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DOE OSTI2023

Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks to segment the leaf body and visible venation of 2,906 Populus trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (a) does not require experimental or image preprocessing, (b) uses the raw RGB images at full resolution, and (c) requires very few samples for training (e.g., just 8 images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (a) methods for fast and accurate image-based feature extraction that require minimal training data and (b) a new population-scale dataset, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Deep Learning Parameterization of Vertical Wind Velocity Variability via Constrained Adversarial Training

Atmospheric models with typical resolution in the tenths of kilometers cannot resolve the dynamics of air parcel ascent, which varies on scales ranging from tens to hundreds of meters. Small-scale wind fluctuations are thus characterized by a subgrid distribution of vertical wind velocity W with standard deviation σ W . The parameterization of σ W is fundamental to the representation of aerosol–cloud interactions, yet it is poorly constrained. Using a novel deep learning technique, this work develops a new parameterization for σ W merging data from global storm-resolving model simulations, high-frequency retrievals of W , and climate reanalysis products. The parameterization reproduces the observed statistics of σ W and leverages learned physical relations from the model simulations to guide extrapolation beyond the observed domain. Incorporating observational data during the training phase was found to be critical for its performance. The parameterization can be applied online within large-scale atmospheric models, or offline using output from weather forecasting and reanalysis products.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Understanding the Spatial Organization of Simultaneous Heavy Precipitation Events Over the Conterminous United States

We introduce the idea of simultaneous heavy precipitation events (SHPEs) to understand whether extreme precipitation has a spatial organization manifested as specified tracks or contiguous fields with inherent scaling relationships. For this purpose, we created a database of SHPEs using ground-based precipitation observations recorded by the daily Global Historical Climatology Network across the conterminous United States during 1900–2014. SHPEs are examined for their seasonality, spatial manifestation, orientation, and areal extent. We quantified the spatial distribution of the centroids and principal axes of SHPEs and their quasi-elliptical manifestations, azimuthal orientations, and areal extents on the ground. Four seasons, December-January-February (DJF), March-April-May (MAM),June-July-August (JJA), and September-October-November (SON) are considered to examine the spatial patterns and associated large-scale atmospheric circulations. Results indicate that there are 54, 58, 103, and204 SHPEs in DJF, MAM, JJA, and SON seasons, and their longest stretches range on average between 650and 1,600, between 850 and 1,500, between 950 and 1,550, and between 750 and 1,450 km, respectively. SHPEs in the DJF, MAM, and JJA seasons occur mostly over the Pacific coast and central and midwestern United States, respectively. The atmospheric circulation patterns and mechanisms of precipitable water vapor and moisture transport in the atmosphere are also discussed in relation to these SHPEs. Power laws explain SHPEs' underlying area scaling behavior in all the four seasons, with stronger evidence in DJF and MAM. A seasonal spatial risk model is developed to predict the likelihood of SHPEs. Quantifying the characteristics of SHPEs and modeling their footprints can improve the projections of flood risk and understanding of damages to interconnected infrastructure systems.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Ultra-low-density digitally architected carbon with a strutted tube-in-tube structure

Porous materials with engineered stretching-dominated lattice designs, which offer attractive mechanical properties with ultra-light weight and large surface area for wide-ranging applications, have recently achieved near-ideal linear scaling between stiffness and density. Here, rather than optimizing the microlattice topology, we explore a different approach to strengthen low-density structural materials by designing tube-in-tube beam structures. We develop a process to transform fully dense, three-dimensional printed polymeric beams into graphitic carbon hollow tube-in-tube sandwich morphologies, where, similar to grass stems, the inner and outer tubes are connected through a network of struts. Compression tests and computational modelling show that this change in beam morphology dramatically slows down the decrease in stiffness with decreasing density. In situ pillar compression experiments further demonstrate large deformation recovery after 30–50% compression and high specific damping merit index. Lastly, our strutted tube-in-tube design opens up the space and realizes highly desirable high modulus–low density and high modulus–high damping material structures.

