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Bayesian methods for predicting interacting protein pairs using domain information

BIOMETRICS 2007年第3期63卷 824-833页

作者： Kim, Inyoung Liu, Yin Zhao, Hongyu Yale Univ Dept Epidemiol & Publ Hlth Sch Med New Haven CT 06520 USA Yale Univ Program Computat Biol & Bioinformat New Haven CT 06520 USA Yale Univ Sch Med Dept Genet New Haven CT 06520 USA

Protein-protein interactions (PPIs) play important roles in most fundamental cellular processes including cell cycle, metabolism, and cell proliferation. Therefore, the development of effective statistical approaches to predicting protein interactions based on recently available large-scale experimental data is very important. Because protein domains are the functional units of proteins and PPIs are mostly achieved through domain-domain interactions (DDIs), the modeling and analysis of protein interactions at the domain level may be more informative and insightful. However, due to the large number of domains, the number of parameters to be estimated is very large, yet the amount of information for statistical inference is quite limited. In this article we propose a full Bayesian method and a semi-Bayesian method for simultaneously estimating DDI probabilities, the false positive rate, and the false negative rate of high-throughput data through integrating data from several organisms. We also propose a model to associate protein interaction probabilities with domain interaction probabilities that reflects the number of domains in each protein, Our Bayesian methods are compared with the likelihood-based approach (Deng et al., 2002, Genome Research 12, 1504-1508;Liu, Liu, and Zhao, 2005, Bioinformatics 21, 3279-3285) developed using the expectation maximization algorithm. We show that the full Bayesian method has the smallest mean square error through both simulations and theoretical justification under a special scenario. The large-scale PPI data obtained from high-throughput yeast two-hybrid experiments are used to demonstrate the advantages of the Bayesian approaches.

关键词： Bayesian method domain-domain interaction expectation maximization algorithm protein-protein interaction

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Anomaly detection of structural health monitoring data using the maximum likelihood estimation-based Bayesian dynamic linear model

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STRUCTURAL HEALTH MONITORING-AN INTERNATIONAL JOURNAL 2021年第6期20卷 2936-2952页

作者： Zhang, Yi-Ming Wang, Hao Wan, Hua-Ping Mao, Jian-Xiao Xu, Yi-Chao Southeast Univ Minist Educ Key Lab C&PC Struct Nanjing 211189 Peoples R China Monash Univ Dept Civil Engn Clayton Vic Australia Zhejiang Univ Coll Civil Engn & Architecture Hangzhou Peoples R China Jiangsu Transportat Res Inst Co Ltd Nanjing Peoples R China State Key Lab Safety & Hlth In Serv Long Span Bri Nanjing Peoples R China

Enormous data are continuously collected by the structural health monitoring system of civil infrastructures. The structural health monitoring data inevitably involve anomalies caused by sensors, transmission errors, or abnormal structural behaviors. It is important to identify the anomalies and find their origin (e.g. sensor fault or structural damage) to make correct interventions. Moreover, online anomaly identification of the structural health monitoring data is critical for timely structural condition assessment and decision-making. This study proposes an online approach for detecting anomalies of the structural health monitoring data based on the Bayesian dynamic linear model. In particular, Bayesian dynamic linear model, consisting of various components, is implemented to characterize the feature of real-time measurements. expectation maximization algorithm and Kalman smoother are combined to estimate the Bayesian dynamic linear model parameters and generate log-likelihood functions. The subspace identification method is introduced to overcome the initialization issue of the expectation maximization algorithm. The log-likelihood difference of consecutive time steps is then used to determine thresholds without introducing extra anomaly detectors. The proposed Bayesian dynamic linear model-based approach is first illustrated by the simulation data and then applied to the structural health monitoring data collected from two long-span bridges. The results indicate that the proposed method exhibits good accuracy and high computational efficiency and also allows for reconstructing the strain measurements to replace anomalies.

