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DOE OSTI2025

CSGL: chemical synthesis graph learning for molecule representation

Abstract Motivation Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. Results Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. Availability and implementation https://github.com/li-2023/CSGL.

Biochemistry & Molecular Biology↗

DOE OSTI2017

Multi-scale visual analysis of time-varying electrocorticography data via clustering of brain regions

There exists a need for effective and easy-to-use software tools supporting the analysis of complex Electrocorticography (ECoG) data. Understanding how epileptic seizures develop or identifying diagnostic indicators for neurological diseases require the in-depth analysis of neural activity data from ECoG. Such data is multi-scale and is of high spatio-temporal resolution. Comprehensive analysis of this data should be supported by interactive visual analysis methods that allow a scientist to understand functional patterns at varying levels of granularity and comprehend its time-varying behavior. We introduce a novel multi-scale visual analysis system, ECoG ClusterFlow, for the detailed exploration of ECoG data. Our system detects and visualizes dynamic high-level structures, such as communities, derived from the time-varying connectivity network. The system supports two major views: 1) an overview summarizing the evolution of clusters over time and 2) an electrode view using hierarchical glyph-based design to visualize the propagation of clusters in their spatial, anatomical context. We present case studies that were performed in collaboration with neuroscientists and neurosurgeons using simulated and recorded epileptic seizure data to demonstrate our system's effectiveness. ECoG ClusterFlow supports the comparison of spatio-temporal patterns for specific time intervals and allows a user to utilize various clustering algorithms. Neuroscientists can identify the site of seizure genesis and its spatial progression during various the stages of a seizure. Our system serves as a fast and powerful means for the generation of preliminary hypotheses that can be used as a basis for subsequent application of rigorous statistical methods, with the ultimate goal being the clinical treatment of epileptogenic zones.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Accurate Characterization of Real Networks from Inaccurate Measurements

Our nation's dependence on information networks makes it vital to anticipate disruptions or find weaknesses in these networks. But networks like the Internet are vast, distributed, and there is no mechanism to completely collect their structure. We are restricted to specific data collection schemes (like traceroute samples from router interfaces) that examine tiny portions of such a network. It has been empirically documented and theoretically proven that these measurements have significant biases, and direct inferences from them will be wrong. But these data collection mechanisms have limited flexibility and cannot be easily modified. Moreover, in many applications there are limits on how much data can be collected. How do we make accurate inferences of network properties with biased and limited measurements? The general problem this report deals with is how to work with incompletely observed networks. We will present several different approaches to this problem. First we will present an approach to estimate the degree distribution of a graph by sampling only a small portion of the vertices. This algorithm provides provably accurate results with sublinear samples. An alternative approach would be to try to enhance the information in the by selective collecting new information by probing for neighbors of a vertex or presence of individual edges. A different setting for working with incomplete arises when we have full access to local information, but do not have any global version of the graph. Can we still identify critical nodes in such a graph? We present an approach to identify such nodes efficiently. Finally, how can we put these ideas together to identify the structure of a network? We present an approach that can complement the existing approaches for network mapping. We start with an estimate of network structure based on existing network mapping methods. Then we find a critical router in the network, use the traffic through this network to selectively collect new data to enhance our prediction.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1990

Performability analysis using semi-Markov reward processes

Beaudry (1978) proposed a simple method of computing the distribution of performability in a Markov reward process. Two extensions of Beaudry's approach are presented. The method is generalized to a semi-Markov reward process by removing the restriction requiring the association of zero reward to absorbing states only. The algorithm proceeds by replacing zero-reward nonabsorbing states by a probabilistic switch; it is therefore related to the elimination of vanishing states from the reachability graph of a generalized stochastic Petri net and to the elimination of fast transient states in a decomposition approach to stiff Markov chains. The use of the approach is illustrated with three applications.

Ciardo, Gianfranco↗

NASA NTRS2012

Jupiter Environment Tool

The Jupiter Environment Tool (JET) is a custom UI plug-in for STK that provides an interface to Jupiter environment models for visualization and analysis. Users can visualize the different magnetic field models of Jupiter through various rendering methods, which are fully integrated within STK s 3D Window. This allows users to take snapshots and make animations of their scenarios with magnetic field visualizations. Analytical data can be accessed in the form of custom vectors. Given these custom vectors, users have access to magnetic field data in custom reports, graphs, access constraints, coverage analysis, and anywhere else vectors are used within STK.

