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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Geometric learning for computational mechanics Part II: Graph embedding for interpretable multiscale plasticity

The history-dependent behaviors of classical plasticity models are often driven by internal variables evolved according to phenomenological laws. The difficulty to interpret how these internal variables represent a history of deformation, the lack of direct measurement of these internal variables for calibration and validation, and the weak physical underpinning of those phenomenological laws have long been criticized as barriers to creating realistic models. In this work, geometric machine learning on graph data (e.g. finite element solutions) is used as a means to establish a connection between nonlinear dimensional reduction techniques and plasticity models. Geometric learning-based encoding on graphs allows the embedding of rich time-history data onto a low-dimensional Euclidean space such that the evolution of plastic deformation can be predicted in the embedded feature space. Finally, a corresponding decoder can then convert these low-dimensional internal variables back into a weighted graph such that the dominating topological features of plastic deformation can be observed and analyzed.

42 ENGINEERING↗
DOE OSTI2026

Universal Workflow Language and Software Enable Geometric Learning and FAIR Scientific Protocol Reporting

Written language and conventional data structures for representing scientific procedures suffer from low process detail, often fail to accurately represent protocols, and lack universality. New strategies for the handling of experimental data are needed to provide viable process information for both humans and machines. In this work, we present the universal workflow language (UWL) and interface (UWLi). UWL is a findable, accessible, interoperable, and reusable (FAIR)-compatible, graph-based data architecture that can capture arbitrary scientific procedures through workflow representation, and UWLi is an accompanying software package for building, manipulating, and interpreting UWL entries. The UWL format was found to be highly effective in identifying deficiencies in the reported process details of high-impact, peer-reviewed scientific journals, and in simulated scenarios, the graph format was shown to be more effective than conventional methods in predictively modeling the outcome of diverse scientific protocols. Implementation of UWL could enable more accurate scientific communication and more impactful process datasets.

14 SOLAR ENERGY↗
DOE OSTI2021

Performance of a geometric deep learning pipeline for HL-LHC particle tracking

The Exa.TrkX project has applied geometric learning concepts such as metric learning and graph neural networks to HEP particle tracking. Exa.TrkX’s tracking pipeline groups detector measurements to form track candidates and filters them. The pipeline, originally developed using the TrackML dataset (a simulation of an LHC-inspired tracking detector), has been demonstrated on other detectors, including DUNE Liquid Argon TPC and CMS High-Granularity Calorimeter. This paper documents new developments needed to study the physics and computing performance of the Exa.TrkX pipeline on the full TrackML dataset, a first step towards validating the pipeline using ATLAS and CMS data. The pipeline achieves tracking efficiency and purity similar to production tracking algorithms. Crucially for future HEP applications, the pipeline benefits significantly from GPU acceleration, and its computational requirements scale close to linearly with the number of particles in the event.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Differentiable modeling and optimization of non-aqueous Li-based battery electrolyte solutions using geometric deep learning

Electrolytes play a critical role in designing next-generation battery systems, by allowing efficient ion transfer, preventing charge transfer, and stabilizing electrode-electrolyte interfaces. In this work, we develop a differentiable geometric deep learning (GDL) model for chemical mixtures, DiffMix, which is applied in guiding robotic experimentation and optimization towards fast charging battery electrolytes. In particular, we extend mixture thermodynamic and transport laws by creating GDL-learnable physical coefficients. We evaluate our model with mixture thermodynamics and ion transport properties, where we show improved prediction accuracy and model robustness of Diff-Mix than its purely data-driven variants. Furthermore, with a robotic experimentation setup, Clio, we improve ionic conductivity of electrolytes by over 18.8% within 10 experimental steps, via differentiable optimization built on DiffMix gradients. By combining GDL, mixture physics laws, and robotic experimentation, DiffMix expands the predictive modeling methods for chemical mixtures and enables efficient optimization in large chemical spaces.

