arXiv subjects

Samuel J. Clark

Publications and source records attributed to Samuel J. Clark.

At least 19 recordsLinked to original sources

arXiv2026

Tomo-center: an AI-based rotation-axis center finder for synchrotron micro- and nano-tomography

Accurate determination of the rotation-axis position is a prerequisite for artifact-free reconstruction in parallel-beam synchrotron micro-tomography. Traditional approaches such as Vo's method rely on sinogram features that can fail for low-contrast or weakly absorbing specimens. We present a learning-based method that treats center selection as a binary classification problem, using a DINOv2-pretrained vision transformer aggregated with attention-based multiple-instance learning, fine-tuned end-to-end on tomographic images. At inference time, the proposed algorithm was applied to a stack of tomograms reconstructed at a sweep of candidate centers to select the optimal center for reconstruction. We tested the estimation accuracy of the proposed method on two independent data sources and consistently achieved a mean absolute error of below 1 pixel. We also tested the method robustness to sparse or noisy acquisitions with the same datasets and demonstrated consistent performance when the number of projections was reduced by a factor of up to 10 or the blank scan factor of the underlying Poisson's noise was increased to 10. We also illustrated the interpretability of the proposed method by mapping out the relative contributions of continuous spatial features to the overall classification task. This method, delivered as tomo-center, an open-source command-line tool, has been integrated into several tomography software packages to assist experiments during the routine beamline operations.

eess.IV↗

arXiv2026

Mortality Forecasting as a Flow Field in Tucker Decomposition Space

Mortality forecasting methods in the Lee-Carter tradition extrapolate temporal components via time-series models, often producing forecasts that systematically underpredict life expectancy at long horizons. This bias is consequential for planning pension funding, healthcare capacity, and social security solvency. The dominant alternative - the Bayesian double-logistic model underlying the UN World Population Prospects - forecasts scalar life expectancy and requires a separate model life table system to recover age-specific rates. We reframe forecasting as integrating a flow field through the low-dimensional score space of a Tucker tensor decomposition of the Human Mortality Database. PCA reduction reveals that the mortality transition is essentially a one-dimensional flow: a scalar speed function advances the level, trajectory functions supply the structural scores, and the Tucker reconstruction produces complete sex-specific, single-year-of-age mortality schedules at each horizon. In leave-country-out cross-validation (9,507 test points, 50-year horizon), the flow-field achieves bias of +1.058 years - substantially smaller than Lee-Carter (-3.2), Hyndman-Ullah (-3.5), and pyBayesLife (+3.3) - because it navigates a score space parameterised by mortality level rather than extrapolating temporal trends into unobserved territory. On 1.66 million sex-age-specific test points, it achieves 2.7x lower error than our de novo Python reimplementation of the UN pipeline trained on the same data - with lower error at every age, every forecast horizon, and for both sexes.

stat.ME↗

arXiv2026

Multi-dimensional Mortality (MDMx): Sex-Age-Specific Model Life Tables, Fitting, Prediction from Summary Mortality Indicators, and Forecasting

Demographers rely on a variety of tools and methods to work with mortality schedules - model life tables, fitting methods, summary-indicator prediction, and forecasting - largely developed independently and not providing structurally coherent sex-specific outputs. The multi-dimensional mortality model (MDMx) unifies all four within one Tucker tensor decomposition demonstrated using the Human Mortality Database (HMD). Period life tables from the HMD are organized as a four-way tensor of logit(1qx) indexed by sex, age, country, and year. Shared factor matrices for sex and age make every output schedule structurally coherent by construction. From this decomposition four capabilities emerge: model life tables via clustering and smooth within-regime trajectories; life table fitting via a three-stage algorithm with Bayes-factor disruption detection; summary-indicator prediction mapping child or adult mortality to complete schedules, reformulating SVD-Comp in tensor coordinates; and forecasting via a damped local linear trend Kalman filter on PCA-reduced core matrices with hierarchical drift.

