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At least 721 records · Page 40

Designing Size Consistent Statistics for Accurate Anomaly Detection in Dynamic Networks

An important task in network analysis is the detection of anomalous events in a network time series. These events could merely be times of interest in the network timeline or they could be examples of malicious activity or network malfunction. Hypothesis testing using network statistics to summarize the behavior of the network provides a robust framework for the anomaly detection decision process. Unfortunately, choosing network statistics that are dependent on confounding factors like the total number of nodes or edges can lead to incorrect conclusions (e.g., false positives and false negatives). In this article, we describe the challenges that face anomaly detection in dynamic network streams regarding confounding factors. We also provide two solutions to avoiding error due to confounding factors: the first is a randomization testing method that controls for confounding factors, and the second is a set of size-consistent network statistics that avoid confounding due to the most common factors, edge count and node count.

97 MATHEMATICS AND COMPUTING↗

Investigation of Structure and Reactivity Relationship in M-N-C Type Catalysts using Density Functional Tight Binding

Catalysts inhibition studies were performed to indisputably confirm the role of various metal, carbon, and nitrogen moieties in the individual steps of oxygen reduction reaction (ORR) on M-N-C catalysts. ORR activity was studied at University of New Mexico by rotating ring disk electrode method in the acidic electrolyte with the addition of Tris (tris(hydroxymethyl)-aminomethane) as inhibiting agent. To understand the interaction of Tris with different defects that exist in Fe-N-C materials and provide the support for the experimental data, we used density functional theory (DFT) and modeled the interaction of protonated Tris (TrisH) with Fe containingcenters (Fe-N 4 and Fe-N 2 C 2 ), pyridinic nitrogen, graphitic nitrogen, and pyrrolic nitrogen both as in plane and edge defects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Portable Data-Parallel Surface Reconstruction on a Uniform Rectilinear Grid

With the increasing heterogeneity and on-node parallelism of high-performance computing hardware, a major challenge is to develop portable and efficient algorithms and software. In this work, we present our implementation of a portable code to perform surface reconstruction using NVIDIA's Thrust library. Surface reconstruction is a technique commonly used in volume tracking methods for simulations of multimaterial flow with interfaces. Here, we have designed a 3D mesh data structure that is easily mapped to the 1D vectors used by Thrust and at the same time is simple to use and uses familiar data structure terminology (such as cells, faces, vertices, and edges). With this new data structure in place, we have implemented a piecewise linear interface reconstruction algorithm in 3 dimensions that effectively exploits the symmetry present in a uniform rectilinear computational cell. Finally, we report performance results, which show that a single implementation of these algorithms can be compiled to multiple backends (specifically, multi-core CPUs, NVIDIA GPUs, and Intel Xeon Phi processors), making efficient use of the available parallelism on each. We also compare performance of our implementation to a legacy FORTRAN implementation in Message Passing Interface (MPI) and show performance parity on single and multi-core CPU and achieved good parallel speed-ups on GPU. In conclusion, our research demonstrates the advantage of performance portability of the underlying data-parallel programming model.

97 MATHEMATICS AND COMPUTING↗

SU-F-R-18: Updates to the Computational Environment for Radiological Research for Image Analysis

