arXiv subjects

Brian Van Essen

Publications and source records attributed to Brian Van Essen.

11 recordsLinked to original sources

arXiv2026

BOOM: Benchmarking Out-Of-distribution Molecular Property Predictions of Machine Learning Models

Data-driven molecular discovery leverages artificial intelligence/machine learning (AI/ML) and generative modeling to filter and design novel molecules. Discovering novel molecules requires accurate out-of-distribution (OOD) predictions, but ML models struggle to generalize OOD. Currently, no systematic benchmarks exist for molecular OOD prediction tasks. We present $\mathbf{BOOM}$, $\mathbf{b}$enchmarks for $\mathbf{o}$ut-$\mathbf{o}$f-distribution $\mathbf{m}$olecular property predictions: a chemically-informed benchmark for OOD performance on common molecular property prediction tasks. We evaluate over 150 model-task combinations to benchmark deep learning models on OOD performance. Overall, we find that no existing model achieves strong generalization across all tasks: even the top-performing model exhibited an average OOD error 3x higher than in-distribution. Current chemical foundation models do not show strong OOD extrapolation, while models with high inductive bias can perform well on OOD tasks with simple, specific properties. We perform extensive ablation experiments, highlighting how data generation, pre-training, hyperparameter optimization, model architecture, and molecular representation impact OOD performance. Developing models with strong OOD generalization is a new frontier challenge in chemical ML. This open-source benchmark is available at https://github.com/FLASK-LLNL/BOOM

cs.LG↗

arXiv2026

Unstructured Hydrodynamics on Spatial Dataflow Architectures: A Joint Code and Data Decomposition Approach

Spatial Dataflow Architectures are an emerging hardware pattern in high-performance computing, whose mesh-connected fixed-memory processing elements are tailored for structured grid kernels with two-dimensional neighborhoods. However, practical multiphysics codes are often computed on unstructured grids, which induce indirect memory accesses and high-dimensional communication patterns, making them infeasible to directly map onto said architectures. This work takes a principled, model-centric approach to partitioning unstructured problems onto spatial dataflow architectures. Through communication and memory modeling, we propose a joint decomposition that considers both the size of the application's fields and its subroutines. In particular, we automate the analysis process of the original code, define a high-dimensional decomposition that minimizes communication via space-filling curves, and apply memory optimization techniques, crucial in this memory-limited environment. We demonstrate mapping the Livermore Unstructured Lagrangian Explicit Shock Hydrodynamics (LULESH) application to the Cerebras Wafer-Scale Engine, showing that larger, unstructured grid codes can still outperform GPUs.

cs.DC↗

arXiv2026

The Open Polymers 2026 (OPoly26) Dataset and Evaluations

Polymers-macromolecular systems composed of repeating chemical units-constitute the molecular foundation of living organisms, while their synthetic counterparts drive transformative advances across medicine, consumer products, and energy technologies. While machine learning (ML) models have been trained on millions of quantum chemical atomistic simulations for materials and/or small molecular structures to enable efficient, accurate, and transferable predictions of chemical properties, polymers have largely not been included in prior datasets due to the computational expense of high quality electronic structure calculations on representative polymeric structures. Here, we address this shortcoming with the creation of the Open Polymers 2026 (OPoly26) dataset, which contains more than 6.57 million density functional theory (DFT) calculations on up to 360 atom clusters derived from polymeric systems, comprising over 1.2 billion total atoms. OPoly26 captures the chemical diversity that makes polymers intrinsically tunable and versatile materials, encompassing variations in monomer composition, degree of polymerization, chain architectures, and solvation environments. We show that augmenting ML model training with the OPoly26 dataset improves model performance for polymer prediction tasks. We also publicly release the OPoly26 dataset to help further the development of ML models for polymers, and more broadly, strive towards universal atomistic models.

physics.chem-ph↗

arXiv2025

Lion Cub: Minimizing Communication Overhead in Distributed Lion

Communication overhead is a key challenge in distributed deep learning, especially on slower Ethernet interconnects, and given current hardware trends, communication is likely to become a major bottleneck. While gradient compression techniques have been explored for SGD and Adam, the Lion optimizer has the distinct advantage that its update vectors are the output of a sign operation, enabling straightforward quantization. However, simply compressing updates for communication and using techniques like majority voting fails to lead to end-to-end speedups due to inefficient communication algorithms and reduced convergence. We analyze three factors critical to distributed learning with Lion: optimizing communication methods, identifying effective quantization methods, and assessing the necessity of momentum synchronization. Our findings show that quantization techniques adapted to Lion and selective momentum synchronization can significantly reduce communication costs while maintaining convergence. We combine these into Lion Cub, which enables up to 5x speedups in end-to-end training compared to Lion. This highlights Lion's potential as a communication-efficient solution for distributed training.

cs.LG↗

arXiv2022

2022 Review of Data-Driven Plasma Science

Data science and technology offer transformative tools and methods to science. This review article highlights latest development and progress in the interdisciplinary field of data-driven plasma science (DDPS). A large amount of data and machine learning algorithms go hand in hand. Most plasma data, whether experimental, observational or computational, are generated or collected by machines today. It is now becoming impractical for humans to analyze all the data manually. Therefore, it is imperative to train machines to analyze and interpret (eventually) such data as intelligently as humans but far more efficiently in quantity. Despite the recent impressive progress in applications of data science to plasma science and technology, the emerging field of DDPS is still in its infancy. Fueled by some of the most challenging problems such as fusion energy, plasma processing of materials, and fundamental understanding of the universe through observable plasma phenomena, it is expected that DDPS continues to benefit significantly from the interdisciplinary marriage between plasma science and data science into the foreseeable future.

physics.plasm-ph↗

arXiv2021

Is Disaggregation possible for HPC Cognitive Simulation?

