Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Markov chain model”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Dark matter clumps as sources of gravitational-wave glitches in LIGO-Virgo-KAGRA data

We consider the hypothetical possibility that nonstationary glitch features in the noise of ground-based gravitational-wave detectors could be produced by small dark matter clumps that pass through the earth in the vicinity of gravitational-wave detectors. Here, we first derive the gravitational-wave strain that would be generated by the passage of such a dark matter clump. We find that the strain is primarily sourced by the Newtonian gravitational acceleration of the mirrors toward the clump and by the Shapiro time delay of the photons in the laser beams as they pass through the gravitational potential created by the dark matter clump. We also find that the Newtonian acceleration effect dominates the gravitational-wave strain for both ground and space-based interferometers. We then compare our dark matter clump, gravitational-wave strain model to 84 Koi-Fish glitches detected during the second observing run of the LIGO/Virgo/KAGRA Collaboration through a Markov chain Monte Carlo Bayesian analysis. We find that all glitches but nine can be confidently rejected as having originated from dark matter clumps. For the remaining glitches, the dark matter hypothesis cannot be excluded, and the maximum a posteriori parameters yield minimum densities of about 10 −7 g⁡/cm 3 , within the model. These results allow us to place the first direct upper limits with gravitational-wave detectors on the local over-density of dark matter in the form of clumps in the local neighborhood of Earth, namely 𝜌 DM ⁢clumps ≲ 10 −15 g⁡/cm −3 .

Astronomy and AstroPhysics↗
DOE OSTI2022

Fracton Hydrodynamics without Time-Reversal Symmetry

Here, we present an effective field theory for the nonlinear fluctuating hydrodynamics of a single conserved charge with or without time-reversal symmetry, based on the Martin-Siggia-Rose formalism. Applying this formalism to fluids with only charge and multipole conservation, and with broken time-reversal symmetry, we predict infinitely many new dynamical universality classes, including some with arbitrarily large upper critical dimensions. Using large scale simulations of classical Markov chains, we find numerical evidence for a breakdown of hydrodynamics in quadrupole-conserving models with broken time-reversal symmetry in one spatial dimension. Our framework can be applied to the hydrodynamics around stationary states of open systems, broadening the applicability of previously developed ideas and methods to a wide range of systems in driven and active matter.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Photometric Objects around Cosmic Webs (PAC) Delineated in a Spectroscopic Survey. I. Methods

We provide a method for estimating the projected density distribution ${\bar{n}}_{2}{w}_{p}({r}_{p})$ of photometric objects around spectroscopic objects in a spectroscopic survey. This quantity describes the distribution of photometric sources with certain physical properties (e.g., luminosity, mass, and color) around cosmic webs (PAC) traced by the spectroscopic objects. The method can make full use of current and future deep and wide photometric surveys to explore the formation of galaxies up to medium redshift (z s < 2) 3 with the aid of cosmological spectroscopic surveys that sample only a fairly limited species of objects (e.g., emission line galaxies). As an example, we apply the PAC method to the CMASS spectroscopic and HSC-SSP PDR2 photometric samples to explore the distribution of galaxies for a wide range of stellar masses from 10 9.0 to 10 12.0 M ⊙ around massive galaxies at z s ≈ 0.6. Using the abundance-matching method, we model ${\bar{n}}_{2}{w}_{p}({r}_{p})$ in N-body simulation using Markov chain Monte Carlo sampling, and we accurately measure the stellar–halo mass relation and stellar mass function for the whole mass range. We can also measure the conditional stellar mass function of satellites for central galaxies of different mass. The PAC method has many potential applications for studying the evolution of galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Bayesian inference of structured latent spaces from neural population activity with the orthogonal stochastic linear mixing model

The brain produces diverse functions, from perceiving sounds to producing arm reaches, through the collective activity of populations of many neurons. Determining if and how the features of these exogenous variables (e.g., sound frequency, reach angle) are reflected in population neural activity is important for understanding how the brain operates. Often, high-dimensional neural population activity is confined to low-dimensional latent spaces. However, many current methods fail to extract latent spaces that are clearly structured by exogenous variables. This has contributed to a debate about whether or not brains should be thought of as dynamical systems or representational systems. Here, we developed a new latent process Bayesian regression framework, the orthogonal stochastic linear mixing model (OSLMM) which introduces an orthogonality constraint amongst time-varying mixture coefficients, and provide Markov chain Monte Carlo inference procedures. We demonstrate superior performance of OSLMM on latent trajectory recovery in synthetic experiments and show superior computational efficiency and prediction performance on several real-world benchmark data sets. We primarily focus on demonstrating the utility of OSLMM in two neural data sets: μ ECoG recordings from rat auditory cortex during presentation of pure tones and multi-single unit recordings form monkey motor cortex during complex arm reaching. We show that OSLMM achieves superior or comparable predictive accuracy of neural data and decoding of external variables (e.g., reach velocity). Most importantly, in both experimental contexts, we demonstrate that OSLMM latent trajectories directly reflect features of the sounds and reaches, demonstrating that neural dynamics are structured by neural representations. Together, these results demonstrate that OSLMM will be useful for the analysis of diverse, large-scale biological time-series datasets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Sensitivity-Informed Bayesian Inference for Home PLC Network Models with Unknown Parameters

