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Lightweight axiom pinpointing via replicated driver and customized SAT-solving

Frontiers of Computer Science 2023年第2期17卷 121-133页

作者： Dantong OUYANG Mengting LIAO Yuxin YE College of Computer Science and Technology Jilin UniversityChangchun 130012China Key Laboratory of Symbolic Computation and Knowledge Engineering(Jilin University) Ministry of EducationChangchun 130012China

In description logic,axiom pinpointing is used to explore defects in ontologies and identify hidden justifications for a logical *** recent years,SAT-based axiom pinpointing techniques,which rely on the enumeration of minimal unsatisfiable subsets(MUSes)of pinpointing formulas,have gained increasing *** with traditional Tableau-based reasoning approaches,SAT-based techniques are more competitive when computing justifications for consequences in large-scale lightweight description logic *** this article,we propose a novel enumeration justification algorithm,working with a replicated *** replicated driver discovers new justifications from the explored justifications through cheap literals resolution,which avoids frequent calls of SAT ***,when the use of SAT solver is inevitable,we adjust the strategies and heuristic parameters of the built-in SAT solver of axiom pinpointing *** adjusted SAT solver is able to improve the checking efficiency of unexplored *** proposed method is implemented as a tool named *** experimental results show that RDMinA outperforms the existing axiom pinpointing tools on practical biomedical ontologies such as Gene,Galen,NCI and Snomed-CT.

关键词： axiom pinpointing description logic SAT solver

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Meta-GPS++: Enhancing Graph Meta-Learning with Contrastive Learning and Self-Training

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ACM Transactions on knowledge Discovery from Data 2024年第9期18卷 1-30页

作者： Liu, Yonghao Li, Mengyu Li, Ximing Huang, Lan Giunchiglia, Fausto Liang, Yanchun Feng, Xiaoyue Guan, Renchu Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Changchun China University of Trento Trento Italy Zhuhai Lab. of the Key Lab. of Symbolic Computation and Knowledge Eng. of the Ministry of Education Zhuhai College of Science and Technology Zhuhai China

Node classification is an essential problem in graph learning. However, many models typically obtain unsatisfactory performance when applied to few-shot scenarios. Some studies have attempted to combine meta-learning with graph neural networks to solve few-shot node classification on graphs. Despite their promising performance, some limitations remain. First, they employ the node encoding mechanism of homophilic graphs to learn node embeddings, even in heterophilic graphs. Second, existing models based on meta-learning ignore the interference of randomness in the learning process. Third, they are trained using only limited labeled nodes within the specific task, without explicitly utilizing numerous unlabeled nodes. Finally, they treat almost all sampled tasks equally without customizing them for their uniqueness. To address these issues, we propose a novel framework for few-shot node classification called Meta-GPS. Specifically, we first adopt an efficient method to learn discriminative node representations on homophilic and heterophilic graphs. Then, we leverage a prototype-based approach to initialize parameters and contrastive learning for regularizing the distribution of node embeddings. Moreover, we apply self-Training to extract valuable information from unlabeled nodes. Additionally, we adopt S (scaling and shifting) transformation to learn transferable knowledge from diverse tasks. The results on real-world datasets show the superiority of Meta-GPS. Our code is available here. © 2024 Copyright held by the owner/author(s).

关键词： Contrastive Learning

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Learning continuous network emerging dynamics from scarce observations via data-adaptive stochastic processes

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Science China(Information Sciences) 2024年第12期67卷 240-255页

作者： Jiaxu CUI Qipeng WANG Bingyi SUN Jiming LIU Bo YANG College of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Public Computer Education and Research Center Jilin University Department of Computer Science Hong Kong Baptist University