关键词： Bayesian dynamic linear model anomaly identification structural health monitoring log-likelihood expectation maximization algorithm

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Estimating the modal parameters from multiple measurement setups using a joint state space model

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MECHANICAL SYSTEMS AND SIGNAL PROCESSING 2014年第1-2期43卷 171-191页

作者： Javier Cara, F. Juan, Jesus Alarcon, Enrique Univ Politecn Madrid ETS Ingenieros Ind Stat Lab E-28006 Madrid Spain Univ Politecn Madrid ETS Ingenieros Ind Dept Struct Mech E-28006 Madrid Spain

Computing the modal parameters of structural systems often requires processing data from multiple non-simultaneously recorded setups of sensors. These setups share some sensors in common, the so-called reference sensors, which are fixed for all measurements, while the other sensors change their position from one setup to the next. One possibility is to process the setups separately resulting in different modal parameter estimates for each setup. Then, the reference sensors are used to merge or glue the different parts of the mode shapes to obtain global mode shapes, while the natural frequencies and damping ratios are usually averaged. In this paper we present a new state space model that processes all setups at once. The result is that the global mode shapes are obtained automatically, and only a value for the natural frequency and damping ratio of each mode is estimated. We also investigate the estimation of this model using maximum likelihood and the expectation maximization algorithm, and apply this technique to simulated and measured data corresponding to different structures. (C) 2013 Elsevier Ltd. All rights reserved.

关键词： Assembled mode shapes Multi-setup operational modal analysis Maximum likelihood estimation expectation maximization algorithm State space model

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Robust algorithm for attack detection based on time-varying hidden Markov model subject to outliers

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INTERNATIONAL JOURNAL OF ADAPTIVE CONTROL AND SIGNAL PROCESSING 2020年第10期34卷 1537-1558页

作者： Lu, Genghong Feng, Dongqin Huang, Biao Zhejiang Univ Inst Cyber Syst & Control State Key Lab Ind Control Technol Zheda Rd 38 Hangzhou Zhejiang Peoples R China Univ Alberta Dept Chem & Mat Engn Edmonton AB Canada

The problem of robust attack detection and prediction for networked control systems in the presence of outliers is discussed in this article. The conventional hidden Markov model (HMM) is trained to learn the system behavior (ie, transitions between different operating modes) in the nominal process. The HMM with time-varying transition probabilities is used to track the attack behavior in which the adversary triggers more hazard modes to hasten fatigue of control devices by injecting attack signals with random magnitude and frequency. For different operating modes, the observations are assumed to follow different multivariate Student'stdistributions instead of Gaussian distributions and thus address the robust estimation problem. The expectation maximization algorithm is used to estimate parameters. Finally, simulations are conducted to verify the effectiveness of the proposed method.

关键词： expectation maximization algorithm hidden Markov models outliers robust attack detection time-varying transition probabilities

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Probabilistic modeling and recognition of 3-D objects

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INTERNATIONAL JOURNAL OF COMPUTER VISION 2000年第3期39卷 229-251页

作者： Hornegger, J Niemann, H Univ Erlangen Nurnberg Lehrstuhl Mustererkennung Informat 5 D-91058 Erlangen Germany

This paper introduces a uniform statistical framework for both 3-D and 2-D object recognition using intensity images as input data. The theoretical part provides a mathematical tool for stochastic modeling. The algorithmic part introduces methods for automatic model generation, localization, and recognition of objects. 2-D images are used for learning the statistical appearance of 3-D objects;both the depth information and the matching between image and model features are missing for model generation. The implied incomplete data estimation problem is solved by the expectation maximization algorithm. This leads to a novel class of algorithms for automatic model generation from projections. The estimation of pose parameters corresponds to a non-linear maximum likelihood estimation problem which is solved by a global optimization procedure. Classification is done by the Bayesian decision rule. This work includes the experimental evaluation of the various facets of the presented approach. An empirical evaluation of learning algorithms and the comparison of different pose estimation algorithms show the feasibility of the proposed probabilistic framework.