Purpose: To present new tools in CERR for Texture Analysis and Visualization. Method: (1) Quantitative Image Analysis: We added the ability to compute Haralick texture features based on local neighbourhood. The Texture features depend on many parameters used in their derivation. For example: (a) directionality, (b) quantization of image, (c) patch-size for the neighborhood, (d) handling of the edge voxels within the region of interest, (e) Averaging co-occurance matrix vs texture features for different directions etc. A graphical user interface was built to set these parameters and then visualize their impact on the resulting texture maps. The entire functionality was written in Matlab. Array indexing was used to speed up the texture calculation. The computation speed is very competitive with the ITK library. Moreover, our implementation works with multiple CPUs and the computation time can be further reduced by using multiple processor threads. In order to reduce the Haralick texture maps into scalar features, we propose the use of Texture Volume Histograms. This lets users make use of the entire distribution of texture values within the region of interest rather than using just the mean and the standard deviations. (2) Qualitative/Visualization tools: The derived texture maps are stored as a new scan (derived) within CERR’s planC data structure. A display that compares various scans was built to show the raw image and the derived texture maps side-by-side. These images are positionally linked and can be navigated together. CERR’s graphics handling was updated and sped-up to be compatible with the newer Matlab versions. As a result, the users can use (a) different window levels and colormaps for different viewports, (b) click-and-drag or use mouse scroll-wheel to navigate slices. Results: The new features and updates are available via https://www.github.com/adityaapte/cerr . Conclusion: Features added to CERR increase its utility in Radiomics and Outcomes modeling.

60 APPLIED LIFE SCIENCES↗

DyG-DPCD: A Distributed Parallel Community Detection Algorithm for Large-Scale Dynamic Graphs

Dynamic (Temporal) graphs capture the valuable evolution of real-world systems, from the continuously evolving patterns of social interactions and genetic pathways to the dynamic fluctuations of economic forces. Detecting communities for such evolving networks poses unique challenges. Detecting and analyzing the evolution of communities within dynamic graphs unlocks valuable insights into the underlying structural and temporal patterns of real-world systems. However, the sheer volume of modern graph data and the inherent complexity of the temporal dimension pose significant challenges to scalable community detection algorithms. Addressing this gap, our work explores the limited landscape of scalable distributed-memory parallel methods specifically designed for dynamic network community detection. We propose a novel parallel algorithm, DyG-DPCD (Dynamic Graph Distributed Parallel Community Detection), to detect communities in dynamic networks using the Message Passing Interface (MPI) framework. We present a vertex-centric approach, allowing us to detect communities through local optimization. Furthermore, we enhance our baseline algorithm by incorporating three heuristics, which improve the algorithm’s performance significantly while maintaining the quality of the solutions. We demonstrate the efficiency of our algorithm by experimenting on several real-world large-scale networks with hundreds of millions of edges spanning diverse domains. Notably, DyG-DPCD achieves speedups between 25× and 30× for large networks that we experimented on using NERSC compute nodes. In conclusion, our algorithm outperforms the STINGER parallel re-agglomeration algorithm by 30×.

97 MATHEMATICS AND COMPUTING↗

Recent Advances in X-ray Absorption Near Edge Structure (XANES) Simulation for Catalysis: Theories and Applications

X-ray absorption spectroscopy (XAS) is a powerful spectroscopic technique for characterizing catalytic active sites. In particular, X-ray Absorption Near Edge Structure (XANES) provides insights into the oxidation state and local coordination environment of the absorbing atom, shedding light on the catalytic structure. Computational XANES simulations provide one-on-one correspondence between the molecular structure and their corresponding spectra, making them an effective approach for interpreting experimental XANES features. This work outlines various theories used to simulate XANES spectra and highlights recent advancements in computational XANES applications for homogeneous, heterogeneous, and single-atom catalysts focusing on identifying the active site structures, the site heterogeneity, and the dynamic evolution of catalysts.

Xu, Jiayi↗

Designing transparent conductors using forbidden optical transitions

Many semiconductors present weak or forbidden transitions at their fundamental band gaps, inducing a widened region of transparency. This occurs in high-performing n-type transparent conductors (TCs) such as Sn-doped In 2 O 3 (ITO); however, thus far, the presence of forbidden transitions has been neglected in the search for new p-type TCs. To address this, we first compute high-throughput absorption spectra across ~18, 000 semiconductors, showing that over half exhibit forbidden or weak optical transitions at their band edges. Next, we demonstrate that compounds with highly localized band-edge states are more likely to present forbidden transitions. Lastly, we search this set for p-type and n-type TCs with forbidden transitions and, by performing defect calculations, propose unexplored TC candidates such as ambipolar BeSiP 2 , p-type wurtzite BAs, and n-type Ba 2 InGaO 5 , among others. In conclusion, we share our dataset and recommend that future screenings for optical properties consider the impact of forbidden transitions.

