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DOE OSTI2024

Uncertainty-aware Continuous Implicit Neural Representations for Remote Sensing Object Counting

Many existing object counting methods rely on density map estimation (DME) of the discrete grid representation by decoding extracted image semantic features from designed convolutional neural networks (CNNs). Relying on discrete density maps not only leads to information loss dependent on the original image resolution, but also has a scalability issue when analyzing high-resolution images with cubically increasing memory complexity. Furthermore, none of the existing methods can offer reliable uncertainty quantification (UQ) for the derived count estimates. To overcome these limitations, we design UNcertainty-aware, hypernetwork-based Implicit neural representations for Counting (UNIC) to assign probabilities and the corresponding counting confidence over continuous spatial coordinates. We derive a sampling-based Bayesian counting loss function and develop the corresponding model training algorithm. UNIC outperforms existing methods on the Remote Sensing Object Counting (RSOC) dataset with reliable UQ and improved interpretability of the derived count estimates. Our code is available at https://github.com/SiyuanXu-tamu/UNIC.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1995

A 3D High-Order Unstructured Finite-Volume Algorithm for Solving Maxwell's Equations

A three-dimensional finite-volume algorithm based on arbitrary basis functions for time-dependent problems on general unstructured grids is developed. The method is applied to the time-domain Maxwell equations. Discrete unknowns are volume integrals or cell averages of the electric and magnetic field variables. Spatial terms are converted to surface integrals using the Gauss curl theorem. Polynomial basis functions are introduced in constructing local representations of the fields and evaluating the volume and surface integrals. Electric and magnetic fields are approximated by linear combinations of these basis functions. Unlike other unstructured formulations used in Computational Fluid Dynamics, the new formulation actually does not reconstruct the field variables at each time step. Instead, the spatial terms are calculated in terms of unknowns by precomputing weights at the beginning of the computation as functions of cell geometry and basis functions to retain efficiency. Since no assumption is made for cell geometry, this new formulation is suitable for arbitrarily defined grids, either smooth or unsmooth. However, to facilitate the volume and surface integrations, arbitrary polyhedral cells with polygonal faces are used in constructing grids. Both centered and upwind schemes are formulated. It is shown that conventional schemes (second order in Cartesian grids) are equivalent to the new schemes using first degree polynomials as the basis functions and the midpoint quadrature for the integrations. In the new formulation, higher orders of accuracy are achieved by using higher degree polynomial basis functions. Furthermore, all the surface and volume integrations are carried out exactly. Several model electromagnetic scattering problems are calculated and compared with analytical solutions. Examples are given for cases based on 0th to 3rd degree polynomial basis functions. In all calculations, a centered scheme is applied in the interior, while an upwind matching scheme is employed at material interfaces and the Engquist-Majda non-reflecting boundary condition is implemented at the numerical outer boundaries. The staggered leapfrog scheme and the Runge-Kutta methods are utilized for the time integration. Excellent agreements are found between the numerical and analytical solutions.

Liu, Yen↗

NASA NTRS2013

Evaluation of MODIS Albedo Product (MCD43A) over Grassland, Agriculture and Forest Surface Types During Dormant and Snow-Covered Periods

This study assesses the Moderate-resolution Imaging Spectroradiometer (MODIS) BRDF/albedo 8 day standard product and products from the daily Direct Broadcast BRDF/albedo algorithm, and shows that these products agree well with ground-based albedo measurements during the more difficult periods of vegetation dormancy and snow cover. Cropland, grassland, deciduous and coniferous forests are considered. Using an integrated validation strategy, analyses of the representativeness of the surface heterogeneity under both dormant and snow-covered situations are performed to decide whether direct comparisons between ground measurements and 500-m satellite observations can be made or whether finer spatial resolution airborne or spaceborne data are required to scale the results at each location. Landsat Enhanced Thematic Mapper Plus (ETM +) data are used to generate finer scale representations of albedo at each location to fully link ground data with satellite data. In general, results indicate the root mean square errors (RMSEs) are less than 0.030 over spatially representative sites of agriculture/grassland during the dormant periods and less than 0.050 during the snow-covered periods for MCD43A albedo products. For forest, the RMSEs are less than 0.020 during the dormant period and 0.025 during the snow-covered periods. However, a daily retrieval strategy is necessary to capture ephemeral snow events or rapidly changing situations such as the spring snow melt.

MODIS↗

DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure --- this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

DOE OSTI2022

SPATIAL GRAPH ATTENTION AND CURIOSITY-DRIVEN POLICY FOR ANTIVIRAL DRUG DISCOVERY

We developed Distilled Graph Attention Policy Network (DGAPN), a reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention (sGAT) mechanism that leverages self-attention over both node and edge attributes as well as encoding the spatial structure - this capability is of considerable interest in synthetic biology and drug discovery. An attentional policy network is introduced to learn the decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with stability. Exploration is driven by the stochasticity of the action space design and the innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while reducing the complexity of paths to chemical synthesis.

