How to Do Spectral Learning at Scale for Science and Engineering

Abstract: Spectral decompositions such as singular value decompositions (SVDs) and eigenvalue decompositions (EVDs) are central tools across a vast swath of scientific computing and machine learning, with abundant engineering applications. Yet many modern methods for learning such decompositions in high dimensions struggle with instability, bias, and poor scalability, even when approximation power is not the limiting factor. I argue that these difficulties are not intrinsic to spectral problems, but instead arise from a shared reliance on Rayleigh-quotient-based constrained optimization, which forces explicit orthogonality handling through penalties, normalization, or whitening.
To address these challenges, I present a reformulation based on unconstrained variational objectives that implicitly encode spectral structure, eliminating the need for orthogonalization and ad-hoc regularization. This perspective leads to a conceptually simpler and scalable parametric framework for learning ordered spectral representations via nested optimization. The resulting framework is well matched to diverse settings in science and engineering. As examples, I demonstrate its effectiveness on eigenvalue problems for linear PDEs such as the Schrödinger equation, spectral (Koopman) analysis of nonlinear dynamical systems such as molecular dynamics, and structured representation learning with deep neural nets. Collectively, these examples illustrate how abandoning Rayleigh-quotient-based formulations resolves long-standing optimization pathologies across domains.

Bio: Jongha (Jon) Ryu is a postdoctoral associate at MIT EECS. He received his Ph.D. in Electrical and Computer Engineering from UC San Diego. His research develops statistical and mathematical foundations for scientific machine learning, with a focus on scalable spectral methods, efficient generative modeling, and reliable uncertainty quantification for scientific and engineering systems.

Location: NCS 120
Abstract: Generative image models trained on massive datasets encode the statistics of our visual world. An off-the-shelf diffusion or flow-matching model can therefore serve as a general-purpose image prior, providing information about images across a wide range of tasks. Harnessing these capabilities, however, requires combining the model at inference time with additional signals or constraints unknown during training. This thesis will develop training-free methods for inference under a generative denoising prior. I first show how sampling from a trained denoiser can be formulated as an optimization problem, which combined with a constraint, can solve tasks ranging from conditional generation and weakly supervised segmentation to combinatorial optimization. I then demonstrate how the inherent properties of denoisers can accelerate inference under such constraints. Replacing gradient descent with an inexact Newton update, based on the symmetry of the denoiser's Jacobian, substantially reduces inference costs without tradeoffs. I also explore a middle ground between model adaptation and fully training-free inference by using the denoiser's robust internal representations to learn constraints from limited labeled data. These methods are applied to gigapixel image domains such as digital histopathology and remote sensing, where generative models can only be trained at a patch scale. To synthesize arbitrarily large images at resolutions unseen during training, I introduce inference-time algorithms that enforce consistency across spatially overlapping patches and image scales. Finally, I propose repurposing inference-time algorithms from sampling tools, to mechanisms for understanding the prior learned by a denoising model. Extending the previously developed techniques, I analyze the Jacobians of generative denoisers, where preliminary results indicate that Jacobian spectra correlates with generative quality. This motivates a Jacobian-spectrum regularization as a way to improve model performance using insights derived from inference-time algorithms.

Speaker: Alexandros Graikos

Location: NCS 220
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Please join us this Friday, February 13th for the CSE 600 seminar given by Associate Professor Debswapna Bhattacharya, from the Department of Computer Science at Virginia Tech.

Abstract: Building a model of a biological system that can provide actionable hypotheses to form a solid foundation for experimental and theoretical analyses is one of the key challenges in biology and medicine. In this talk, I will present my group's ongoing work in developing, evaluating, and disseminating a new generation of computational methods for biomolecular modeling powered by artificial intelligence (AI) and machine learning (ML). First, I will introduce a new generation of AI/ML methods for improved modeling and characterization of protein-nucleic acid assemblies by deep graph learning using embeddings from biological large language models (LLMs) as well as geometric attention-enabled pairing of heterogeneous biological LLMs, a previously unexplored avenue. Then, I will present a novel generative deep learning model based on equivariant flow matching for end-to-end generation of all-atom RNA 3D structural ensemble. Finally, I will outline my future research directions on attaining atomic-level accuracy in computational modeling of biomolecules and their assemblies at scale.

Speaker: Debswapna Bhattacharya is an Associate Professor in the Department of Computer Science at Virginia Tech. He received his Ph.D. in Computer Science from the University of Missouri-Columbia in 2016. Before joining Virginia Tech in 2022, he was an Assistant Professor at Auburn University from 2017 to 2021. His research interests lie at the intersection of computational biology and machine learning, with a particular focus on artificial intelligence for computational structural biology, specifically in modeling and characterization of biomolecular structures and interactions. His research group has been developing novel computational and data-driven methods, software, and information systems for diverse biomolecular modeling problems, ranking among the best methods in community-wide blind assessments and serving the worldwide community of biomedical users. He received various research awards (NSF CAREER Award, NIH Maximizing Investigators' Research Award, NSF National AI Research Resource Award) and numerous institutional honors (National Distinction and Outstanding Contributor at Virginia Tech, Ginn Faculty Fellowship at Auburn University, Outstanding Engineering Faculty Award at Auburn University).
Location: NCS 120
How Language Makes us Smart (without Big Data) presented by Charles Yang

Abstract: Language provides the glue that combines simpler concepts into complex ones. To study how language guides conceptual development, we need precise accounts of how rules are learned from the child's linguistic experience, which is extremely limited in comparison to the amount of data available to current machine learning methods. In this talk, I discuss a mathematical model of inductive generalization, which enables language learning with very small amount of data. Such a view of learning has strong implications for the cross-cultural/linguistic variation of development. As a case study, I show that Hong Kong children learning Cantonese, which has a relatively simpler formal counting system, develop understanding of symbolic numbers a full year ahead of English-learning children in the United States, which is precisely predictable from the learning model. The new conception of learning adds another wrinkle to the eternal question of how language and thought are related to each other.