stat.ME↗

arXiv2026

Aeroacoustic signatures reveal fast transient dynamics of vapor-jet-driven cavity oscillations in metallic additive manufacturing

Aeroacoustic emissions from intense evaporation are widely measured yet often treated as noisy byproducts and used mainly in empirical monitoring. Here, we show that airborne sound encodes physics-governed sub-millisecond fingerprints of vapor-jet dynamics in excessive vaporization, exemplified by vapor keyholes in laser metal processing. From first principles, we develop a vapor-jet-cavity oscillation framework and incorporate it into an aeroacoustic formulation, thereby coupling measured sound to transient cavity depth and oscillation frequency. Reconciled with synchronized multimodal in-situ data, airborne acoustics enable accurate tracking of vapor-cavity properties within tens to hundreds of microseconds. Combined with newly discovered correlations, cavity-jet-acoustic theory recasts the transition from steady, pore-free to pore-shedding vaporizations as a critical-frequency event. Aeroacoustic emissions thus become scalable, physics-guided, and cost-efficient probes of rapidly evolving liquid-vapor systems.

physics.app-ph↗

arXiv2025

A Mechanistic Study on Environment Gases in Metal Additive Manufacturing

A variety of protective or reactive environmental gases have recently gained growing attention in laser-based metal additive manufacturing (AM) technologies due to their unique thermophysical properties and the potential improvements they can bring to the build processes. However, much remains unclear regarding the effects of different gas environments on critical phenomena in laser AM, such as rapid cooling, energy coupling, and defect generation. Through simultaneous high-speed synchrotron x-ray imaging and thermal imaging, we identify distinct effects of various environmental gases in laser AM and gained a deeper understanding of the underlying mechanisms. Compared to the commonly used protective gas, argon, it is found that helium has a negligible effect on cooling the part. However, helium can suppress unstable keyholes by decreasing effective energy absorption, thus mitigating keyhole porosity generation and reducing pore size under certain processing conditions. These observations provide guidelines for the strategic use of environmental gases in laser AM to produce parts with improved quality.

physics.gen-ph↗

arXiv2024

Deep learning-based spatio-temporal fusion for high-fidelity ultra-high-speed x-ray radiography

Full-field ultra-high-speed (UHS) x-ray imaging experiments have been well established to characterize various processes and phenomena. However, the potential of UHS experiments through the joint acquisition of x-ray videos with distinct configurations has not been fully exploited. In this paper, we investigate the use of a deep learning-based spatio-temporal fusion (STF) framework to fuse two complementary sequences of x-ray images and reconstruct the target image sequence with high spatial resolution, high frame rate, and high fidelity. We applied a transfer learning strategy to train the model and compared the peak signal-to-noise ratio (PSNR), average absolute difference (AAD), and structural similarity (SSIM) of the proposed framework on two independent x-ray datasets with those obtained from a baseline deep learning model, a Bayesian fusion framework, and the bicubic interpolation method. The proposed framework outperformed the other methods with various configurations of the input frame separations and image noise levels. With 3 subsequent images from the low resolution (LR) sequence of a 4-time lower spatial resolution and another 2 images from the high resolution (HR) sequence of a 20-time lower frame rate, the proposed approach achieved an average PSNR of 37.57 dB and 35.15 dB, respectively. When coupled with the appropriate combination of high-speed cameras, the proposed approach will enhance the performance and therefore scientific value of the UHS x-ray imaging experiments.

eess.IV↗

arXiv2024

High-speed synchrotron X-ray imaging of melt pool dynamics during ultrasonic melt processing of Al6061