Sturm, Erick J.↗

DOE OSTI2013

A Flow-Channel Analysis for the Mars Hopper

The Mars Hopper is an exploratory vehicle designed to fly on Mars using carbon dioxide from the Martian atmosphere as a rocket propellant. The propellent gasses are thermally heated while traversing a radioisotope ther- mal rocket (RTR) engine’s core. This core is comprised of a radioisotope surrounded by a heat capacitive material interspersed with tubes for the propellant to travel through. These tubes, or flow channels, can be manu- factured in various cross-sectional shapes such as a special four-point star or the traditional circle. Analytical heat transfer and computational fluid dynamics (CFD) anal- yses were performed using flow channels with either a circle or a star cross- sectional shape. The nominal total inlet pressure was specified at 2,805,000 Pa; and the outlet pressure was set to 2,785,000 Pa. The CO2 inlet tem- perature was 300 K; and the channel wall was 1200 K. The steady-state CFD simulations computed the smooth-walled star shape’s outlet temper- ature to be 959 K on the finest mesh. The smooth-walled circle’s outlet temperature was 902 K. A circle with a surface roughness specification at 0.01 mm gave 946 K and at 0.1 mm yielded 989 K. The The effects of a slightly varied inlet pressure were also examined. The analytical calculations were based on the mass flow rates computed in the CFD simulations and provided significantly higher outlet temperature results while displaying the same comparison trends. Research relating to the flow channel heat transfer studies was also done. Mathematical methods to geometrically match the cross-sectional areas of the circle and star, along with a square and equilateral triangle, were derived. A Wolfram Mathematica 8 module was programmed to analyze CFD results using Richardson Extrapolation and calculate the grid convergence index (GCI). A Mathematica notebook, also composed, computes and graphs the bulk mean temperature along a flow channel’s length while the user dynam- ically provides the input variables, allowing their effects on the temperature to be more easily observed.

33 ADVANCED PROPULSION SYSTEMS↗

DOE OSTI2023

Scalable Incremental Checkpointing using GPU-Accelerated De-Duplication

Writing large amounts of data concurrently to stable storage is a typical I/O pattern of many HPC workflows. This pattern introduces high I/O overheads and results in increased storage space utilization especially for workflows that need to capture the evolution of data structures with high frequency as checkpoints. In this context, many applications, such as graph pattern matching, perform sparse updates to large data structures between checkpoints. For these applications, incremental checkpointing techniques that save only the differences from one checkpoint to another can dramatically reduce the checkpoint sizes, I/O bottlenecks, and storage space utilization. However, such techniques are not without challenges: it is non-trivial to transparently determine what data has changed since a previous checkpoint and assemble the differences in a compact fashion that does not result in excessive metadata. State-of-art data reduction techniques (e.g., compression and de-duplication) have significant limitations when applied to modern HPC applications that leverage GPUs: slow at detecting the differences, generate a large amount of metadata to keep track of the differences, and ignore crucial spatiotemporal checkpoint data redundancy. This paper addresses these challenges by proposing a Merkle tree-based incremental checkpointing method to exploit GPUs' high memory bandwidth and massive parallelism. Experimental results at scale show a significant reduction of the I/O overhead and space utilization of checkpointing compared with state-of-the-art incremental checkpointing and compression techniques.