36 MATERIALS SCIENCE↗

DOE OSTI2023

EPiC-GAN: Equivariant point cloud generation for particle jets

With the vast data-collecting capabilities of current and future high-energy collider experiments, there is an increasing demand for computationally efficient simulations. Generative machine learning models enable fast event generation, yet so far these approaches are largely constrained to fixed data structures and rigid detector geometries. In this paper, we introduce EPiC-GAN - equivariant point cloud generative adversarial network - which can produce point clouds of variable multiplicity. This flexible framework is based on deep sets and is well suited for simulating sprays of particles called jets. The generator and discriminator utilize multiple EPiC layers with an interpretable global latent vector. Crucially, the EPiC layers do not rely on pairwise information sharing between particles, which leads to a significant speed-up over graph- and transformer-based approaches with more complex relation diagrams. We demonstrate that EPiC-GAN scales well to large particle multiplicities and achieves high generation fidelity on benchmark jet generation tasks.

Buhmann, Erik↗

DOE OSTI2021

ForSE: A GAN-based Algorithm for Extending CMB Foreground Models to Subdegree Angular Scales

We present ForSE (Foreground Scale Extender), a novel Python package that aims to overcome the current limitations in the simulation of diffuse Galactic radiation, in the context of cosmic microwave background (CMB) experiments. ForSE exploits the ability of generative adversarial neural networks (GANs) to learn and reproduce complex features present in a set of images, with the goal of simulating realistic and non-Gaussian foreground radiation at subdegree angular scales. This is of great importance in order to estimate the foreground contamination to lensing reconstruction, delensing, and primordial B-modes for future CMB experiments. We applied this algorithm to Galactic thermal dust emission in both total intensity and polarization. Our results show how ForSE is able to generate small-scale features (at 12') having as input the large-scale ones (80'). The injected structures have statistical properties, evaluated by means of the Minkowski functionals, in good agreement with those of the real sky and which show the correct amplitude scaling as a function of the angular dimension. Furthermore, the obtained thermal dust Stokes Q and U full-sky maps as well as the ForSE package are publicly available for download.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2023

A GPU-Accelerated Population Generation, Sorting, and Mutation Kernel for an Optimization-Based Causal Inference Model

We develop a GPU-accelerated machine learning generative adversarial network model that can be used with observational data for the purpose of constructing causal inferences. The theoretical basis of our machine learning model is novel and is conceptualized to be operable and scalable for high performance computing platforms. Our GPU-accelerated code enables large-scale parallelization of the computation within a common and accessible computing environment. This will expand the reach of our model and empower research in new substantive domains while maintaining the underlying theoretical properties.

Cho, Wendy K. Tam↗

DOE OSTI2021

Data for Adoption of Perennial Energy Crops in the U.S. Midwest, Causal and Heterogeneous Determinants

The success of a bioenergy policy relies largely on the wide adoption of perennial energy crops at the farm scale. This study uses survey data to examine potential adoption decisions by farmers in the U.S. Midwest and the causal effects of various direct and indirect influencing factors, especially heterogeneous preferences of farmers. A Bayesian network (BN) model is developed to delineate the causal relationship between farmers adoption decisions and the influencing factors. We find a dominating role of economic factors and a non-negligible impact of non-economic factors, such as the perceived environmental benefits and the extent of familiarity with perennial energy crops. To examine the effect of heterogeneity in farmer preferences, we classify the surveyed farmers into four categories based on their attitudes toward the economic, social, and environmental dimensions of perennial energy crops. We identified statistically significant between-group differences in the responses of the four types of farmers to the various influencing factors. Our findings contribute to disentangling the complicated motivations that will influence perennial energy crop adoption decisions and provide implications for more targeted policy development that need to consider the heterogeneous drivers of farmer decisions about land use.

