arXiv subjects

George Biros

Publications and source records attributed to George Biros.

At least 19 recordsLinked to original sources

arXiv2026

Interactive Debugger for Performance Portable Python HPC Kernels

We propose PKDB, the first interactive debugger for GPU and multithreaded low-level kernels written in Python. Python is widely used in high performance computing (HPC), with frameworks such as PyKokkos translating Python-embedded domain-specific languages to native code that runs across OpenMP-threaded CPUs and various GPUs. Yet interactive debugging support for such code is absent: developers resort to print statements, framework-specific assertions, or CPU-only execution, the last of which requires altering the program or its data and can mask device-specific bugs. PKDB enables standard interactive debugging like breakpoints, stepping, and variable inspection while preserving actual on-device execution without source modification. Beyond these fundamentals, PKDB introduces two advanced capabilities that exploit the dynamic nature of Python and PyKokkos: (i) Live code evaluation, which lets developers execute arbitrary Python expressions or entire kernels in the middle of a paused kernel without restarting the process; (ii) Kernel call site substitution, which allows an actively running kernel to be updated and reloaded on the fly, so only the kernel is recompiled and re-executed without restarting the application. Our performance evaluation on Intel, AMD, and NVIDIA CPUs, and NVIDIA and AMD GPUs shows that PKDB introduces limited overhead and is practical for everyday use while introducing critical debugging features to the Python HPC ecosystem.

cs.DC↗

arXiv2026

VesNet: Neural network accelerated solver for simulating Stokesian vesicle suspensions

Numerical simulation of deformable particle suspensions in Stokes flow is computationally expensive due to nonlinear fluid-structure interactions, evolving interfaces, and multiscale hydrodynamics. We present VesNet, a hybrid framework that accelerates two-dimensional vesicle suspension simulations by approximating vesicle self interactions, including background flow coupling and short-range lubrication forces, while retaining conventional modules for boundary reparameterization and far-field hydrodynamics. A GPU-accelerated implementation achieves over 100x speedup compared to a multithreaded MATLAB CPU boundary integral solver and about 5x relative to its GPU counterpart. VesNet accurately captures key dynamics, including single-vesicle phase behavior, pair interactions, and large-scale suspensions in Taylor-Green and Poiseuille flows, enabling efficient simulations of thousands of vesicles on modest computational resources.

physics.flu-dyn↗

arXiv2026

A performance portable fast Ewald summation for Stokes flow

We present GPU algorithms for Ewald summation methods for accelerating N-body Stokes flow problems in periodic domains. Like most N-body codes, Ewald sums use a near-field/far-field decomposition. The near field involves particle-to-particle (P2P) interactions. The far field primarily involves particle-to-grid (P2G) and grid-to-particle (G2P) interactions, as well as Fast Fourier Transforms. For each interaction, we investigate several algorithmic variants. Our implementation uses PyKokkos, a Python interface for the Kokkos C++ parallel programming framework, which supports portability to AMD/NVIDIA GPU and ARM/x86 CPU architectures. Double and single-precision numerical results, alongside analytical performance models, confirm the efficiency of our algorithms on AMD and NVIDIA GPU and on ARM and AMD CPU architectures. The P2P interaction achieves around 73% compute efficiency on NVIDIA H200, 84% on NVIDIA A100, 60% on AMD MI300, 52% on Grace CPU, and 68% on AMD Epyc CPU. A straightforward implementation of the P2G kernel can become a computational bottleneck. We introduce a novel P2G algorithm that achieves up to 16$\times$ speedup compared to a baseline GPU implementation. The overall Ewald sum code processes approximately 8 million particles per second on a H200 GPU, and about a half-million particles per second on a Grace CPU, for nine digits of accuracy. We also perform a multi-GPU weak scaling test on up to 256 million particles (64 GPUs) that shows bounded communication cost for all stages except the all-to-all particle sorting, which can be reduced to neighbor communication in the relevant time-stepping regime.

math.NA↗

arXiv2026

IV-Net: A neural network for elliptic PDEs with random and highly varying coefficients