Bayesian inference is used to calibrate a bottom-up home PLC network model with unknown loads and wires at frequencies up to 30 MHz. A network topology with over 50 parameters is calibrated using global sensitivity analysis and transitional Markov Chain Monte Carlo (TMCMC). The sensitivity-informed Bayesian inference computes Sobol indices for each network parameter and applies TMCMC to calibrate the most sensitive parameters for a given network topology. A greedy random search with TMCMC is used to refine the discrete random variables of the network. This results in a model that can accurately compute the transfer function despite noisy training data and a high dimensional parameter space. The model is able to infer some parameters of the network used to produce the training data, and accurately computes the transfer function under extrapolative scenarios.

42 ENGINEERING↗
DOE OSTI2025

Discrete generative diffusion models without stochastic differential equations: A tensor network approach

Diffusion models (DMs) are a class of generative machine learning methods that sample a target distribution by transforming samples of a trivial (often Gaussian) distribution using a learned stochastic differential equation. In standard DMs, this is done by learning a “score function” that reverses the effect of adding diffusive noise to the distribution of interest. Here we consider the generalisation of DMs to lattice systems with discrete degrees of freedom, and where noise is added via Markov chain jump dynamics. We show how to use tensor networks (TNs) to efficiently define and sample such “discrete diffusion models” (DDMs) without explicitly having to solve a stochastic differential equation. We show the following: (i) by parametrising the data and evolution operators as TNs, the denoising dynamics can be represented exactly; (ii) the auto-regressive nature of TNs allows to generate samples efficiently and without bias; (iii) for sampling Boltzmann-like distributions, TNs allow to construct an efficient learning scheme that integrates well with Monte Carlo. We illustrate this approach to study the equilibrium of two models with non-trivial thermodynamics, the d = 1 constrained Fredkin chain and the d = 2 Ising model. Published by the American Physical Society 2025

Causer, Luke (ORCID:0000000194243473)↗
DOE OSTI2021

Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes

Objective: Currently, next generation sequencing (NGS) is widely used to decode potential novel or variant pathogens both in emergent outbreaks and in routine clinical practice. However, the efficient identification of novel or diverged pathogenomic compositions remains a big challenge. It is especially true for short DNA sequence fragments from NGS, since sequence similarity searching is vulnerable to false negatives or false positives, as is mismatching or matching with unrelated proteins. Therefore, this study aimed to establish a bioinformatics approach that can generate unique motif sequences for profiling searching, resulting in high specificity and sensitivity. Results: In this study, we introduced a Shortest Unique Representative Hidden Markov Model (HMM) approach to identify bacterial toxin, virulence factor (VF), and antimicrobial resistance (AR) in short sequence reads. We first construct unique representative domain sequences of toxin genes, VFs, and ARs to avoid potential false positives, and then to use HMM models to accurately identify potential toxin, VF, and AR fragments. The benchmark shows this approach can achieve relatively high specificity and sensitivity if the appropriate cutoff value is applied. Our approach can be used to recognize the protein sequences of known toxins and pathogens, identifies their common characteristics and then searches for similar sequences in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

On decoupling the integrals of cosmological perturbation theory

ABSTRACT Perturbation theory (PT) is often used to model statistical observables capturing the translation and rotation-invariant information in cosmological density fields. PT produces higher order corrections by integration over linear statistics of the density fields weighted by kernels resulting from recursive solution of the fluid equations. These integrals quickly become high dimensional and naively require increasing computational resources the higher the order of the corrections. Here, we show how to decouple the integrands that often produce this issue, enabling PT corrections to be computed as a sum of products of independent 1D integrals. Our approach is related to a commonly used method for calculating multiloop Feynman integrals in quantum field theory, the Gegenbauer Polynomial x-Space Technique. We explicitly reduce the three terms entering the 2-loop power spectrum, formally requiring 9D integrations, to sums over successive 1D radial integrals. These 1D integrals can further be performed as convolutions, rendering the scaling of this method Nglog Ng with Ng the number of grid points used for each fast Fourier transform. This method should be highly enabling for upcoming large-scale structure redshift surveys where model predictions at an enormous number of cosmological parameter combinations will be required by Monte Carlo Markov Chain searches for the best-fitting values.

