arXiv subjects

J. Tinsley Oden

Publications and source records attributed to J. Tinsley Oden.

18 recordsLinked to original sources

arXiv2023

Bayesian model calibration for diblock copolymer thin film self-assembly using power spectrum of microscopy data and machine learning surrogate

Identifying parameters of computational models from experimental data, or model calibration, is fundamental for assessing and improving the predictability and reliability of computer simulations. In this work, we propose a method for Bayesian calibration of models that predict morphological patterns of diblock copolymer (Di-BCP) thin film self-assembly while accounting for various sources of uncertainties in pattern formation and data acquisition. This method extracts the azimuthally-averaged power spectrum (AAPS) of the top-down microscopy characterization of Di-BCP thin film patterns as summary statistics for Bayesian inference of model parameters via the pseudo-marginal method. We derive the analytical and approximate form of a conditional likelihood for the AAPS of image data. We demonstrate that AAPS-based image data reduction retains the mutual information, particularly on important length scales, between image data and model parameters while being relatively agnostic to the aleatoric uncertainties associated with the random long-range disorder of Di-BCP patterns. Additionally, we propose a phase-informed prior distribution for Bayesian model calibration. Furthermore, reducing image data to AAPS enables us to efficiently build surrogate models to accelerate the proposed Bayesian model calibration procedure. We present the formulation and training of two multi-layer perceptrons for approximating the parameter-to-spectrum map, which enables fast integrated likelihood evaluations. We validate the proposed Bayesian model calibration method through numerical examples, for which the neural network surrogate delivers a fivefold reduction of the number of model simulations performed for a single calibration task.

physics.comp-ph↗

arXiv2023

Bridging Scales: a Hybrid Model to Simulate Vascular Tumor Growth and Treatment Response

Cancer is a disease driven by random DNA mutations and the interaction of many complex phenomena. To improve the understanding and ultimately find more effective treatments, researchers leverage computer simulations mimicking the tumor growth in silico. The challenge here is to account for the many phenomena influencing the disease progression and treatment protocols. This work introduces a computational model to simulate vascular tumor growth and the response to drug treatments in 3D. It consists of two agent-based models for the tumor cells and the vasculature. Moreover, partial differential equations govern the diffusive dynamics of the nutrients, the vascular endothelial growth factor, and two cancer drugs. The model focuses explicitly on breast cancer cells over-expressing HER2 receptors and a treatment combining standard chemotherapy (Doxorubicin) and monoclonal antibodies with anti-angiogenic properties (Trastuzumab). However, large parts of the model generalize to other scenarios. We show that the model qualitatively captures the effects of the combination therapy by comparing our simulation results with previously published pre-clinical data. Furthermore, we demonstrate the scalability of the model and the associated C++ code by simulating a vascular tumor occupying a volume of 400mm3 using a total of 92.5 million agents.

physics.comp-ph↗

arXiv2023

A phase-field model for non-small cell lung cancer under the effects of immunotherapy

Formulating tumor models that predict growth under therapy is vital for improving patient-specific treatment plans. In this context, we present our recent work on simulating non-small-scale cell lung cancer (NSCLC) in a simple, deterministic setting for two different patients receiving an immunotherapeutic treatment. At its core, our model consists of a Cahn-Hilliard-based phase-field model describing the evolution of proliferative and necrotic tumor cells. These are coupled to a simplified nutrient model that drives the growth of the proliferative cells and their decay into necrotic cells. The applied immunotherapy decreases the proliferative cell concentration. Here, we model the immunotherapeutic agent concentration in the entire lung over time by an ordinary differential equation (ODE). Finally, reaction terms provide a coupling between all these equations. By assuming spherical, symmetric tumor growth and constant nutrient inflow, we simplify this full 3D cancer simulation model to a reduced 1D model. We can then resort to patient data gathered from computed tomography (CT) scans over several years to calibrate our model. For the reduced 1D model, we show that our model can qualitatively describe observations during immunotherapy by fitting our model parameters to existing patient data. Our model covers cases in which the immunotherapy is successful and limits the tumor size, as well as cases predicting a sudden relapse, leading to exponential tumor growth. Finally, we move from the reduced model back to the full 3D cancer simulation in the lung tissue. Thereby, we show the predictive benefits a more detailed patient-specific simulation including spatial information could yield in the future.

