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Isoform Function Prediction Based on Heterogeneous Graph Attention Networks

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Isoform Function Prediction Based on Heterogeneous Graph Att...

2023 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2023

作者： Guo, Kuo Li, Yifan Chen, Hao Shen, Hong-Bin Yang, Yang Shanghai Jiao Tong University Key Lab. of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Department of Computer Science and Engineering Shanghai200240 China Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Institute of Image Processing and Pattern Recognition Shanghai200240 China Carnegie Mellon University School of Computer Science Computational Biology Department PittsburghPA15213 United States

ISBN: (纸本)9798350337488

Isoforms refer to different mRNA molecules transcribed from the same gene, which can be translated into proteins with varying structures and functions. Predicting the functions of isoforms is an essential topic in bioinformatics as it can provide valuable insights into the intricate mechanisms of gene regulation and biological processes. Conventionally, gene function labels are standardized in Gene Ontology (GO) terms. However, traditional methods for predicting isoform function are largely limited by the absence of isoform-specific labels, sparse annotations, and the vast number of GO terms. To address these issues, we propose HANIso, a deep learning-based method for isoform function prediction. HANIso leverages a pretrained protein language model to extract features from protein sequences. It also integrates heterogeneous information, such as isoform sequence features, GO annotations, and isoform interaction data, using a Heterogeneous Graph Attention Network (HAN). This allows the model to learn the importance of different sources of information and their semantic relationships through the attention mechanism. Our method can predict function labels at both the gene level and isoform level. We conduct experiments on two species datasets, and the results demonstrate that our method outperforms existing methods on both AUROC and AUPRC. HANIso has the potential to overcome the limitations of traditional methods and provide a more accurate and comprehensive understanding of isoform function. © 2023 IEEE.

关键词： alternative splicing gene ontology heterogeneous graph attention network isoform function prediction protein language model

Binary system modes of matrix-coupled multidimensional Kuramoto oscillators

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arXiv 2023年

作者： Wang, Chongzhi Shao, Haibin Li, Dewei Department of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Engineering Research Center of Intelligent Control and Management Shanghai200240 China

Synchronization and desynchronization are the two ends on the spectrum of emergent phenomena that somehow often coexist in biological, neuronal, and physical networks. However, previous studies essentially regard their coexistence as a partition of the network units: those that are in relative synchrony and those that are not. In real-world systems, desynchrony bears subtler divisions because the interacting units are high-dimensional, like fish schooling with varying speeds in a circle, synchrony and desynchrony may occur to the different dimensions of the population. In this work, we show with an ensemble of multidimensional Kuramoto oscillators, that this property is generalizable to arbitrary dimensions: for a d dimensional population, there exist 2d system modes where each dimension is either synchronized or desynchronized, represented by a set of almost binary order parameters. Such phenomena are induced by a matrix coupling mechanism that goes beyond the conventional scalar-valued coupling by capturing the inter-dimensional dependence amongst multidimensional individuals, which arises naturally from physical, sociological and engineering systems. As verified by our theory, the property of the coupling matrix thoroughly affects the emergent system modes and the phase transitions toward them. By numerically demonstrating that these system modes are interchangeable through matrix manipulation, we also observe explosive synchronization/desynchronization that is induced without the conditions that are previously deemed essential. Our discovery provides theoretical analogy to the cerebral activity where the resting state and the activated state coexist unihemispherically, it also evokes a new possibility of information storage in oscillatory neural networks. Copyright © 2023, The Authors. All rights reserved.

关键词： Synchronization

A Multimodal Fault Diagnosis Model Utilizing GAF Transformation for controllable Pitch Propeller Hydraulic system

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A Multimodal Fault Diagnosis Model Utilizing GAF Transformat...

International Conference on control, Decision and information Technologies (CoDIT)

作者： Huihuang Cai Wei Chen Huanglong Fu Hua Wang Jingcheng Wang Department of Automation Key Laboratory of System Control and Information Processing Ministry of Education of China and Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai China Shanghai Marine Equipment Research Institute Shanghai China Department of Automation the Key Laboratory of System Control and Information Processing Ministry of Education of China and the Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai China Autonomous Systems and Intelligent Control International Joint Research Center Xi'an Technological University Xi'an China

ISBN: (数字)9798350373974

ISBN: (纸本)9798350373981

The hydraulic system of the controllable pitch propeller (CPP) serves as the power source for adjusting the blade pitch. Due to its structural complexity and harsh operating conditions, any malfunction of this system could significantly impair the vessel's navigation. Apart from the pitch command and the pitch feedback of CPP itself, the number and types of sensors added for fault diagnosis are not fixed. Therefore, this study establishes a multimodal fault diagnosis model based on Gramian angular field(GAF). By considering the deviation values of pitch feedback and pitch command as key variables, this model transforms them into a two-dimensional image using GAF, thereby obtaining more effective feature information. Image features are extracted using ResNet, while the temporal features of additional sensors are extracted using GRU. Finally, a multi-head attention mechanism is employed for feature fusion. This method achieves a classification accuracy of 100% in the classification of four types of hydraulic system faults simulated on the experimental platform.