Bio: Charles Yang studied at the MIT AI lab and now teaches linguistics, computer science and psychology and directs the Program in Cognitive Science at the University of Pennsylvania. He is the author of several books: The Price of Linguistic Productivity (2016 MIT Press) won the Leonard Bloomfield Award from the Linguistic Society of America. His honors include a Guggenheim fellowship.
Title: Cyberinfrastructure for forward prediction and inversion estimation with uncertainty quantification

Seminar Speaker: Dr. Mengyang Gu, Assistant Professor, Department of Statistics and Applied Probability, University of California, Santa Barbara

Abstract: In this talk, we introduce four useful tools for forward prediction and inversion estimation. The first tool is the parallel partial Gaussian process surrogate model for emulating expensive computer simulations with massive coordinates. The tool is implemented in the RobustGaSP package available in R, MATLAB, and Python, for predicting both scalar- and vector-valued outputs with uncertainty assessment. The second tool is implemented in the RobustCalibration package, which handles Bayesian data inversion or model calibration by one or multiple types of experimental observations. A unique feature of the package is the inclusion of fast surrogate models of both scalar- and vector-valued computer simulations that bypass the expensive simulation in one line of code. The third tool is implemented in the AIUQ package, available in both R and MATLAB. In this approach, we show that differential dynamic microscopy, a scattering-based analysis tool that extracts dynamical information from microscopy videos, is equivalent to fitting the temporal auto-covariance in Fourier space, based on a latent factor model we construct. We develop a more efficient estimator and reduce the computational cost to pseudolinear order with respect to the number of observations without approximation, by utilizing the generalized Schur algorithm for the Toeplitz covariance. In the last tool, we developed a new method called the inverse Kalman filter, which enables fast matrix-vector multiplication between a covariance matrix from a dynamic linear model and any real-valued vector with a linear computational cost. These new approaches outline a wide range of applications that include emulating expensive simulation at molecular-, meso- and macro-scales, active learning with error control, nonparametric estimation of particle interaction functions, and data inversion from microscopy and velocity fields.

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CSE 600 Talk: Squeezing Software Performance via Eliminating Wasteful Operations presented by Xu Liu

ABSTRACT: Inefficiencies abound in complex, layered software. A variety of inefficiencies show up as wasteful memory operations, such as redundant or useless memory loads and stores. Aliasing, limited optimization scopes, and insensitivity to input and execution contexts act as severe deterrents to static program analysis. Microscopic observation of whole executions at instruction- and operand-level granularity breaks down abstractions and helps recognize redundancies that masquerade in complex programs. In this talk, I will describe various wasteful memory operations, which pervasively exist in modern
software packages and expose great potential for optimization. I will discuss the design of a fine-grained instrumentation-based profiling framework that identifies wasteful operations in their contexts, which guides nontrivial performance improvement. Furthermore, I will show our recent improvement to the profiling framework by abandoning
instrumentation, which reduces the runtime overhead from 10x to 3% on average. I will show how our approach works for native binaries and various managed languages such as Java, yielding new performance insights for optimization.

BIO: Xu Liu is an assistant professor in the Department of Computer Science at College of William & Mary. He obtained his PhD from Rice University in 2014 and joined the College of William & Mary in the same year. Prof. Liu works on building performance tools to pinpoint and optimize inefficiencies in HPC code bases. He has developed several open-source profiling tools, which are used worldwide at universities, DOE national laboratories and industrial companies. Prof. Liu has published a number of papers in high-quality venues. His papers received Best Paper Award at SC'15, PPoPP'18, PPoPP'19 and ASPLOS'17 Highlights, as well as Distinguished Paper Award at ICSE'19. His recent ASPLOS'18 paper has been selected as ACM SIGPLAN Research Highlights in 2019 and nominated for CACM Research Highlights. Prof. Liu is the receipt of 2019 IEEE TCHPC Early Career Researchers Award for Excellence in High Performance Computing. Prof. Liu served on the program committee of conferences such as SC, PPoPP, IPDPS, CGO, HPCA and ASPLOS.

You are cordially invited to attend the biweekly Brookhaven AI Mixer (BAM). BAM includes three short talks on AI research happening at BNL, followed by an open mixer over coffee and snacks for everyone to network and discuss all things AI. The first half hour will consist of presentations that will be available via ZOOM, and the second half hour will be for in person only networking.

Join us every other Tuesday at noon in CDSD's Training Room (building 725, 2nd floor) to learn about interesting AI methods and applications, engage with potential collaborators, prepare for pending FASST funding calls, and build a community of AI for Science at BNL.

Speakers

Kriti Chopra, Computing & Data Sciences (CDS)
Thomas Flynn, Computing & Data Sciences (CDS)
Wenjie Liao, Chemistry Division

Tuesday, January 7, 2025, 12:00 pm -- CDS, Bldg. 725, Training Room

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