25 - ENERGY STORAGE↗
DOE OSTI2021

Selecting XFEL single-particle snapshots by geometric machine learning

A promising new route for structural biology is single-particle imaging with an X-ray Free-Electron Laser (XFEL). This method has the advantage that the samples do not require crystallization and can be examined at room temperature. However, high-resolution structures can only be obtained from a sufficiently large number of diffraction patterns of individual molecules, so-called single particles. Here, we present a method that allows for efficient identification of single particles in very large XFEL datasets, operates at low signal levels, and is tolerant to background. This method uses supervised Geometric Machine Learning (GML) to extract low-dimensional feature vectors from a training dataset, fuse test datasets into the feature space of training datasets, and separate the data into binary distributions of “single particles” and “non-single particles.” As a proof of principle, we tested simulated and experimental datasets of the Coliphage PR772 virus. We created a training dataset and classified three types of test datasets: First, a noise-free simulated test dataset, which gave near perfect separation. Second, simulated test datasets that were modified to reflect different levels of photon counts and background noise. These modified datasets were used to quantify the predictive limits of our approach. Third, an experimental dataset collected at the Stanford Linear Accelerator Center. The single-particle identification for this experimental dataset was compared with previously published results and it was found that GML covers a wide photon-count range, outperforming other single-particle identification methods. Moreover, a major advantage of GML is its ability to retrieve single particles in the presence of structural variability.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Learning Distributed Geometric Koopman Operator for Sparse Networked Dynamical Systems

Koopman operator theory provides an alternative to study nonlinear networked dynamical systems by mapping the state space to an abstract higher dimensional space where the system evolution is linear. Recent works show the application of graph neural networks (GNNs) to learn state to object-centric embeddings and achieve centralized block-wise computation of Koopman operator (KO) under additional assumptions on the underlying agents properties and constraints on the KO structure. However, the computational complexity of learning the Koopman increases exponentially for networked systems where the number of possible system states grows in a combinatorial fashion with the number of nodes. The learning challenge is further amplified for sparse networks by two factors: 1) sample sparsity for learning the Koopman operator in the non-linear space, and 2) the divergence in the dynamics of individual nodes or from one subgraph to another. Our work aims to address these challenge by formulating the representation learning of networked dynamical systems into a multi-agent paradigm and learning the Koopman operator in a distributive manner. The computational as well as performance advantages of distributed Koopman is predominant for sparse networks whereas for fully connected networks, it is shown to coincide with the centralized one. The empirical study on rope system, network of oscillators and a synthetic power system show comparable and superior performance along with computational benefits with the state-of-the-art methods.

Mukherjee, Sayak↗
DOE OSTI2021

Geometric deep learning of RNA structure

RNA molecules adopt three-dimensional structures that are critical to their function and of interest in drug discovery. Few RNA structures are known, however, and predicting them computationally has proven challenging. We introduce a machine learning approach that enables identification of accurate structural models without assumptions about their defining characteristics, despite being trained with only 18 known RNA structures. The resulting scoring function, the Atomic Rotationally Equivariant Scorer (ARES), substantially outperforms previous methods and consistently produces the best results in community-wide blind RNA structure prediction challenges. By learning effectively even from a small amount of data, our approach overcomes a major limitation of standard deep neural networks. Because it uses only atomic coordinates as inputs and incorporates no RNA-specific information, this approach is applicable to diverse problems in structural biology, chemistry, materials science, and beyond.

Townshend, Raphael J. L.↗
DOE OSTI2020

PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein function, many functional prediction tasks use only protein sequence. In this work, we isolate protein structure to make functional annotations for proteins in the Protein Data Bank in order to study the expressiveness of different structure-based prediction schemes. We present PersGNN - an end-to-end trainable deep learning model that combines graph representation learning with topological data analysis to capture a complex set of both local and global structural features. While variations of these techniques have been successfully applied to proteins before, we demonstrate that our hybridized approach, PersGNN, outperforms either method on its own as well as a baseline neural network that learns from the same information. PersGNN achieves a 9.3% boost in area under the precision recall curve (AUPR) compared to the best individual model, as well as high F1 scores across different gene ontology categories, indicating the transferability of this approach.

Swenson, Nicolas↗
DOE OSTI2024

Geometric Measures of Trustworthiness for Machine Learning Predictions

his report details the findings from the research and investigation of Geometric Measures of Trustworthiness for Machine Learning Predictions. We explored the trustworthiness of machine learning (ML) models’ predictions using geometric measures to quantify the similarity of a query point with the training data. Predictive uncertainty in ML can originate from at least three sources: (1) Model uncertainty, which represents the uncertainty in model form (e.g. decision tree, vs neural network) and estimating the model parameters from the training data, (2) Data uncertainty, which represents the natural complexities of the data such as class overlap and inherent noise, and (3) Distributional uncertainty, which represents the mismatch between the training and operational distributions. The proposed measures focus on measuring and explaining the data and distributional uncertainties by measuring the relationships of operational data with the training data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

