Expectation Maximization Research Articles

Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.

Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.

Hybrid Thresholding for Image Deconvolution in Expectation Maximization framework

ABSTRACT In this study, we proposed an image deconvolution method in the expectation maximization (EM) framework. This method involves two steps: (i) E-step: utilizing the fast Fourier transform (FFT) for computationally efficient inversion of the convolution operator and (ii) M-step: employing the discrete wavelet transform (DWT) for estimating the original image from the image obtained in the E-step. In M-step, we proposed a modified L1-clipped penalty resulting in a hybrid thresholding scheme that integrates conventional hard and soft thresholds. This hybrid threshold ameliorates the inherent bias-variance trade-offs associated with traditional hard and soft thresholding schemes. The mathematical expressions for the risk, bias, and variance of the proposed hybrid threshold are derived and the performance is evaluated through simulation. Experimental results show that the proposed method achieves optimal values for variance and bias, thereby minimizing the risk. Moreover, the proposed method outperforms state-of-the-art methods in terms of performance metrics: PSNR, ISNR, and SSIM.

Simulation Assessment of Expectation-maximization Algorithm in Pseudo-convex Mixtures Generated by the Exponential Distribution

The use of pseudo-convex mixtures generated from stable distributions for extremes offers a valuable approach for handling reliability-related data challenges. This framework encompasses pseudo-convex mixtures stemming from exponential distribution. However, precise parameter estimation, particularly in cases where the weight parameter ω is negative, remains a challenge. This work assesses the performance of the Expectation- Maximization algorithm in estimating parameters for pseudo-convex mixtures generated by the exponential distribution through simulation.

Population Pharmacokinetics and Limited Sampling Strategy of Mycophenolate Mofetil for Indian Patients with Lupus Nephritis

Background: Mycophenolic acid is widely used to treat lupus nephritis (LN). However, it exhibits complex pharmacokinetics with large interindividual variability. This study aimed to develop a population pharmacokinetic (popPK) model and a 3-sample limited sampling strategy (LSS) to optimize therapeutic drug monitoring in Indian patients with LN. Methods: Five blood samples from each LN patient treated with mycophenolic acid were collected at steady-state predose and 1, 2, 4, and 6 hours postdose. Demographic parameters were tested as covariates to explain interindividual variability. PopPK analysis was performed using Monolix and the stochastic approximation expectation-maximization algorithm. An LSS was derived from 500 simulated pharmacokinetic (PK) profiles using maximum a posteriori Bayesian estimation to estimate individual PK parameters and area under the curve (AUC). The LSS-calculated AUC was compared with the AUC calculated using the trapezoidal rule and all the simulated samples. Results: A total of 51 patients were included in this study. Based on the 245 mycophenolic acid concentrations, a 1-compartmental model with double absorption using gamma distributions best fitted the data. None of the covariates improved the model significantly. The model was internally validated using diagnostic plots, prediction-corrected visual predictive checks, and bootstrapping. The best LSS included samples at 1, 2, and 4 hours postdose and exhibited good performances in an external dataset (root mean squared error, 21.9%; mean bias, −4.20%). Conclusions: The popPK model developed in this study adequately estimated the PK of mycophenolic acid in adult Indian patients with LN. This simple LSS can optimize TDM based on the AUC in routine practice.

Evaluation of lesion contrast in the walk-through long axial FOV PET scanner simulated with XCAT anthropomorphic phantoms