Cognitive simulation (CogSim) is an important and emerging workflow for HPC scientific exploration and scientific machine learning (SciML). One challenging workload for CogSim is the replacement of one component in a complex physical simulation with a fast, learned, surrogate model that is "inside" of the computational loop. The execution of this in-the-loop inference is particularly challenging because it requires frequent inference across multiple possible target models, can be on the simulation's critical path (latency bound), is subject to requests from multiple MPI ranks, and typically contains a small number of samples per request. In this paper we explore the use of large, dedicated Deep Learning / AI accelerators that are disaggregated from compute nodes for this CogSim workload. We compare the trade-offs of using these accelerators versus the node-local GPU accelerators on leadership-class HPC systems.

cs.DC↗

arXiv2021

Enabling Machine Learning-Ready HPC Ensembles with Merlin

With the growing complexity of computational and experimental facilities, many scientific researchers are turning to machine learning (ML) techniques to analyze large scale ensemble data. With complexities such as multi-component workflows, heterogeneous machine architectures, parallel file systems, and batch scheduling, care must be taken to facilitate this analysis in a high performance computing (HPC) environment. In this paper, we present Merlin, a workflow framework to enable large ML-friendly ensembles of scientific HPC simulations. By augmenting traditional HPC with distributed compute technologies, Merlin aims to lower the barrier for scientific subject matter experts to incorporate ML into their analysis. In addition to its design, we describe some example applications that Merlin has enabled on leadership-class HPC resources, such as the ML-augmented optimization of nuclear fusion experiments and the calibration of infectious disease models to study the progression of and possible mitigation strategies for COVID-19.

cs.DC↗

arXiv2020

The Case for Strong Scaling in Deep Learning: Training Large 3D CNNs with Hybrid Parallelism

We present scalable hybrid-parallel algorithms for training large-scale 3D convolutional neural networks. Deep learning-based emerging scientific workflows often require model training with large, high-dimensional samples, which can make training much more costly and even infeasible due to excessive memory usage. We solve these challenges by extensively applying hybrid parallelism throughout the end-to-end training pipeline, including both computations and I/O. Our hybrid-parallel algorithm extends the standard data parallelism with spatial parallelism, which partitions a single sample in the spatial domain, realizing strong scaling beyond the mini-batch dimension with a larger aggregated memory capacity. We evaluate our proposed training algorithms with two challenging 3D CNNs, CosmoFlow and 3D U-Net. Our comprehensive performance studies show that good weak and strong scaling can be achieved for both networks using up 2K GPUs. More importantly, we enable training of CosmoFlow with much larger samples than previously possible, realizing an order-of-magnitude improvement in prediction accuracy.

cs.DC↗

arXiv2019

Parallelizing Training of Deep Generative Models on Massive Scientific Datasets

Training deep neural networks on large scientific data is a challenging task that requires enormous compute power, especially if no pre-trained models exist to initialize the process. We present a novel tournament method to train traditional as well as generative adversarial networks built on LBANN, a scalable deep learning framework optimized for HPC systems. LBANN combines multiple levels of parallelism and exploits some of the worlds largest supercomputers. We demonstrate our framework by creating a complex predictive model based on multi-variate data from high-energy-density physics containing hundreds of millions of images and hundreds of millions of scalar values derived from tens of millions of simulations of inertial confinement fusion. Our approach combines an HPC workflow and extends LBANN with optimized data ingestion and the new tournament-style training algorithm to produce a scalable neural network architecture using a CORAL-class supercomputer. Experimental results show that 64 trainers (1024 GPUs) achieve a speedup of 70.2 over a single trainer (16 GPUs) baseline, and an effective 109% parallel efficiency.

cs.DC↗

arXiv2019

Improving Strong-Scaling of CNN Training by Exploiting Finer-Grained Parallelism

Scaling CNN training is necessary to keep up with growing datasets and reduce training time. We also see an emerging need to handle datasets with very large samples, where memory requirements for training are large. Existing training frameworks use a data-parallel approach that partitions samples within a mini-batch, but limits to scaling the mini-batch size and memory consumption makes this untenable for large samples. We describe and implement new approaches to convolution, which parallelize using spatial decomposition or a combination of sample and spatial decomposition. This introduces many performance knobs for a network, so we develop a performance model for CNNs and present a method for using it to automatically determine efficient parallelization strategies. We evaluate our algorithms with microbenchmarks and image classification with ResNet-50. Our algorithms allow us to prototype a model for a mesh-tangling dataset, where sample sizes are very large. We show that our parallelization achieves excellent strong and weak scaling and enables training for previously unreachable datasets.

cs.DC↗

arXiv2015

Large-Scale Deep Learning on the YFCC100M Dataset

We present a work-in-progress snapshot of learning with a 15 billion parameter deep learning network on HPC architectures applied to the largest publicly available natural image and video dataset released to-date. Recent advancements in unsupervised deep neural networks suggest that scaling up such networks in both model and training dataset size can yield significant improvements in the learning of concepts at the highest layers. We train our three-layer deep neural network on the Yahoo! Flickr Creative Commons 100M dataset. The dataset comprises approximately 99.2 million images and 800,000 user-created videos from Yahoo's Flickr image and video sharing platform. Training of our network takes eight days on 98 GPU nodes at the High Performance Computing Center at Lawrence Livermore National Laboratory. Encouraging preliminary results and future research directions are presented and discussed.

cs.LG↗