Guodong Li;Bowei Zhao;Xiaorui Su;Dongxu Li;Yue Yang;Zhi Zeng;Lun Hu
{"title":"Learning Sequential and Structural Dependencies Between Nucleotides for RNA N6-Methyladenosine Site Identification","authors":"Guodong Li;Bowei Zhao;Xiaorui Su;Dongxu Li;Yue Yang;Zhi Zeng;Lun Hu","doi":"10.1109/JAS.2024.124233","DOIUrl":"https://doi.org/10.1109/JAS.2024.124233","url":null,"abstract":"N6-methyladenosine (m6A) is an important RNA methylation modification involved in regulating diverse biological processes across multiple species. Hence, the identification of m6A modification sites provides valuable insight into the biological mechanisms of complex diseases at the post-transcriptional level. Although a variety of identification algorithms have been proposed recently, most of them capture the features of m6A modification sites by focusing on the sequential dependencies of nucleotides at different positions in RNA sequences, while ignoring the structural dependencies of nucleotides in their three-dimensional structures. To overcome this issue, we propose a cross-species end-to-end deep learning model, namely CR-NSSD, which conduct a cross-domain representation learning process integrating nucleotide structural and sequential dependencies for RNA m6A site identification. Specifically, CR-NSSD first obtains the pre-coded representations of RNA sequences by incorporating the position information into single-nucleotide states with chaos game representation theory. It then constructs a cross-domain reconstruction encoder to learn the sequential and structural dependencies between nucleotides. By minimizing the reconstruction and binary cross-entropy losses, CR-NSSD is trained to complete the task of m6A site identification. Extensive experiments have demonstrated the promising performance of CR-NSSD by comparing it with several state-of-the-art m6A identification algorithms. Moreover, the results of cross-species prediction indicate that the integration of sequential and structural dependencies allows CR-NSSD to capture general features of m6A modification sites among different species, thus improving the accuracy of cross-species identification.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 10","pages":"2123-2134"},"PeriodicalIF":15.3,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142137513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Fuzzy-Model-Based Finite Frequency Fault Detection Filtering Design for Two-Dimensional Nonlinear Systems","authors":"Meng Wang;Huaicheng Yan;Jianbin Qiu;Wenqiang Ji","doi":"10.1109/JAS.2024.124452","DOIUrl":"https://doi.org/10.1109/JAS.2024.124452","url":null,"abstract":"This article studies the fault detection filtering design problem for Roesser type two-dimensional (2-D) nonlinear systems described by uncertain 2-D Takagi-Sugeno (T-S) fuzzy models. Firstly, fuzzy Lyapunov functions are constructed and the 2-D Fourier transform is exploited, based on which a finite frequency fault detection filtering design method is proposed such that a residual signal is generated with robustness to external disturbances and sensitivity to faults. It has been shown that the utilization of available frequency spectrum information of faults and disturbances makes the proposed filtering design method more general and less conservative compared with a conventional non-frequency based filtering design approach. Then, with the proposed evaluation function and its threshold, a novel mixed finite frequency \u0000<tex>$mathcal{H}_{infty}/mathcal{H}_{-}$</tex>\u0000 fault detection algorithm is developed, based on which the fault can be immediately detected once the evaluation function exceeds the threshold. Finally, it is verified with simulation studies that the proposed method is effective and less conservative than conventional non-frequency and/or common Lyapunov function based filtering design methods.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 10","pages":"2099-2110"},"PeriodicalIF":15.3,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142137530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shouyong Jiang;Jinglei Guo;Yong Wang;Shengxiang Yang
{"title":"Evolutionary Multi/Many-Objective Optimisation via Bilevel Decomposition","authors":"Shouyong Jiang;Jinglei Guo;Yong Wang;Shengxiang Yang","doi":"10.1109/JAS.2024.124515","DOIUrl":"https://doi.org/10.1109/JAS.2024.124515","url":null,"abstract":"Decomposition of a complex multi-objective optimisation problem (MOP) to multiple simple subMOPs, known as M2M for short, is an effective approach to multi-objective optimisation. However, M2M facilitates little communication/collaboration between subMOPs, which limits its use in complex optimisation scenarios. This paper extends the M2M framework to develop a unified algorithm for both multi-objective and many-objective optimisation. Through bilevel decomposition, an MOP is divided into multiple subMOPs at upper level, each of which is further divided into a number of single-objective subproblems at lower level. Neighbouring subMOPs are allowed to share some subproblems so that the knowledge gained from solving one sub-MOP can be transferred to another, and eventually to all the sub-MOPs. The bilevel decomposition is readily combined with some new mating selection and population update strategies, leading to a high-performance algorithm that competes effectively against a number of state-of-the-arts studied in this paper for both multi- and many-objective optimisation. Parameter analysis and component analysis have been also carried out to further justify the proposed algorithm.