math.NA↗

arXiv2022

Residual-based error correction for neural operator accelerated infinite-dimensional Bayesian inverse problems

We explore using neural operators, or neural network representations of nonlinear maps between function spaces, to accelerate infinite-dimensional Bayesian inverse problems (BIPs) with models governed by nonlinear parametric partial differential equations (PDEs). Neural operators have gained significant attention in recent years for their ability to approximate the parameter-to-solution maps defined by PDEs using as training data solutions of PDEs at a limited number of parameter samples. The computational cost of BIPs can be drastically reduced if the large number of PDE solves required for posterior characterization are replaced with evaluations of trained neural operators. However, reducing error in the resulting BIP solutions via reducing the approximation error of the neural operators in training can be challenging and unreliable. We provide an a priori error bound result that implies certain BIPs can be ill-conditioned to the approximation error of neural operators, thus leading to inaccessible accuracy requirements in training. To reliably deploy neural operators in BIPs, we consider a strategy for enhancing the performance of neural operators, which is to correct the prediction of a trained neural operator by solving a linear variational problem based on the PDE residual. We show that a trained neural operator with error correction can achieve a quadratic reduction of its approximation error, all while retaining substantial computational speedups of posterior sampling when models are governed by highly nonlinear PDEs. The strategy is applied to two numerical examples of BIPs based on a nonlinear reaction--diffusion problem and deformation of hyperelastic materials. We demonstrate that posterior representations of the two BIPs produced using trained neural operators are greatly and consistently enhanced by error correction.

math.NA↗

arXiv2022

Goal-Oriented A-Posteriori Estimation of Model Error as an Aid to Parameter Estimation

In this work, a Bayesian model calibration framework is presented that utilizes goal-oriented a-posterior error estimates in quantities of interest (QoIs) for classes of high-fidelity models characterized by PDEs. It is shown that for a large class of computational models, it is possible to develop a computationally inexpensive procedure for calibrating parameters of high-fidelity models of physical events when the parameters of low-fidelity (surrogate) models are known with acceptable accuracy. The main ingredients in the proposed model calibration scheme are goal-oriented a-posteriori estimates of error in QoIs computed using a so-called lower fidelity model compared to those of an uncalibrated higher fidelity model. The estimates of error in QoIs are used to define likelihood functions in Bayesian inversion analysis. A standard Bayesian approach is employed to compute the posterior distribution of model parameters of high-fidelity models. As applications, parameters in a quasi-linear second-order elliptic boundary-value problem (BVP) are calibrated using a second-order linear elliptic BVP. In a second application, parameters of a tumor growth model involving nonlinear time-dependent PDEs are calibrated using a lower fidelity linear tumor growth model with known parameter values.

math.NA↗

arXiv2022

Optimal design of chemoepitaxial guideposts for directed self-assembly of block copolymer systems using an inexact-Newton algorithm

Directed self-assembly (DSA) of block-copolymers (BCPs) is one of the most promising developments in the cost-effective production of nanoscale devices. The process makes use of the natural tendency for BCP mixtures to form nanoscale structures upon phase separation. The phase separation can be directed through the use of chemically patterned substrates to promote the formation of morphologies that are essential to the production of semiconductor devices. Moreover, the design of substrate pattern can formulated as an optimization problem for which we seek optimal substrate designs that effectively produce given target morphologies. In this paper, we adopt a phase field model given by a nonlocal Cahn--Hilliard partial differential equation (PDE) based on the minimization of the Ohta--Kawasaki free energy, and present an efficient PDE-constrained optimization framework for the optimal design problem. The design variables are the locations of circular- or strip-shaped guiding posts that are used to model the substrate chemical pattern. To solve the ensuing optimization problem, we propose a variant of an inexact Newton conjugate gradient algorithm tailored to this problem. We demonstrate the effectiveness of our computational strategy on numerical examples that span a range of target morphologies. Owing to our second-order optimizer and fast state solver, the numerical results demonstrate five orders of magnitude reduction in computational cost over previous work. The efficiency of our framework and the fast convergence of our optimization algorithm enable us to rapidly solve the optimal design problem in not only two, but also three spatial dimensions.

