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Quorum sensing-based interactions among drugs,microbes,and diseases

science China(Life sciences) 2023年第1期66卷 137-151页

作者： Shengbo Wu Shujuan Yang Manman Wang Nan Song Jie Feng Hao Wu Aidong Yang Chunjiang Liu Yanni Li Fei Guo Jianjun Qiao School of Chemical Engineering and Technology Tianjin UniversityTianjin 300072China School of Computer Science and Engineering Central South UniversityChangsha 410083China State Key Laboratory of Chemical Engineering Tianjin UniversityTianjin 300072China Collaborative Innovation Center of Chemical Science and Engineering(Tianjin) Tianjin 300072China Key Laboratory of Systems Bioengineering Ministry of Education(Tianjin University)Tianjin 300072China School of Computer Science and Technology College of Intelligence and ComputingTianjin UniversityTianjin 300350China Department of Engineering Science University of OxfordOxford OX13PJUK Institute of Shaoxing Tianjin UniversityShaoxing 312300China

Many diseases and health conditions are closely related to various microbes,which participate in complex interactions with diverse drugs;nonetheless,the detailed targets of such drugs remain to be *** existing studies have reported causal associations among drugs,gut microbes,or diseases,calling for a workflow to reveal their intricate *** this study,we developed a systematic workflow comprising three modules to construct a Quorum Sensing-based Drug-Microbe-Disease(QSDMD)database(http://***/),which includes diverse interactions for more than 8,000 drugs,163 microbes,and 42 common *** interactions between microbes and more than 8,000 drugs have been systematically studied by targeting microbial QS receptors combined with a docking-based virtual screening technique and in vitro experimental ***,we have constructed a QS-based drug-receptor interaction network,proposed a systematic framework including various drug-receptor-microbe-disease connections,and mapped a paradigmatic circular interaction network based on the QS-DMD,which can provide the underlying QS-based mechanisms for the reported causal *** QS-DMD will promote an understanding of personalized medicine and the development of potential therapies for diverse *** work contributes to a paradigm for the construction of a molecule-receptor-microbe-disease interaction network for human health that may form one of the key knowledge maps of precision medicine in the future.

关键词： quorum sensing drugs microbe-disease association microbe-host interaction gut microbiota personalized medicine

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Boundary-Preserving Parallel Refinement for Tetrahedral Meshes

Boundary-Preserving Parallel Refinement for Tetrahedral Mesh...

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high performance and Smart computing (HPSC), IEEE International Conference on

作者： Tinghao Yang Xiang Zhang Chunye Gong Xiang Gao Chuanfu Xu Jie Liu College of Computer Science and Technology National University of Defense Technology Changsha PR. China Laboratory of Digitizing Software for Frontier Equipment National University of Defense Technology Changsha PR. China State Key Laboratory of High Performance Computing National University of Defense Technology Changsha PR. China

ISBN: (数字)9798331596637

ISBN: (纸本)9798331596644

Mesh refinement is to increase the number of mesh elements by cutting each mesh element into multiple sub-ones. Though it can accelerate meshing and optimize mesh quality, the boundary of mesh elements as usual deviate from the respective complex geometry, especially with sharp curvatures. Besides, it demands more memory footprint for large problem size. Here, this paper devises a parallel boundary preserving mesh refinement method to addresses the above issues. Particularly, it seeks the longest edges for new point insertion so that mesh elements decouple with each other for high parallelism. More importantly, when the boudary mesh elements are refined, some new points sampled from the geometry will be inserted into their faces so that the new mesh elements are aware of boundary. As compared to refinement algorithms tailored for standalone machines and used by mainstream commercial softwares, the proposed refinement method offers promising efficiency.

关键词： Geometry Costs high performance computing Fitting Parallel processing Data structures Surface fitting Software Surface treatment Faces

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Unknown-Aware Bilateral Dependency Optimization for Defending Against Model Inversion Attacks

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IEEE Transactions on Pattern Analysis and Machine Intelligence 2025年第8期PP卷 PP页

作者： Peng, Xiong Liu, Feng Wang, Nannan Lan, Long Liu, Tongliang Cheung, Yiu-Ming Han, Bo Hong Kong Baptist University Department of Computer Science Hong Kong The University of Melbourne School of Computing and Information Systems Australia Xidian University State Key Laboratory of Integrated Services Networks School of Telecommunications Engineering Shaanxi Xi'an710071 China National University of Defense Technology State Key Laboratory of High Performance Computing School of Computer Hunan Changsha410000 China The University of Sydney Sydney AI Centre School of Computer Science Faculty of Engineering Australia