Ultrasonic processing of solidifying metals in additive manufacturing can provide grain refinement and advantageous mechanical properties. However, the specific physical mechanisms of microstructural refinement relevant to laser-based additive manufacturing have not been directly observed because of sub-millimeter length scales and rapid solidification rates associated with melt pools. Here, high-speed synchrotron X-ray imaging is used to observe the effect of ultrasonic vibration directly on melt pool dynamics and solidification of Al6061 alloy. The high temporal and spatial resolution enabled direct observation of cavitation effects driven by a 20.2 kHz ultrasonic source. We utilized multiphysics simulations to validate the postulated connection between ultrasonic treatment and solidification. The X-ray results show a decrease in melt pool and keyhole depth fluctuations during melting and promotion of pore migration toward the melt pool surface with applied sonication. Additionally, the simulation results reveal increased localized melt pool flow velocity, cooling rates, and thermal gradients with applied sonication. This work shows how ultrasonic treatment can impact melt pools and its potential for improving part quality.

physics.app-ph↗

arXiv2024

Bayesian analysis of verbal autopsy data using factor models with age- and sex-dependent associations between symptoms

Verbal autopsies (VAs) are extensively used to investigate the population-level distributions of deaths by cause in low-resource settings without well-organized vital statistics systems. Computer-based methods are often adopted to assign causes of death to deceased individuals based on the interview responses of their family members or caregivers. In this article, we develop a new Bayesian approach that extracts information about cause-of-death distributions from VA data considering the age- and sex-related variation in the associations between symptoms. Its performance is compared with that of existing approaches using gold-standard data from the Population Health Metrics Research Consortium. In addition, we compute the relevance of predictors to causes of death based on information-theoretic measures.

stat.AP↗

arXiv2023

Ultrafast Radiographic Imaging and Tracking: An overview of instruments, methods, data, and applications

Ultrafast radiographic imaging and tracking (U-RadIT) use state-of-the-art ionizing particle and light sources to experimentally study sub-nanosecond dynamic processes in physics, chemistry, biology, geology, materials science and other fields. These processes, fundamental to nuclear fusion energy, advanced manufacturing, green transportation and others, often involve one mole or more atoms, and thus are challenging to compute by using the first principles of quantum physics or other forward models. One of the central problems in U-RadIT is to optimize information yield through, e.g. high-luminosity X-ray and particle sources, efficient imaging and tracking detectors, novel methods to collect data, and large-bandwidth online and offline data processing, regulated by the underlying physics, statistics, and computing power. We review and highlight recent progress in: a.) Detectors; b.) U-RadIT modalities; c.) Data and algorithms; and d.) Applications. Hardware-centric approaches to U-RadIT optimization are constrained by detector material properties, low signal-to-noise ratio, high cost and long development cycles of critical hardware components such as ASICs. Interpretation of experimental data, including comparisons with forward models, is frequently hindered by sparse measurements, model and measurement uncertainties, and noise. Alternatively, U-RadIT make increasing use of data science and machine learning algorithms, including experimental implementations of compressed sensing. Machine learning and artificial intelligence approaches, refined by physics and materials information, may also contribute significantly to data interpretation, uncertainty quantification, and U-RadIT optimization.

physics.ins-det↗

arXiv2023

Bayesian Nested Latent Class Models for Cause-of-Death Assignment using Verbal Autopsies Across Multiple Domains

Understanding cause-specific mortality rates is crucial for monitoring population health and designing public health interventions. Worldwide, two-thirds of deaths do not have a cause assigned. Verbal autopsy (VA) is a well-established tool to collect information describing deaths outside of hospitals by conducting surveys to caregivers of a deceased person. It is routinely implemented in many low- and middle-income countries. Statistical algorithms to assign cause of death using VAs are typically vulnerable to the distribution shift between the data used to train the model and the target population. This presents a major challenge for analyzing VAs as labeled data are usually unavailable in the target population. This article proposes a Latent Class model framework for VA data (LCVA) that jointly models VAs collected over multiple heterogeneous domains, assign cause of death for out-of-domain observations, and estimate cause-specific mortality fractions for a new domain. We introduce a parsimonious representation of the joint distribution of the collected symptoms using nested latent class models and develop an efficient algorithm for posterior inference. We demonstrate that LCVA outperforms existing methods in predictive performance and scalability. Supplementary materials for this article and the R package to implement the model are available online.