math.OC↗

arXiv2022

Mutual-Information Based Optimal Experimental Design for Hyperpolarized $^{13}$C-Pyruvate MRI

A key parameter of interest recovered from hyperpolarized (HP) MRI measurements is the apparent pyruvate-to-lactate exchange rate, $k_{PL}$, for measuring tumor metabolism. This manuscript presents an information-theory-based optimal experimental design (OED) approach that minimizes the uncertainty in the rate parameter, $k_{PL}$, recovered from HP-MRI measurements. Mutual information (MI) is employed to measure the information content of the HP measurements with respect to the first-order exchange kinetics of the pyruvate conversion to lactate. Flip angles of the pulse sequence acquisition are optimized with respect to the mutual information. Further, a spatially varying model (high-fidelity) based on the Block-Torrey equations is proposed and utilized as a control. A time-varying flip angle scheme leads to a higher parameter optimization that can further improve the quantitative value of mutual information over a constant flip angle scheme. However, the constant flip angle scheme leads to the best accuracy and precision when considering inference from noise-corrupted data. For the particular MRI data examined here, pyruvate and lactate flip angles of 35 and 28 degrees, respectively, were the best choice in terms of accuracy and precision of the parameter recovery. Moreover, the recovery of rate parameter $k_{PL}$ from the data generated from the high-fidelity model highlights the influence of diffusion and strength of vascular source on the recovered rate parameter. Since the existing pharmacokinetic models for HP-MRI do not account for spatial variation, the optimized design parameters may not be fully optimal in a more general 3D setting.

cs.IT↗

arXiv2022

Bayesian model calibration for block copolymer self-assembly: Likelihood-free inference and expected information gain computation via measure transport

We consider the Bayesian calibration of models describing the phenomenon of block copolymer (BCP) self-assembly using image data produced by microscopy or X-ray scattering techniques. To account for the random long-range disorder in BCP equilibrium structures, we introduce auxiliary variables to represent this aleatory uncertainty. These variables, however, result in an integrated likelihood for high-dimensional image data that is generally intractable to evaluate. We tackle this challenging Bayesian inference problem using a likelihood-free approach based on measure transport together with the construction of summary statistics for the image data. We also show that expected information gains (EIGs) from the observed data about the model parameters can be computed with no significant additional cost. Lastly, we present a numerical case study based on the Ohta--Kawasaki model for diblock copolymer thin film self-assembly and top-down microscopy characterization. For calibration, we introduce several domain-specific energy- and Fourier-based summary statistics, and quantify their informativeness using EIG. We demonstrate the power of the proposed approach to study the effect of data corruptions and experimental designs on the calibration results.

physics.comp-ph↗

arXiv2022

A 1D-0D-3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic PDEs is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D-0D-3D coupled models for simulating blood flow and transport processes: The first 1D-0D-3D model covers the whole path from the aorta to the breast, while the second model is a sub-model obtained by restriction to breast vasculature and tissue making possible a significant reduction in computational cost. Several numerical experiments are conducted that demonstrate realistic flow simulations compared to existing data on blood flow in human breast and vascular system.

q-bio.TO↗

arXiv2021

Modeling and simulation of vascular tumors embedded in evolving capillary networks