By abusing access to a well-trained classifier, model inversion (MI) attacks pose a significant threat as they can recover the original training data, leading to privacy leakage. Previous studies mitigated MI attacks by imposing regularization to reduce the dependency between input features and outputs during classifier training, a strategy known as unilateral dependency optimization. However, this strategy contradicts the objective of minimizing the supervised classification loss, which inherently seeks to maximize the dependency between input features and outputs. Consequently, there is a trade-off between improving the model's robustness against MI attacks and maintaining its classification performance. To address this issue, we propose the bilateral dependency optimization strategy (BiDO), a dual-objective approach that minimizes the dependency between input features and latent representations, while simultaneously maximizing the dependency between latent representations and labels. BiDO is remarkable for its privacy-preserving capabilities. However, models trained with BiDO exhibit diminished capabilities in out-of-distribution (OOD) detection compared to models trained with standard classification supervision. Given the open-world nature of deep learning systems, this limitation could lead to significant security risks, as encountering OOD inputs—whose label spaces do not overlap with the in-distribution (ID) data used during training-is inevitable. To address this, we leverage readily available auxiliary OOD data to enhance the OOD detection performance of models trained with BiDO. This leads to the introduction of an upgraded framework, unknown-aware BiDO (BiDO+), which mitigates both privacy and security concerns. As a highlight, with comparable model utility, BiDO-HSIC+ reduces the FPR95 by 55.02% and enhances the AUCROC by 9.52% compared to BiDO-HSIC, while also providing superior MI robustness. © 1979-2012 IEEE.

关键词： Differential privacy

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A Cross-domain Radar Emitter Recognition Method with Few-shot Learning

A Cross-domain Radar Emitter Recognition Method with Few-sho...

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computer Engineering and Intelligent Communications (ISCEIC), International Symposium on

作者： Yixian Luo Tianrui Liu Xueqiong Li Hengzhu Liu Institute for Quantum Information & State Key Laboratory of High Performance Computing National University of Defense Technology Changsha China College of Computer National University of Defense Technology Changsha China

In many realistic scenarios, it is necessary but challenging to acquire a large number of annotated radar emitter samples for training a recognition model. This study proposes a cross-domain radar emitter recognition method with few-shot learning, which introduces model-agnostic meta-learning (MAML) to recognize radar emitter and improves it to adapt to various types of radar emitter in different domains without spending a lot of time and data to retrain the model. This method can learn an ideal initialization parameter with a few source domain samples, and then initialize with this parameter on a completely different target domain. It can obtain good generalization effect by fine-tuning with fewer samples, so as to realize cross-domain recognition of radar emitter. Simulation results show that the accuracy of the proposed method can reach more than 90% in high-noise target domains with completely different data distribution from the source domain, which shows its superiority in recognition performance and sample size compared with other radar emitter recognition methods.

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New Advanced computing Architecture for Cryptography Design and Analysis by D-Wave Quantum Annealer

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Tsinghua science and technology 2022年第4期27卷 751-759页

作者： Xiangmin Ji Baonan Wang Feng Hu Chao Wang Huanguo Zhang College of Computer Information Science Fujian Agriculture and Forestry UniversityFuzhou 350002China School of Cyber Science and Engineering Wuhan UniversityWuhan 430072China College of Computer Science and Technology Shanghai University of Electric PowerShanghai 200090China International Research Laboratory of Specialty Fiber Optics and Advanced Communication Shanghai UniversityShanghai 200444 State Key Laboratory of Cryptology Beijing 100878China laboratory of Specialty Fiber Optics and Optical Access Networks Joint International Research Laboratory of Specialty Fiber Optics and Advanced CommunicationShanghai UniversityShanghai 200444 State Key Laboratory of Cryptology Beijing 100878and also with Center for Quantum ComputingPeng Cheng LaboratoryShenzhen 518000China School of Cyber Science and Engineering Wuhan UniversityWuhan 430072