We introduce a novel neural operator architecture designed to approximate solutions of linear elliptic partial differential equations with high-contrast, spatially varying coefficients. The network, termed the Iterated V-shaped Net (IV-Net), realizes a mapping from the input coefficients and righthand side to the corresponding solution field. The architecture of IV-Net is informed by, and closely resembles, a V-cycle multigrid solver. The IV-Net model is parameterized via convolutional layers defined in the physical domain. For coercive problems with highly heterogeneous coefficients, the proposed network exhibits superior performance relative to a proper orthogonal decomposition (POD) approach and several existing neural operator architectures. For low-frequency oscillatory Helmholtz problems with smooth coefficients, its performance is similar to that of a Fourier neural operator. We analyze the approximation error and convergence behavior of IV-Net, its data efficiency, and its dependence on the underlying discretization mesh. Furthermore, we demonstrate the practical effectiveness of the architecture through a series of numerical experiments, including applications to uncertainty quantification, inverse problems, and prediction of quantities of interest.

math.NA↗

arXiv2026

LNODE: latent dynamics reveal the shared spatiotemporal structure of amyloid-$\beta$ progression

We present and analyze LNODE, a mechanism-based phenomenological model for amyloid beta (A$\beta$) dynamics, calibrated using positron emission tomography (PET) imaging. A$\beta$ is a key biomarker of Alzheimer's disease. LNODE is designed to support the fusion, harmonization, quantitative analysis, and interpretation of A$\beta$ PET scans. We evaluate LNODE on 1461 subjects in the ADNI cohort and 1,070 subjects in the A4 Study, using MUSE and DKT anatomical atlases. LNODE is formulated as a regional neural ordinary differential equation (ODE) model that is jointly calibrated on all available scans within a cohort. The model captures the spatial propagation, proliferation, and clearance of A$\beta$ and incorporates a latent-state representation that modulates A$\beta$ dynamics. The temporal evolution of these latent states is governed by cohort-shared parameters, enabling LNODE to represent both population-level trajectories and subject-specific deviations. The proposed model demonstrates strong parameter identifiability and stability properties, supported by synthetic experiments and analysis of the Hessian condition number. To mitigate overfitting and reduce spurious correlations, LNODE is intentionally underparameterized, employing approximately five to ten parameters per subject. Despite this parsimonious parameterization, LNODE achieves cohort $R^2 > 0.99$ in both the ADNI and A4 datasets. LNODE exhibits strong predictive performance: in the A4 cohort, it accurately forecasts the A$\beta$ PET signal in previously unseen follow-up scans, including cases with inter-scan intervals exceeding four years. Clustering in the learned latent-state space reveals distinct subgroups, consistent with the existence of different subtypes of Alzheimer's disease progression.

q-bio.QM↗

arXiv2026

Proximal-IMH: Proximal Posterior Proposals for Independent Metropolis-Hastings with Approximate Operators

We consider the problem of sampling from a posterior distribution arising in Bayesian inverse problems in science, engineering, and imaging. Our method belongs to the family of independence Metropolis-Hastings (IMH) sampling algorithms, which are common in Bayesian inference. Relying on the existence of an approximate posterior distribution that is cheaper to sample from but may have significant bias, we introduce Proximal-IMH, a scheme that removes this bias by correcting samples from the approximate posterior through an auxiliary optimization problem. This yields a local adjustment that trades off adherence to the exact model against stability around the approximate reference point. For idealized settings, we prove that the proximal correction tightens the match between approximate and exact posteriors, thereby improving acceptance rates and mixing. The method applies to both linear and nonlinear input-output operators and is particularly suitable for inverse problems where exact posterior sampling is too expensive. We present numerical experiments including multimodal and data-driven priors with nonlinear input-output operators. The results show that Proximal-IMH reliably outperforms existing IMH variants.

cs.LG↗

arXiv2026

Latent-IMH: Efficient Bayesian Inference for Inverse Problems with Approximate Operators

We study sampling from posterior distributions in Bayesian linear inverse problems where $A$, the parameters to observables operator, is computationally expensive. In many applications, $A$ can be factored in a manner that facilitates the construction of a cost-effective approximation $\tilde{A}$. In this framework, we introduce Latent-IMH, a sampling method based on the Metropolis-Hastings independence (IMH) sampler. Latent-IMH first generates intermediate latent variables using the approximate $\tilde{A}$, and then refines them using the exact $A$. Its primary benefit is that it shifts the computational cost to an offline phase. We theoretically analyze the performance of Latent-IMH using KL divergence and mixing time bounds. Using numerical experiments on several model problems, we show that, under reasonable assumptions, it outperforms state-of-the-art methods such as the No-U-Turn sampler (NUTS) in computational efficiency. In some cases, Latent-IMH can be orders of magnitude faster than existing schemes.

