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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

MATEY: multiscale adaptive transformer models for spatiotemporal physical systems

Accurate representation of the multiscale features in spatiotemporal physical systems using vision transformer architectures requires extremely long, computationally prohibitive token sequences. To address this issue, we propose two novel adaptive tokenization schemes that dynamically adjust patch sizes based on local features: one ensures convergent behavior to uniform patch refinement, while the other offers better computational efficiency. Moreover, we present a set of spatiotemporal attention schemes, where the temporal or axial spatial dimensions are decoupled, to evaluate their baseline computational and data efficiencies and to determine whether adaptive tokenization can improve this performance. We assess the performance of the proposed multiscale adaptive model, MATEY, in a sequence of experiments. Compared to a full spatiotemporal attention scheme or a scheme that decouples only the temporal dimension, we find that fully decoupled axial attention is less efficient and expressive, requiring more training time and model parameters to achieve the same accuracy. The experiments on the adaptive tokenization schemes show that, compared to a uniformly refined model, the proposed schemes achieve comparable or improved accuracy at a much lower cost in the tested two-dimensional settings. While the asymptotic analysis suggests the potential for favorable scaling, empirical validation at substantially longer sequence lengths remains to be performed in future work. Finally, we demonstrate in two fine-tuning tasks featuring different physics that models pretrained on PDEBench data outperform the ones trained from scratch, especially in the low data regime with frozen attention.

adaptive tokenization↗
DOE OSTI2025

SHF: Symmetrical Hierarchical Forest with Pretrained Vision Transformer Encoder for High-Resolution Medical Segmentation

This paper presents a novel approach to addressing the long-sequence problem in high-resolution medical images for Vision Transformers (ViTs). Using smaller patches as tokens can enhance ViT performance, but quadratically increases computation and memory requirements. Therefore, the common practice for applying ViTs to high-resolution images is either to: (a) employ complex sub-quadratic attention schemes or (b) use large to medium-sized patches and rely on additional mechanisms within the model to capture the spatial hierarchy of details. We propose Symmetrical Hierarchical Forest (SHF), a lightweight approach that adaptively patches the input image to increase token information density and encode hierarchical spatial structures into the input embedding. We then apply a reverse depatching scheme to the output embeddings of the transformer encoder, eliminating the need for convolution-based decoders. Unlike previous methods that modify attention mechanisms or use a complex hierarchy of interacting models, SHF can be retrofitted to any ViT model to allow it to learn the hierarchical structure of details in high-resolution images without requiring architectural changes. Experimental results demonstrate significant gains in computational efficiency and performance: on the PAIP WSI dataset, we achieved a 3∼32×speedup or a 2.95%∼7.03% increase in accuracy (measured by Dice score) at a 64K2 resolution with the same computational budget, compared to state-of-the-art production models. On the 3D medical datasets BTCV and KiTS, training was 6×faster, with accuracy gains of 6.93% and 5.9%, respectively, compared to models without SHF.

Zhang, Enzhi [Hokkaido University, Japan]↗
DOE OSTI2025

Towards Automatically Matching Security Advisories to CPEs: String Similarity-based Vendor Matching

When a vulnerability is reported by the National Vulnerability Database (NVD), affected products are listed in the structured Common Platform Enumeration (CPE) format. Unfortunately, if the vulnerability is in a software library (e.g., Log4j), it will not include CPEs for each product containing that library. In these cases, security operators need to manually read the vendor's or third-party security advisories to see if their product is affected. However, these advisories do not report affected products in a structured format, which prevents automated processing, This paper makes the first effort towards automatically constructing structured CPEs for the vulnerable products in a non-NVD security advisory from the unstructured data in the advisory. Since this is a very challenging problem, this paper specifically focuses on the initial but key step of matching the un-structured vendor names in security advisories to the structured vendor representations in the standard CPE format. We explore the feasibility of using string similarity to solve the problem. The basic idea is to compare a vendor name from the non-NVD advisory with each vendor in the official CPE dictionary. The CPE vendor with the highest similarity score to the advisory's vendor will be considered as the match. We first conduct an experimental, comparative study of multiple mainstream string similarity metrics for this matching problem. To improve the performance, we then design a new string similarity metric that is adapted from an existing metric by weighing different tokens in the advisory's vendor name differently.

