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All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Integrating multi-modal remote sensing, deep learning, and attention mechanisms for yield prediction in plant breeding experiments

In both plant breeding and crop management, interpretability plays a crucial role in instilling trust in AI-driven approaches and enabling the provision of actionable insights. The primary objective of this research is to explore and evaluate the potential contributions of deep learning network architectures that employ stacked LSTM for end-of-season maize grain yield prediction. A secondary aim is to expand the capabilities of these networks by adapting them to better accommodate and leverage the multi-modality properties of remote sensing data. In this study, a multi-modal deep learning architecture that assimilates inputs from heterogeneous data streams, including high-resolution hyperspectral imagery, LiDAR point clouds, and environmental data, is proposed to forecast maize crop yields. The architecture includes attention mechanisms that assign varying levels of importance to different modalities and temporal features that, reflect the dynamics of plant growth and environmental interactions. The interpretability of the attention weights is investigated in multi-modal networks that seek to both improve predictions and attribute crop yield outcomes to genetic and environmental variables. This approach also contributes to increased interpretability of the model's predictions. The temporal attention weight distributions highlighted relevant factors and critical growth stages that contribute to the predictions. The results of this study affirm that the attention weights are consistent with recognized biological growth stages, thereby substantiating the network's capability to learn biologically interpretable features. Accuracies of the model's predictions of yield ranged from 0.82-0.93 R 2 ref in this genetics-focused study, further highlighting the potential of attention-based models. Further, this research facilitates understanding of how multi-modality remote sensing aligns with the physiological stages of maize. The proposed architecture shows promise in improving predictions and offering interpretable insights into the factors affecting maize crop yields, while demonstrating the impact of data collection by different modalities through the growing season. By identifying relevant factors and critical growth stages, the model's attention weights provide valuable information that can be used in both plant breeding and crop management. The consistency of attention weights with biological growth stages reinforces the potential of deep learning networks in agricultural applications, particularly in leveraging remote sensing data for yield prediction. To the best of our knowledge, this is the first study that investigates the use of hyperspectral and LiDAR UAV time series data for explaining/interpreting plant growth stages within deep learning networks and forecasting plot-level maize grain yield using late fusion modalities with attention mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

Abstract The information about the domain architecture of proteins is useful for studying protein structure and function. However, accurate prediction of protein domain boundaries (i.e., sequence regions separating two domains) from sequence remains a significant challenge. In this work, we develop a deep learning method based on multi-head U-Nets (called DistDom) to predict protein domain boundaries utilizing 1D sequence features and predicted 2D inter-residue distance map as input. The 1D features contain the evolutionary and physicochemical information of protein sequences, whereas the 2D distance map includes the structural information of proteins that was rarely used in domain boundary prediction before. The 1D and 2D features are processed by the 1D and 2D U-Nets respectively to generate hidden features. The hidden features are then used by the multi-head attention to predict the probability of each residue of a protein being in a domain boundary, leveraging both local and global information in the features. The residue-level domain boundary predictions can be used to classify proteins as single-domain or multi-domain proteins. It classifies the CASP14 single-domain and multi-domain targets at the accuracy of 75.9%, 13.28% more accurate than the state-of-the-art method. Tested on the CASP14 multi-domain protein targets with expert annotated domain boundaries, the average per-target F1 measure score of the domain boundary prediction by DistDom is 0.263, 29.56% higher than the state-of-the-art method.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Unsupervised atomic data mining via multi-kernel graph autoencoders for machine learning force fields

Constructing a chemically diverse dataset while avoiding sampling bias is critical to training efficient and generalizable force fields. However, in computational chemistry and materials science, many common dataset generation techniques are prone to oversampling regions of the potential energy surface. Furthermore, these regions can be difficult to identify and isolate from each other or may not align well with human intuition, making it challenging to systematically remove bias in the dataset. While traditional clustering and pruning (down-sampling) approaches can be useful for this, they can often lead to information loss or a failure to properly identify distinct regions of the potential energy surface due to difficulties associated with the high dimensionality of atomic descriptors. In this work, we introduce the Multi-kernel Edge Attention-based Graph Autoencoder (MEAGraph) model, an unsupervised approach for analyzing atomic datasets. MEAGraph combines multiple linear kernel transformations with attention-based message passing to capture geometric sensitivity and enable effective dataset pruning without relying on labels or extensive training. Demonstrated applications on niobium, tantalum, and iron datasets show that MEAGraph efficiently groups similar atomic environments, allowing for the use of basic pruning techniques for removing sampling bias. This approach provides an effective method for representation learning and clustering that can be used for data analysis, outlier detection, and dataset optimization.