Tan, Nigel↗

DOE OSTI2020

A conservative, consistent, and scalable meshfree mimetic method

Mimetic methods discretize divergence by restricting the Gauss theorem to mesh cells. Because point clouds lack such geometric entities, construction of a compatible meshfree divergence remains a challenge. In this work, we define an abstract Meshfree Mimetic Divergence (MMD) operator on point clouds by contraction of field and virtual face moments. This MMD satisfies a discrete divergence theorem, provides a discrete local conservation principle, and is first-order accurate. We consider two MMD instantiations. The first one assumes a background mesh and uses generalized moving least squares (GMLS) to obtain the necessary field and face moments. This MMD instance is appropriate for settings where a mesh is available but its quality is insufficient for a robust and accurate mesh-based discretization. The second MMD operator retains the GMLS field moments but defines virtual face moments using computationally efficient weighted graph-Laplacian equations. This MMD instance does not require a background grid and is appropriate for applications where mesh generation creates a computational bottleneck. It allows one to trade an expensive mesh generation problem for a scalable algebraic one, without sacrificing compatibility with the divergence operator. We demonstrate the approach by using the MMD operator to obtain a virtual finite-volume discretization of conservation laws on point clouds. Finally, numerical results in the paper confirm the mimetic properties of the method and show that it behaves similarly to standard finite volume methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2025

Geometric GNNs for charged particle tracking at GlueX

Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a point cloud and can be structured as graphs, graph neural networks (GNNs) emerge as an intuitive and effective choice for this task. In this study, we evaluate the GNN model for track finding on the data from the GlueX experiment at Jefferson Lab. We use simulation data to train the model and test on both simulation and real GlueX measurements. We demonstrate that GNN-based track finding outperforms the currently used traditional method at GlueX in terms of segment-based efficiency at a fixed purity while providing faster inferences. We show that the GNN model can achieve significant speedup by processing multiple events in batches, which exploits the parallel computation capability of graphical processing units (GPUs). Finally, we compare the GNN implementation on GPU and field-programmable gate array and describe the trade-off.

batched GNN pipeline↗

DOE OSTI2026

Energy-Screened Many-Body Expansion for Protein–Ligand Interactions: Examining Convergence for Metalloenzymes Through Seven–Body Interactions

Fragment-based quantum chemistry is a powerful strategy for calculating protein−ligand interaction energies using quantum chemistry methods. Rigorous convergence often requires hundreds of atoms in the protein binding-site model, especially if that model is constructed using distance-based criteria to select amino acid residues, while three- and four-body calculations exhibit instability related to combinatorial proliferation in the number of subsystem calculations. Here, we report an energy-based screening protocol for the many-body expansion applied to protein−ligand interactions, implemented in the open-source FRAGME∩T code. Using a combination of aggressive screening based on semiempirical quantum chemistry, with an improved graph-theoretical algorithm to eliminate unimportant subsystems, we are able to perform n-body calculations up to n = 7 using density functional theory in triple-ζ basis sets. Distance cutoffs further reduce the cost without compromising accuracy. Rapid and stable convergence of the many-body expansion is obtained by n = 4, for a pair of metalloenzymes in which a divalent ion coordinates directly to the ligand. As compared to previous results that relied solely on distance cutoffs, oscillations in the n-body corrections are reduced or eliminated, although residual errors remain in one case. This work demonstrates that benchmark-quality protein−ligand interaction energies can be systematically converged using a method with excellent parallel efficiency and scalability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1990

Thematic Conference on Remote Sensing for Exploration Geology - Methods, Integration, Solutions, 7th, Calgary, Canada, Oct. 2-6, 1989, Proceedings. Volumes 1 & 2

Recent advances in airborne and satellite remote-sensing technology for application to geological exploration are discussed in reviews and reports. Sections are devoted to basement tectonics and their surface expressions, spectral geology, hydrocarbon exploration applications, radar applications and future systems, engineering and environment issues, geobotanical remote sensing, advanced image processing, data integration and mapping, and mineral exploration. Extensive diagrams, graphs, and sample images are provided.

Source record↗

DOE OSTI2019

An Agile Design-to-Simulation Workflow Using a New Conforming Moving Least Squares Method

This report summarizes the accomplishments and challenges of a two year LDRD effort focused on improving design-to-simulation agility. The central bottleneck in most solid mechanics simulations is the process of taking CAD geometry and creating a discretization of suitable quality, i.e., the "meshing" effort. This report revisits meshfree methods and documents some key advancements that allow their use on problems with complex geometries, low quality meshes, nearly incompressible materials or that involve fracture. The resulting capability was demonstrated to be an effective part of an agile simulation process by enabling rapid discretization techniques without increasing the time to obtain a solution of a given accuracy. The first enhancement addressed boundary-related challenges associated with meshfree methods. When using point clouds and Euclidean metrics to construct approximation spaces, the boundary information is lost, which results in low accuracy solutions for non-convex geometries and mate rial interfaces. This also complicates the application of essential boundary conditions. The solution involved the development of conforming window functions which use graph and boundary information to directly incorporate boundaries into the approximation space.