36 MATERIALS SCIENCE↗

De novo design of proteins housing excitonically coupled chlorophyll special pairs

Natural photosystems couple light harvesting to charge separation using a ‘special pair’ of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C 2 -symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.

59 BASIC BIOLOGICAL SCIENCES↗

Operando structural and chemical evolutions of TiS 2 in Na-ion batteries

Titanium disulfide (TiS 2 ) with high electric conductivity, fast rate capability, and good cycling performance is a promising candidate for electrode material in sodium (Na)-ion batteries. Despite the well-studied electrochemical behaviors of TiS 2 in Li-ion batteries, the detailed reaction mechanism of TiS 2 in Na-ion batteries is not yet fully understood due to a more complex multi-phase conversion process. In this work, reactions of TiS 2 in Na-ion batteries are investigated via a multi-modal synchrotron approach: operando X-ray Absorption Spectroscopy (XAS) – including X-ray Absorption Near-Edge Structure (XANES) and Extended X-ray Absorption Fine Structure (EXAFS) – and ex situ X-ray Powder Diffraction (XPD), coupled with computational modeling. Operando XANES spectra indicate that the redox reactions occur in both Ti and S during the electrochemically driven phase transformation. Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) analysis of XAS suggests that different numbers of components are involved in the lithiation and sodiation of TiS 2 , with the sodiation including at least one intermediate phase in addition to the starting material and the final sodiation product. Ex situ XPD and Rietveld refinement further determined and quantified the unknown phases, showing that three phases, TiS 2 , Na 0.55 TiS 2 , and NaTiS 2 , participate in the sodiation of TiS 2 . Operando EXAFS results show the changes in the Ti–Ti coordination number and interatomic distance. This explains the coulombic efficiency decay due to the incomplete recovery of the coordination number of Ti after cycling. Overall, this work reveals the reaction mechanism occurring in Na–TiS 2 batteries with a greater quantitative understanding of the structural evolution. By combining the multi-modal synchrotron approach and computational work, this study provides a framework for studying a broader range of electrochemically driven phase-transformation systems towards advanced energy storage and conversion applications.

25 ENERGY STORAGE↗

Effect of scrape-off-layer current on reconstructed tokamak equilibrium

Methods are described that extend fields from reconstructed equilibria to include scrape-off-layer current through extrapolated parametrized and experimental fits. The extrapolation includes both the effects of the toroidal-field and pressure gradients which produce scrape-off-layer current after recomputation of the Grad-Shafranov solution. To quantify the degree that inclusion of scrape-off-layer current modifies the equilibrium, the χ-squared goodness-of-fit parameter is calculated for cases with and without scrape-off-layer current. The change in χ-squared is found to be minor when scrape-off-layer current is included however flux surfaces are shifted by up to 3 cm. Here the impact on edge modes of these scrape-off-layer modifications is also found to be small and the importance of these methods to nonlinear computation is discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

End-to-end deep learning pipeline for real-time Bragg peak segmentation: from training to large-scale deployment

X-ray crystallography reconstruction, which transforms discrete X-ray diffraction patterns into three-dimensional molecular structures, relies critically on accurate Bragg peak finding for structure determination. As X-ray free electron laser (XFEL) facilities advance toward MHz data rates (1 million images per second), traditional peak finding algorithms that require manual parameter tuning or exhaustive grid searches across multiple experiments become increasingly impractical. While deep learning approaches offer promising solutions, their deployment in high-throughput environments presents significant challenges in automated dataset labeling, model scalability, edge deployment efficiency, and distributed inference capabilities. We present an end-to-end deep learning pipeline with three key components: (1) a data engine that combines traditional algorithms with our peak matching algorithm to generate high-quality training data at scale, (2) a modular architecture that scales from a few million to hundreds of million parameters, enabling us to train large expert-level models offline while deploying smaller, distilled models at the edge, and (3) a decoupled producer-consumer architecture that separates specialized data source layer from model inference, enabling flexible deployment across diverse computing environments. Using this integrated approach, our pipeline achieves accuracy comparable to traditional methods tuned by human experts while eliminating the need for experiment-specific parameter tuning. Although current throughput requires optimization for MHz facilities, our system's scalable architecture and demonstrated model compression capabilities provide a foundation for future high-throughput XFEL deployments.