Materials science↗
DOE OSTI2023

DeePMD-kit v2: A software package for deep potential models

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

A comparison of histopathology imaging comprehension algorithms based on multiple instance learning

Whole slide imaging (WSI), also called digital virtual microscopy, is a new imaging modality. It allows for the application of AI and machine learning methods to cancer pathology to help establish a means for the automatic diagnosis of cancer cases. However, designing machine-learning models for WSI is computationally challenging due to its required ultra-high resolution. The current state-of-the-art models use multiple instance learning (MIL). MIL is a weakly-supervised learning method in which the model uses an array of inferences from many smaller instances to make a final classification about the entire set. In the context of WSI, researchers divide the ultra-high-resolution image into many patches. The model then classifies the slide based on an array of inferences from the patches. Among several ways of making the final classification, attention-based mechanisms have resulted in superb accuracy scores. The Transformer, one attention-based algorithm, has reported substantial improvements for WSI comprehension tasks. In this project, we studied and compared several WSI comprehension algorithms. We used the following three datasets: CAMELYON16+17, TCGALung, and TCGA-Kidney. We found that attention-based MIL algorithms performed better than standard MIL algorithms for classifying WSI images, achieving a higher mean accuracy and AUC. However, none of the attention-based algorithms performed significantly better than the others, reporting accuracy scores that varied widely. Presumably, it is due to the limited availability of training samples in the data corpus. Since it is not easy to increase the samples from human subjects, some machine learning techniques like transfer learning could help mitigate this issue.

Saunders, Adam↗
DOE OSTI2026

Predicting river turbidity in Pine Island Bayou using machine learning techniques coupled with variational mode decomposition

Elevated turbidity levels pose significant public health risks by facilitating the transport of harmful pollutants, including metals, organic compounds, and pathogenic microorganisms into the surface water. These conditions create serious challenges for public recreational water use and drinking water treatment, leading to economic losses and health risks. This study utilizes water monitoring data in Pine Island Bayou, Texas, and develops a Sequence-to-Sequence (S2S) model to predict turbidity using Attention-based Gated Recurrent Units with Encoder-Decoder (AT-GRU-ED) and Long Short-Term Memory (LSTM), coupled with Variational Mode Decomposition (VMD). Compared to the model without VMD, the model demonstrates satisfactory 72-hour turbidity prediction performance, achieving MAEs of 2.60 and 3.29 NTU (reductions of 53% and 58%), RMSEs of 21.08 and 31.49 NTU (reductions of 82% and 80%), and R² values of 0.96 and 0.84 on the validation and test sets, respectively. Feature importance analysis reveals that water temperature is the dominant factor influencing seasonal turbidity patterns, while real-time hourly rainfall significantly contributes to short-term variability. Turbidity typically peaks within 48 hours after rainfall events due to lagged effects from surface runoff and upstream flow. Findings suggest suspending recreational water use and water supply pumping for three days after heavy rainfall can benefit public health and improve water treatment processes. Discharges above 100 m3/s are found to accelerate sediment dilution and transport, reducing turbidity levels more quickly after the peak. In conclusion, the proposed model demonstrates reliable 72-hour turbidity prediction, supporting decision-making for water treatment plant operations and providing early warning for public recreational water use.

Deep learning↗
DOE OSTI2023

Investigating Anomalies in Compute Clusters: An Unsupervised Learning Approach

As compute clusters continue to grow in scale and complexity, the frequency of detected anomalies in their operation significantly increases. Timely detection of anomalous events is vital to maintain system efficiency and availability. This study presents an attentionbased graph neural network (GNN) for detecting anomalies in clusters at the compute node level and for providing detailed root cause analysis. We show the effectiveness of attention-based GNNs to accurately detect and localize anomalies on real-world datasets.