Wu, Y↗

DOE OSTI2021

Protein conformational switch discerned via network centrality properties

Network analysis has emerged as a powerful tool for examining structural biology systems. The spatial organization of the components of a biomolecular structure has been rendered as a graph representation and analyses have been performed to deduce the biophysical and mechanistic properties of these components. For proteins, the analysis of protein structure networks (PSNs), especially via network centrality measurements and cluster coefficients, has led to identifying amino acid residues that play key functional roles and classifying amino acid residues in general. Whether these network properties examined in various studies are sensitive to subtle (yet biologically significant) conformational changes remained to be addressed. Here, we focused on four types of network centrality properties (betweenness, closeness, degree, and eigenvector centralities) for conformational changes upon ligand binding of a sensor protein (constitutive androstane receptor) and an allosteric enzyme (ribonucleotide reductase). We found that eigenvector centrality is sensitive and can distinguish salient structural features between protein conformational states while other centrality measures, especially closeness centrality, are less sensitive and rather generic with respect to the structural specificity. We also demonstrated that an ensembleinformed, modified PSN with static edges removed (which we term PSN*) has enhanced sensitivity at discerning structural changes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Is turning down the sun a good proxy for stratospheric sulfate geoengineering?

Deliberately blocking out a small portion of the incoming solar radiation would cool the climate. One such approach would be injecting SO2 into the stratosphere, which would produce sulfate aerosols that would remain in the atmosphere for 1–3 years, reflecting part of the incoming shortwave radiation. The cooling produced by the aerosols can offset the warming produced by increased greenhouse gas (GHG) concentrations, but it would also affect the climate differently, leading to residual differences compared to a climate not affected by either. Many climate model simulations of geoengineering have used a uniform reduction of the incoming solar radiation as a proxy for stratospheric aerosols, both because many models are not designed to adequately capture relevant stratospheric aerosol processes, and because a solar reduction has often been assumed to capture the most important differences between how stratospheric aerosols and GHG would affect the climate. Here we show that dimming the sun does not produce the same surface climate effects as simulating aerosols in the stratosphere. By more closely matching the spatial pattern of solar reduction to that of the aerosols, some improvements in this idealized representation are possible, with further improvements if the stratospheric heating produced by the aerosols is included. This is relevant both for our understanding of the physical mechanisms driving the changes observed in stratospheric-sulfate geoengineering simulations, and in terms of the relevance of impact assessments that use a uniform solar dimming.

Visioni, Daniele↗

NASA NTRS1971

Spatial transform coding of color images.

The application of the transform-coding concept to the coding of color images represented by three primary color planes of data is discussed. The principles of spatial transform coding are reviewed and the merits of various methods of color-image representation are examined. A performance analysis is presented for the color-image transform-coding system. Results of a computer simulation of the coding system are also given. It is shown that, by transform coding, the chrominance content of a color image can be coded with an average of 1.0 bits per element or less without serious degradation. If luminance coding is also employed, the average rate reduces to about 2.0 bits per element or less.

Pratt, W. K.↗

NASA NTRS1994

Two-Layer Variable Infiltration Capacity Land Surface Representation for General Circulation Models

A simple two-layer variable infiltration capacity (VIC-2L) land surface model suitable for incorporation in general circulation models (GCMs) is described. The model consists of a two-layer characterization of the soil within a GCM grid cell, and uses an aerodynamic representation of latent and sensible heat fluxes at the land surface. The effects of GCM spatial subgrid variability of soil moisture and a hydrologically realistic runoff mechanism are represented in the soil layers. The model was tested using long-term hydrologic and climatalogical data for Kings Creek, Kansas to estimate and validate the hydrological parameters. Surface flux data from three First International Satellite Land Surface Climatology Project Field Experiments (FIFE) intensive field compaigns in the summer and fall of 1987 in central Kansas, and from the Anglo-Brazilian Amazonian Climate Observation Study (ABRACOS) in Brazil were used to validate the mode-simulated surface energy fluxes and surface temperature.