stat.ML↗

arXiv2026

Inverse problems for history-enriched linear model reduction

Standard projection-based model reduction for dynamical systems incurs closure error because it only accounts for instantaneous dependence on the resolved state. From the Mori-Zwanzig (MZ) perspective, projecting the full dynamics onto a low-dimensional resolved subspace induces additional noise and memory terms arising from the dynamics of the unresolved component in the orthogonal complement. The memory term makes the resolved dynamics explicitly history dependent. In this work, based on the MZ identity, we derive exact, history-enriched models for the resolved dynamics of linear driven dynamical systems and formulate inverse problems to learn model operators from discrete snapshot data via least-squares regression. We propose a greedy time-marching scheme to solve the inverse problems efficiently and analyze operator identifiability under full and partial observation data availability. For full observation data, we show that, under mild assumptions, the operators are identifiable even when the full-state dynamics are governed by a general time-varying linear operator, whereas with partial observation data the inverse problem has a unique solution only when the full-state operator is time-invariant. To address the resulting non-uniqueness in the time-varying case, we introduce a time-smoothing Tikhonov regularization. Numerical results demonstrate that the operators can be faithfully reconstructed from both full and partial observation data and that the learned history-enriched MZ models yield accurate trajectories of the resolved state.

math.DS↗

arXiv2025

VLCs: Managing Parallelism with Virtualized Libraries

As the complexity and scale of modern parallel machines continue to grow, programmers increasingly rely on composition of software libraries to encapsulate and exploit parallelism. However, many libraries are not designed with composition in mind and assume they have exclusive access to all resources. Using such libraries concurrently can result in contention and degraded performance. Prior solutions involve modifying the libraries or the OS, which is often infeasible. We propose Virtual Library Contexts (VLCs), which are process subunits that encapsulate sets of libraries and associated resource allocations. VLCs control the resource utilization of these libraries without modifying library code. This enables the user to partition resources between libraries to prevent contention, or load multiple copies of the same library to allow parallel execution of otherwise thread-unsafe code within the same process. In this paper, we describe and evaluate C++ and Python prototypes of VLCs. Experiments show VLCs enable a speedup up to 2.85x on benchmarks including applications using OpenMP, OpenBLAS, and LibTorch. Source code of VLCs is available at https://github.com/pecos/Virtual-Library-Context.

cs.DC↗

arXiv2025

A Portable Multi-GPU Solver for Collisional Plasmas with Coulombic Interactions

We study parallel particle-in-cell (PIC) methods for low-temperature plasmas (LTPs), which discretize kinetic formulations that capture the time evolution of the probability density function of particles as a function of position and velocity. We use a kinetic description for electrons and a fluid approximation for heavy species. In this paper, we focus on GPU acceleration of algorithms for velocity-space interactions and in particular, collisions of electrons with neutrals, ions, and electrons. Our work has two thrusts. The first is algorithmic exploration and analysis. The second is examining the viability of rapid-prototyping implementations using Python-based HPC tools, in particular PyKokkos. We discuss several common PIC kernels and present performance results on NVIDIA Volta V100 and AMD MI250X GPUs. Overall, the MI250X is slightly faster for most kernels but shows more sensitivity to register pressure. We also report scaling results for a distributed memory implementation on up to 16 MPI ranks.

cs.CE↗

arXiv2025

Extensions of the regret-minimization algorithm for optimal design

We consider the problem of selecting a subset of points from a dataset of $n$ unlabeled examples for labeling, with the goal of training a multiclass classifier. To address this, we build upon the regret minimization framework introduced by Allen-Zhu et al. in "Near-optimal design of experiments via regret minimization" (ICML, 2017). We propose an alternative regularization scheme within this framework, which leads to a new sample selection objective along with a provable sample complexity bound that guarantees a $(1+\epsilon)$-approximate solution. Additionally, we extend the regret minimization approach to handle experimental design in the ridge regression setting. We evaluate the selected samples using logistic regression and compare performance against several state-of-the-art methods. Our empirical results on MNIST, CIFAR-10, and a 50-class subset of ImageNet demonstrate that our method consistently outperforms competing approaches across most scenarios.