Lu, Yiyang↗
DOE OSTI2024

Explaining Neural Spike Activity for Simulated Bio-plausible Network through Deep Sequence Learning

With significant improvements in large-scale simulations of brain models, there is a growing need to develop tools for rapid analysis and interpreting the simulation results. In this work, we explore the potential of sequential deep learning models to understand and explain the network dynamics among the neurons extracted from a large-scale neural simulation in STACS (Simulation Tool for Asynchronous Cortical Stream). Our method employs a representative neuroscience model that abstracts the cortical dynamics with a reservoir of randomly connected spiking neurons with a low stable spike firing rate throughout the simulation duration. We subsequently analyze the spike dynamics of the simulated spiking neural network through an autoencoder model and an attention-based mechanism.

Kulkarni, Shruti↗
DOE OSTI2023

Eco-PiNN: A Physics-informed Neural Network for Eco-toll Estimation

The eco-toll estimation problem quantifies the expected environmental cost (e.g., energy consumption, exhaust emissions) for a vehicle to travel along a path. This problem is important for societal applications such as eco-routing, which aims to find paths with the lowest exhaust emissions or energy need. The challenges of this problem are threefold: (1) the dependence of a vehicle's eco-toll on its physical parameters; (2) the lack of access to data with eco-toll information; and (3) the influence of contextual information (i.e. the connections of adjacent segments in the path) on the eco-toll of road segments. Prior work on eco-toll estimation has mostly relied on pure data-driven approaches and has high estimation errors given the limited training data. To address these limitations, we propose a novel Eco-toll estimation Physics-informed Neural Network framework (Eco-PiNN) using three novel ideas, namely, (1) a physics-informed decoder that integrates the physical laws governing vehicle dynamics into the network, (2) an attention-based contextual information encoder, and (3) a physics-informed regularization to reduce overfitting. Experiments on real-world heavy-duty truck data show that the proposed method can greatly improve the accuracy of eco-toll estimation compared with state-of-the-art methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Peak2Patch: High-Fidelity Functional Group Identification through Attention-Based Fusion of Infrared and Mass Spectra

Identifying molecular structure based on spectroscopic readings is a key task in a variety of chemical and biological applications. Common spectroscopy techniques, such as Infrared (IR) Spectroscopy and Mass Spectrometry (MS), provide detailed information on the structure of molecular compounds but nonetheless require expert-level knowledge to decode. Machine learning has emerged as a potential solution for automating structure prediction from chemical spectra; however, current approaches generally focus on single sensor modalities, neglecting to leverage the complementary information contained within differing spectra. In this paper, we introduce Peak2Patch, a novel approach to fusion-enhanced prediction of functional groups from IR and mass spectra. First, we perform a detailed comparison of backbone networks for encoding both sparse mass spectra and dense IR spectra and demonstrate the superior performance of transformer neural networks over current state-of-the-art convolutional neural networks. Second, we evaluate three broad categories of fusion: early (raw feature), middle (deep feature), and late (decision) fusion, demonstrating the potential of a deep feature fusion-based approach. Lastly, we present Peak2Patch, our attention-based fusion scheme, which leverages cross-attention to mix features between encoded tokens of the two modalities. We validate our approach on a publicly available multimodal spectroscopic data set of 790k simulated molecules, demonstrating a large improvement in functional group prediction over both the previous state-of-the-art and our own strong single-modal baselines.