stat.ME↗

arXiv2022

The openVA Toolkit for Verbal Autopsies

Verbal autopsy (VA) is a survey-based tool widely used to infer cause of death (COD) in regions without complete-coverage civil registration and vital statistics systems. In such settings, many deaths happen outside of medical facilities and are not officially documented by a medical professional. VA surveys, consisting of signs and symptoms reported by a person close to the decedent, are used to infer the cause of death for an individual, and to estimate and monitor the cause of death distribution in the population. Several classification algorithms have been developed and widely used to assign cause of death using VA data. However, The incompatibility between different idiosyncratic model implementations and required data structure makes it difficult to systematically apply and compare different methods. The openVA package provides the first standardized framework for analyzing VA data that is compatible with all openly available methods and data structure. It provides an open-sourced, R implementation of several most widely used VA methods. It supports different data input and output formats, and customizable information about the associations between causes and symptoms. The paper discusses the relevant algorithms, their implementations in R packages under the openVA suite, and demonstrates the pipeline of model fitting, summary, comparison, and visualization in the R environment.

stat.AP↗

arXiv2021

Health and Demographic Surveillance Systems and the 2030 Agenda: Sustainable Development Goals

The health and demographic surveillance system (HDSS) is an old method for intensively monitoring a population to assess the effects of healthcare or other population-level interventions - often clinical trials. The strengths of HDSS include very detailed descriptions of whole populations with frequent updates. This often provides long time series of accurate population and health indicators for the HDSS study population. The primary weakness of HDSS is that the data describe only the HDSS study population and cannot be generalized beyond that. The 2030 agenda is the ecosystem of activities - many including population-level monitoring - that relate to the United Nations (UN) Sustainable Development Goals (SDG). With respect to the 2030 agenda, HDSS can contribute by: continuing to conduct cause-and-effect studies; contributing to data triangulation or amalgamation initiatives; characterizing the bias in and calibrating 'big data'; and contributing more to the rapid training of data-oriented professionals, especially in the population and health fields.

stat.OT↗

arXiv2020

Correlative Synchrotron X-ray Imaging and Diffraction of Directed Energy Deposition Additive Manufacturing

The governing mechanistic behaviour of Directed Energy Deposition Additive Manufacturing (DED-AM) is revealed by a combined in situ and operando synchrotron X-ray imaging and diffraction study of a nickel-base superalloy, IN718. Using a unique process replicator, real-space phase-contrast imaging enables quantification of the melt-pool boundary and flow dynamics during solidification. This imaging knowledge informed precise diffraction measurements of temporally resolved microstructural phases during transformation and stress development with a spatial resolution of 100 $μ$m. The diffraction quantified thermal gradient enabled a dendritic solidification microstructure to be predicted and coupled to the stress orientation and magnitude. The fast cooling rate entirely suppressed the formation of secondary phases or recrystallisation in the solid-state. Upon solidification, the stresses rapidly increase to the yield strength during cooling. This insight, combined with IN718 $'$s large solidification range suggests that the accumulated plasticity exhausts the alloy$'$s ductility, causing liquation cracking. This study has revealed additional fundamental mechanisms governing the formation of highly non-equilibrium microstructures during DED-AM.

physics.app-ph↗

arXiv2020

In situ and Operando X-ray Imaging of Directed Energy Deposition Additive Manufacturing