42 ENGINEERING↗

NASA NTRS1995

Model checking

Automatic formal verification methods for finite-state systems, also known as model-checking, successfully reduce labor costs since they are mostly automatic. Model checkers explicitly or implicitly enumerate the reachable state space of a system, whose behavior is described implicitly, perhaps by a program or a collection of finite automata. Simple properties, such as mutual exclusion or absence of deadlock, can be checked by inspecting individual states. More complex properties, such as lack of starvation, require search for cycles in the state graph with particular properties. Specifications to be checked may consist of built-in properties, such as deadlock or 'unspecified receptions' of messages, another program or implicit description, to be compared with a simulation, bisimulation, or language inclusion relation, or an assertion in one of several temporal logics. Finite-state verification tools are beginning to have a significant impact in commercial designs. There are many success stories of verification tools finding bugs in protocols or hardware controllers. In some cases, these tools have been incorporated into design methodology. Research in finite-state verification has been advancing rapidly, and is showing no signs of slowing down. Recent results include probabilistic algorithms for verification, exploitation of symmetry and independent events, and the use symbolic representations for Boolean functions and systems of linear inequalities. One of the most exciting areas for further research is the combination of model-checking with theorem-proving methods.

Dill, David L.↗

DOE OSTI2020

ExpoKids: An R-based tool for characterizing aggregate chemical exposure during childhood

Background: Aggregate exposure, the combined exposures to a single chemical from all pathways, is a critical children’s health issue. Objective: The primary objective is to develop a tool to illustrate potential differences in aggregate exposure at various childhood lifestages and the adult lifestage. Methods: We developed ExpoKids (an R-based tool) using oral exposure estimates across lifestages generated by US EPA’s Exposure Factors Interactive Resource for Scenarios Tool (ExpoFIRST). Results: ExpoKids is applied to illustrate aggregate oral exposure, for ten media, as average daily doses (ADD) and lifetime average daily doses (LADD) in five graphs organized across seven postnatal childhood lifestages and the adult lifestage. This data visualization tool conveys ExpoFIRST findings, from available exposure data, to highlight the relative contributions of media and lifestages to chemical exposure. To evaluate the effectiveness of ExpoKids, three chemical case examples (di[2-ethylhexyl] phthalate [DEHP], manganese, and endosulfan) were explored. Data available from the published literature and databases for each case example were used to explore research questions regarding media and lifestage contributions to aggregate exposure. Significance: These illustrative case examples demonstrate ExpoKids’ versatile application to explore a diverse set of children’s health risk assessment and management questions by visually depicting specific media and lifestage contributions to aggregate exposure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Enhancing stability, magnetic anisotropy, and coercivity of manganese aluminum: Machine learning, ab initio , and micromagnetic modeling

The binary manganese aluminum (MnAl) alloy with L⁢1 0 crystal structure is a promising rare earth (RE) element-free permanent magnetic material because of its exceptional magnetic properties. However, experimentally synthesizing it in a stable bulk form is extremely challenging. Here, in this study, an alternative method of stabilizing the material, a pathway for experimental synthesis and validation, is proposed and theoretically verified. This is done by partially substituting Mn and Al sites with Fe and Ni and identifying its enhanced phase stability, saturation magnetization density, magnetic anisotropy, and coercivity from density functional theory (DFT), machine learning (ML) crystal graph convolution neural network (CGCNN), and micro-magnetic modeling. When considering a fixed 50% Ni, the magnetic anisotropy increases with the increasing Fe content but decreases the formation energy. The calculated formation energies, elastic constants, and phonon frequencies demonstrate that the binary and quaternary compositions are stable. Most importantly, in 50% Fe and Ni-substituted-equiatomic phase, magnetic anisotropy constants and saturation magnetization density increase by 56% and 23% as compared to the MnAl. Further, the coercivity of the equiatomic phase predicted with micro-magnetic modeling is higher by 17% than the parent compound.