Learning network dynamics from the empirical structure and spatio-temporal observation data is crucial to revealing the interaction mechanisms of complex networks in a wide range of domains. However,most existing methods only aim at learning network dynamic behaviors generated by a specific ordinary differential equation instance, resulting in ineffectiveness for new ones, and generally require dense *** observed data, especially from network emerging dynamics, are usually difficult to obtain, which brings trouble to model learning. Therefore, learning accurate network dynamics with sparse, irregularly-sampled,partial, and noisy observations remains a fundamental challenge. We introduce a new concept of the stochastic skeleton and its neural implementation, i.e., neural ODE processes for network dynamics(NDP4ND), a new class of stochastic processes governed by stochastic data-adaptive network dynamics, to overcome the challenge and learn continuous network dynamics from scarce observations. Intensive experiments conducted on various network dynamics in ecological population evolution, phototaxis movement, brain activity, epidemic spreading, and real-world empirical systems, demonstrate that the proposed method has excellent data adaptability and computational efficiency, and can adapt to unseen network emerging dynamics, producing accurate interpolation and extrapolation with reducing the ratio of required observation data to only about 6% and improving the learning speed for new dynamics by three orders of magnitude.

关键词： complex networks network dynamics emerging spatio-temporal dynamics neural processes

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Efficient Sharing of Energy Consumption Data: A Privacy-Preserving Threshold Aggregation Approach

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IEEE Internet of Things Journal 2025年第13期12卷 23988-24002页

作者： Li, Guohao Zhou, Lu Lian, Jiale Liu, Siyi Yang, Li Zhong, Yantao Li, Qiang Xidian University School of Computer Science and Technology Xi’an China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun China Co. Ltd Guangdong Shenzhen China

Energy consumption data collected by smart meters is increasingly used by various subscribers in the smart grid for load management, energy monitoring, and policy planning. To protect user privacy, edge-assisted privacy-preserving data aggregation (PPDA) techniques are commonly employed. However, existing methods face several challenges: i) limited scalability, ii) strict trust requirements, and iii) the risk of revealing unique consumption patterns to data collectors. To address these challenges, we propose a privacy-preserving threshold aggregation method that is easily scalable and facilitates efficient energy data sharing under limited trust assumptions. Specifically, we design VFPNTRU, a quantum-resistant homomorphic proxy re-encryption scheme with fault tolerance and re-encryption verification. In VFP-NTRU, smart meters can encrypt data with a public key without the need for prior negotiation of decryption keys with multiple subscribers. Additionally, we develop a privacy threshold collection protocol that uses a verifiable oblivious pseudorandom function to provide privacy guarantees similar to k-anonymity for SM data collection. We further introduce an energy consumption model to determine optimal collection strategies, improving system responsiveness. We provide correctness analysis and prove the security of our scheme. Experimental results demonstrate that our approach outperforms existing PPDA methods, making it particularly suitable for resource-constrained smart meters and central servers managing large-scale energy data. © 2014 IEEE.

关键词： Differential privacy

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PBCounter:weighted model counting on pseudo-boolean formulas

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Frontiers of Computer Science 2025年第3期19卷 55-63页

作者： Yong LAI Zhenghang XU Minghao YIN College of Computer Science and Technology Jilin UniversityChangchun 130012China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin UniversityChangchun 130012China School of Computer Science and Information Technology Northeast Normal UniversityChangchun 130017China

In Weighted Model Counting(WMC),we assign weights to literals and compute the sum of the weights of the models of a given propositional formula where the weight of an assignment is the product of the weights of its *** current WMC solvers work on Conjunctive Normal Form(CNF)***,CNF is not a natural representation for human-being in many *** by the stronger expressive power of Pseudo-Boolean(PB)formulas than CNF,we propose to perform WMC on PB *** on a recent dynamic programming algorithm framework called ADDMC for WMC,we implement a weighted PB counting tool *** compare PBCounter with the state-of-the-art weighted model counters SharpSAT-TD,ExactMC,D4,and ADDMC,where the latter tools work on CNF with encoding methods that convert PB constraints into a CNF *** experiments on three domains of benchmarks show that PBCounter is superior to the model counters on CNF formulas.

关键词： weighted model counting pseudo-boolean constraint algebraic decision diagrams preprocessing techniques

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Migration: An Efficient Explorer Operator to Guide Swarm Evolution 1

Migration: An Efficient Explorer Operator to Guide Swarm Evo...