BackgroundThis study evaluates the lesion contrast in a cost-effective long axial field of view (FOV) PET scanner, called the walk-through PET (WT-PET). The scanner consists of two flat detector panels covering the entire torso and head, scanning patients in an upright position for increased throughput. High-resolution, depth-of-interaction capable, monolithic detector technology is used to provide good spatial resolution and enable detection of smaller lesions.MethodsMonte Carlo GATE simulations are used in conjunction with XCAT anthropomorphic phantoms to evaluate lesion contrast in lung, liver and breast for various lesion diameters (10, 7 and 5 mm), activity concentration ratios (8:1, 4:1 and 2:1) and patient BMIs (18–37). Images were reconstructed iteratively with listmode maximum likelihood expectation maximization, and contrast recovery coefficients (CRCs) were obtained for the reconstructed lesions.ResultsResults shows notable variations in contrast recovery coefficients (CRC) across different lesion sizes and organ locations within the XCAT phantoms. Specifically, our findings reveal that 10 mm lesions consistently exhibit higher CRC compared to 7 mm and 5 mm lesions, with increases of approximately 54% and 330%, respectively, across all investigated organs. Moreover, high contrast recovery is observed in most liver lesions regardless of diameter or activity ratio (average CRC = 42%), as well as in the 10 mm lesions in the lung. Notably, for the 10 mm lesions, the liver demonstrates 42% and 62% higher CRC compared to the lung and breast, respectively. This trend remains consistent across lesion sizes, with the liver consistently exhibiting higher CRC values compared to the lung and breast: 7 mm lesions show an increase of 96% and 41%, while 5 mm lesions exhibit approximately 294% and 302% higher CRC compared to the lung and breast, respectively.ConclusionA comparison with a conventional pixelated LSO long axial FOV PET shows similar performance, achieved at a reduced cost for the WT-PET due to a reduction in required number of detectors.

FGO-MFI: factor graph optimization-based multi-sensor fusion and integration for reliable localization

Reliable and precise information pertaining to the position, velocity, and attitude is essential for automated driving. This paper proposes FGO-MFI, a cost-effective and robust multi-sensor fusion and integration localization framework that utilizes factor graph optimization. Firstly, a tightly coupled Global Navigation Satellite Systems (GNSS)/on-board sensor fusion localization framework is established to estimate vehicle states, including position, velocity, and attitude. To address the large drift rate of the Inertial Measurement Unit (IMU), this study introduces a novel IMU/Dynamics pre-integration method based on the vehicle dynamics model. We establish a two-degree-of-freedom vehicle dynamics model utilizing measurements from the wheel speed sensor and steering wheel angle sensor. The IMU/Dynamics factor is devised through a close integration of the model output and IMU pre-integration, enabling the construction of precise odometry with low-cost on-board sensors. Then, to address the issue of the non-Gaussian distribution of GNSS pseudorange error, this paper employs a Gaussian Mixture Model (GMM) to characterize the pseudorange noise, which is then applied to further sensor fusion. Given the time-varying nature of pseudorange noise, the expectation maximization algorithm is utilized to estimate GMM parameters online, leveraging the pseudorange residuals within a sliding window. Comprehensive experiments, inclusive of challenging scenarios such as urban canyons, tunnels, and wooded areas, have been carried out. They affirm the superior performance of the proposed method. Experiments have shown that our method demonstrates reliable localization across different statuses of GNSS signal, exhibiting a 39.4% improvement in the root mean square error of position error when compared to the state-of-the-art. Additionally, this FGO-MFI is a general sensor data fusion framework and is able to incorporate diverse sensor measurements, for example, from cameras and LiDARs to provide more reliable and accurate localization information.

Anatomy-guided multi-resolution image reconstruction in PET

Objective. In this paper, we propose positron emission tomography image reconstruction using a multi-resolution triangular mesh. The mesh can be adapted based on patient specific anatomical information that can be in the form of a computed tomography or magnetic resonance imaging image in the hybrid imaging systems. The triangular mesh can be adapted to high resolution in localized anatomical regions of interest (ROI) and made coarser in other regions, leading to an imaging model with high resolution in the ROI with clearly reduced number of degrees of freedom compared to a conventional uniformly dense imaging model. Approach. We compare maximum likelihood expectation maximization reconstructions with the multi-resolution model to reconstructions using a uniformly dense mesh, a sparse mesh and regular rectangular pixel mesh. Two simulated cases are used in the comparison, with the first one using the NEMA image quality phantom and the second the XCAT human phantom. Main results. When compared to the results with the uniform imaging models, the locally refined multi-resolution mesh retains the accuracy of the dense mesh reconstruction in the ROI while being faster to compute than the reconstructions with the uniformly dense mesh. The locally dense multi-resolution model leads also to more accurate reconstruction than the pixel-based mesh or the sparse triangular mesh. Significance. The findings suggest that triangular multi-resolution mesh, which can be made patient and application specific, is a potential alternative for pixel-based reconstruction.