Jacobson, Philip [Sandia National Laboratories (SN↗
DOE OSTI2025

Deep Point Cloud Building Envelope Segmentation (DeeP-CuBES) using Deep Learning

Building Information Modeling (BIM) plays an important role in building design and construction, particularly for achieving energy-efficient retrofits. Building envelope retrofits using panelized prefabricated system, such as those popularized by the Energiesprong program, need accurate as-built dimensions of facade features (windows, doors, etc.) to achieve the desired thermal and air tightness. Traditionally, building surveying is done manually, resulting in a time-consuming and labor-intensive process. Recently, 3D point clouds from terrestrial LiDAR have been used to automate the generation of as-built dimensions of existing buildings. However, automated BIM using LiDAR relies on solving the point cloud semantic segmentation (PCSS) problem. In this work, we propose a robust pipeline for solving the PCSS problem using deep neural networks, focusing on overcoming challenges posed by imbalanced datasets and complex architectural features. We introduce the first high-density, labeled, and validated building envelope point cloud dataset derived from multiple building scans, specifically curated to tackle challenges in facade-level segmentation. Results from the trained neural networks show that advanced attention-based architectures and incorporating radiometry (light intensity and RGB) features significantly boost segmentation accuracy for windows and doors.

Selvakumar, Balaji [ORNL]↗
DOE OSTI2022

Data-driven modeling of power generation for a coal power plant under cycling

Increased penetration of renewables for power generation has negatively impacted the dynamics of conventional fossil fuel-based power plants. The power plants operating on the base load are forced to cycle, to adjust to the fluctuating power demands. This results in an inefficient operation of the coal power plants, which leads up to higher operating losses. To overcome such operational challenge associated with cycling and to develop an optimal process control, this work analyzes a set of models for predicting power generation. Moreover, the power generation is intrinsically affected by the state of the power plant components, and therefore our model development also incorporates additional power plant process variables while forecasting the power generation. We present and compare multiple state-of-the-art forecasting data-driven methods for power generation to determine the most adequate and accurate model. We also develop an interpretable attention-based transformer model to explain the importance of process variables during training and forecasting. The trained deep neural network (DNN) LSTM model has good accuracy in predicting gross power generation under various prediction horizons with/without cycling events and outperforms the other models for long-term forecasting. The DNN memory-based models show significant superiority over other state-of-the-art machine learning models for short, medium and long range predictions. The transformer-based model with attention enhances the selection of historical data for multi-horizon forecasting, and also allows to interpret the significance of internal power plant components on the power generation. This newly gained insights can be used by operation engineers to anticipate and monitor the health of power plant equipment during high cycling periods.

01 COAL, LIGNITE, AND PEAT↗
DOE OSTI2022

Distilling Knowledge from Ensembles of Cluster-Constrained-Attention Multiple-Instance Learners for Whole Slide Image Classification

The peculiar nature of whole slide imaging (WSI), digitizing conventional glass slides to obtain multiple high resolution images which capture microscopic details of a patient’s histopathological features, has garnered increased interest from the computer vision research community over the last two decades. Given the unique computational space and time complexity inherent to gigapixel-size whole slide image data, researchers have proposed novel machine learning algorithms to aid in the performance of diagnostic tasks in clinical pathology. One effective algorithm represents a Whole slide image as a bag of smaller image patches, which can be represented as low-dimension image patch embeddings. Weakly supervised deep-learning methods, such as cluster-constrained-attention multiple instance learning (CLAM), have shown promising results when combined with image patch embeddings. While traditional ensemble classifiers yield improved task performance, such methods come with a steep cost in model complexity. Through knowledge distillation, it is possible to retain some performance improvements from an ensemble, while minimizing costs to model complexity. In this work, we implement a weakly supervised ensemble using clustering-constrained-attention multiple-instance learners (CLAM), which uses attention and instance-level clustering to identify task salient regions and feature extraction in whole slides. By applying logit-based and attention-based knowledge distillation, we show it is possible to retain some performance improvements resulting from the ensemble at zero cost to model complexity.

Alamudun, Folami↗
DOE OSTI2023

Attention-Augmented Parametric Kernel Graph Neural Network (APKGNN) for Node Classification

We present a new graph neural network, the Attention-based Parametric-Kernel augmented Graph Neural Network (APKGNN), developed for node classification tasks. Despite extensive work on modeling multi-faceted relationships between connected nodes of a graph, the effect of attention on edge features mapped to relationships has not yet been analyzed through learning representation. This study derives such an attention vector by first calculating node features corresponding to endpoints of an edge and then aggregating these with extracted local intrinsic patches of a given graph to generate augmented local patch vectors. This process uses a parametric kernel based on Gaussian mixture models (GMMs) to embed local neighborhoods of the graph in local patches. The patch vectors then convolve with the above node features to produce an updated node representation. We show that this new learning representation (APKGNN) achieves higher node classification accuracy on tasks - both standard benchmarks (Cora, PubMed, Citeseer) and new experimental short text corpora where nodes correspond to text documents and words. This implementation of the GNN convolution layer outperforms state-of-the-art (SOTA) algorithms, achieving higher training, validation, and test accuracy by a significant margin on three standard benchmark data sets under both SOTA experimental settings and those for new testbeds.