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1st IEEE International Conference on Medical Artificial Intelligence, MedAI 2023

作者： Han, Xiaosong Zhou, Chengyang Liang, Yanchun Guan, Renchu College of Computer Science and Technology Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering National Education Ministry Changchun China College of Computer Science and Technology Zhuhai Laboratory of Key Laboratory for Symbol Computation and Knowledge Engineering Ministry of Education Jilin University Zhuhai College of Science and Technology Key Laboratory for Symbol Computation and Knowledge Engineering National Education Ministry Zhuhai China

ISBN: (纸本)9798350358780

Particle Swarm Optimization with Migration (MPSO) is proposed to solve the issue that PSO will encounter unbearable time cost problems when dealing with High-dimension, Expensive and Black-box objective function tasks. The Migration operator is inspired by the migration of Salmon. Salmon will start a dangerous journey from the ocean to the home rivers for reproduction. The process of the entire behavior is similar to the reduction and recovery of dimension. Therefore, we design the Migration operator where a pretrained Wasserstein Autoencoders (WAE) is applied to simulate the migration behavior to accelerate the process of evolution in PSO, and we use Least-Squares Regression in lower space to produce better generation. In comparison with famous baseline methods in some benchmark functions, MPSO converges faster and more accurately, which shows the great potential of migration operations. © 2023 IEEE.

关键词： Particle swarm optimization (PSO)

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Multiparticipant Federated Feature Selection Algorithm With Particle Swarm Optimization for Imbalanced Data Under Privacy Protection

IEEE Transactions on Artificial Intelligence

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IEEE Transactions on Artificial Intelligence 2023年第5期4卷 1002-1016页

作者： Hu, Ying Zhang, Yong Gong, Dunwei Sun, Xiaoyan China University of Mining and Technology School of Information and Control Engineering Xuzhou221008 China Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Changchun130012 China

In the real world, data describing the same learning task may be distributed in different institutions (called participants), and these participants cannot share their own data due to the need of privacy protection. How to select an optimal feature subset on the basis of ensuring the data privacy of each participant is an important and challenging topic. At the same time, data on part participants show imbalanced or even miss some classes, further increasing the difficulty of solving this kind of problem. In view of this, by introducing a trusted third party to process and integrate optimal information from participants, this article proposes a multiparticipant federated evolutionary feature selection algorithm for imbalanced data under privacy protection. First, a multilevel joint sample filling strategy with multiple participants (called sampling-rough selection-fine tuning strategy) is proposed to fill imbalanced or empty classes on each participant while ensuring data privacy. Then, a federated evolutionary feature selection method based on particle swarm optimization (PSO) is proposed by periodically sharing the optimal feature subsets obtained by PSOs on participants. Finally, the proposed algorithm is applied to 15 test datasets, and compared with several typical imbalanced feature selection algorithms and two kinds of ensemble feature selection algorithms. The experimental results show that the proposed algorithm can significantly promote the ability of each participant on processing imbalanced datasets, and improve the classification accuracy of obtained feature subsets while protecting the participants' data privacy. © 2020 IEEE.

关键词： Clustering algorithms

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Foundation models in bioinformatics

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National Science Review 2025年第4期12卷 400-418页

作者： Fei Guo Renchu Guan Yaohang Li Qi Liu Xiaowo Wang Can Yang Jianxin Wang Hunan Provincial Key Lab on Bioinformatics School of Computer Science and Engineering Central South University Xiangjiang Laboratory Key Laboratory for Symbol Computation and Knowledge Engineering of the Ministry of Education College of Computer Science and Technology Jilin University Department of Computer Science Old Dominion University School of Life Sciences and Technology Tongji University Department of Automation Tsinghua University Department of Mathematics State Key Laboratory of Molecular Neuroscience and Big Data Bio-Intelligence Lab The Hong Kong University of Science and Technology

With the adoption of foundation models(FMs),artificial intelligence(AI) has become increasingly significant in bioinformatics and has successfully addressed many historical challenges,such as pre-training frameworks,model evaluation and *** demonstrate notable proficiency in managing large-scale,unlabeled datasets,because experimental procedures are costly and labor *** various downstream tasks,FMs have consistently achieved noteworthy results,demonstrating high levels of accuracy in representing biological entities.A new era in computational biology has been ushered in by the application of FMs,focusing on both general and specific biological *** this review,we introduce recent advancements in bioinformatics FMs employed in a variety of downstream tasks,including genomics,transcriptomics,proteomics,drug discovery and single-cell *** aim is to assist scientists in selecting appropriate FMs in bioinformatics,according to four model types:language FMs,vision FMs,graph FMs and multimodal *** addition to understanding molecular landscapes,AI technology can establish the theoretical and practical foundation for continued innovation in molecular biology.