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1973-1986"},"PeriodicalIF":15.3,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141993916","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Risk-Informed Model-Free Safe Control of Linear Parameter-Varying Systems","authors":"Babak Esmaeili;Hamidreza Modares","doi":"10.1109/JAS.2024.124479","DOIUrl":"https://doi.org/10.1109/JAS.2024.124479","url":null,"abstract":"This paper presents a risk-informed data-driven safe control design approach for a class of stochastic uncertain nonlinear discrete-time systems. The nonlinear system is modeled using linear parameter-varying (LPV) systems. A model-based probabilistic safe controller is first designed to guarantee probabilistic \u0000<tex>$lambda$</tex>\u0000-contractivity (i.e., stability and invariance) of the LPV system with respect to a given polyhedral safe set. To obviate the requirement of knowing the LPV system model and to bypass identifying its open-loop model, its closed-loop data-based representation is provided in terms of state and scheduling data as well as a decision variable. It is shown that the variance of the closed-loop system, as well as the probability of safety satisfaction, depends on the decision variable and the noise covariance. A minimum-variance direct data-driven gain-scheduling safe control design approach is presented next by designing the decision variable such that all possible closed-loop system realizations satisfy safety with the highest confidence level. This minimum-variance approach is a control-oriented learning method since it minimizes the variance of the state of the closed-loop system with respect to the safe set, and thus minimizes the risk of safety violation. Unlike the certainty-equivalent approach that results in a risk-neutral control design, the minimum-variance method leads to a risk-averse control design. It is shown that the presented direct risk-averse learning approach requires weaker data richness conditions than existing indirect learning methods based on system identification and can lead to a lower risk of safety violation. Two simulation examples along with an experimental validation on an autonomous vehicle are provided to show the effectiveness of the presented approach.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1918-1932"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Regional Multi-Agent Cooperative Reinforcement Learning for City-Level Traffic Grid Signal Control","authors":"Yisha Li;Ya Zhang;Xinde Li;Changyin Sun","doi":"10.1109/JAS.2024.124365","DOIUrl":"https://doi.org/10.1109/JAS.2024.124365","url":null,"abstract":"This article studies the effective traffic signal control problem of multiple intersections in a city-level traffic system. A novel regional multi-agent cooperative reinforcement learning algorithm called RegionSTLight is proposed to improve the traffic efficiency. Firstly a regional multi-agent Q-learning framework is proposed, which can equivalently decompose the global Q value of the traffic system into the local values of several regions. Based on the framework and the idea of human-machine cooperation, a dynamic zoning method is designed to divide the traffic network into several strong-coupled regions according to real-time traffic flow densities. In order to achieve better cooperation inside each region, a lightweight spatio-temporal fusion feature extraction network is designed. The experiments in synthetic, real-world and city-level scenarios show that the proposed RegionSTLight converges more quickly, is more stable, and obtains better asymptotic performance compared to state-of-the-art models.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1987-1998"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Target Controllability of Multi-Layer Networks with High-Dimensional Nodes","authors":"Lifu Wang;Zhaofei Li;Ge Guo;Zhi Kong","doi":"10.1109/JAS.2023.124152","DOIUrl":"https://doi.org/10.1109/JAS.2023.124152","url":null,"abstract":"This paper studies the target controllability of multi-layer complex networked systems, in which the nodes are high-dimensional linear time invariant (LTI) dynamical systems, and the network topology is directed and weighted. The influence of inter-layer couplings on the target controllability of multi-layer networks is discussed. It is found that even if there exists a layer which is not target controllable, the entire multi-layer network can still be target controllable due to the inter-layer couplings. For the multi-layer networks with general structure, a necessary and sufficient condition for target controllability is given by establishing the relationship between uncontrollable subspace and output matrix. By the derived condition, it can be found that the system may be target controllable even if it is not state controllable. On this basis, two corollaries are derived, which clarify the relationship between target controllability, state controllability and output controllability. For the multi-layer networks where the inter-layer couplings are directed chains and directed stars, sufficient conditions for target controllability of networked systems are given, respectively. These conditions are easier to verify than the classic criterion.