Bose, Avishek↗
DOE OSTI2025

Graph-Based Attention Mechanisms for Solving the AC Optimal Power Flow Problem in Electrical Power Networks

With the increasing complexity and data availability in modern power systems, learning-based approaches to AC Optimal Power Flow (AC OPF) have garnered significant attention. In particular, the structure of smart grids lends itself naturally to graph-based representations, where Graph Neural Networks (GNNs) can capture spatial and relational dependencies. This paper investigates attention-based GNN architectures tailored to heterogeneous graph representations of electric grids. We evaluate two major paradigms: relational attention, which distinguishes between edge types during message passing, and meta-path attention, which captures high-level semantics through multi-hop, typed paths. Using a large corpus of public AC OPF scenarios, we benchmark representative models of each type of attention. Our results demonstrate the benefits of heterogeneous attention-based models in accurately capturing grid dynamics; heterogeneous attention models achieve superior performance in both standard and perturbed settings. The findings highlight the importance of semantic-aware architectures for improving prediction robustness and interpretability in power system applications.

Trigui, Ali [Qubit Engineering Inc.]↗
DOE OSTI2022

A Length Adaptive Algorithm-Hardware Co-design of Transformer on FPGA Through Sparse Attention and Dynamic Pipelining

Transformers are considered one of the most important deep learning models since 2018, in part because it establishes state-of-the-art (SOTA) records and could potentially replace existing Deep Neural Networks (DNNs). Despite the remarkable triumphs, the prolonged turnaround time of Transformer models is a widely recognized roadblock. The variety of sequence lengths imposes additional computing overhead where inputs need to be zero-padded to the maximum sentence length in the batch to accommodate the parallel computing platforms. This paper targets the field-programmable gate array (FPGA) and proposes a coherent sequence length adaptive algorithm–hardware co-design for Transformer acceleration. Particularly, we develop a hardware-friendly sparse attention operator and a length-aware hardware resource scheduling algorithm. The proposed sparse attention operator brings the complexity of attention-based models down to linear complexity and alleviates the off-chip memory traffic. The proposed length-aware resource hardware scheduling algorithm dynamically allocates the hardware resources to fill up the pipeline slots and eliminates bubbles for NLP tasks. Experiments show that our design has very small accuracy loss and has 80.2 × and 2.6 × speedup compared to CPU and GPU implementation, and 4 × higher energy efficiency than state-of-the-art GPU accelerator optimized via CUBLAS GEMM.

Peng, Hongwu↗
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↗
DOE OSTI2024

Reconstructing Richtmyer–Meshkov instabilities from noisy radiographs using low dimensional features and attention-based neural networks

We develop an ML-based approach for density reconstruction based on transformer neural networks. This approach is demonstrated in the setting of ICF-like double shell hydrodynamic simulations wherein the parameters related to material properties and initial conditions are varied. The new method can robustly recover the complex topologies given by the Richtmyer-Meshkoff instability (RMI) from a sequence of hydrodynamic features derived from radiographic images corrupted with blur, scatter, and noise. A noise model is developed to characterize errors in extracting features from synthetic radiographs of the simulated density field. The key component of the network is a transformer encoder that acts on a sequence of features extracted from noisy radiographs. This encoder includes numerous self-attention layers that act to learn temporal dependencies in the input sequences and increase the expressiveness of the model. This approach is shown to exhibit an excellent ability to accurately recover the RMI growth rates, despite the gas-metal interface being greatly obscured by radiographic noise. Our approach can be applied in a broad array of fields involving shock physics and material science.

47 OTHER INSTRUMENTATION↗