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At least 1,009 records · Page 56

The Carnegie Supernova Project I: Spectroscopic analysis of stripped-envelope supernovae

An analysis leveraging 170 optical spectra of 35 stripped-envelope (SE) core-collapse supernovae (SNe) observed by the Carnegie Supernova Project I and published in a companion paper is presented. Mean template spectra were constructed for the SNe IIb, Ib, and Ic subtypes, and parent ions associated with designated spectral features are identified with the aid of the spectral synthesis code SYNAPPS. Our modeled mean spectra suggest the ~6150 Å feature in SNe IIb may have an underlying contribution due to silicon, while the same feature in some SNe Ib may have an underlying contribution due to hydrogen. Standard spectral line diagnostics consisting of pseudo-equivalent widths (pEWs) and blue-shifted Doppler velocity were measured for each of the spectral features. Correlation matrices and rolling mean values of both spectral diagnostics were constructed. A principle component analysis (PCA) was applied to various wavelength ranges of the entire dataset and suggests clear separation among the different SE SN subtypes, which follows from trends previously identified in the literature. In addition, our findings reveal the presence of two SNe IIb subtypes, a select number of SNe Ib displaying signatures of weak, high-velocity hydrogen, and a single SN Ic with evidence of weak helium features. Our PCA results can be leveraged to obtain robust subtyping of SE SNe based on a single spectrum taken during the so-called photospheric phase, separating SNe IIb from SNe Ib with ~80% completion.

79 ASTRONOMY AND ASTROPHYSICS↗

ATAT: Astronomical Transformer for time series and Tabular data

Context. The advent of next-generation survey instruments, such as theVera C. RubinObservatory and its Legacy Survey of Space and Time (LSST), is opening a window for new research in time-domain astronomy. The Extended LSST Astronomical Time-Series Classification Challenge (ELAsTiCC) was created to test the capacity of brokers to deal with a simulated LSST stream. Aims. Our aim is to develop a next-generation model for the classification of variable astronomical objects. We describe ATAT, the Astronomical Transformer for time series And Tabular data, a classification model conceived by the ALeRCE alert broker to classify light curves from next-generation alert streams. ATAT was tested in production during the first round of the ELAsTiCC campaigns. Methods. ATAT consists of two transformer models that encode light curves and features using novel time modulation and quantile feature tokenizer mechanisms, respectively. ATAT was trained on different combinations of light curves, metadata, and features calculated over the light curves. We compare ATAT against the current ALeRCE classifier, a balanced hierarchical random forest (BHRF) trained on human-engineered features derived from light curves and metadata. Results. When trained on light curves and metadata, ATAT achieves a macro F1 score of 82.9 ± 0.4 in 20 classes, outperforming the BHRF model trained on 429 features, which achieves a macro F1 score of 79.4 ± 0.1. Conclusions. The use of transformer multimodal architectures, combining light curves and tabular data, opens new possibilities for classifying alerts from a new generation of large etendue telescopes, such as theVera C. RubinObservatory, in real-world brokering scenarios.

Astronomy & Astrophysics↗

Origins of epitaxial macro-terraces and macro-steps on GaN substrates

Localized lattice distortions in GaN substrates can serve as nucleation sites for epitaxial macro-steps and macro-terraces. These detrimental macro-scale features give rise to optically hazy homoepitaxial GaN surfaces. After nucleating, these macro-features grow laterally along the surface and coalesce, leading to significant coverage of the wafer surface. Dot-core GaN substrates consisting of a periodic array of cores were used as a defect-engineered system, where dislocations are intentionally concentrated at the cores. The high density of threading dislocations at the cores induced localized lattice distortions. Here, these distortions are associated predominantly with lattice tilt on the order of hundreds of arcsec across ~0.5 mm laterally along the wafer surface. The resulting macro-features that nucleated at these localized distorted sites were made up of macro-terraces with lengths ranging ~30–~150 μm and macro-step heights ranging ~200–~400 nm. Another source of localized distortion was threading screw dislocations or GaN nanopipes that resulted in spiral growth and hillock formation. Based on x-ray topography and optical microscopy measurements, we speculate that the coalescence of hillocks evolves into macro-terraces and macro-steps. While previous studies focused on the substrate miscut as a means to control macro-feature formation, we show that localized lattice tilt from defects is another important contributor to macro-feature formation.