cs.LG↗

arXiv2025

Boltzsim: A fast solver for the 1D-space electron Boltzmann equation with applications to radio-frequency glow discharge plasmas

We present an algorithm for solving the one-dimensional space collisional Boltzmann transport equation (BTE) for electrons in low-temperature plasmas (LTPs). Modeling LTPs is useful in many applications, including advanced manufacturing, material processing, and hypersonic flows, to name a few. The proposed BTE solver is based on an Eulerian formulation. It uses Chebyshev collocation method in physical space and a combination of Galerkin and discrete ordinates in velocity space. We present self-convergence results and cross-code verification studies compared to an in-house particle-in-cell (PIC) direct simulation Monte Carlo (DSMC) code. Boltzsim is our open source implementation of the solver. Furthermore, we use Boltzsim to simulate radio-frequency glow discharge plasmas (RF-GDPs) and compare with an existing methodology that approximates the electron BTE. We compare these two approaches and quantify their differences as a function of the discharge pressure. The two approaches show an 80x, 3x, 1.6x, and 0.98x difference between cycle-averaged time periodic electron number density profiles at 0.1 Torr, 0.5 Torr, 1 Torr, and 2 Torr discharge pressures, respectively. As expected, these differences are significant at low pressures, for example less than 1 Torr.

physics.plasm-ph↗

arXiv2024

FIRAL: An Active Learning Algorithm for Multinomial Logistic Regression

We investigate theory and algorithms for pool-based active learning for multiclass classification using multinomial logistic regression. Using finite sample analysis, we prove that the Fisher Information Ratio (FIR) lower and upper bounds the excess risk. Based on our theoretical analysis, we propose an active learning algorithm that employs regret minimization to minimize the FIR. To verify our derived excess risk bounds, we conduct experiments on synthetic datasets. Furthermore, we compare FIRAL with five other methods and found that our scheme outperforms them: it consistently produces the smallest classification error in the multiclass logistic regression setting, as demonstrated through experiments on MNIST, CIFAR-10, and 50-class ImageNet.

cs.LG↗

arXiv2024

A Scalable Algorithm for Active Learning

FIRAL is a recently proposed deterministic active learning algorithm for multiclass classification using logistic regression. It was shown to outperform the state-of-the-art in terms of accuracy and robustness and comes with theoretical performance guarantees. However, its scalability suffers when dealing with datasets featuring a large number of points $n$, dimensions $d$, and classes $c$, due to its $\mathcal{O}(c^2d^2+nc^2d)$ storage and $\mathcal{O}(c^3(nd^2 + bd^3 + bn))$ computational complexity where $b$ is the number of points to select in active learning. To address these challenges, we propose an approximate algorithm with storage requirements reduced to $\mathcal{O}(n(d+c) + cd^2)$ and a computational complexity of $\mathcal{O}(bncd^2)$. Additionally, we present a parallel implementation on GPUs. We demonstrate the accuracy and scalability of our approach using MNIST, CIFAR-10, Caltech101, and ImageNet. The accuracy tests reveal no deterioration in accuracy compared to FIRAL. We report strong and weak scaling tests on up to 12 GPUs, for three million point synthetic dataset.

cs.LG↗

arXiv2024

A fast solver for the spatially homogeneous electron Boltzmann equation

We present a numerical method for the velocity-space, spatially homogeneous, collisional Boltzmann equation for electron transport in low-temperature plasma (LTP) conditions. Modeling LTP plasmas is useful in many applications, including advanced manufacturing, material processing, semiconductor processing, and hypersonics, to name a few. Most state-of-the-art methods for electron kinetics are based on Monte-Carlo sampling for collisions combined with Lagrangian particle-in-cell methods. We discuss an Eulerian solver that approximates the electron velocity distribution function using spherical harmonics (angular components) and B-splines (energy component). Our solver supports electron-heavy elastic and inelastic binary collisions, electron-electron Coulomb interactions, steady-state and transient dynamics, and an arbitrary nmber of angular terms in the electron distribution function. We report convergence results and compare our solver to two other codes: an in-house particle Monte-Carlo ethod; and Bolsig+, a state-of-the-art Eulerian solver for electron transport in LTPs. Furthermore, we use our solver to study the relaxation time scales of the higher-order anisotropic correction terms. Our code is open-source and provides an interface that allows coupling to multiphysics simulations of low-temperature plasmas.