关键词： Fault diagnosis Propellers Navigation Hydraulic systems Transforms Sensor phenomena and characterization Feature extraction Sensor systems Marine vehicles Load modeling

DSLO: Deep Sequence LiDAR Odometry Based on Inconsistent Spatio-temporal Propagation

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DSLO: Deep Sequence LiDAR Odometry Based on Inconsistent Spa...

IEEE/RSJ International Conference on Intelligent Robots and systems (IROS)

作者： Huixin Zhang Guangming Wang Xinrui Wu Chenfeng Xu Mingyu Ding Masayoshi Tomizuka Wei Zhan Hesheng Wang Department of Automation Key Laboratory of System Control and Information Processing of Ministry of Education Key Laboratory of Marine Intelligent Equipment and System of Ministry of Education Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai China Department of Engineering University of Cambridge Cambridge U.K. UC Berkeley Berkeley CA USA

ISBN: (数字)9798350377705

ISBN: (纸本)9798350377712

This paper introduces a 3D point cloud sequence learning model based on inconsistent spatio-temporal propagation for LiDAR odometry, termed DSLO. It consists of a pyramid structure with a spatial information reuse strategy, a sequential pose initialization module, a gated hierarchical pose refinement module, and a temporal feature propagation module. First, spatial features are encoded using a point feature pyramid, with features reused in successive pose estimations to reduce computational overhead. Second, a sequential pose initialization method is introduced, leveraging the high-frequency sampling characteristic of LiDAR to initialize the LiDAR pose. Then, a gated hierarchical pose refinement mechanism refines poses from coarse to fine by selectively retaining or discarding motion information from different layers based on gate estimations. Finally, temporal feature propagation is proposed to incorporate the historical motion information from point cloud sequences, and address the spatial inconsistency issue when transmitting motion information embedded in point clouds between frames. Experimental results on the KITTI odometry dataset and Argoverse dataset demonstrate that DSLO outperforms state-of-the-art methods, achieving at least a 15.67% improvement on RTE and a 12.64% improvement on RRE, while also achieving a 34.69% reduction in runtime compared to baseline methods. Our implementation will be available at https://***/IRMVLab/DSLO.

关键词： Point cloud compression Solid modeling Laser radar Accuracy Three-dimensional displays Runtime Logic gates Robot sensing systems Real-time systems Odometry

Differential Private Discrete Noise-Adding Mechanism: Conditions, Properties, and Optimization

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Differential Private Discrete Noise-Adding Mechanism: Condit...

作者： Qin, Shuying He, Jianping Fang, Chongrong Lam, James Shanghai Jiao Tong University Department of Automation Shanghai200240 China Key Laboratory of System Control and Information Processing Ministry of Education of China Beijing100816 China Shanghai Engineering Research Center of Intelligent Control and Management Shanghai200240 China Shenzhen Institute of Research and Innovation Shenzhen518055 China The University of Hong Kong Department of Mechanical Engineering Hong Kong999077 Hong Kong

Differential privacy is a widely used framework for evaluating privacy loss in data anonymization. While the continuous noise-adding mechanism has been extensively studied, there is a dearth of research on discrete random mechanisms for discretely distributed data. This study addresses this gap by examining the primary differential privacy conditions and properties for general discrete random mechanisms, and investigating the trade-off between data privacy and data utility. We establish sufficient and necessary conditions for discrete ϵ-differential privacy and sufficient conditions for discrete (ϵδ)-differential privacy, with closed-form expressions for differential privacy parameters. These conditions can be applied to evaluate the differential privacy properties of discrete noise-adding mechanisms with various types of noise. Moreover, we propose an optimal discrete ϵ-differential private noise-adding mechanism under the utility-maximization framework. Here, the utility is characterized by the similarity of the statistical properties between the mechanism's input and output. Our findings suggest that the optimal class of discrete noise probability distributions in the mechanism is staircase-shaped. © 1991-2012 IEEE.

关键词： Probability distributions

Optimal Linear Attack in Cyber-Physical systems with Periodic Detection

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Optimal Linear Attack in Cyber-Physical Systems with Periodi...

IEEE Conference on Decision and control

作者： Jia Qi Chongrong Fang Jianping He Dept. of Automation Key Laboratory of System Control and Information Processing Shanghai Jiao Tong University Ministry of Education of China and Shanghai Engineering Research Center of Intelligent Control and Management Shanghai China

Security issues are of significant importance for cyber-physical systems (CPS), where the attack design is a major concern. Most related studies on attack design implicitly consider that the control period and detection period are the same. However, the two periods could be different in practical systems with remote detection such as supervisory control and data acquisition (SCADA) systems, which could lead to new vulnerabilities for attackers. In this paper, we consider the design of innovation-based linear attack strategies for CPS when the control period and detection period are inconsistent. Specifically, we propose an attack framework that consists of attack strategies for detection and non-detection instants under the period discrepancy. On this basis, we design the optimal stealthy innovation-based linear attack strategies for state estimation and LQG control to maximize the estimation error or control cost, respectively. Simulations are given to demonstrate the effectiveness of the proposed attack strategies.