McClanahan, Kylie↗
DOE OSTI2023

Adaptive language model training for molecular design

Abstract The vast size of chemical space necessitates computational approaches to automate and accelerate the design of molecular sequences to guide experimental efforts for drug discovery. Genetic algorithms provide a useful framework to incrementally generate molecules by applying mutations to known chemical structures. Recently, masked language models have been applied to automate the mutation process by leveraging large compound libraries to learn commonly occurring chemical sequences (i.e., using tokenization) and predict rearrangements (i.e., using mask prediction). Here, we consider how language models can be adapted to improve molecule generation for different optimization tasks. We use two different generation strategies for comparison, fixed and adaptive. The fixed strategy uses a pre-trained model to generate mutations; the adaptive strategy trains the language model on each new generation of molecules selected for target properties during optimization. Our results show that the adaptive strategy allows the language model to more closely fit the distribution of molecules in the population. Therefore, for enhanced fitness optimization, we suggest the use of the fixed strategy during an initial phase followed by the use of the adaptive strategy. We demonstrate the impact of adaptive training by searching for molecules that optimize both heuristic metrics, drug-likeness and synthesizability, as well as predicted protein binding affinity from a surrogate model. Our results show that the adaptive strategy provides a significant improvement in fitness optimization compared to the fixed pre-trained model, empowering the application of language models to molecular design tasks.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

WLCG Authorisation from X.509 to Tokens

The WLCG Authorisation Working Group was formed in July 2017 with the objective to understand and meet the needs of a future-looking Authentication and Authorisation Infrastructure (AAI) for WLCG experiments. Much has changed since the early 2000s when X.509 certificates presented the most suitable choice for authorisation within the grid; progress in token based authorisation and identity federation has provided an interesting alternative with notable advantages in usability and compatibility with external (commercial) partners. The need for interoperability in this new model is paramount as infrastructures and research communities become increasingly interdependent. Over the past two years, the working group has made significant steps towards identifying a system to meet the technical needs highlighted by the community during staged requirements gathering activities. Enhancement work has been possible thanks to externally funded projects, allowing existing AAI solutions to be adapted to our needs. A cornerstone of the infrastructure is the reliance on a common token schema in line with evolving standards and best practices, allowing for maximum compatibility and easy cooperation with peer infrastructures and services. We present the work of the group and an analysis of the anticipated changes in authorisation model by moving from X.509 to token based authorisation. A concrete example of token integration in Rucio is presented.

Bockelman, Brian↗
DOE OSTI2025

Sequence length scaling in vision transformers for scientific images on frontier

Vision Transformers (ViTs) are pivotal for foundational models in scientific imagery, including Earth science applications, due to their capability to process large sequence lengths. While transformers for text have inspired scaling sequence lengths in ViTs, adapting these for ViTs introduces unique challenges. We develop distributed sequence parallelism for ViTs, enabling them to handle up to 1M tokens. Our approach, leveraging DeepSpeed-Ulysses and Long-Sequence-Segmentation with model sharding, is the first to apply sequence parallelism in ViT training, achieving a 94% batch scaling efficiency on 2,048 AMD-MI250X GPUs. Evaluating sequence parallelism in ViTs, particularly in models up to 10B parameters, highlighted substantial bottlenecks. We countered these with hybrid sequence, pipeline, and flash attention strategies, to scale beyond single GPU memory limits. Our method significantly enhances climate modeling accuracy by 20% in temperature predictions, marking the first training of a vision transformer model to convergence with a sequence length of 188K tokens, using full self-attention.

Tsaris, Aristeidis (aris) [ORNL] (ORCID:0000000277↗
DOE OSTI2024

Adaptive Patching for High-resolution Image Segmentation with Transformers

Attention-based models are proliferating in the space of image analytics, including segmentation. The standard method of feeding images to transformer encoders is to divide the images into patches and then feed the patches to the model as a linear sequence of tokens. For high-resolution images, e.g. microscopic pathology images, the quadratic compute and memory cost prohibits the use of an attention-based model, if we are to use smaller patch sizes that are favorable in segmentation. The solution is to either use custom complex multi-resolution models or approximate attention schemes. We take inspiration from Adapative Mesh Refinement (AMR) methods in HPC by adaptively patching the images, as a pre-processing step, based on the image details to reduce the number of patches being fed to the model, by orders of magnitude. This method has a negligible overhead, and works seamlessly with any attention-based model, i.e. it is a pre-processing step that can be adopted by any attention-based model without friction. We demonstrate superior segmentation quality over SoTA segmentation models for realworld pathology datasets while gaining a geomean speedup of 6.9× for resolutions up to 64K2, on up to 2, 048 GPUs.