A bi-endpoint expectation-maximisation algorithm for re-estimating sample size for the time-to-event endpoint under the blind condition

Abstract The expectation-maximisation (EM) algorithm can be used to adjust the sample size for the time-to-event endpoint without unblinding. Nevertheless, censoring or unreliable initial estimates may render inconsistent estimates by the EM algorithm. To address these limitations, we propose a bi-endpoint EM algorithm that incorporates the time-to-event endpoint and another endpoint, which can encompass various endpoint types and is not limited to efficacy indicators, during the EM iterations. Additionally, we suggest 2 approaches for choosing initial estimates. The application conditions are as follows: (i) at least one endpoint’s initial estimate is reliable and (ii) the influence of this endpoint on the posterior distribution of the latent variable exceeds that of another endpoint.

Consumer electronics based smart technologies for enhanced terahertz healthcare having an integration of split learning with medical imaging

The proposed work contains three major contribution, such as smart data collection, optimized training algorithm and integrating Bayesian approach with split learning to make privacy of the patent data. By integrating consumer electronics device such as wearable devices, and the Internet of Things (IoT) taking THz image, perform EM algorithm as training, used newly proposed slit learning method the technology promises enhanced imaging depth and improved tissue contrast, thereby enabling early and accurate disease detection the breast cancer disease. In our hybrid algorithm, the breast cancer model achieves an accuracy of 97.5 percent over 100 epochs, surpassing the less accurate old models which required a higher number of epochs, such as 165.

Comparison of quantitative whole body PET parameters on [68Ga]Ga-PSMA-11 PET/CT using ordered Subset Expectation Maximization (OSEM) vs. bayesian penalized likelihood (BPL) reconstruction algorithms in men with metastatic castration-resistant prostate cancer

BackgroundPSMA PET/CT is a predictive and prognostic biomarker for determining response to [177Lu]Lu-PSMA-617 in patients with metastatic castration resistant prostate cancer (mCRPC). Thresholds defined to date may not be generalizable to newer image reconstruction algorithms. Bayesian penalized likelihood (BPL) reconstruction algorithm is a novel reconstruction algorithm that may improve contrast whilst preventing introduction of image noise. The aim of this study is to compare the quantitative parameters obtained using BPL and the Ordered Subset Expectation Maximization (OSEM) reconstruction algorithms.MethodsFifty consecutive patients with mCRPC who underwent [68Ga]Ga-PSMA-11 PET/CT using OSEM reconstruction to assess suitability for [177Lu]Lu-PSMA-617 therapy were selected. BPL algorithm was then used retrospectively to reconstruct the same PET raw data. Quantitative and volumetric measurements such as tumour standardised uptake value (SUV)max, SUVmean and Molecular Tumour Volume (MTV-PSMA) were calculated on both reconstruction methods. Results were compared (Bland-Altman, Pearson correlation coefficient) including subgroups with low and high-volume disease burdens (MTV-PSMA cut-off 40 mL).ResultsThe SUVmax and SUVmean were higher, and MTV-PSMA was lower in the BPL reconstructed images compared to the OSEM group, with a mean difference of 8.4 (17.5%), 0.7 (8.2%) and − 21.5 mL (-3.4%), respectively. There was a strong correlation between the calculated SUVmax, SUVmean, and MTV-PSMA values in the OSEM and BPL reconstructed images (Pearson r values of 0.98, 0.99, and 1.0, respectively). No patients were reclassified from low to high volume disease or vice versa when switching from OSEM to BPL reconstruction.Conclusions[68Ga]Ga-PSMA-11 PET/CT quantitative and volumetric parameters produced by BPL and OSEM reconstruction methods are strongly correlated. Differences are proportional and small for SUVmean, which is used as a predictive biomarker. Our study suggests that both reconstruction methods are acceptable without clinical impact on quantitative or volumetric findings. For longitudinal comparison, committing to the same reconstruction method would be preferred to ensure consistency.