We Know Where We Don't Know: 3D Bayesian CNNs for Credible Geometric Uncertainty

Deep learning has been successfully applied to the segmentation of 3D Computed Tomography (CT) scans. Establishing the credibility of these segmentations requires uncertainty quantification (UQ) to identify untrustworthy predictions. Recent UQ architectures include Monte Carlo dropout networks (MCDNs), which approximate deep Gaussian processes, and Bayesian neural networks (BNNs), which learn the distribution of the weight space. BNNs are advantageous over MCDNs for UQ but are thought to be computationally infeasible in high dimension, and neither architecture has produced interpretable geometric uncertainty maps. We propose a novel 3D Bayesian convolutional neural network (BCNN), the first deep learning method which generates statistically credible geometric uncertainty maps and scales for application to 3D data. We present experimental results on CT scans of graphite electrodes and laser-welded metals and show that our BCNN outperforms an MCDN in recent uncertainty metrics. The geometric uncertainty maps generated by our BCNN capture distributions of sigmoid values that are interpretable as confidence intervals, critical for applications that rely on deep learning for high-consequence decisions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Geometry-complete perceptron networks for 3D molecular graphs

Abstract Motivation The field of geometric deep learning has recently had a profound impact on several scientific domains such as protein structure prediction and design, leading to methodological advancements within and outside of the realm of traditional machine learning. Within this spirit, in this work, we introduce GCPNet, a new chirality-aware SE(3)-equivariant graph neural network designed for representation learning of 3D biomolecular graphs. We show that GCPNet, unlike previous representation learning methods for 3D biomolecules, is widely applicable to a variety of invariant or equivariant node-level, edge-level, and graph-level tasks on biomolecular structures while being able to (1) learn important chiral properties of 3D molecules and (2) detect external force fields. Results Across four distinct molecular-geometric tasks, we demonstrate that GCPNet’s predictions (1) for protein–ligand binding affinity achieve a statistically significant correlation of 0.608, more than 5%, greater than current state-of-the-art methods; (2) for protein structure ranking achieve statistically significant target-local and dataset-global correlations of 0.616 and 0.871, respectively; (3) for Newtownian many-body systems modeling achieve a task-averaged mean squared error less than 0.01, more than 15% better than current methods; and (4) for molecular chirality recognition achieve a state-of-the-art prediction accuracy of 98.7%, better than any other machine learning method to date. Availability and implementation The source code, data, and instructions to train new models or reproduce our results are freely available at https://github.com/BioinfoMachineLearning/GCPNet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Time-series forecasting using manifold learning, radial basis function interpolation, and geometric harmonics

We address a three-tier numerical framework based on nonlinear manifold learning for the forecasting of high-dimensional time series, relaxing the “curse of dimensionality” related to the training phase of surrogate/machine learning models. At the first step, we embed the high-dimensional time series into a reduced low-dimensional space using nonlinear manifold learning (local linear embedding and parsimonious diffusion maps). Then, we construct reduced-order surrogate models on the manifold (here, for our illustrations, we used multivariate autoregressive and Gaussian process regression models) to forecast the embedded dynamics. Finally, we solve the pre-image problem, thus lifting the embedded time series back to the original high-dimensional space using radial basis function interpolation and geometric harmonics. The proposed numerical data-driven scheme can also be applied as a reduced-order model procedure for the numerical solution/propagation of the (transient) dynamics of partial differential equations (PDEs). In conclusion, we assess the performance of the proposed scheme via three different families of problems: (a) the forecasting of synthetic time series generated by three simplistic linear and weakly nonlinear stochastic models resembling electroencephalography signals, (b) the prediction/propagation of the solution profiles of a linear parabolic PDE and the Brusselator model (a set of two nonlinear parabolic PDEs), and (c) the forecasting of a real-world data set containing daily time series of ten key foreign exchange rates spanning the time period 3 September 2001–29 October 2020.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

KamNet: An integrated spatiotemporal deep neural network for rare event searches in KamLAND-Zen

Rare event searches allow us to search for new physics at energy scales inaccessible with other means by leveraging specialized large-mass detectors. Machine learning provides a new tool to maximize the information provided by these detectors. The information is sparse, which forces these algorithms to start from the lowest level data and exploit all symmetries in the detector to produce results. In this work we present KamNet, which harnesses breakthroughs in geometric deep learning and spatiotemporal data analysis to maximize the physics reach of KamLAND-Zen, a kiloton scale spherical liquid scintillator detector searching for 0⁢νβ⁢β. Using a simplified background model for KamLAND, we show that KamNet outperforms a conventional convolutional neural network (CNN) on benchmarking Monte Carlo simulations with an increasing level of robustness. Using simulated data, we then demonstrate KamNet's ability to increase KamLAND-Zen's sensitivity to 0ν⁢ββ and 2⁢ν⁢β⁢β decay to excited states. A key component of this work is the addition of an attention mechanism to elucidate the underlying physics KamNet is using for the background rejection.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