Slepian, Zachary↗
DOE OSTI2025

High-dimensional maximum-entropy phase space tomography

Reconstructing 4D or 6D phase space distributions from 1D or 2D measurements is a challenging inverse problem encountered in particle accelerators. Entropy maximization is an established method to incorporate prior information in the reconstruction, but it is typically infeasible in high-dimensional spaces. In this paper, I review two recent approaches to high-dimensional entropy maximization. The first approach utilizes differentiable simulations and a class of generative models known as normalizing flows, whereas the second approach employs the method of Lagrange multipliers and Markov Chain Monte Carlo (MCMC) sampling. My aim is to provide a short explanation of each method using a common notation. I conclude by mentioning several unsolved problems in phase space tomography.

Hoover, Austin [ORNL] (ORCID:0000000153136962)↗
DOE OSTI2022

Decoding Golden Eagle Movement Behavior from High-Resolution, Variable-Rate Telemetry Data Through Bayesian Filtering

The recent advances in animal tracking technology have enabled the collection of a vast amount of in situ data regarding the movement of wildlife at high spatiotemporal resolution. These data are usually available at variable time resolutions and contains noise (error) originating from GPS fixes. Decoding movement characteristics, particularly of flying animals, from telemetry data while handling these factors is a challenging yet important task for conservation purposes. Typically, this task is broken into two subtasks: resampling, and model calibration. The resampling subtask converts the variable rate positional data into a constant time interval data, while the model calibration subtask uses the resampled data to tune time-invariant parameters of the proposed models. For telemetry data at high temporal resolutions (order of 1 second), it is very challenging to decouple noise from actual movements using interpolation-based resampling techniques. Any errors introduced during resampling can significantly alter the the calibration and prediction attributes of the movement model. We address this problem through a unified Bayesian state-space framework that can handle both the resampling and calibration tasks in a single step. In addition, we use the speed and heading of the bird from telemetry data to regularize the position information of the bird. We use a Kalman filtering approach to include these nonlinearly related motion parameters within the state space framework. We cross-validated to quantify how this inclusion affects the model performance in estimating true bird movements. The relationship between the true state of the bird and environmental and topographical covariates is then represented parametrically. These parameters are then tuned using stochastic sampling strategies like Markov Chain Monte Carlo (MCMC). We use the telemetry data collected from golden eagles in the western USA to demonstrate the applicability of this approach to build a predictive, probabilistic movement model. Our preliminary results show that this approach provides improved predictive performance in terms of capturing higher-order motion parameters such as angular and horizontal accelerations, which may have simpler and more direct relationships with environmental covariates than corresponding speeds. In this talk, we will demonstrate how this state-space approach benefits the prediction capabilities of a movement model in simulating golden eagle paths through a wind power plant in Wyoming given certain atmospheric conditions. The model outcomes are aimed at informing mitigation strategies that can minimize the potential for collisions of golden eagles with wind turbines.

Bayesian methods↗
DOE OSTI2025

Combining Observations and Models: A Review of the CARDAMOM Framework for Data‐Constrained Terrestrial Ecosystem Modeling

The rapid increase in the volume and variety of terrestrial biosphere observations (i.e., remote sensing data and in situ measurements) offers a unique opportunity to derive ecological insights, refine process‐based models, and improve forecasting for decision support. However, despite their potential, ecological observations have primarily been used to benchmark process‐based models, as many past and current models lack the capability to directly integrate observations and their associated uncertainties for parameterization. In contrast, data assimilation frameworks such as the CARbon DAta MOdel fraMework (CARDAMOM) and its suite of process‐based models, known as the Data Assimilation Linked Ecosystem Carbon Model (DALEC), are specifically designed for model‐data fusion. This review, motivated by a recent CARDAMOM community workshop, examines the development and applications of CARDAMOM, with an emphasis on its role in advancing ecosystem process understanding. CARDAMOM employs a Bayesian approach, using a Markov Chain Monte Carlo algorithm to enable data‐driven calibration of DALEC parameters and initial states (i.e., carbon pool sizes) through observation operators. CARDAMOM's unique ability to retrieve localized model process parameters from diverse datasets—ranging from in situ measurements to global satellite observations—makes it a highly flexible tool for analyzing spatially variable ecosystem responses to environmental change. However, assimilating these data also presents challenges, including data quality issues that propagate into model skill, as well as trade‐offs between model complexity, parameter equifinality, and predictive performance. We discuss potential solutions to these challenges, such as reducing parameter equifinality by incorporating new observations. This review also offers community recommendations for incorporating emerging datasets, integrating machine learning techniques, strengthening collaboration with remote sensing, field, and modeling communities, and expanding CARDAMOM's relevance for localized ecosystem monitoring and decision‐making. CARDAMOM enables a deep, mechanistic understanding of terrestrial ecosystem dynamics that cannot be achieved through empirical analyses of observational datasets or weakly constrained models alone.