关键词： statistical object recognition pose estimation expectation maximization algorithm mixture densities hidden Markov models marginalization global optimization adaptive random search

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Identification of nonlinear state-space time-delay system

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ASSEMBLY AUTOMATION 2020年第1期40卷 22-30页

作者： Liu, Xin Zhang, Hang Zhu, Pengbo Yang, Xianqiang Du, Zhiwei Harbin Inst Technol Harbin Peoples R China North China Inst Sci & Technol Langfang Peoples R China

Purpose This paper aims to investigate an identification strategy for the nonlinear state-space model (SSM) in the presence of an unknown output time-delay. The equations to estimate the unknown model parameters and output time-delay are derived simultaneously in the proposed strategy. Design/methodology/approach The unknown integer-valued time-delay is processed as a latent variable which is uniformly distributed in a priori known range. The estimations of the unknown time-delay and model parameters are both realized using the expectation-maximization (EM) algorithm, which has a good performance in dealing with latent variable issues. Moreover, the particle filter (PF) with an unknown time-delay is introduced to calculated the Q-function of the EM algorithm. Findings Although amounts of effective approaches for nonlinear SSM identification have been developed in the literature, the problem of time-delay is not considered in most of them. The time-delay is commonly existed in industrial scenario and it could cause extra difficulties for industrial process modeling. The problem of unknown output time-delay is considered in this paper, and the validity of the proposed approach is demonstrated through the numerical example and a two-link manipulator system. Originality/value The novel approach to identify the nonlinear SSM in the presence of an unknown output time-delay with EM algorithm is put forward in this work.

关键词： Particle filter expectation maximization algorithm Latent variables Nonlinear system identification State-space time-delay model

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Film hole layout optimization for multi-row film cooling plate in continuous parameter space under non-uniform inlet temperature distribution

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APPLIED THERMAL ENGINEERING 2024年 257卷

作者： Huang, Junjie Zhu, Jianqin Cheng, Zeyuan Tong, Zixiang Qiu, Lu Wang, Yanjia Beihang Univ Sch Energy & Power Engn Natl Key Lab Sci & Technol Aeroengine Aerothermody Beijing 100191 Peoples R China Tianmushan Lab Hangzhou 310023 Peoples R China

Film cooling is an advanced external cooling technology for protecting gas turbine blades from excessive temperatures. To counteract non-uniform heat loads caused by hot streak and swirl effects at the combustion chamber outlet, fine design of film hole positions is necessary. However, the complexity due to the numerous film holes and their positional parameters presents challenges in the independent optimization of film hole positions in a continuous parameter space. This study proposed an optimization method grounded in the divide and conquer approach to address optimization for film hole layout. The film hole layout was decomposed into multiple single rows and optimized systematically by iteratively refining the single-row film hole layout along the streamwise direction using the expectation maximization algorithm. Optimized layouts for five different inlet temperature distributions were obtained using the proposed method and adiabatic wall temperature distributions were compared and analyzed for optimized and staggered layouts. Additionally, the cooling performance of the optimized layout was evaluated against the staggered layout under conjugate heat transfer conditions and the robustness of the optimized layout under various blowing ratios and peak temperature positions was tested. The results demonstrated that the proposed method can optimize the positions of 52 film holes within 0.3 h, and it was generalized to various inlet temperature distributions. By enhancing lateral interactions among downstream film jets, the lifting effect of kidney vortex in the optimized layout was weakened, bringing the film jets closer to the wall and significantly increasing coolant coverage during streamwise development. Comparative analysis reveals the superior cooling performance of the optimized layout at the blowing ratio of 1.0, evidenced by a 15.1% reduction in total input heat transfer rate and a 12.3% enhancement in overall cooling efficiency relative to the staggered l

关键词： Non-uniform temperature distribution Film cooling Hole layout optimization Divide and conquer approach expectation maximization algorithm

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Classical and Bayesian Estimation for the Parameters of a Competing Risk Model Based on Minimum of Exponential and Gamma Failures

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IEEE TRANSACTIONS ON RELIABILITY 2016年第3期65卷 1522-1535页