Zhang, Enzhi↗
DOE OSTI2021

Secure Command Line Solution for Token-based Authentication

The WLCG is modernizing its security infrastructure, replacing X.509 client authentication with the newer industry standard of JSON Web Tokens (JWTs) obtained through the Open ID Connect (OIDC) protocol. There is a wide variety of software available using the standards, but most of it is for Web browser-based applications and doesn’t adapt well to the command line-based software used heavily in High Throughput Computing (HTC). OIDC command line client software did exist, but it did not meet our requirements for security and convenience. This paper discusses a command line solution we have made based on the popular existing secrets management software from Hashicorp called vault. We made a package called htvault-config to easily configure a vault service and another called htgettoken to be the vault client. In addition, we have integrated use of the tools into the HTCondor workload management system, although they also work well independent of HTCondor. All of the software is open source, under active development, and ready for use.

Dykstra, Dave↗
DOE OSTI2024

Masked Particle Modeling on Sets: Towards Self-Supervised High Energy Physics Foundation Models

Abstract We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a novel scheme to perform masked modeling based pre-training to learn permutation invariant functions on sets. More generally, this work provides a step towards building large foundation models for HEP that can be generically pre-trained with self-supervised learning and later fine-tuned for a variety of down-stream tasks. In MPM, particles in a set are masked and the training objective is to recover their identity, as defined by a discretized token representation of a pre-trained vector quantized variational autoencoder. We study the efficacy of the method in samples of high energy jets at collider physics experiments, including studies on the impact of discretization, permutation invariance, and ordering. We also study the fine-tuning capability of the model, showing that it can be adapted to tasks such as supervised and weakly supervised jet classification, and that the model can transfer efficiently with small fine-tuning data sets to new classes and new data domains.

Heinrich, Lukas (ORCID:0000000240487584)↗
DOE OSTI2020

Efficient Generalized Boundary Detection Using a Sliding Information Distance

In this work, we present a general machine learning algorithm for boundary detection within general signals based on an efficient, accurate, and robust approximation of the universal normalized information distance. Our approach uses an adaptive sliding information distance (SLID) combined with a wavelet-based approach for peak identification to locate the boundaries. Special emphasis is placed on developing an adaptive formulation of SLID to handle general signals with multiple unknown and/or drifting section lengths. Although specialized algorithms may outperform SLID when domain knowledge is available, these algorithms are limited to specific applications and do not generalize. SLID excels in these cases. We demonstrate the versatility and efficacy of SLID on a variety of signal types, including synthetically generated sequences of tokens, binary executables for reverse engineering applications, and time series of seismic events.

42 ENGINEERING↗
DOE OSTI2025

Learning-Based Quantum Compilation: Translating QASM to QIR with CodeBERT

We propose a learning-based approach to quantum compilation by translating OpenQASM to Quantum Intermediate Representation (QIR) using a fine-tuned CodeBERT model. Trained on 10,000 synthetic QASM-QIR pairs, the model captures code semantics while addressing QIR verbosity and the 512-token limit via a custom token compression scheme. Finetuning was performed on the Frontier supercomputer, with results showing syntactic correctness and stable validation loss reduction. Our method moves toward enabling flexible, language-modeldriven quantum software tools. It also introduces syntax error handling and the possibility of incorporating classical control constructs, addressing limitations in existing rule-based compilers like qBraid-QIR. While the current model has been validated on quantum-only circuits, we propose future evaluations on hybrid quantum-classical examples. This poster will provide architecture insights, compression examples, training loss plots, and QIR outputs. Our work highlights the potential for scalable, adaptable compilation in future quantum toolchains.

Afrose, Sharmin [ORNL]↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