GENERAL CIRCULATION MODELS↗

NASA NTRS2006

Sensing Super-position: Visual Instrument Sensor Replacement

The coming decade of fast, cheap and miniaturized electronics and sensory devices opens new pathways for the development of sophisticated equipment to overcome limitations of the human senses. This project addresses the technical feasibility of augmenting human vision through Sensing Super-position using a Visual Instrument Sensory Organ Replacement (VISOR). The current implementation of the VISOR device translates visual and other passive or active sensory instruments into sounds, which become relevant when the visual resolution is insufficient for very difficult and particular sensing tasks. A successful Sensing Super-position meets many human and pilot vehicle system requirements. The system can be further developed into cheap, portable, and low power taking into account the limited capabilities of the human user as well as the typical characteristics of his dynamic environment. The system operates in real time, giving the desired information for the particular augmented sensing tasks. The Sensing Super-position device increases the image resolution perception and is obtained via an auditory representation as well as the visual representation. Auditory mapping is performed to distribute an image in time. The three-dimensional spatial brightness and multi-spectral maps of a sensed image are processed using real-time image processing techniques (e.g. histogram normalization) and transformed into a two-dimensional map of an audio signal as a function of frequency and time. This paper details the approach of developing Sensing Super-position systems as a way to augment the human vision system by exploiting the capabilities of the human hearing system as an additional neural input. The human hearing system is capable of learning to process and interpret extremely complicated and rapidly changing auditory patterns. The known capabilities of the human hearing system to learn and understand complicated auditory patterns provided the basic motivation for developing an image-to-sound mapping system.

Maluf, David A.↗

NASA NTRSDate not supplied

Regional Impacts of Ice Sheet Surface Representation Improvements in an Earth System Model

Ice sheet surface conditions and their subsequent impact on surface mass balance play an important role in ice sheet dynamics and ice sheet interaction with the overlying atmosphere and surrounding ocean. The NASA Global Modeling and Assimilation Office’s (GMAO) Goddard Earth Observing System (GEOS) ecosystem of models and reanalyses model ice sheet and glacier surface mass balance with a moderately complex snow and ice module, including prognostic surface albedo evolution, fractional snow cover, and snowpack hydrology and meltwater retention. With this configuration, Greenland near surface air temperatures and ice sheet melt are well represented in MERRA-2, GMAO’s current atmospheric reanalysis; however, the similarity to observations in some regions is due, in part, to compensating biases in surface energy budget. Recent improvements to GEOS’ cloud microphysics and longwave radiation parameterizations reduced biases in surface net longwave radiation and exacerbated surface net shortwave radiation biases, effectively increasing near surface temperatures and melting, particularly during the summer months. Here, we demonstrate the Earth system response to an improved representation of the ice sheet surface focused on minimizing the surface energy biases and increasing spatial and temporal representativeness. New changes to the surface albedo parameterization, including the introduction of a prognostic aerosol darkening scheme, help mitigate shortwave biases, while modifications to surface roughness characteristics improve near surface sensible heat fluxes. Focusing on the Arctic and Greenland, we examine the combined impact on these changes on regional weather conditions and ice sheet surface mass balance using a high resolution atmospheric only experiment, and we use a coupled model configuration to assess the impact on oceanic conditions and subseasonal-to-seasonal prediction. Overall, these improvements increase modeled ice sheet surface realism and provide a strong basis for more accurate ice sheet mass balance in GMAO’s future reanalyses and forecasting systems.

Lauren C Andrews↗

NASA NTRSDate not supplied

Regional Impacts of Ice Sheet Surface Representation Improvements in an Earth System Model

Lauren C. Andrews↗

DOE OSTI2020

Development of a Convolutional Neural Network Classifier for Data Starved Spectra - 20199

The Institute for Clean Energy Technology (ICET) at Mississippi State University is exploring the utility of machine learning in augmenting its mobile radiation surveying platforms, which are currently being developed as means to survey depleted uranium contaminated areas in support of remediation and decommissioning efforts. Mobile survey platforms provide a means to efficiently scan large areas of interest while reducing human exposure to radiation and other hazards. The survey platforms can also be used for scanning for any gamma emitting isotope in addition to depleted uranium. The spectral data that the platforms collect may be data starved with relatively low counts and poorly defined spectral features depending on the speed of the platforms and scintillation detector selection. Such data-starved spectra are difficult to use for isotope identification, requiring advanced knowledge of the possible radionuclides that could be present and environmental factors that could attenuate signals or introduce background noise. These factors in combination with the volume of survey data increases the time it takes to perform analysis of survey data when the source type is unknown. There are a number of algorithms in the field of machine learning that can be used to classify data that would be challenging and time-consuming for a human to identify. Supervised machine learning algorithms train models based on extensive amounts of human-labeled training data. Once sufficiently trained, these models can be used to quickly make high-fidelity predictions on new data. Convolutional neural networks are machine learning algorithms that excel in learning representations of 'shapes'. They do this by taking numerical input data and convolving them with spatial feature detectors referred to as filters. These filters are incrementally adjusted to reduce the prediction error on the data during the backpropagation step of training. Discussed in this paper is the development of a convolutional neural network classifier (CNNC) that can utilize spectral survey data for source discrimination and isotope identification. Bench-top laboratory experiments data using LaBr{sub 3}(Ce) scintillation detectors were used to train and evaluate the performance of the developed CNNC. The CNNC is capable of discriminating a variety of gamma emitting source types, differentiating different forms of uranium (depleted vs. natural), and estimating the amount of uranium for a known geometry. The discussed CNNC may be useful in scenarios where survey systems are deployed in situations where hazardous radioactive material maybe present, but the type is unknown. When used in remediation applications the CNNC can be used to screen-out false positives, helping reduce remediation costs. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