Bhandari, Churna [Ames National Laboratory, and Io↗

DOE OSTI2015

SU-E-T-250: Determining VMAT Machine Limitations of An Elekta Linear Accelerator with Agility MLC for Accurate Modeling in RayStation and Robust Delivery

Purpose: To implement VMAT in RayStation with the Elekta Synergy linac with the new Agility MLC, and to utilize the same vendor softwares to determine the optimum Elekta VMAT machine parameters in RayStation for accurate modeling and robust delivery. Methods: iCOMCat is utilized to create various beam patterns with user defined dose rate, gantry, MLC and jaw speed for each control point. The accuracy and stability of the output and beam profile are qualified for each isolated functional component of VMAT delivery using ion chamber and Profiler2 with isocentric mounting fixture. Service graphing on linac console is used to verify the mechanical motion accuracy. The determined optimum Elekta VMAT machine parameters were configured in RayStation v4.5.1. To evaluate the system overall performance, TG-119 test cases and nine retrospective VMAT patients were planned on RayStation, and validated using both ArcCHECK (with plug and ion chamber) and MapCHECK2. Results: Machine output and profile varies <0.3% when only variable is dose rate (35MU/min-600MU/min). <0.9% output and <0.3% profile variation are observed with additional gantry motion (0.53deg/s–5.8deg/s both directions). The output and profile variation are still <1% with additional slow leaf motion (<1.5cm/s both direction). However, the profile becomes less symmetric, and >1.5% output and 7% profile deviation is seen with >2.5cm/s leaf motion. All clinical cases achieved comparable plan quality as treated IMRT plans. The gamma passing rate is 99.5±0.5% on ArcCheck (<3% iso center dose deviation) and 99.1±0.8% on MapCheck2 using 3%/3mm gamma (10% lower threshold). Mechanical motion accuracy in all VMAT deliveries is <1°/1mm. Conclusion: Accurate RayStation modeling and robust VMAT delivery is achievable on Elekta Agility for <2.5cm/s leaf motion and full range of dose rate and gantry speed determined by the same vendor softwares. Our TG-119 and patient results have provided us with the confidence to use VMAT clinically.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1994

An Interactive Educational Tool for Compressible Aerodynamics

A workstation-based interactive educational tool was developed to aid in the teaching of undergraduate compressible aerodynamics. The tool solves for the supersonic flow past a wedge using the equations found in NACA 1135. The student varies the geometry or flow conditions through a graphical user interface and the new conditions are calculated immediately. Various graphical formats present the variation of flow results to the student. One such format leads the student to the generation of some of the graphs found in NACA-1135. The tool includes interactive questions and answers to aid in both the use of the tool and to develop an understanding of some of the complexities of compressible aerodynamics. A series of help screens make the simulator easy to learn and use. This paper will detail the numerical methods used in the tool and describe how it can be used and modified.

Benson, Thomas J.↗

DOE OSTI2024

Data-Driven Unit Commitment Refinement - a Scalable Approach for Complex Modern Power Grids

Integration of renewable generation, which is often intermittent and decentralized, substantially increases the stochasticity and complexity of power grid operations. Future power systems planning will require significant computational capability to evaluate balance between demand and supply under varying conditions, both temporally and spatially. The standard approach for generation unit commitment is to use mixed-integer linear programming to find the optimal generation schedule considering ramping and generator constraints. In the future grid this poses computational scalability challenges because generation and demand are not known with certainty due to stochasticity in weather and complexity of the grid. To address this challenge, we present a data-driven unit commitment approach that can efficiently include stochastic weather impacts and contingency considerations to improve unit commitment. Our approach uses graph-based data analytics techniques on solutions to the security constrained (and possibly stochastic) economic dispatch problem to identify potential improvements to a given unit commitment. Recent breakthroughs in fully-parallel stochastic economic dispatch software allow this approach to be scalably deployed. Simulations on synthetic South Carolina and Texas grids show this method can improve grid reliability with security constraints over a set of contingencies, while also meaningfully lowering total generation cost.

Holt, Timothy↗