Modeling↗

DOE OSTI2024

Addressing GPU memory limitations for Graph Neural Networks in High-Energy Physics applications

Introduction Reconstructing low-level particle tracks in neutrino physics can address some of the most fundamental questions about the universe. However, processing petabytes of raw data using deep learning techniques poses a challenging problem in the field of High Energy Physics (HEP). In the Exa.TrkX Project, an illustrative HEP application, preprocessed simulation data is fed into a state-of-art Graph Neural Network (GNN) model, accelerated by GPUs. However, limited GPU memory often leads to Out-of-Memory (OOM) exceptions during training, due to the large size of models and datasets. This problem is exacerbated when deploying models on High-Performance Computing (HPC) systems designed for large-scale applications. Methods We observe a high workload imbalance issue during GNN model training caused by the irregular sizes of input graph samples in HEP datasets, contributing to OOM exceptions. We aim to scale GNNs on HPC systems, by prioritizing workload balance in graph inputs while maintaining model accuracy. Our paper introduces diverse balancing strategies aimed at decreasing the maximum GPU memory footprint and avoiding the OOM exception, across various datasets. Results Our experiments showcase memory reduction of up to 32.14% compared to the baseline. We also demonstrate the proposed strategies can avoid OOM in application. Additionally, we create a distributed multi-GPU implementation using these samplers to demonstrate the scalability of these techniques on the HEP dataset. Discussion By assessing the performance of these strategies as data loading samplers across multiple datasets, we can gauge their effectiveness in both single-GPU and distributed environments. Our experiments, conducted on datasets of varying sizes and across multiple GPUs, broaden the applicability of our work to various GNN applications that handle input datasets with irregular graph sizes.

Lee, Claire Songhyun↗

DOE OSTI2023

Skyrmion‐Excited Spin‐Wave Fractal Networks

Magnetic skyrmions exhibit unique, technologically relevant pseudo-particle behaviors which arise from their topological protection, including well-defined, 3D dynamic modes that occur at microwave frequencies. During dynamic excitation, spin waves are ejected into the interstitial regions between skyrmions, creating the magnetic equivalent of a turbulent sea. However, since the spin waves in these systems have a well-defined length scale, and the skyrmions are on an ordered lattice, ordered structures from spin-wave interference can precipitate from the chaos. This work uses small-angle neutron scattering (SANS) to capture the dynamics in hybrid skyrmions and investigate the spin-wave structure. Performing simultaneous ferromagnetic resonance and SANS, the diffraction pattern shows a large increase in low-angle scattering intensity, which is present only in the resonance condition. This scattering pattern is best fit using a mass fractal model, which suggests the spin waves form a long-range fractal network. The fractal structure is constructed of fundamental units with a size that encodes the spin-wave emissions and are constrained by the skyrmion lattice. Furthermore, these results offer critical insights into the nanoscale dynamics of skyrmions, identify a new dynamic spin-wave fractal structure, and demonstrate SANS as a unique tool to probe high-speed dynamics.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Adoption of perennial energy crops in the US Midwest: Causal and heterogeneous determinants

The success of a bioenergy policy relies largely on the wide adoption of perennial energy crops at the farm-scale. This study uses survey data to examine potential adoption decisions by farmers in the US Midwest and the causal effects of various direct and indirect influencing factors, especially heterogeneous preferences of farmers. A Bayesian network (BN) model is developed to delineate the causal-relationship between farmers adoption decisions and the influencing factors. Here, we find a dominating role of economic factors and a non-negligible impact of non-economic factors, such as the perceived environmental benefits and the extent of familiarity with perennial energy crops. To examine the effect of heterogeneity in farmer preferences, we classify the surveyed farmers into four categories based on their attitudes toward the economic, social, and environmental dimensions of perennial energy crops. We identify statistically significant between-group differences in the responses of the four types of farmers to the various influencing factors. Our findings contribute to disentangling the complicated motivations that will influence perennial energy crop adoption decisions and provide implications for more targeted policy development that need to consider the heterogeneous drivers of farmer decisions about land use.