Brain MR image segmentation for tumor detection based on Riesz probability distributions

ABSTRACT This research introduces a new approach using the Riesz mixture model for medical image segmentation, specifically for diagnosing and treating brain tumors. We developed a novel technique for pixel classification based on the Riesz distribution, which is generated using an extended Bartlett decomposition. Our work is pioneering, as there are no existing studies addressing this issue in the literature. We aim to demonstrate the effectiveness of this distribution for brain image segmentation. We used the Expectation-Maximization algorithm to estimate the mixture parameters. To validate our segmentation algorithm, we conducted a comparative study with a recent method based on the Wishart distribution using Matlab software. Experiments with the Riesz mixture model showed that our method produces more intuitive results with a recognition rate of 94.52%. These results confirm the reliability of our method in detecting tumors using both synthetic and real brain images.

Efficient inference of parent-of-origin effect using case-control mother-child genotype data

Parent-of-origin effect plays an important role in mammal development and disorder. Case-control mother-child pair genotype data can be used to detect parent-of-origin effect and is often convenient to collect in practice. Most existing methods for assessing parent-of-origin effect do not incorporate any covariates, which may be required to control for confounding factors. We propose to model the parent-of-origin effect through a logistic regression model, with predictors including maternal and child genotypes, parental origins, and covariates. The parental origins may not be fully inferred from genotypes of a target genetic marker, so we propose to use genotypes of markers tightly linked to the target marker to increase inference efficiency. A robust statistical inference procedure is developed based on a modified profile log-likelihood in a retrospective way. A computationally feasible expectation–maximization algorithm is devised to estimate all unknown parameters involved in the modified profile log-likelihood. This algorithm differs from the conventional expectation–maximization algorithm in the sense that it is based on a modified instead of the original profile log-likelihood function. The convergence of the algorithm is established under some mild regularity conditions. This expectation–maximization algorithm also allows convenient handling of missing child genotypes. Large sample properties, including weak consistency, asymptotic normality, and asymptotic efficiency, are established for the proposed estimator under some mild regularity conditions. Finite sample properties are evaluated through extensive simulation studies and the application to a real dataset.

Room impulse response reshaping-based expectation maximization in an underdetermined reverberant environment

Source separation in an underdetermined reverberation environment is a very challenging issue. The classical method is based on the expectation–maximization algorithm. However, it is limited to high reverberation environments, resulting in bad or even invalid separation performance. To eliminate this restriction, a room impulse response reshaping-based expectation maximization method is designed to solve the problem of source separation in an underdetermined reverberant environment. Firstly, a room impulse response reshaping technology is designed to eliminate the influence of audible echo on the reverberant environment, improving the quality of the received signals. Then, a new mathematical model of time-frequency mixing signals is established to reduce the approximation error of model transformation caused by high reverberation. Furthermore, an improved expectation maximization method is proposed for real-time update learning rules of model parameters, and then the sources are separated using the estimators provided by the improved expectation maximization method. Experimental results based on source separation of speech and music mixtures demonstrate that the proposed algorithm achieves better separation performance while maintaining much better robustness than popular expectation maximization methods.

A Flexible EM-Like Clustering Algorithm for Noisy Data.