Universal quantum computers are far from achieving practical *** D-Wave quantum computer is initially designed for combinatorial ***,exploring the potential applications of the D-Wave device in the field of cryptography is of great ***,although we optimize the general quantum Hamiltonian on the basis of the structure of the multiplication table(factor up to 1005973),this study attempts to explore the simplification of Hamiltonian derived from the binary structure of the integers to be factored.A simple factorization on 143 with four qubits is provided to verify the potential of further advancing the integer-factoring ability of the D-Wave ***,by using the quantum computing cryptography based on the D-Wave 2000 Q system,this research further constructs a simple version of quantum-classical computing architecture and a Quantum-Inspired Simulated Annealing(QISA)*** functions and a high-performance platform are introduced,and additional balanced Boolean functions with high nonlinearity and optimal algebraic immunity can be *** comparison between QISA and Quantum Annealing(QA)on six-variable bent functions not only shows the potential speedup of QA,but also suggests the potential of architecture to be a scalable way of D-Wave annealer toward a practical cryptography design.

关键词： Quantum Annealing(QA) factorization Boolean functions brain-inspired cognition

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Cluster-guided Contrastive Class-imbalanced Graph Classification 39

Cluster-guided Contrastive Class-imbalanced Graph Classifica...

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39th Annual AAAI Conference on Artificial Intelligence, AAAI 2025

作者： Ju, Wei Mao, Zhengyang Yi, Siyu Qin, Yifang Gu, Yiyang Xiao, Zhiping Shen, Jianhao Qiao, Ziyue Zhang, Ming College of Computer Science Sichuan University Chengdu China School of Computer Science State Key Laboratory for Multimedia Information Processing PKU-Anker LLM Lab Peking University Beijing China College of Mathematics Sichuan University Chengdu China Paul G. Allen School of Computer Science and Engineering University of Washington SeattleWA United States Huawei Hisilicon Shanghai China School of Computing and Information Technology Great Bay University Dongguan China

ISBN: (纸本)157735897X

This paper studies the problem of class-imbalanced graph classification, which aims at effectively classifying the graph categories in scenarios with imbalanced class distributions. While graph neural networks (GNNs) have achieved remarkable success, their modeling ability on imbalanced graph-structured data remains suboptimal, which typically leads to predictions biased towards the majority classes. On the other hand, existing class-imbalanced learning methods in vision may overlook the rich graph semantic substructures of the majority classes and excessively emphasize learning from the minority classes. To address these challenges, we propose a simple yet powerful approach called C3GNN that integrates the idea of clustering into contrastive learning to enhance class-imbalanced graph classification. Technically, C3GNN clusters graphs from each majority class into multiple subclasses, with sizes comparable to the minority class, mitigating class imbalance. It also employs the Mixup technique to generate synthetic samples, enriching the semantic diversity of each subclass. Furthermore, supervised contrastive learning is used to hierarchically learn effective graph representations, enabling the model to thoroughly explore semantic substructures in majority classes while avoiding excessive focus on minority classes. Extensive experiments on real-world graph benchmark datasets verify the superior performance of our proposed method against competitive baselines. Copyright © 2025, Association for the Advancement of Artificial Intelligence (***). All rights reserved.

关键词： Contrastive Learning

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Super-Resolution of Diffusion-Weighted Images via TDI-Conditioned Diffusion Model 15th

Super-Resolution of Diffusion-Weighted Images via TDI-Cond...

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15th International Workshop on Computational Diffusion MRI, CDMRI 2024, held in conjunction with 27th International Conference on Medical Image computing and computer-Assisted Intervention, MICCAI 2024

作者： Ma, Jiquan Teng, Yujun Chen, Geng Jiang, Haotian Zhang, Kai Liu, Feihong Rekik, Islem Shen, Dinggang School of Computer Science and Technology Heilongjiang University Harbin China National Engineering Laboratory for Integrated Aero-Space-Ground-Ocean Big Data Application Technology School of Computer Science and Engineering Northwestern Polytechnical University Xi’an China School of Biomedical Engineering and State Key Laboratory of Advanced Medical Materials and Devices ShanghaiTech University Shanghai China School of Information Science and Technology Northwest University Xi’an China BASIRA Lab Imperial-X and Department of Computing Imperial College London London United Kingdom