09 BIOMASS FUELS↗

DOE OSTI2022

Resolving the structure of phage–bacteria interactions in the context of natural diversity

Microbial communities are shaped by viral predators. Yet, resolving which viruses (phages) and bacteria are interacting is a major challenge in the context of natural levels of microbial diversity. Thus, fundamental features of how phage-bacteria interactions are structured and evolve in the wild remain poorly resolved. Here we use large-scale isolation of environmental marine Vibrio bacteria and their phages to obtain estimates of strain-level phage predator loads, and use all-by-all host range assays to discover how phage and host genomic diversity shape interactions. We show that lytic interactions in environmental interaction networks (as observed in agar overlay) are sparse—with phage predator loads being low for most bacterial strains, and phages being host-strain-specific. Paradoxically, we also find that although overlap in killing is generally rare between tailed phages, recombination is common. Together, these results suggest that recombination during cryptic co-infections is an important mode of phage evolution in microbial communities. In the development of phages for bioengineering and therapeutics it is important to consider that nucleic acids of introduced phages may spread into local phage populations through recombination, and that the likelihood of transfer is not predictable based on lytic host range.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A new large-scale suspended sediment model and its application over the United States

Abstract. Suspended sediment plays a vital role in the regional and global cycling of carbon and nutrients by carrying carbon and nutrients from headwaters into lowland rivers and the oceans. Sediment transport through river systems is often fundamentally modified by human activities such as reservoir management. However, a physically based representation of sediment transport is still missing in most existing Earth system models (ESMs), which are essential tools for modeling and predicting Earth system changes. Here, we introduce a multi-process river sediment module for ESMs, which includes (1) hillslope soil erosion and sediment discharge into streams, (2) sediment transport processes through river networks, (3) reservoir operation based on the inflows from upstream areas and water demand from downstream areas, and (4) sediment trapping by reservoirs. All model parameters are estimated a priori without calibration. We apply this new sediment modeling framework to the contiguous United States and validate it against historical observations of monthly streamflow and sediment discharges at 35 river gauges. The model reasonably well captures the long-term balance and seasonal variations of suspended sediment in large river systems. Furthermore, our model results show that suspended sediment discharge in managed rivers is affected more by reservoirs' direct trapping of sediment particles than by their flow regulation. This new sediment module enables future modeling of the transportation and transformation of carbon and nutrients carried by the fine sediment along the river–ocean continuum to close the global carbon and nutrient cycles.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Data efficiency and extrapolation trends in neural network interatomic potentials

Abstract Recently, key architectural advances have been proposed for neural network interatomic potentials (NNIPs), such as incorporating message-passing networks, equivariance, or many-body expansion terms. Although modern NNIP models exhibit small differences in test accuracy, this metric is still considered the main target when developing new NNIP architectures. In this work, we show how architectural and optimization choices influence the generalization of NNIPs, revealing trends in molecular dynamics (MD) stability, data efficiency, and loss landscapes. Using the 3BPA dataset, we uncover trends in NNIP errors and robustness to noise, showing these metrics are insufficient to predict MD stability in the high-accuracy regime. With a large-scale study on NequIP, MACE, and their optimizers, we show that our metric of loss entropy predicts out-of-distribution error and data efficiency despite being computed only on the training set. This work provides a deep learning justification for probing extrapolation and can inform the development of next-generation NNIPs.

36 MATERIALS SCIENCE↗

DOE OSTI2023

An finite element analysis surrogate model with boundary oriented graph embedding approach for rapid design

Abstract In this work, we present a boundary oriented graph embedding (BOGE) approach for the graph neural network to assist in rapid design and digital prototyping. The cantilever beam problem has been solved as an example to validate its potential of providing physical field results and optimized designs using only 10 ms. Providing shortcuts for both boundary elements and local neighbor elements, the BOGE approach can embed unstructured mesh elements into the graph and performs an efficient regression on large-scale triangular-mesh-based finite element analysis (FEA) results, which cannot be realized by other machine-learning-based surrogate methods. It has the potential to serve as a surrogate model for other boundary value problems. Focusing on the cantilever beam problem, the BOGE approach with 3-layer DeepGCN model achieves the regression with mean square error (MSE) of 0.011 706 (2.41% mean absolute percentage error) for stress field prediction and 0.002 735 MSE (with 1.58% elements having error larger than 0.01) for topological optimization. The overall concept of the BOGE approach paves the way for a general and efficient deep-learning-based FEA simulator that will benefit both industry and Computer Aided Design (CAD) design-related areas.