Though very popular, it is well known that the Expectation-Maximisation (EM) algorithm for the Gaussian mixture model performs poorly for non-Gaussian distributions or in the presence of outliers or noise. In this paper, we propose a Flexible EM-like Clustering Algorithm (FEMCA): a new clustering algorithm following an EM procedure is designed. It is based on both estimations of cluster centers and covariances. In addition, using a semi-parametric paradigm, the method estimates an unknown scale parameter per data point. This allows the algorithm to accommodate heavier tail distributions, noise, and outliers without significantly losing efficiency in various classical scenarios. We first present the general underlying model for independent, but not necessarily identically distributed, samples of elliptical distributions. We then derive and analyze the proposed algorithm in this context, showing in particular important distribution-free properties of the underlying data distributions. The algorithm convergence and accuracy properties are analyzed by considering the first synthetic data. Finally, we show that FEMCA outperforms other classical unsupervised methods of the literature, such as k-means, EM for Gaussian mixture models, and its recent modifications or spectral clustering when applied to real data sets as MNIST, NORB, and 20newsgroups.

A Global-Local collaborative approach to quantifying spatial non-stationarity in three-dimensional mineral prospectivity modeling

The three-dimensional (3D) modeling of mineral prospectivity plays a pivotal role in the mineral exploration process, enabling explorers to identify, evaluate, and prioritize deep-seated targets more effectively.Accurately predicting the 3D distribution of mineral prospectivity relies on effectively quantifying correlations to mineralization. The ore formation process is extremely intricate, marked by spatial non-stationary correlations. While state-of-the-art 3D mineral prospectivity modeling methods use machine learning (including deep learning) to capture correlation between geological evidence and mineralization hidden in the geosciences data, limited attention has been given to quantifying the local non-stationary nature in ore formation. This paper proposes a novel method that adapts to local spatial non-stationarity in 3D mineral prospectivity modeling. The approach integrates a prospectively model with a local regression model, creating a global–local collaborative model to quantify spatial non-stationary associations with mineralization. Random Forest (RF) and Reset are employed to construct mineral prospectivity models that quantify the global associations with mineralization. Simultaneously, the geographically weighted regression (GWR) model serves as a local model to capture the local non-stationarity within mineralization association. An Expectation Maximization algorithm is tailored to bridge the gap between global and local models, resulting in an iterative framework that progressively fuses global spatial associations and local non-stationarity related to mineralization. The iterative process generates a mineral perspectivity model that adapts to local non-stationarity in predictive areas. A case study on the Dingjiashan Pb-Zn deposit validates the effectiveness of the proposed method. The results demonstrate that the global–local collaborative mineral perspectivity model significantly boosts prediction accuracy in predictive areas. Moreover, the regression parameters of GWR derived from the model construction process effectively reveal the spatial non-stationary impacts of different ore-controlling factors, thereby improving the interpretability and reliability of predicted mineral prospectivity.

Development of Quench Detection Method Around the Joint Box for HTS Cable Using TFDR and EM Algorithm

Development of Quench Detection Method Around the Joint Box for HTS Cable Using TFDR and EM Algorithm

PiCO+: Contrastive Label Disambiguation for Robust Partial Label Learning.

Partial label learning (PLL) is an important problem that allows each training example to be labeled with a coarse candidate set with the ground-truth label included. However, in a more practical but challenging scenario, the annotator may miss the ground-truth and provide a wrong candidate set, which is known as the noisy PLL problem. To remedy this problem, we propose the PiCO+ framework that simultaneously disambiguates the candidate sets and mitigates label noise. Core to PiCO+, we develop a novel label disambiguation algorithm PiCO that consists of a contrastive learning module along with a novel class prototype-based disambiguation method. Theoretically, we show that these two components are mutually beneficial, and can be rigorously justified from an expectation-maximization (EM) algorithm perspective. To handle label noise, we extend PiCO to PiCO+, which further performs distance-based clean sample selection, and learns robust classifiers by a semi-supervised contrastive learning algorithm. Beyond this, we further investigate the robustness of PiCO+ in the context of out-of-distribution noise and incorporate a novel energy-based rejection method for improved robustness. Extensive experiments demonstrate that our proposed methods significantly outperform the current state-of-the-art approaches in standard and noisy PLL tasks and even achieve comparable results to fully supervised learning.

