arXiv subjects

Daniele E. Schiavazzi

Publications and source records attributed to Daniele E. Schiavazzi.

29 records · Page 2Linked to original sources

arXiv2023

Differentially Private Normalizing Flows for Density Estimation, Data Synthesis, and Variational Inference with Application to Electronic Health Records

Electronic health records (EHR) often contain sensitive medical information about individual patients, posing significant limitations to sharing or releasing EHR data for downstream learning and inferential tasks. We use normalizing flows (NF), a family of deep generative models, to estimate the probability density of a dataset with differential privacy (DP) guarantees, from which privacy-preserving synthetic data are generated. We apply the technique to an EHR dataset containing patients with pulmonary hypertension. We assess the learning and inferential utility of the synthetic data by comparing the accuracy in the prediction of the hypertension status and variational posterior distribution of the parameters of a physics-based model. In addition, we use a simulated dataset from a nonlinear model to compare the results from variational inference (VI) based on privacy-preserving synthetic data, and privacy-preserving VI obtained from directly privatizing NFs for VI with DP guarantees given the original non-private dataset. The results suggest that synthetic data generated through differentially private density estimation with NF can yield good utility at a reasonable privacy cost. We also show that VI obtained from differentially private NF based on the free energy bound loss may produce variational approximations with significantly altered correlation structure, and loss formulations based on alternative dissimilarity metrics between two distributions might provide improved results.

stat.ML↗

arXiv2022

Data-driven synchronization-avoiding algorithms in the explicit distributed structural analysis of soft tissue

We propose a data-driven framework to increase the computational efficiency of the explicit finite element method in the structural analysis of soft tissue. An encoder-decoder long short-term memory deep neural network is trained based on the data produced by an explicit, distributed finite element solver. We leverage this network to predict synchronized displacements at shared nodes, minimizing the amount of communication between processors. We perform extensive numerical experiments to quantify the accuracy and stability of the proposed synchronization-avoiding algorithm.

cs.DC↗

arXiv2022

Multifidelity data fusion in convolutional encoder/decoder networks

We analyze the regression accuracy of convolutional neural networks assembled from encoders, decoders and skip connections and trained with multifidelity data. Besides requiring significantly less trainable parameters than equivalent fully connected networks, encoder, decoder, encoder-decoder or decoder-encoder architectures can learn the mapping between inputs to outputs of arbitrary dimensionality. We demonstrate their accuracy when trained on a few high-fidelity and many low-fidelity data generated from models ranging from one-dimensional functions to Poisson equation solvers in two-dimensions. We finally discuss a number of implementation choices that improve the reliability of the uncertainty estimates generated by Monte Carlo DropBlocks, and compare uncertainty estimates among low-, high- and multifidelity approaches.

cs.LG↗

arXiv2022

Variational Inference with NoFAS: Normalizing Flow with Adaptive Surrogate for Computationally Expensive Models

Fast inference of numerical model parameters from data is an important prerequisite to generate predictive models for a wide range of applications. Use of sampling-based approaches such as Markov chain Monte Carlo may become intractable when each likelihood evaluation is computationally expensive. New approaches combining variational inference with normalizing flow are characterized by a computational cost that grows only linearly with the dimensionality of the latent variable space, and rely on gradient-based optimization instead of sampling, providing a more efficient approach for Bayesian inference about the model parameters. Moreover, the cost of frequently evaluating an expensive likelihood can be mitigated by replacing the true model with an offline trained surrogate model, such as neural networks. However, this approach might generate significant bias when the surrogate is insufficiently accurate around the posterior modes. To reduce the computational cost without sacrificing inferential accuracy, we propose Normalizing Flow with Adaptive Surrogate (NoFAS), an optimization strategy that alternatively updates the normalizing flow parameters and surrogate model parameters. We also propose an efficient sample weighting scheme for surrogate model training that preserves global accuracy while effectively capturing high posterior density regions. We demonstrate the inferential and computational superiority of NoFAS against various benchmarks, including cases where the underlying model lacks identifiability. The source code and numerical experiments used for this study are available at https://github.com/cedricwangyu/NoFAS.