DOE OSTI2022

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

DOE OSTI2026

Model data for infrastructure-aware simulation of compound flooding at Alligator Bayou Watershed, southeast Texas

This dataset supports infrastructure-aware hydrologic modeling and flood scenario analysis for the Alligator Bayou Watershed, a highly managed urban watershed in Southeast Texas. It includes Jupyter notebooks for figure reproduction, model configuration files, simulation outputs, and derived products used to quantify the influence of engineered stormwater infrastructure on flood behavior across multiple spatial scales. The dataset was generated using the Watershed Workflow Python package and the Advanced Terrestrial Simulator (ATS), enabling integrated surface–subsurface hydrologic simulations on a channel-aligned mesh with explicit representations of pump stations, gate structures, detention basins, and impervious surfaces. Outputs include time series of gate and pump flows, stage observations, and water balance components, as well as spatially explicit fields of peak ponded depth and flood duration across multiple infrastructure scenarios spanning a single-location detention basin expansion, distributed drainage limitations, and compound coastal flooding. These data facilitate full reproducibility of the manuscript figures and support further research on urban flood dynamics and the role of stormwater infrastructure in shaping watershed-scale flood response.

EARTH SCIENCE > OCEANS > COASTAL PROCESSES↗

DOE OSTI2021

Spatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery

We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. Here, the framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.

Wu, Yulun↗

NASA NTRS2024

Evaluation of a Combined Drought Indicator Against Crop Yield Estimations and Simulations Over the Argentine Humid Pampas

Droughts pose serious threats to the agricultural sector, especially in rainfed-dominated agricultural regions like those in Argentina’s Humid Pampas. This region was recently impacted by slow-evolving and long-lasting droughts as well as by flash droughts, resulting in losses reaching thousands of millions of US dollars. Improvements of drought early warning systems are essential, particularly given the projected increase in drought frequency and severity over southern South America. The spatial and temporal relationship between precipitation deficits, soil moisture and vegetation health anomalies are crucial for better understanding and representation of the agricultural droughts and their impacts. In this context, the Combined Drought Indicator (CDI) considers the causal and time-lagged relationship of these three variables. The study’s objective is twofold: (1) Analyze the time-lagged response between precipitation deficits, soil moisture and satellite fAPAR anomalies; and (2) Evaluate the CDI’s capability to characterize the severity of drought events on the Humid Pampas against agricultural yield estimations and simulations, as well as agricultural emergency declarations. The correlation among the variables shows strong spatial variability. The highest Pearson correlation values (r > 0.42) are observed over parts of the Humid Pampas for time lags of 0, 10, and 20 days between the variables. Although the CDI has limitations, such as its coarse spatial resolution and monthly temporal resolution of precipitation data, it effectively tracks the progression of major drought events in the region. The CDI’s performance aligns well with estimations and simulations of soybean and corn yields, as well as official declarations of agricultural emergencies. Insights from this study also provide a basis for discussing potential improvements to the CDI. This study highlights the global and regional significance of evaluating and enhancing the CDI for effective drought monitoring, emphasizing the role of collaborative efforts for future advancements in drought early warning systems.

Combined Drought Indicator↗

DOE OSTI2022

CoordNet: Data Generation and Visualization Generation for Time-Varying Volumes via a Coordinate-Based Neural Network

Although deep learning has demonstrated its capability in solving diverse scientific visualization problems, it still lacks generalization power across different tasks. To address this challenge, we propose CoordNet, a single coordinate-based framework that tackles various tasks relevant to time-varying volumetric data visualization without modifying the network architecture. The core idea of our approach is to decompose diverse task inputs and outputs into a unified representation (i.e., coordinates and values) and learn a function from coordinates to their corresponding values. We achieve this goal using a residual block-based implicit neural representation architecture with periodic activation functions. We evaluate CoordNet on data generation (i.e., temporal super-resolution and spatial super-resolution) and visualization generation (i.e., view synthesis and ambient occlusion prediction) tasks using time-varying volumetric data sets of various characteristics. Here, the experimental results indicate that CoordNet achieves better quantitative and qualitative results than the state-of-the-art approaches across all the evaluated tasks. Source code and pre-trained models are available at https://github.com/stevenhan1991/CoordNet.

97 MATHEMATICS AND COMPUTING↗