Wang, Cong↗

Ergodicity, lack thereof, and the performance of reservoir computing with memristive networks

Abstract Networks composed of nanoscale memristive components, such as nanowire and nanoparticle networks, have recently received considerable attention because of their potential use as neuromorphic devices. In this study, we explore ergodicity in memristive networks, showing that the performance on machine leaning tasks improves when these networks are tuned to operate at the edge between two global stability points. We find this lack of ergodicity is associated with the emergence of memory in the system. We measure the level of ergodicity using the Thirumalai-Mountain metric, and we show that in the absence of ergodicity, two different memristive network systems show improved performance when utilized as reservoir computers (RC). We highlight that it is also important to let the system synchronize to the input signal in order for the performance of the RC to exhibit improvements over the baseline.

97 MATHEMATICS AND COMPUTING↗

Multinode Multi-GPU Two-Electron Integrals: Code Generation Using the Regent Language

The computation of two-electron repulsion integrals (ERIs) is often the most expensive step of integral-direct self-consistent field methods. Formally it scales as O(N 4 ), where N is the number of Gaussian basis functions used to represent the molecular wave function. In practice, this scaling can be reduced to O(N 2 ) or less by neglecting small integrals with screening methods. The contributions of the ERIs to the Fock matrix are of Coulomb (J) and exchange (K) type and require separate algorithms to compute matrix elements efficiently. We previously implemented highly efficient GPU-accelerated J-matrix and K-matrix algorithms in the electronic structure code TeraChem. Although these implementations supported the use of multiple GPUs on a node, they did not support the use of multiple nodes. This presents a key bottleneck to cutting-edge ab initio simulations of large systems, e.g., excited state dynamics of photoactive proteins. We present our implementation of multinode multi-GPU J- and K-matrix algorithms in TeraChem using the Regent programming language. Regent directly supports distributed computation in a task-based model and can generate code for a variety of architectures, including NVIDIA GPUs. We demonstrate multinode scaling up to 45 GPUs (3 nodes) and benchmark against hand-coded TeraChem integral code. Finally, we also outline our metaprogrammed Regent implementation, which enables flexible code generation for integrals of different angular momenta.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A Volcanic Hydrogen Habitable Zone

The classical habitable zone (HZ) is the circular region around a star in which liquid water could exist on the surface of a rocky planet. The outer edge of the traditional N{sub 2}–CO{sub 2}–H{sub 2}O HZ extends out to nearly ∼1.7 au in our solar system, beyond which condensation and scattering by CO{sub 2} outstrips its greenhouse capacity. Here, we show that volcanic outgassing of atmospheric H{sub 2} can extend the outer edge of the HZ to ∼2.4 au in our solar system. This wider volcanic-hydrogen HZ (N{sub 2}–CO{sub 2}–H{sub 2}O–H{sub 2}) can be sustained as long as volcanic H{sub 2} output offsets its escape from the top of the atmosphere. We use a single-column radiative-convective climate model to compute the HZ limits of this volcanic hydrogen HZ for hydrogen concentrations between 1% and 50%, assuming diffusion-limited atmospheric escape. At a hydrogen concentration of 50%, the effective stellar flux required to support the outer edge decreases by ∼35%–60% for M–A stars. The corresponding orbital distances increase by ∼30%–60%. The inner edge of this HZ only moves out ∼0.1%–4% relative to the classical HZ because H{sub 2} warming is reduced in dense H{sub 2}O atmospheres. The atmospheric scale heights of such volcanic H{sub 2} atmospheres near the outer edge of the HZ also increase, facilitating remote detection of atmospheric signatures.