42 ENGINEERING↗

DOE OSTI2022

PythonFOAM: In-situ data analyses with OpenFOAM and Python

Here, we outline the development of a general-purpose Python-based data analysis tool for OpenFOAM. Our implementation relies on the construction of OpenFOAM applications that have bindings to data analysis libraries in Python. Double precision data in OpenFOAM is cast to a NumPy array using the NumPy C-API and Python modules may then be used for arbitrary data analysis and manipulation on flow-field information. We highlight how the proposed wrapper may be used for an in-situ online singular value decomposition (SVD) implemented in Python and accessed from the OpenFOAM solver PimpleFOAM. Here, 'in-situ' refers to a programming paradigm that allows for a concurrent computation of the data analysis on the same computational resources utilized for the partial differential equation solver. In addition, to demonstrate parallel deployments, we deploy a distributed SVD, which collects snapshot data across the ranks of a distributed simulation to compute the global left singular vectors. Crucially, both OpenFOAM and Python share the same message passing interface (MPI) communicator for this deployment which allows Python objects and functions to exchange NumPy arrays across ranks. Subsequently, we provide scaling assessments of this distributed SVD on multiple nodes of Intel Broadwell and KNL architectures for canonical test cases such as the large eddy simulations of a backward facing step and a channel flow at friction Reynolds number of 395. Finally, we demonstrate the deployment of a deep neural network for compressing the flow-field information using an autoencoder to demonstrate an ability to use state-of-the-art machine learning tools in the Python ecosystem.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2021

Cost function dependent barren plateaus in shallow parametrized quantum circuits

Variational quantum algorithms (VQAs) optimize the parameters θ of a parametrized quantum circuit V(θ) to minimize a cost function C. While VQAs may enable practical applications of noisy quantum computers, they are nevertheless heuristic methods with unproven scaling. Here, we rigorously prove two results, assuming V(θ) is an alternating layered ansatz composed of blocks forming local 2-designs. Our first result states that defining C in terms of global observables leads to exponentially vanishing gradients (i.e., barren plateaus) even when V(θ) is shallow. Hence, several VQAs in the literature must revise their proposed costs. On the other hand, our second result states that defining C with local observables leads to at worst a polynomially vanishing gradient, so long as the depth of V(θ) is Ο(logn). Our results establish a connection between locality and trainability. We illustrate these ideas with large-scale simulations, up to 100 qubits, of a quantum autoencoder implementation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

The soil environment is constantly changing due to shifts in soil moisture, nutrient availability and other conditions. To contend with these changes, soil microorganisms have evolved a variety of ways to adapt to environmental perturbations, including regulation of gene expression. However, it is challenging to untangle the complex phenotypic response of the soil to environmental change, partly due to the absence of predictive modeling frameworks that can mechanistically link molecular-level changes in soil microorganisms to a community’s functional phenotypes (or metaphenome). Towards filling this gap, we performed a combined analysis of metabolic and gene co-expression networks to explore how the soil microbiome responded to changes in soil moisture and nutrient conditions and to determine which genes were expressed under a given condition. Our integrated modeling approach revealed previously unknown, but critically important aspects of the soil microbiomes’ response to environmental perturbations. Incorporation of metabolomic and transcriptomic data into metabolic reaction networks identified condition-specific signature genes that are uniquely associated with dry, wet, and glycine-amended conditions. A subsequent gene co-expression network analysis revealed that drought-associated genes occupied more central positions in a network model of the soil community, compared to the genes associated with wet, and glycine-amended conditions. These results indicate the occurrence of system-wide metabolic coordination when soil microbiomes cope with moisture or nutrient perturbations. Importantly, the approach that we demonstrate here to analyze large-scale multi-omics data from a natural soil environment is applicable to other microbiome systems for which multi-omics data are available.

54 ENVIRONMENTAL SCIENCES↗