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1999-2010"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Safe Efficient Policy Optimization Algorithm for Unsignalized Intersection Navigation","authors":"Xiaolong Chen;Biao Xu;Manjiang Hu;Yougang Bian;Yang Li;Xin Xu","doi":"10.1109/JAS.2024.124287","DOIUrl":"https://doi.org/10.1109/JAS.2024.124287","url":null,"abstract":"Unsignalized intersections pose a challenge for autonomous vehicles that must decide how to navigate them safely and efficiently. This paper proposes a reinforcement learning (RL) method for autonomous vehicles to navigate unsignalized intersections safely and efficiently. The method uses a semantic scene representation to handle variable numbers of vehicles and a universal reward function to facilitate stable learning. A collision risk function is designed to penalize unsafe actions and guide the agent to avoid them. A scalable policy optimization algorithm is introduced to improve data efficiency and safety for vehicle learning at intersections. The algorithm employs experience replay to overcome the on-policy limitation of proximal policy optimization and incorporates the collision risk constraint into the policy optimization problem. The proposed safe RL algorithm can balance the trade-off between vehicle traffic safety and policy learning efficiency. Simulated intersection scenarios with different traffic situations are used to test the algorithm and demonstrate its high success rates and low collision rates under different traffic conditions. The algorithm shows the potential of RL for enhancing the safety and reliability of autonomous driving systems at unsignalized intersections.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"2011-2026"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A Generalized Array Factor for Time-Modulated Hexagonal Based Antenna Array Geometry with Novel Trapezoidal Switching","authors":"Gopi Ram","doi":"10.1109/JAS.2024.124458","DOIUrl":"https://doi.org/10.1109/JAS.2024.124458","url":null,"abstract":"The concept of the time-modulated array has been emerging as an alternative to the complex phase shifters, which lowers the cost of the array feeding network due to the utilization of radio frequency (RF) switches. The various forms of hexagonal antenna array geometries can be used for applications like surveillance tracking in phased array radar and wireless communication systems. This work proposes the generalized array factor (AF) for the hexagonal antenna array geometry based on time modulation. The time modulation in generalized hexagonal geometry can maintain the fixed static amplitude excitation, giving more flexibility over time. Furthermore, a novel trapezoidal switching function is also proposed and applied to the generalized array factor to enable future researchers to use this array factor in the field of advancement to observe how switching schemes like trapezoidal and rectangular affect the array pattern's side lobe level (SLL). The generalized equation can be utilized for the analysis and synthesis of radiation characteristics of the time-modulated hexagonal array (TMHA), time-modulated concentric hexagonal array (TMCHA), time-modulated hexagonal cylindrical array (TMHCA), and time-modulated hexagonal concentric cylindrical array (TMHCCA). The numerical result illustrates the generation of AF of time-modulated hexagonal structures and also shows that the trapezoidal switching sequence outperforms the rectangular switch using the cat swarm optimization (CSO) approach.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1967-1972"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"RMPC-Based Visual Servoing for Trajectory Tracking of Quadrotor UAVs with Visibility Constraints","authors":"Qifan Yang;Huiping Li","doi":"10.1109/JAS.2024.124533","DOIUrl":"https://doi.org/10.1109/JAS.2024.124533","url":null,"abstract":"Dear Editor, This letter deals with the tracking problem of quadrotors subject to external disturbances and visibility constraints by designing a robust model predictive control (RMPC) scheme. According to the image-based visual servoing (IBVS) method, a virtual camera is constructed to express image moments of the tracking target. Furthermore, we design time-varying visibility constraints to cater to UAV attitudes in the RMPC optimization problem so that the tracking target always stays within the field of view (FoV) of the aerial camera. Moreover, the RMPC algorithm is proved to be recursively feasible, and the closed-loop system is stable. Finally, numerical experiments verify the efficacy of the proposed method.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"2027-2029"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10637429","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Data Driven Vibration Control: A Review","authors":"Weiyi Yang;Shuai Li;Xin Luo","doi":"10.1109/JAS.2024.124431","DOIUrl":"https://doi.org/10.1109/JAS.2024.124431","url":null,"abstract":"With the ongoing advancements in sensor networks and data acquisition technologies across various systems like manufacturing, aviation, and healthcare, the data driven vibration control (DDVC) has attracted broad interests from both the industrial and academic communities. Input shaping (IS), as a simple and effective feedforward method, is greatly demanded in DDVC methods. It convolves the desired input command with impulse sequence without requiring parametric dynamics and the closed-loop system structure, thereby suppressing the residual vibration separately. Based on a thorough investigation into the state-of-the-art DDVC methods, this survey has made the following efforts: 1) Introducing the IS theory and typical input shapers; 2) Categorizing recent progress of DDVC methods; 3) Summarizing commonly adopted metrics for DDVC; and 4) Discussing the engineering applications and future trends of DDVC. By doing so, this study provides a systematic and comprehensive overview of existing DDVC methods from designing to optimizing perspectives, aiming at promoting future research regarding this emerging and vital issue.","PeriodicalId":54230,"journal":{"name":"Ieee-Caa Journal of Automatica Sinica","volume":"11 9","pages":"1898-1917"},"PeriodicalIF":15.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141991488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}