John Lowengrub

Arvind Baskaran, John Lowengrub, Cheng Wang et al.

In this paper we provide a detailed convergence analysis for an unconditionally energy stable, second-order accurate convex splitting scheme for the Modified Phase Field Crystal equation, a generalized damped wave equation for which the usual Phase Field Crystal equation is a special degenerate case. The fully discrete, fully second-order finite difference scheme in question was derived in a recent work [2]. An introduction of a new variable ψ, corresponding to the temporal derivative of the phase variable ϕ, could bring an accuracy reduction in the formal consistency estimate, because of the hyperbolic nature of the equation. A higher order consistency analysis by an asymptotic expansion is performed to overcome this difficulty. In turn, second order convergence in both time and space is established in a discrete L^\infty (0,T; H^3) norm.

Ray Zirui Zhang, Ivan Ezhov, Michal Balcerak et al.

Predicting the infiltration of Glioblastoma (GBM) from medical MRI scans is crucial for understanding tumor growth dynamics and designing personalized radiotherapy treatment plans.Mathematical models of GBM growth can complement the data in the prediction of spatial distributions of tumor cells. However, this requires estimating patient-specific parameters of the model from clinical data, which is a challenging inverse problem due to limited temporal data and the limited time between imaging and diagnosis. This work proposes a method that uses Physics-Informed Neural Networks (PINNs) to estimate patient-specific parameters of a reaction-diffusion PDE model of GBM growth from a single 3D structural MRI snapshot. PINNs embed both the data and the PDE into a loss function, thus integrating theory and data. Key innovations include the identification and estimation of characteristic non-dimensional parameters, a pre-training step that utilizes the non-dimensional parameters and a fine-tuning step to determine the patient specific parameters. Additionally, the diffuse domain method is employed to handle the complex brain geometry within the PINN framework. Our method is validated both on synthetic and patient datasets, and shows promise for real-time parametric inference in the clinical setting for personalized GBM treatment.

Wenqiang Feng, Zhen Guan, John Lowengrub et al.

We present and analyze an unconditionally energy stable and convergent finite difference scheme for the Functionalized Cahn-Hilliard equation. One key difficulty associated with the energy stability is based on the fact that one nonlinear energy functional term in the expansion appears as non-convex, non-concave. To overcome this subtle difficulty, we add two auxiliary terms to make the combined term convex, which in turns yields a convex-concave decomposition of the physical energy. As a result, an application of the convex splitting methodology assures both the unique solvability and the unconditional energy stability of the proposed numerical scheme. To deal with a 4-Laplacian solver in an $H^{-1}$ gradient flow at each time step, we apply an efficient preconditioned steepest descent algorithm to solve the corresponding nonlinear systems. In addition, a global in time $H_{\rm per}^2$ stability of the numerical scheme is established at a theoretical level, which in turn ensures the full order convergence analysis of the scheme. A few numerical results are presented, which confirm the stability and accuracy of the proposed numerical scheme.

Ray Zirui Zhang, Christopher E. Miles, Xiaohui Xie et al.

We propose a new neural network based method for solving inverse problems for partial differential equations (PDEs) by formulating the PDE inverse problem as a bilevel optimization problem. At the upper level, we minimize the data loss with respect to the PDE parameters. At the lower level, we train a neural network to locally approximate the PDE solution operator in the neighborhood of a given set of PDE parameters, which enables an accurate approximation of the descent direction for the upper level optimization problem. The lower level loss function includes the L2 norms of both the residual and its derivative with respect to the PDE parameters. We apply gradient descent simultaneously on both the upper and lower level optimization problems, leading to an effective and fast algorithm. The method, which we refer to as BiLO (Bilevel Local Operator learning), is also able to efficiently infer unknown functions in the PDEs through the introduction of an auxiliary variable. We provide a theoretical analysis that justifies our approach. Through extensive experiments over multiple PDE systems, we demonstrate that our method enforces strong PDE constraints, is robust to sparse and noisy data, and eliminates the need to balance the residual and the data loss, which is inherent to the soft PDE constraints in many existing methods.

Ray Zirui Zhang, Christopher E. Miles, Xiaohui Xie et al.

Uncertainty quantification and inverse problems governed by partial differential equations (PDEs) are central to a wide range of scientific and engineering applications. In this second part of a two part series, we extend Bilevel Local Operator Learning (BiLO) for PDE-constrained optimization problems developed in Part 1 to the Bayesian inference framework. At the lower level, we train a network to approximate the local solution operator by minimizing the local operator loss with respect to the weights of the neural network. At the upper level, we sample the PDE parameters from the posterior distribution. We achieve efficient sampling through gradient-based Markov Chain Monte Carlo (MCMC) methods and low-rank adaptation (LoRA). Compared with existing methods based on Bayesian neural networks, our approach bypasses the challenge of sampling in the high-dimensional space of neural network weights and does not require specifying a prior distribution on the neural network solution. Instead, uncertainty propagates naturally from the data through the PDE constraints. By enforcing strong PDE constraints, the proposed method improves the accuracy of both parameter inference and uncertainty quantification. We analyze the dynamic error of the gradient in the MCMC sampler and the static error in the posterior distribution due to inexact minimization of the lower level problem and demonstrate a direct link between the tolerance for solving the lower level problem and the accuracy of the resulting uncertainty quantification. Through numerical experiments across a variety of PDE models, we demonstrate that our method delivers accurate inference and quantification of uncertainties while maintaining high computational efficiency.

Patrick Bilic, Patrick Christ, Hongwei Bran Li et al.

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}.

Mariano Franco-de-León, John Lowengrub

In this paper, we implement non-stiff interface tracking methods for the evolution of 2-D curves that follow Airy flow, a curvature-dependent dispersive geometric evolution law. The curvature of the curve satisfies the modified Korteweg-de Vries equation, a dispersive non-linear soliton equation. We present a fully discrete space-time analysis of the equations (proof of convergence) and numerical evidence that confirms the accuracy, convergence, efficiency, and stability of the methods.

Jana Lipková, Markus Rempfler, Patrick Christ et al.

The segmentation of liver lesions is crucial for detection, diagnosis and monitoring progression of liver cancer. However, design of accurate automated methods remains challenging due to high noise in CT scans, low contrast between liver and lesions, as well as large lesion variability. We propose a 3D automatic, unsupervised method for liver lesions segmentation using a phase separation approach. It is assumed that liver is a mixture of two phases: healthy liver and lesions, represented by different image intensities polluted by noise. The Cahn-Hilliard equation is used to remove the noise and separate the mixture into two distinct phases with well-defined interfaces. This simplifies the lesion detection and segmentation task drastically and enables to segment liver lesions by thresholding the Cahn-Hilliard solution. The method was tested on 3Dircadb and LITS dataset.

Edward Meeds, Michael Chiang, Mary Lee et al.

In many domains, scientists build complex simulators of natural phenomena that encode their hypotheses about the underlying processes. These simulators can be deterministic or stochastic, fast or slow, constrained or unconstrained, and so on. Optimizing the simulators with respect to a set of parameter values is common practice, resulting in a single parameter setting that minimizes an objective subject to constraints. We propose a post optimization posterior analysis that computes and visualizes all the models that can generate equally good or better simulation results, subject to constraints. These optimization posteriors are desirable for a number of reasons among which easy interpretability, automatic parameter sensitivity and correlation analysis and posterior predictive analysis. We develop a new sampling framework based on approximate Bayesian computation (ABC) with one-sided kernels. In collaboration with two groups of scientists we applied POPE to two important biological simulators: a fast and stochastic simulator of stem-cell cycling and a slow and deterministic simulator of tumor growth patterns.