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LHMap-loc: Cross-Modal Monocular Localization Using LiDAR Point Cloud Heat Map

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arXiv 2024年

作者： Wu, Xinrui Xu, Jianbo Hu, Puyuan Wang, Guangming Wang, Hesheng Department of Automation Key Laboratory of System Control and Information Processing of Ministry of Education Key Laboratory of Marine Intelligent Equipment and System of Ministry of Education Shanghai Engineering Research Center of Intelligent Control and Management Shanghai Jiao Tong University Shanghai200240 China Department of Engineering University of Cambridge CambridgeCB2 1PZ United Kingdom

— Localization using a monocular camera in the pre-built LiDAR point cloud map has drawn increasing attention in the field of autonomous driving and mobile robotics. However, there are still many challenges (e.g. difficulties of map storage, poor localization robustness in large scenes) in accurately and efficiently implementing cross-modal localization. To solve these problems, a novel pipeline termed LHMap-loc is proposed, which achieves accurate and efficient monocular localization in LiDAR maps. Firstly, feature encoding is carried out on the original LiDAR point cloud map by generating offline heat point clouds, by which the size of the original LiDAR map is compressed. Then, an end-to-end online pose regression network is designed based on optical flow estimation and spatial attention to achieve real-time monocular visual localization in a pre-built map. In addition, a series of experiments have been conducted to prove the effectiveness of the proposed method. Our code is available at: https://***/IRMVLab/LHMaploc. Copyright © 2024, The Authors. All rights reserved.

关键词： Optical radar

Preserving Topology of Network systems: Metric, Analysis, and Optimal Design

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arXiv 2023年

作者： Li, Yushan Wang, Zitong He, Jianping Chen, Cailian Guan, Xinping Dept. of Automation Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai Engineering Research Center of Intelligent Control and Management Shanghai China

Preserving the topology from being inferred by external adversaries has become a paramount security issue for network systems (NSs), and adding random noises to the nodal states provides a promising way. Nevertheless, recent works have revealed that the topology cannot be preserved under i.i.d. noises in the asymptotic sense. How to effectively characterize the non-asymptotic preservation performance still remains an open issue. Inspired by the deviation quantification of concentration inequalities, this paper proposes a novel metric named trace-based variance-expectation ratio. This metric effectively captures the decaying rate of the topology inference error, where a slower rate indicates better non-asymptotic preservation performance. We prove that the inference error will always decay to zero asymptotically, as long as the added noises are non-increasing and independent (milder than the i.i.d. condition). Then, the optimal noise design that produces the slowest decaying rate for the error is obtained. More importantly, we amend the noise design by introducing one-lag time dependence, achieving the zero state deviation and the non-zero topology inference error in the asymptotic sense simultaneously. Extensions to a general class of noises with multi-lag time dependence are provided. Comprehensive simulations verify the theoretical findings. Copyright © 2023, The Authors. All rights reserved.

关键词： Topology

Simultaneously Infer Cell Pseudotime,Velocity Field and Gene Interaction from Multi-Branch scRNA-seq Data with scPN

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arXiv 2024年

作者： Zhou, Zhen Li, Jiachen Xin, Hongyi Pan, Xiaoyong Shen, Hong-Bin Institute of Image Processing and Pattern Recognition Shanghai Jiao Tong University Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai200240 China Global Institute of Future Technology Shanghai Jiao Tong University Shanghai200240 China

Modeling cellular dynamics from single-cell RNA sequencing (scRNA-seq) data is critical for understanding cell development and underlying gene regulatory relationships. Many current methods rely on single-cell velocity to obtain pseudotime, which can lead to inconsistencies between pseudotime and velocity. It is challenging to simultaneously infer cell pseudotime and gene interaction networks, especially in multi-branch differentiation scenarios. We present single-cell Piecewise Network (scPN), a novel high-dimensional dynamical modeling approach that iteratively extracts temporal patterns and inter-gene relationships from scRNA-seq data. To tackle multi-branch differentiation challenges, scPN models gene regulatory dynamics using piecewise gene-gene interaction networks, offering an interpretable framework for deciphering complex gene regulation patterns over time. Results on synthetic data and multiple scRNA-seq datasets demonstrate the superior performance of scPN in reconstructing cellular dynamics and identifying key transcription factors involved in development compared to existing methods. To the best of our knowledge, scPN is the first attempt at modeling that can recover pseudotime, velocity fields, and gene interactions all at once on multi-branch datasets. Copyright © 2024, The Authors. All rights reserved.

关键词： Transcription