Bayesian inference↗
DOE OSTI2023

Quantification of early nonpharmaceutical interventions aimed at slowing transmission of Coronavirus Disease 2019 in the Navajo Nation and surrounding states (Arizona, Colorado, New Mexico, and Utah)

During an early period of the Coronavirus Disease 2019 (COVID-19) pandemic, the Navajo Nation, much like New York City, experienced a relatively high rate of disease transmission. Yet, between January and October 2020, it experienced only a single period of growth in new COVID-19 cases, which ended when cases peaked in May 2020. The daily number of new cases slowly decayed in the summer of 2020 until late September 2020. In contrast, the surrounding states of Arizona, Colorado, New Mexico, and Utah all experienced at least two periods of growth in the same time frame, with second surges beginning in late May to early June. Here, we investigated these differences in disease transmission dynamics with the objective of quantifying the contributions of non-pharmaceutical interventions (NPIs) (e.g., behaviors that limit disease transmission). We considered a compartmental model accounting for distinct periods of NPIs to analyze the epidemic in each of the five regions. We used Bayesian inference to estimate region-specific model parameters from regional surveillance data (daily reports of new COVID-19 cases) and to quantify uncertainty in parameter estimates and model predictions. Our results suggest that NPIs in the Navajo Nation were sustained over the period of interest, whereas in the surrounding states, NPIs were relaxed, which allowed for subsequent surges in cases. Our region-specific model parameterizations allow us to quantify the impacts of NPIs on disease incidence in the regions of interest.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Analytical gradient-based optimization of CALPHAD model parameters

The calibration of CALPHAD (CALculation of PHAse Diagrams) models involves the solution of a very challenging high-dimensional multiobjective optimization problem. Traditional approaches to parameter fitting predominantly rely on gradient-free methods, which while robust, are computationally inefficient and often scale poorly with model complexity. In this work, we introduce and demonstrate a generalizable framework for analytic gradient-based optimization of the parameters of the CALPHAD model enabled by the recently formalized Jansson derivative technique. This method allows for efficient evaluation of gradients of thermodynamic properties at equilibrium with respect to model parameters, even in the presence of arbitrarily complex internal degrees of freedom. Leveraging these semi-analytic gradients, we employ the conjugate gradient (CG) method to optimize thermodynamic model parameters for four binary alloy systems: Cu-Mg, Fe-Ni, Cr-Ni, and Cr-Fe. Across all systems, CG achieves comparable or superior optimality relative to Bayesian ensemble Markov Chain Monte Carlo (MCMC) with improvements in computational efficiency ranging from one to three orders of magnitude. Furthermore, our results establish a new paradigm for CALPHAD assessments in which high fidelity data-rich model calibration becomes tractable using deterministic gradient-informed algorithms.

CALPHAD↗
DOE OSTI2023

Bayesian Cloud Property Retrievals from ARM Active and Passive Measurements

The optimum use of the continuous measurements of thermodynamics, radiation, aerosols, clouds and precipitation from the DOE Atmospheric Radiation Measurement (ARM) program is key to achieve the DOE Atmospheric System Research (ASR)’s objectives. One of the key mission requirements is to retrieve cloud and precipitation properties, as well as vertical motion parameters, along the vertical cross- section defined by the profiling active sensors. Such retrievals are challenging to perform continuously in the entire spectrum of cloud and precipitation conditions due to the large natural microphysical and dynamical variability, the often-limited information content in the measurements, and the lack of proper characterization of measurement quality and uncertainty. Today, the acquisition of new remote and in-situ sensors by the ARM program creates opportunities to address the microphysical retrieval problem by exploiting new, more robust retrieval techniques and integrating various scattered advancements in both sensor techniques and retrieval algorithms. During this project, we constructed a robust Bayesian Markov chain Monte Carlo (MCMC) cloud property retrieval algorithm that includes a state of the art radar forward model. Our MCMC-based retrieval produces both the best estimate of height-resolved cloud and precipitation properties in the radar profile, as well as an estimate of the in-cloud vertical motion and turbulence. In addition, the MCMC algorithm automatically produces robust and flexible estimates of retrieval uncertainty. We tested the algorithm on several synthetic cloud profiles obtained from large eddy simulation (LES) models with bin-resolved microphysics.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Fast matrix algebra for Bayesian model calibration