79 ASTRONOMY AND ASTROPHYSICS↗

Enhancing the accuracy of XPS calculations: Exploring hybrid basis set schemes for CVS-EOMIP-CCSD calculations

Reliable computational methodologies and basis sets for modeling x-ray spectra are essential for extracting and interpreting electronic and structural information from experimental x-ray spectra. In particular, the trade-off between numerical accuracy and computational cost due to the size of the basis set is a major challenge, since molecular orbitals undergo extreme relaxation in the core-hole state. To gain clarity on the changes in electronic structure induced by the formation of a core-hole, the use of sufficiently flexible basis for expanding the orbitals, particularly for the core region, has been shown to be essential. This work focuses on the refinement of core-hole ionized state calculations using the equation-of-motion coupled cluster family of methods through an extensive analysis on the effectiveness of “hybrid” and mixed basis sets. In this investigation, we utilize the CVS-EOMIP-CCSD method in combination and construct hybrid basis sets piecewise from readily available Dunning’s correlation consistent basis sets in order to calculate x-ray ionization energies (IEs) for a set of small gas phase molecules. Our results provide insights into the impact of basis sets on the CVS-EOMIP-CCSD calculations of K-edge IEs of first-row p-block elements. Furthermore, these insights enable us to understand more about the basis set dependence of the core IEs computed and allow us to establish a protocol for deriving reliable and cost-effective theoretical estimates for computing IEs of small molecules containing such elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fuzzy cyber detection pattern matching

Mechanisms for identifying a pattern of computing resource activity of interest, in activity data characterizing activities of computer system elements, are provided. A temporal graph of the activity data is generated and a filter is applied to the temporal graph to generate one or more first vector representations, each characterizing nodes and edges within a moving window defined by the filter. The filter is applied to a pattern graph representing a pattern of entities and events indicative of the pattern of interest, to generate a second vector representation. The second vector representation is compared to the one or more first vector representations to identify one or more nearby vectors, and one or more corresponding subgraph instances are output to an intelligence console computing system as inexact matches of the temporal graph.

Shu, Xiaokui↗

Ergodicity, lack thereof, and the performance of reservoir computing with memristive networks and nanowire

Networks composed of nanoscale memristive components, such as nanowire and nanoparticle networks, have recently received considerable attention because of their potential use as neuromorphic devices. In this study, we explore ergodicity in memristive networks, showing that the performance on machine leaning tasks improves when these networks are tuned to operate at the edge between two global stability points. We find this lack of ergodicity is associated with the emergence of memory in the system. We measure the level of ergodicity using the Thirumalai-Mountain metric, and we show that in the absence of ergodicity, two different memristive network systems show improved performance when utilized as reservoir computers (RC). We highlight that it is also important to let the system synchronize to the input signal in order for the performance of the RC to exhibit improvements over the baseline.

97 MATHEMATICS AND COMPUTING↗

First-principles identification of novel double perovskites for water-splitting applications

Identification of new materials for photo-electrochemical conversion of water into hydrogen and oxygen using visible solar light is one of the grand challenges of our times. Toward this goal, here we employ a hierarchy of down-selection steps based on structural constraints, thermodynamic stability, constraints on bandgap and band-edge positions to identify potential candidates residing in a target double perovskite chemical space. The adopted screening strategy results in four new promising candidate materials, which were studied in greater detail using first-principles computations for their thermodynamic stability, electronic structure and octahedral structural distortions. In conclusion, our theoretical investigation is expected to serve as a motivation for future experimental efforts targeted toward realizing these identified promising materials.

36 MATERIALS SCIENCE↗