physics.plasm-ph↗

arXiv2024

Inverse Problem Regularization for 3D Multi-Species Tumor Growth Models

We present a multi-species partial differential equation (PDE) model for tumor growth and a an algorithm for calibrating the model from magnetic resonance imaging (MRI) scans. The model is designed for glioblastoma (GBM) brain tumors. The modeled species correspond to proliferative, infiltrative, and necrotic tumor cells. The model calibration is formulated as an inverse problem and solved a PDE-constrained optimization method. The data that drives the calibration is derived by a single multi-parametric MRI image. This a typical clinical scenario for GBMs. The unknown parameters that need to be calibrated from data include ten scalar parameters and the infinite dimensional initial condition (IC) for proliferative tumor cells. This inverse problem is highly ill-posed as we try to calibrate a nonlinear dynamical system from data taken at a single time. To address this ill-posedness, we split the inversion into two stages. First we regularize the IC reconstruction by solving a single-species compressed sensing problem. Then, using the IC reconstruction, we invert for model parameters using a weighted regularization term. We construct the regularization term by using auxiliary 1D inverse problems. We apply our proposed scheme to clinical data. We compare our algorithm with single-species reconstruction and unregularized reconstructions. Our scheme enables the stable estimation of non-observable species and quantification of infiltrative tumor cells.

math.NA↗

arXiv2024

A single-snapshot inverse solver for two-species graph model of tau pathology spreading in human Alzheimer disease

We propose a method that uses a two-species ordinary differential equation (ODE) model to characterize misfolded tau (or simply tau) protein spreading in Alzheimer's disease (AD) and calibrates it from clinical data. The unknown model parameters are the initial condition (IC) for tau and three scalar parameters representing the migration, proliferation, and clearance of tau proteins. Driven by imaging data, these parameters are estimated by formulating a constrained optimization problem with a sparsity regularization for the IC. This optimization problem is solved with a projection-based quasi-Newton algorithm. We investigate the sensitivity of our method to different algorithm parameters. We evaluate the performance of our method on both synthetic and clinical data. The latter comprises cases from the AD Neuroimaging Initiative (ADNI) datasets: 455 cognitively normal (CN), 212 mild cognitive impairment (MCI), and 45 AD subjects. We compare the performance of our approach to the commonly used Fisher-Kolmogorov (FK) model with a fixed IC at the entorhinal cortex (EC). Our method demonstrates an average improvement of 25.7% relative error compared to the FK model on the AD dataset. HFK also achieves an R-squared score of 0.664 for fitting AD data compared with 0.55 from FK model results under the same optimization scheme. Furthermore, for cases that have longitudinal data, we estimate a subject-specific AD onset time.

q-bio.QM↗

arXiv2024

GrainGNN: A dynamic graph neural network for predicting 3D grain microstructure

We propose GrainGNN, a surrogate model for the evolution of polycrystalline grain structure under rapid solidification conditions in metal additive manufacturing. High fidelity simulations of solidification microstructures are typically performed using multicomponent partial differential equations (PDEs) with moving interfaces. The inherent randomness of the PDE initial conditions (grain seeds) necessitates ensemble simulations to predict microstructure statistics, e.g., grain size, aspect ratio, and crystallographic orientation. Currently such ensemble simulations are prohibitively expensive and surrogates are necessary. In GrainGNN, we use a dynamic graph to represent interface motion and topological changes due to grain coarsening. We use a reduced representation of the microstructure using hand-crafted features; we combine pattern finding and altering graph algorithms with two neural networks, a classifier (for topological changes) and a regressor (for interface motion). Both networks have an encoder-decoder architecture; the encoder has a multi-layer transformer long-short-term-memory architecture; the decoder is a single layer perceptron. We evaluate GrainGNN by comparing it to high-fidelity phase field simulations for in-distribution and out-of-distribution grain configurations for solidification under laser power bed fusion conditions. GrainGNN results in 80\%--90\% pointwise accuracy; and nearly identical distributions of scalar quantities of interest (QoI) between phase field and GrainGNN simulations compared using Kolmogorov-Smirnov test. GrainGNN's inference speedup (PyTorch on single x86 CPU) over a high-fidelity phase field simulation (CUDA on a single NVIDIA A100 GPU) is 150$\times$--2000$\times$ for 100-initial grain problem. Further, using GrainGNN, we model the formation of 11,600 grains in 220 seconds on a single CPU core.

cs.CE↗