In Bayesian model calibration, evaluation of the likelihood function usually involves finding the inverse and determinant of a covariance matrix. When Markov Chain Monte Carlo (MCMC) methods are used to sample from the posterior, hundreds of thousands of likelihood evaluations may be required. In this paper, we demonstrate that the structure of the covariance matrix can be exploited, leading to substantial time savings in practice. Here, we also derive two simple equations for approximating the inverse of the covariance matrix in this setting, which can be computed in near-quadratic time. The practical implications of these strategies are demonstrated using a simple numerical case study and the "quack" R package. For a covariance matrix with 1000 rows, application of these strategies for a million likelihood evaluations leads to a speedup of roughly 4000 compared to the naive implementation

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Confronting interacting dark radiation scenarios with cosmological data

Dark radiation (DR) is generally predicted in new physics scenarios that address fundamental puzzles of the Standard Model or tensions in the cosmological data. Cosmological data have the sensitivity to constrain not only the energy density of DR but also whether it is interacting. In this paper, we present a systematic study of five types of interacting DR (free-streaming, fluid, decoupling, instantaneous decoupling, and recoupling DR) and their impact on cosmological observables. We modify the Boltzmann hierarchy to describe all these types of interacting DR under the relaxation time approximation. We, for the first time, robustly calculate the collision terms for recoupling scalar DR and provide a better estimation of the recoupling transition redshift. We demonstrate the distinct features of each type of DR on the cosmic microwave background and matter power spectra. We perform Markov-chain Monte Carlo scans using the Planck 2018 data and baryon acoustic oscillation data. Assuming no new physics in the standard model neutrino sector, we find no statistically significant constraints on the couplings of DR, although there is a slight preference for the fluidlike limit of all the cases. In the case of instantaneous decoupling DR, this limit corresponds to a late transition redshift around recombination. Furthermore, the ΔN eff constraint varies marginally depending on the type of DR.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Plug & play directed evolution of proteins with gradient-based discrete MCMC

Abstract A long-standing goal of machine-learning-based protein engineering is to accelerate the discovery of novel mutations that improve the function of a known protein. We introduce a sampling framework for evolving proteins in silico that supports mixing and matching a variety of unsupervised models, such as protein language models, and supervised models that predict protein function from sequence. By composing these models, we aim to improve our ability to evaluate unseen mutations and constrain search to regions of sequence space likely to contain functional proteins. Our framework achieves this without any model fine-tuning or re-training by constructing a product of experts distribution directly in discrete protein space. Instead of resorting to brute force search or random sampling, which is typical of classic directed evolution, we introduce a fast Markov chain Monte Carlo sampler that uses gradients to propose promising mutations. We conduct in silico directed evolution experiments on wide fitness landscapes and across a range of different pre-trained unsupervised models, including a 650 M parameter protein language model. Our results demonstrate an ability to efficiently discover variants with high evolutionary likelihood as well as estimated activity multiple mutations away from a wild type protein, suggesting our sampler provides a practical and effective new paradigm for machine-learning-based protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Radiation Source Localization Using Surrogate Models Constructed from 3-D Monte Carlo Transport Physics Simulations

Recent research has focused on the development of surrogate models for radiation source localization in a simulated urban domain. We employ the Monte Carlo N-Particle (MCNP) code to provide high- delity simulations of radiation transport within an urban domain. The model is constructed to employ a source location (x, y, z) as input and return the estimated count rate for a set of speci ed detector locations. Because MCNP simulations are computationally expensive, we develop e cient and accurate surrogate models of the detector responses. We construct surrogate models using Gaussian processes (GP) and neural networks (NN) that we train and verify using the MCNP simulations. The trained surrogate models provide an e cient framework for Bayesian inference and experimental design. We employ Delayed Rejection Adaptive Metropolis (DRAM), a Markov Chain Monte Carlo (MCMC) algorithm, to infer the location and intensity of an unknown source. The DRAM results yield a posterior probability distribution for the source's location conditioned on the observed detector count rates. The posterior distribution exhibits regions of high and low probability within the simulated environment identifying potential source locations. In this manner, we can quantify the source location to within at least one of these regions of high probability in the considered cases. Employing these methods, we are able to reduce the space of potential source locations by at least 60%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