as a new paradigm for assessing large language models (LLMs), concerns have been raised regarding the alignment, bias, and stability of LLM evaluators. While substantial work has focused on alignment and bias, little research has concentrated on the stability of LLM evaluators. In this paper, we conduct extensive experiments involving 9 widely used LLM evaluators across 2 different evaluation settings to investigate the uncertainty in model-based LLM evaluations. We pinpoint that LLM evaluators exhibit varying uncertainty based on model families and sizes. With careful comparative analyses, we find that employing special prompting strategies, whether during inference or post-training, can alleviate evaluation uncertainty to some extent. By utilizing uncertainty to enhance LLM’s reliability and detection capability in Out-Of-Distribution (OOD) data, we further fine-tune an uncertainty-aware LLM evaluator named ConfiLM using a human-annotated fine-tuning set and assess ConfiLM’s OOD evaluation ability on a manually designed test set sourced from the 2024 Olympics. Experimental results demonstrate that incorporating uncertainty as additional information during the fine-tuning phase can largely improve the model’s evaluation performance in OOD scenarios. The code and data are released at: https://***/hasakiXie123/LLM-Evaluator-Uncertainty. © 2025, CC BY-NC-SA.

关键词： Digital elevation model

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