Frame-wise speech extraction with recursive expectation maximization for partially deformable microphone arrays

Large-apertured wearable and deformable microphone arrays have shown their better performance than conventional small wearable and rigid microphone arrays for speech extraction tasks, especially when the desired speech is far away from the arrays or there exist a great number of directional noises in practical applications. Most existing beamforming methods that require the information of the desired sound direction often cannot be used directly on deformable arrays because their shape might continuously change over time. To tackle the problem of utilizing partially deformable microphone arrays for target speech extraction, this paper derives a frame-wise speech extraction method, which is referred to as the recursive multichannel Wiener filter with generalized Gamma priors. In this method, the complex spectrum of the desired speech is assumed to follow a zero-mean complex Gaussian distribution with time-varying variance, and the reciprocal of this time-varying variance known as the precision is further assumed to follow a Gamma distribution, while the complex spectrum of the noise is assumed to follow a zero-mean complex Gaussian distribution. Under these two assumptions, we derive the recursive expectation maximization algorithm to extract the desired speech in a frame-by-frame manner. Experimental results show the promising performance of the proposed method in terms of multiple objective metrics.

Advanced Microstructural Characterization in High-Strength Steels Via Machine Learning-Enhanced High-Speed Nanoindentation and EBSD Mapping

This research investigates the nanoscopic features of Advanced High-Strength Steels (AHSS) through a bottom-up approach employing high-speed nanoindentation mapping (HSNM) to elucidate structure-property relationships. The influence of grain boundaries on nanomechanical properties was documented, highlighting the challenge of SEM-EBSD analysis in differentiating phases with identical crystal structures (BCC, FCC, etc.). Integrating SEM-EBSD with HSNM in the same region of interest is essential for detailed insights into phase/microstructure distribution and accurate grain boundary identification.A modular four-step analysis protocol, designed and validated on ferritic-bainitic TRIP steels (TBF), leverages machine learning-enhanced HSNM for significant advancements in AHSS design. The initial phase involves the application of the expectation-maximization algorithm for probability distribution fitting of HSNM data, deriving primary mechanical phase statistics. This exclusively facilitates the correlation of elastic modulus and hardness for each phase/microstructure using nanoindentation data. Further refinement of phase/microstructure to mechanical property correlations was achieved through a supervised machine learning approach, ensuring precise association between EBSD and nanoindentation data. This includes detailed image analysis and clustering of nanoindentation data, enhancing the precision in phase recognition.This methodology addresses the critical challenges in developing 3rd Generation AHSS, aiming to fill the gap in accurately identifying and quantifying phases such as martensite, austenite, bainite, and ferrite, thereby reducing classification and measurement uncertainties. The approach contributes to the fundamental understanding of AHSS microstructures and provides a scalable framework for the comprehensive characterization of structural materials.

Loss Modeling with the Size-biased Lognormal Mixture and the Entropy Regularized EM Algorithm

The Erlang mixture with a common scale parameter is one of many popular models for modeling insurance losses. However, the actuarial literature recognizes and discusses some limitations of aforementioned model in approximate heavy-tailed distributions. In this paper, a size-biased left-truncated Lognormal (SB-ltLN) mixture is proposed as a robust alternative to the Erlang mixture for modeling left-truncated insurance losses with a heavy tail. The weak denseness property of the weighted Lognormal mixture is studied along with the tail behavior. Explicit analytical solutions are derived for moments and Tail Value at Risk based on the proposed model. An extension of the regularized expectation–maximization (REM) algorithm with Shannon's entropy weights (ewREM) is introduced for parameter estimation and variability assessment. The Operational Riskdata eXchange's left-truncated internal fraud loss data set is used to illustrate applications of the proposed model. Finally, the results of a simulation study show promising performance of the proposed SB-ltLN mixture in different simulation settings.