cs.LG↗

arXiv2022

AdaAnn: Adaptive Annealing Scheduler for Probability Density Approximation

Approximating probability distributions can be a challenging task, particularly when they are supported over regions of high geometrical complexity or exhibit multiple modes. Annealing can be used to facilitate this task which is often combined with constant a priori selected increments in inverse temperature. However, using constant increments limit the computational efficiency due to the inability to adapt to situations where smooth changes in the annealed density could be handled equally well with larger increments. We introduce AdaAnn, an adaptive annealing scheduler that automatically adjusts the temperature increments based on the expected change in the Kullback-Leibler divergence between two distributions with a sufficiently close annealing temperature. AdaAnn is easy to implement and can be integrated into existing sampling approaches such as normalizing flows for variational inference and Markov chain Monte Carlo. We demonstrate the computational efficiency of the AdaAnn scheduler for variational inference with normalizing flows on a number of examples, including density approximation and parameter estimation for dynamical systems.

stat.CO↗

arXiv2022

An analysis of reconstruction noise from undersampled 4D flow MRI

Novel Magnetic Resonance (MR) imaging modalities can quantify hemodynamics but require long acquisition times, precluding its widespread use for early diagnosis of cardiovascular disease. To reduce the acquisition times, reconstruction methods from undersampled measurements are routinely used, that leverage representations designed to increase image compressibility. Reconstructed anatomical and hemodynamic images may present visual artifacts. Although some of these artifact are essentially reconstruction errors, and thus a consequence of undersampling, others may be due to measurement noise or the random choice of the sampled frequencies. Said otherwise, a reconstructed image becomes a random variable, and both its bias and its covariance can lead to visual artifacts; the latter leads to spatial correlations that may be misconstrued for visual information. Although the nature of the former has been studied in the literature, the latter has not received as much attention. In this study, we investigate the theoretical properties of the random perturbations arising from the reconstruction process, and perform a number of numerical experiments on simulated and MR aortic flow. Our results show that the correlation length remains limited to two to three pixels when a Gaussian undersampling pattern is combined with recovery algorithms based on $\ell_1$-norm minimization. However, the correlation length may increase significantly for other undersampling patterns, higher undersampling factors (i.e., 8x or 16x compression), and different reconstruction methods.

eess.IV↗

arXiv2021

An ensemble solver for segregated cardiovascular FSI

Computational models are increasingly used for diagnosis and treatment of cardiovascular disease. To provide a quantitative hemodynamic understanding that can be effectively used in the clinic, it is crucial to quantify the variability in the outputs from these models due to multiple sources of uncertainty. To quantify this variability, the analyst invariably needs to generate a large collection of high-fidelity model solutions, typically requiring a substantial computational effort. In this paper, we show how an explicit-in-time ensemble cardiovascular solver offers superior performance with respect to the embarrassingly parallel solution with implicit-in-time algorithms, typical of an inner-outer loop paradigm for non-intrusive uncertainty propagation. We discuss in detail the numerics and efficient distributed implementation of a segregated FSI cardiovascular solver on both CPU and GPU systems, and demonstrate its applicability to idealized and patient-specific cardiovascular models, analyzed under steady and pulsatile flow conditions.

cs.CE↗

arXiv2020

Multi-fidelity estimators for coronary circulation models under clinically-informed data uncertainty

Numerical models are increasingly used for non-invasive diagnosis and treatment planning in coronary artery disease, where service-based technologies have proven successful in identifying hemodynamically significant and hence potentially dangerous vascular anomalies. Despite recent progress towards clinical adoption, many results in the field are still based on a deterministic characterization of blood flow, with no quantitative assessment of the variability of simulation outputs due to uncertainty from multiple sources. In this study, we focus on parameters that are essential to construct accurate patient-specific representations of the coronary circulation, such as aortic pressure waveform, intramyocardial pressure and quantify how their uncertainty affects clinically relevant model outputs. We construct a deformable model of the left coronary artery subject to a prescribed inlet pressure and with open-loop outlet boundary conditions, treating fluid-structure interaction through an Arbitrary-Lagrangian-Eulerian frame of reference. Random input uncertainty is estimated directly from repeated clinical measurements from intra-coronary catheterization and complemented by literature data. We also achieve significant computational cost reductions in uncertainty propagation thanks to multifidelity Monte Carlo estimators of the outputs of interest, leveraging the ability to generate, at practically no cost, one- and zero-dimensional low-fidelity representations of left coronary artery flow, with appropriate boundary conditions. The results demonstrate how the use of multi-fidelity control variate estimators leads to significant reductions in variance and accuracy improvements with respect to traditional Monte-Carlo.

physics.med-ph↗

arXiv2020

Multilevel and multifidelity uncertainty quantification for cardiovascular hemodynamics