ISBN: (纸本)9783031869198

Diffusion-Weighted Imaging (DWI) is a significant technique for studying white matter. However, it suffers from low-resolution obstacles in clinical settings. Post-acquisition Super-Resolution (SR) can enhance the resolution of DWIs and has gained increasing research interest in recent years. An advanced generative model, the Diffusion Model (DM), exhibits particularly promising performance in image SR. However, effective conditions are required to bootstrap the DM for DWI SR. To this end, we proposed the first DM-based DWI SR model with two effective conditions based on low-solution DWIs and Track Density Imaging (TDI) maps, which possess rich high-resolution prior knowledge Additionally, we consider another condition based on features from low-resolution DWIs. These two conditions are integrated into our model, which comprises three components: DWI Resolution Enhancer (DRE), DWI Feature Extractor (DFE), and TDI Feature Extractor (TFE). DRE combines low-resolution DWI features from DFE with TDI features from TFE to progressively generate high-resolution DWIs. We performed extensive experiments on DWIs of normal subjects from human connectome projects and patients with Parkinson’s disease. The results demonstrate that our model outperforms existing DWI SR models, both qualitatively and quantitatively. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2025.

关键词： Neurodegenerative diseases

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high Quality Global Routing Algorithm Based on Multi-Stage Optimization

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Jisuanji Fuzhu Sheji Yu Tuxingxue Xuebao/Journal of computer-Aided Design and computer Graphics 2024年第4期36卷 607-614页

作者： Genggeng, Liu Zhenyu, Pei Ning, Xu College of Computer and Data Science Fuzhou University Fuzhou350116 China State Key Laboratory of Computer Architecture Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China School of Information Engineering Wuhan University of Technology Wuhan430070 China

Global routing is a crucial step in VLSI physical design. To address the problems that the low utilization rate of capacity and easy to fall into local optimum in the existing global routing algorithms, a high-quality global routing algorithm based on multi-stage optimization is proposed. First, the virtual capacity dynamic adjustment strategy is introduced in the pre-connection stage and the routing reorganization stage to improve the utilization rate of capacity. Then, in the routing reorganization stage, the routing subarea adaptive expansion strategy is proposed to narrow the search space and improve the routing efficiency. Finally, the A* algorithm heuristic search is combined with the global search capability of the particle swarm algorithm to avoid the algorithm to choose the shortest path in the routing process, and thus avoid the algorithm to fall into the local optimum. Experimental results comparing with existing global routing algorithms on ISPD benchmark circuits show that the routing results of proposed algorithm reduce the wirelength by 6.0% to 22.8%. © 2024 Institute of computing technology. All rights reserved.

关键词： Routing algorithms

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Symbolic Execution of MPI Programs with One-Sided Communications

Symbolic Execution of MPI Programs with One-Sided Communicat...

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Asia-Pacific Conference on Software Engineering

作者： Nenghui Hu Zheng Bian Ziqi Shuai Zhenbang Chen Yufeng Zhang College of Computer National University of Defense Technology China Key Laboratory of Software Engineering for Complex Systems National University of Defense Technology China State Key Laboratory of High Performance Computing National University of Defense Technology China College of Computer Science and Electronic Engineering Hunan University Changsha China

Message-passing interface (MPI) programs are non-deterministic and challenging to ensure correctness. The introduction of one-sided communications makes the problem of non-determinism more severe for MPI programs. This paper reports our in-progress work of symbolic execution for the MPI programs with one-sided communications. Our approach can cover the non-determinism caused by the inputs, one-sided communication, and message- passing operations of MPI programs. The preliminary evaluation's results indicate the promising of our approach.

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Unsatisfiable Core Based Constraint Solving Cache in Symbolic Execution

Unsatisfiable Core Based Constraint Solving Cache in Symboli...

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Asia-Pacific Conference on Software Engineering

作者： Ziqi Shuai Zhenbang Chen Yufeng Zhang Hengbiao Yu Ji Wang College of Computer National University of Defense Technology China Key Laboratory of Software Engineering for Complex Systems National University of Defense Technology China State Key Laboratory of High Performance Computing National University of Defense Technology China College of Computer Science and Electronic Engineering Hunan University Changsha China

Constraint solving stands out as a significant bot-tleneck in symbolic execution. Caching is a commonly adopted approach to alleviate this bottleneck. However, the cutting-edge caching technique targeting unsatisfiable constraints, known as unsatisfiable core caching, primarily involves checking whether the constraint being solved contains an unsatisfiable core that has been previously collected. Such straightforward reuse frequently proves less effective in numerous scenarios. In this paper, we present a novel method to enhance the utilization of unsatisfiable cores. By excavating unsatisfiable cores, our method can compute an easily solvable over-approximation that tends to be unsatis-fiable for each constraint, which facilitates the determination of the satisfiability of the original constraint. We implemented our method on KLEE symbolic executor. The evaluation results on 27 real-world programs are encouraging.

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