作者： Ranjan, Rakesh Upadhyay, Satyanshu K. Banaras Hindu Univ Dept Stat Varanasi 221005 Uttar Pradesh India Banaras Hindu Univ DST Ctr Interdisciplinary Math Sci Varanasi 221005 Uttar Pradesh India

The paper provides both classical and Bayesian estimation of the parameters of a competing risk model defined on the basis of minimum of exponential and gamma failure modes. Usually such situations are the examples of incomplete specification of data that naturally opens the way to expectation maximization algorithm for obtaining maximum likelihood estimates of model parameters. This incomplete specification of the data simultaneously explores the possibility of sampling importance resampling strategy with intermediate Markov chain Monte Carlo steps for the Bayesian estimation of parameters. Although this paper focuses primarily on estimation of model parameters, other inferential developments can be routinely done. Numerical illustration is provided based on both simulated and real-data examples.

关键词： Competing risk model exponential model expectation maximization algorithm gamma model increasing hazard rate sampling importance resampling

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Generative factor analyzed HMM for automatic speech recognition

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SPEECH COMMUNICATION 2005年第4期45卷 435-454页

作者： Yao, KS Paliwal, KK Lee, TW Univ Calif San Diego Inst Neural Computat La Jolla CA 92093 USA Griffith Univ Sch Microelect Engn Brisbane Qld 4111 Australia

We present a generative factor analyzed hidden Markov model (GFA-HMM) for automatic speech recognition. In a standard HMM, observation vectors are represented by mixture of Gaussians (MoG) that are dependent on discrete-valued hidden state sequence. The GFA-HMM introduces a hierarchy of continuous-valued latent representation of observation vectors, where latent vectors in one level are acoustic-unit dependent and latent vectors in a higher level are acoustic-unit independent. An expectation maximization (EM) algorithm is derived for maximum likelihood estimation of the model. We show through a set of experiments to verify the potential of the GFA-HMM as an alternative acoustic modeling technique. In one experiment, by varying the latent dimension and the number of mixture components in the latent spaces, the GFA-HMM attained more compact representation than the standard HMM. In other experiments with varies noise types and speaking styles, the GFA-HMM was able to have (statistically significant) improvement with respect to the standard HMM, (c) 2005 Elsevier B.V. All rights reserved.

关键词： hidden Markov models factor analysis mixture of Gaussian speech recognition expectation maximization algorithm

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Constellation Learning-Based Signal Detection for Ambient Backscatter Communication Systems

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IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS 2019年第2期37卷 452-463页

作者： Zhang, Qianqian Guo, Huayan Liang, Ying-Chang Yuan, Xiaojun Univ Elect Sci & Technol China Natl Key Lab Sci & Technol Commun Chengdu 611731 Sichuan Peoples R China Univ Elect Sci & Technol China Ctr Intelligent Networking & Commun Chengdu 611731 Sichuan Peoples R China

Ambient backscatter communication (AmBC) is a promising solution to energy-efficient and spectrum-efficient Internet of Things with stringent power and cost constraints. In an AmBC system, recovering the tag information at the reader, however, is a challenging task due to the difficulty in acquiring the relevant channel-state information (CSI). To eliminate the need to estimate the CSI, in this paper, we propose a label-assisted transmission framework, in which two known labels are transmitted from the tag before data transmission. By exploring the received signal constellation information, we propose modulation-constrained expectation maximization algorithm, based on which two detection methods are developed. One method, referred to as constellation learning with labeled signals, learns the parameters by clustering the labeled signals and recovers the unlabeled signals by the learnt parameters. The other method, referred to as constellation learning with labeled and unlabeled signals, uses all received signals in clustering. Efficient initialization techniques are provided for the two clustering algorithms. Finally, extensive simulation results show that the proposed constellation learning methods achieve comparable performance as the optimal detector with perfect CSI.

关键词： Ambient backscatter communication (AmBC) constellation learning signal detection clustering expectation maximization algorithm

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