Standard approaches for uncertainty quantification in cardiovascular modeling pose challenges due to the large number of uncertain inputs and the significant computational cost of realistic three-dimensional simulations. We propose an efficient uncertainty quantification framework utilizing a multilevel multifidelity Monte Carlo estimator to improve the accuracy of hemodynamic quantities of interest while maintaining reasonable computational cost. This is achieved by leveraging three cardiovascular model fidelities, each with varying spatial resolution to rigorously quantify the variability in hemodynamic outputs. We employ two low-fidelity models to construct several different estimators. Our goal is to investigate and compare the efficiency of estimators built from combinations of these low-fidelity and high-fidelity models. We demonstrate this framework on healthy and diseased models of aortic and coronary anatomy, including uncertainties in material property and boundary condition parameters. We seek to demonstrate that for this application it is possible to accelerate the convergence of the estimators by utilizing a MLMF paradigm. Therefore, we compare our approach to Monte Carlo and multilevel Monte Carlo estimators based only on three-dimensional simulations. We demonstrate significant reduction in total computational cost with the MLMF estimators. We also examine the differing properties of the MLMF estimators in healthy versus diseased models, as well as global versus local quantities of interest. As expected, global quantities and healthy models show larger reductions than local quantities and diseased model, as the latter rely more heavily on the highest fidelity model evaluations. In all cases, our workflow coupling Dakota's MLMF estimators with the SimVascular cardiovascular modeling framework makes uncertainty quantification feasible for constrained computational budgets.

q-bio.QM↗

arXiv2020

The effects of clinically-derived parametric data uncertainty in patient-specific coronary simulations with deformable walls

Cardiovascular simulations are increasingly used for non-invasive diagnosis of cardiovascular disease, to guide treatment decisions, and in the design of medical devices. Quantitative assessment of the variability of simulation outputs due to input uncertainty is a key step toward further integration of cardiovascular simulations in the clinical workflow. In this study, we present uncertainty quantification in computational models of the coronary circulation to investigate the effect of uncertain parameters, including coronary pressure waveform, intramyocardial pressure, morphometry exponent, and the vascular wall Young's modulus. We employ a left coronary artery model with deformable vessel walls, simulated via an ALE framework for FSI, with a prescribed inlet pressure and open-loop lumped parameter network outlet boundary conditions. Stochastic modeling of the uncertain inputs is determined from intra-coronary catheterization data or gathered from the literature. Uncertainty propagation is performed using several approaches including Monte Carlo, Quasi MC, stochastic collocation, and multiwavelet stochastic expansion. Variabilities in QoI, including branch pressure, flow, wall shear stress, and wall deformation are assessed. We find that uncertainty in inlet pressures and intramyocardial pressures significantly affect all resulting QoIs, while uncertainty in elastic modulus only affects the mechanical response of the vascular wall. Variability in the morphometry exponent has little effect on coronary hemodynamics or wall mechanics. Finally, we compare convergence behaviors of statistics of QoIs using several uncertainty propagation methods. From the simulation results, we conclude that the multi-wavelet stochastic expansion shows superior accuracy and performance against Quasi Monte Carlo and stochastic collocation methods.

physics.med-ph↗

arXiv2019

Performance of preconditioned iterative linear solvers for cardiovascular simulations in rigid and deformable vessels

Computing the solution of linear systems of equations is invariably the most time consuming task in the numerical solutions of PDEs in many fields of computational science. In this study, we focus on the numerical simulation of cardiovascular hemodynamics with rigid and deformable walls, discretized in space and time through the variational multi-scale finite element method. We focus on three approaches: the problem agnostic generalized minimum residual (GMRES) and stabilized bi-conjugate gradient (BICGS) methods, and a recently proposed, problem specific, bi-partitioned (BIPN) method. We also perform a comparative analysis of several preconditioners, including diagonal, block-diagonal, incomplete factorization, multi-grid, and resistance based methods. Solver performance and matrix characteristics (diagonal dominance, symmetry, sparsity, bandwidth and spectral properties) are first examined for an idealized cylindrical geometry with physiologic boundary conditions and then successively tested on several patient-specific anatomies representative of realistic cardiovascular simulation problems. Incomplete factorization pre-conditioners provide the best performance and results in terms of both strong and weak scalability. The BIPN method was found to outperform other methods in patient-specific models with rigid walls. In models with deformable walls, BIPN was outperformed by BICG with diagonal and Incomplete LU preconditioners.

physics.comp-ph↗