In this work, we present a coupled 3D-1D model of solid tumor growth within a dynamically changing vascular network to facilitate realistic simulations of angiogenesis. Additionally, the model includes erosion of the extracellular matrix, interstitial flow, and coupled flow in blood vessels and tissue. We employ continuum mixture theory with stochastic Cahn--Hilliard type phase-field models of tumor growth. The interstitial flow is governed by a mesoscale version of Darcy's law. The flow in the blood vessels is controlled by Poiseuille flow, and Starling's law is applied to model the mass transfer in and out of blood vessels. The evolution of the network of blood vessels is orchestrated by the concentration of the tumor angiogenesis factors (TAFs); blood vessels grow towards the increasing TAFs concentrations. This process is not deterministic, allowing random growth of blood vessels and, therefore, due to the coupling of nutrients in tissue and vessels, makes the growth of tumors stochastic. We demonstrate the performance of the model by applying it to a variety of scenarios. Numerical experiments illustrate the flexibility of the model and its ability to generate satellite tumors. Simulations of the effects of angiogenesis on tumor growth are presented as well as sample-independent features of cancer.

q-bio.TO↗

arXiv2021

Analysis of a new multispecies tumor growth model coupling 3D phase-fields with a 1D vascular network

In this work, we present and analyze a mathematical model for tumor growth incorporating ECM erosion, interstitial flow, and the effect of vascular flow and nutrient transport. The model is of phase-field or diffused-interface type in which multiple phases of cell species and other constituents are separated by smooth evolving interfaces. The model involves a mesoscale version of Darcy's law to capture the flow mechanism in the tissue matrix. Modeling flow and transport processes in the vasculature supplying the healthy and cancerous tissue, one-dimensional (1D) equations are considered. Since the models governing the transport and flow processes are defined together with cell species models on a three-dimensional (3D) domain, we obtain a 3D-1D coupled model. We show some mathematical results on the existence of weak solutions. Furthermore, simulation results are presented illustrating the evolution of tumors and the effects of ECM erosion.

math.AP↗

arXiv2021

Quantitative in vivo imaging to enable tumor forecasting and treatment optimization

Current clinical decision-making in oncology relies on averages of large patient populations to both assess tumor status and treatment outcomes. However, cancers exhibit an inherent evolving heterogeneity that requires an individual approach based on rigorous and precise predictions of cancer growth and treatment response. To this end, we advocate the use of quantitative in vivo imaging data to calibrate mathematical models for the personalized forecasting of tumor development. In this chapter, we summarize the main data types available from both common and emerging in vivo medical imaging technologies, and how these data can be used to obtain patient-specific parameters for common mathematical models of cancer. We then outline computational methods designed to solve these models, thereby enabling their use for producing personalized tumor forecasts in silico, which, ultimately, can be used to not only predict response, but also optimize treatment. Finally, we discuss the main barriers to making the above paradigm a clinical reality.

q-bio.TO↗

arXiv2020

A globally convergent modified Newton method for the direct minimization of the Ohta-Kawasaki energy with application to the directed self-assembly of diblock copolymers

We propose a fast and robust scheme for the direct minimization of the Ohta-Kawasaki energy that characterizes the microphase separation of diblock copolymer melts. The scheme employs a globally convergent modified Newton method with line search which is shown to be mass-conservative, energy-descending, asymptotically quadratically convergent, and three orders of magnitude more efficient than the commonly-used gradient flow approach. The regularity and the first-order condition of minimizers are analyzed. A numerical study of the chemical substrate guided directed self-assembly of diblock copolymer melts, based on a novel polymer-substrate interaction model and the proposed scheme, is provided.

physics.comp-ph↗

arXiv2019

A statistical framework for generating microstructures of two-phase random materials: application to fatigue analysis