关键词： foundation model bioinformatics genomics transcriptomics proteomics drug discovery single-cell analysis

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Auxiliary Tasks Benefit Skeleton-based Action Recognition

Auxiliary Tasks Benefit Skeleton-based Action Recognition

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2025 IEEE International Conference on Acoustics, Speech, and Signal Processing, ICASSP 2025

作者： Yang, Yuheng Chen, Haipeng College of Computer Science and Technology Key Laboratory of Symbolic Computation and Knowledge Engineering Ministry of Education Jilin University Changchun China

ISBN: (纸本)9798350368741

Skeleton-based action recognition has long been a fundamental and intriguing problem in machine intelligence. This task is challenging due to pose occlusion and rapid motion, which typically results in incomplete or noisy skeleton data. State-of-the-art methods tend to learn human motion directly from these corrupted skeletons as if they were reliable. Unfortunately, this might lead to unsatisfactory results when key regions of the skeleton are occluded or disturbed. To tackle the problem, we propose a novel framework that integrates auxiliary tasks into a motion modeling network. These auxiliary tasks corrupt partial human skeletons with masking or noise and then force the network to recover the corrupted data, explicitly facilitating robust feature representation learning. We further propose supervising the auxiliary tasks with mutual information losses, mathematically ensuring feature consistency and spatial alignment between the recovered and original skeleton data. Empirically, our approach sets the new state-of-the-art performance on three benchmark datasets. © 2025 IEEE.

关键词： auxiliary task mutual information skeleton-based action recognition

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PNESR-DDI: An Effective Drug-Drug Interaction Prediction Model Based on Pretraining Method and Enhanced Subgraph Reconstruction

PNESR-DDI: An Effective Drug-Drug Interaction Prediction Mod...

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2024 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2024

作者： Chen, Ke Han, Xiaosong Li, Xiaoran Liang, Yanchun Xu, Dong Guan, Renchu Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Software Changchun China Jilin University Key Laboratory for Symbol Computation and Knowledge Engineering of National Education Ministry College of Computer Science and Technology Changchun China Zhuhai College of Science and Technology Zhuhai Laboratory of Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education School of Computer Science Zhuhai China University of Missouri Christopher S. Bond Life Sciences Center Department of Electrical Engineering and Computer Science Columbia United States

ISBN: (纸本)9798350386226

Drug-Drug Interaction (DDI) task plays a crucial role in clinical treatment and drug development. Recently, deep learning methods have been successfully applied for DDI prediction. However, training deep learning models always need large amount of data, while known DDIs are scarce. To address this challenge, a graph neural network-based DDI prediction model named PNESR-DDI is proposed, which compensates for the lack of DDIs by enriching drug representations. First, to obtain initial node representations that incorporate rich semantic information from the biomedical knowledge graph (KG), a link prediction pre-training method on external KG is proposed in the node embedding pre-training module. Then, considering the large scale of the KG, subgraph extraction for the target drug pairs is introduced to reduce noise and decrease computational complexity in the subgraph anchoring module. After that, the subgraph is updated, and node similarities are propagated in the subgraph reconstruction module. Based on the node similarity scores, the subgraph is pruned and reconstructed, which adjusts node representations to be more conducive to DDI prediction. Finally, the drug embeddings, subgraph representations, and drug fingerprint features are concatenated to predict DDIs. PNESRDDI is evaluated on two benchmark DDI datasets: DrugBank and TWOSIDES. Experiment results show that PNESR-DDI achieves better performance than baselines. Ablation results validate the effectiveness of the pre-training method and the adaptive subgraph reconstruction strategy. © 2024 IEEE.

关键词： knowledge graph

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