The mechanical performance of Directed Energy Deposition Additive Manufactured (DED-AM) components can be highly material dependent. Through in situ and operando synchrotron X-ray imaging we capture the underlying phenomena controlling build quality of stainless steel (SS316) and titanium alloy (Ti6242 or Ti-6Al-2Sn-4Zr-2Mo). We reveal three mechanisms influencing the build efficiency of titanium alloys compared to stainless steel: blown powder sintering; reduced melt-pool wetting due to the sinter; and pore pushing in the melt-pool. The former two directly increase lack of fusion porosity, while the later causes end of track porosity. Each phenomenon influences the melt-pool characteristics, wetting of the substrate and hence build efficacy and undesirable microstructural feature formation. We demonstrate that porosity is related to powder characteristics, pool flow, and solidification front morphology. Our results clarify DED-AM process dynamics, illustrating why each alloy builds differently, facilitating the wider application of additive manufacturing to new materials.

physics.app-ph↗

arXiv2019

Verbal Autopsy in Civil Registration and Vital Statistics: The Symptom-Cause Information Archive

The burden of disease is fundamental to understanding, prioritizing, and monitoring public health interventions. Cause of death is required to calculate the burden of disease, but in many parts of the developing world deaths are neither detected nor given a cause. Verbal autopsy is a feasible way of assigning a cause to a death based on an interview with those who cared for the person who died. As civil registration and vital statistics systems improve in the developing world, verbal autopsy is playing and increasingly important role in providing information about cause of death and the burden of disease. This note motivates the creation of a global symptom-cause archive containing reference deaths with both a verbal autopsy and a cause assigned through an independent mechanism. This archive could provide training and validation data for refining, developing, and testing machine-based algorithms to automate cause assignment from verbal autopsy data. This, in turn, would improve the comparability of machine-assigned causes and provide a means to fine-tune individual cause assignment within specific contexts.

stat.AP↗

arXiv2019

Using Bayesian latent Gaussian graphical models to infer symptom associations in verbal autopsies

Learning dependence relationships among variables of mixed types provides insights in a variety of scientific settings and is a well-studied problem in statistics. Existing methods, however, typically rely on copious, high quality data to accurately learn associations. In this paper, we develop a method for scientific settings where learning dependence structure is essential, but data are sparse and have a high fraction of missing values. Specifically, our work is motivated by survey-based cause of death assessments known as verbal autopsies (VAs). We propose a Bayesian approach to characterize dependence relationships using a latent Gaussian graphical model that incorporates informative priors on the marginal distributions of the variables. We demonstrate such information can improve estimation of the dependence structure, especially in settings with little training data. We show that our method can be integrated into existing probabilistic cause-of-death assignment algorithms and improves model performance while recovering dependence patterns between symptoms that can inform efficient questionnaire design in future data collection.

stat.AP↗

arXiv2019

Bayesian Joint Spike-and-Slab Graphical Lasso

In this article, we propose a new class of priors for Bayesian inference with multiple Gaussian graphical models. We introduce fully Bayesian treatments of two popular procedures, the group graphical lasso and the fused graphical lasso, and extend them to a continuous spike-and-slab framework to allow self-adaptive shrinkage and model selection simultaneously. We develop an EM algorithm that performs fast and dynamic explorations of posterior modes. Our approach selects sparse models efficiently with substantially smaller bias than would be induced by alternative regularization procedures. The performance of the proposed methods are demonstrated through simulation and two real data examples.

stat.ML↗

arXiv2018

Bayesian factor models for probabilistic cause of death assessment with verbal autopsies

The distribution of deaths by cause provides crucial information for public health planning, response, and evaluation. About 60% of deaths globally are not registered or given a cause, limiting our ability to understand disease epidemiology. Verbal autopsy (VA) surveys are increasingly used in such settings to collect information on the signs, symptoms, and medical history of people who have recently died. This article develops a novel Bayesian method for estimation of population distributions of deaths by cause using verbal autopsy data. The proposed approach is based on a multivariate probit model where associations among items in questionnaires are flexibly induced by latent factors. Using the Population Health Metrics Research Consortium labeled data that include both VA and medically certified causes of death, we assess performance of the proposed method. Further, we estimate important questionnaire items that are highly associated with causes of death. This framework provides insights that will simplify future data collection.

stat.AP↗