Random microstructures of heterogeneous materials play a crucial role in the material macroscopic behavior and in predictions of its effective properties. A common approach to modeling random multiphase materials is to develop so-called surrogate models approximating statistical features of the material. However, the surrogate models used in fatigue analysis usually employ simple microstructure, consisting of ideal geometries such as ellipsoidal inclusions, which generally does not capture complex geometries. In this paper, we introduce a simple but flexible surrogate microstructure model for two-phase materials through a level-cut of a Gaussian random field with covariance of Matérn class. Such parametrization of the covariance function allows for the representation of a few key design parameters while representing the geometry of inclusions in a more general setting for a large class of random heterogeneous two-phase media. In addition to the traditional morphology descriptors such as porosity, size and aspect ratio, it provides control of the regularity of the inclusions interface and sphericity. These parameters are estimated from a small number of real material images using Bayesian inversion. An efficient process of evaluating the samples, based on the Fast Fourier Transform, makes possible the use of Monte-Carlo methods to estimate statistical properties for the quantities of interest in a given material class. We demonstrate the overall framework of the use of the surrogate material model in application to the uncertainty quantification in fatigue analysis, its feasibility and efficiency, and its role in the microstructure design.

physics.app-ph↗

arXiv2019

On the unsteady Darcy-Forchheimer-Brinkman equation in local and nonlocal tumor growth models

A mathematical analysis of local and nonlocal phase-field models of tumor growth is presented that includes time-dependent Darcy-Forchheimer-Brinkman models of convective velocity fields and models of long-range cell interactions. A complete existence analysis is provided. In addition, a parameter-sensitivity analysis is described that quantifies the sensitivity of key quantities of interest to changes in parameter values. Two sensitivity analyses are examined; one employing statistical variances of model outputs and another employing the notion of active subspaces based on existing observational data. Remarkably, the two approaches yield very similar conclusions on sensitivity for certain quantities of interest. The work concludes with the presentation of numerical approximations of solutions of the governing equations and results of numerical experiments on tumor growth produced using finite element discretizations of the full tumor model for representative cases.

math.AP↗

arXiv2019

Local and nonlocal phase-field models of tumor growth and invasion due to ECM degradation

We present and analyze new multi-species phase-field mathematical models of tumor growth and ECM invasion. The local and nonlocal mathematical models describe the evolution of volume fractions of tumor cells, viable cells (proliferative and hypoxic cells), necrotic cells, and the evolution of MDE and ECM, together with chemotaxis, haptotaxis, apoptosis, nutrient distribution, and cell-to-matrix adhesion. We provide a rigorous proof of the existence of solutions of the coupled system with gradient-based and adhesion-based haptotaxis effects. In addition, we discuss finite element discretizations of the model, and we present the results of numerical experiments designed to show the relative importance and roles of various effects, including cell mobility, proliferation, necrosis, hypoxia, and nutrient concentration on the generation of MDEs and the degradation of the ECM.

math.AP↗

arXiv2019

Goal-Oriented Adaptive Modeling of Random Heterogeneous Media and Model-Based Multilevel Monte Carlo Methods

Methods for generating sequences of surrogates approximating fine scale models of two-phase random heterogeneous media are presented that are designed to adaptively control the modeling error in key quantities of interest (QoIs). For specificity, the base models considered involve stochastic partial differential equations characterizing, for example, steady-state heat conduction in random heterogeneous materials and stochastic elastostatics problems in linear elasticity. The adaptive process involves generating a sequence of surrogate models defined on a partition of the solution domain into regular subdomains and then, based on estimates of the error in the QoIs, assigning homogenized effective material properties to some subdomains and full random fine scale properties to others, to control the error so as to meet a preset tolerance. New model-based Multilevel Monte Carlo (mbMLMC) methods are presented that exploit the adaptive sequencing and are designed to reduce variances and thereby accelerate convergence of Monte Carlo sampling. Estimates of cost and mean squared error of the method are presented. The results of several numerical experiments are discussed that confirm that substantial saving in computer costs can be realized through the use of controlled surrogate models and the associated mbMLMC algorithms.

math.NA↗

arXiv2018

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.

cs.CE↗