36 MATERIALS SCIENCE↗

X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction

Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. Here, to better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ~13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe–Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO 3 ) and K-citrate [K 3 (C 6 H 5 O 7 )·H 2 O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO 3 has both the lowest and highest lying energy features, and K 3 (C 6 H 5 O 7 )·H 2 O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Seabed bathymetry and friction modeling in MoorDyn

This paper presents the implementation and verification of a seabed bathymetry feature and seabed friction feature to the open-source, lumped-mass mooring system dynamics modeler, MoorDyn, which is part of the National Renewable Energy Laboratory’s aero-hydro-servo-elastic simulation tool, OpenFAST. Variations in seabed slope, as well as the frictional effects of mooring lines moving along the seabed, will affect the mooring line tensions of a floating platform and the consequent platform response. These new features are especially relevant for modeling mooring systems in deep-water coastal areas where seabed depth can change significantly over an entire mooring footprint. The bathymetry feature models the seabed as a rectangular grid of variable water depths in place of the existing, uniform water depth in MoorDyn. The friction force is primarily represented as a Coulombic friction force, or the product of a kinetic friction coefficient and the seabed contact normal force, with the ability to differentiate between transverse and axial motion of a line node on the seabed in any bathymetry grid. These capabilities were tested by running MoorDyn and OpenFAST simulations over a variety of seabed and environmental conditions; the resulting fairlead tensions, node tensions, and mooring line kinematics were verified against equivalent OrcaFlex simulations. The results match closely, meaning the features are verified, which will increase the overall fidelity of OpenFAST and FAST.Farm simulations.

17 WIND ENERGY↗

Improving deep learning-based protein distance prediction in CASP14

Abstract Motivation Accurate prediction of residue–residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Results Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions [i.e. classifying distances between two residues into two categories: in contact (<8 Angstrom) and not in contact otherwise] and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the precision of distance classification. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps. Availability and implementation The software package, source code and data of DeepDist2 are freely available at https://github.com/multicom-toolbox/deepdist and https://zenodo.org/record/4712084#.YIIM13VKhQM. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Shocks in the stacked Sunyaev-Zel’dovich profiles of clusters II: Measurements from SPT-SZ + Planck Compton- y map

ABSTRACT We search for the signature of cosmological shocks in stacked gas pressure profiles of galaxy clusters using data from the South Pole Telescope (SPT). Specifically, we stack the latest Compton-y maps from the 2500 deg2 SPT-SZ survey on the locations of clusters identified in that same data set. The sample contains 516 clusters with mean mass $\langle M_{\rm 200m}\rangle = 10^{14.9} \, {\rm M}_\odot$ and redshift 〈z〉 = 0.55. We analyse in parallel a set of zoom-in hydrodynamical simulations from the three hundred project. The SPT-SZ data show two features: (i) a pressure deficit at R/R200m = 1.08 ± 0.09, measured at 3.1σ significance and not observed in the simulations, and; (ii) a sharp decrease in pressure at R/R200m = 4.58 ± 1.24 at 2.0σ significance. The pressure deficit is qualitatively consistent with a shock-induced thermal non-equilibrium between electrons and ions, and the second feature is consistent with accretion shocks seen in previous studies. We split the cluster sample by redshift and mass, and find both features exist in all cases. There are also no significant differences in features along and across the cluster major axis, whose orientation roughly points towards filamentary structure. As a consistency test, we also analyse clusters from the Planck and Atacama Cosmology Telescope Polarimeter surveys and find quantitatively similar features in the pressure profiles. Finally, we compare the accretion shock radius ($R_{\rm sh,\, acc}$) with existing measurements of the splashback radius (Rsp) for SPT-SZ and constrain the lower limit of the ratio, $R_{\rm sh,\, acc}/R_{\rm sp}\gt 2.16 \pm 0.59$.

79 ASTRONOMY AND ASTROPHYSICS↗

Analysis of the impact of broad absorption lines on quasar redshift measurements with synthetic observations

ABSTRACT Accurate quasar classifications and redshift measurements are increasingly important to precision cosmology experiments. Broad absorption line (BAL) features are present in 15–20 per cent of all quasars, and these features can introduce systematic redshift errors, and in extreme cases produce misclassifications. We quantitatively investigate the impact of BAL features on quasar classifications and redshift measurements with synthetic spectra that were designed to match observations by the Dark Energy Spectroscopic Instrument (DESI) survey. Over the course of 5 yr, DESI aims to measure spectra for 40 million galaxies and quasars, including nearly three million quasars. Our synthetic quasar spectra match the signal-to-noise ratio and redshift distributions of the first year of DESI observations, and include the same synthetic quasar spectra both with and without BAL features. We demonstrate that masking the locations of the BAL features decreases the redshift errors by about 1 per cent and reduces the number of catastrophic redshift errors by about 80 per cent. We conclude that identifying and masking BAL troughs should be a standard part of the redshift determination step for DESI and other large-scale spectroscopic surveys of quasars.

(galaxies:) quasars: absorption↗

Predictive Models of Genetic Redundancy in Arabidopsis thaliana

Abstract Genetic redundancy refers to a situation where an individual with a loss-of-function mutation in one gene (single mutant) does not show an apparent phenotype until one or more paralogs are also knocked out (double/higher-order mutant). Previous studies have identified some characteristics common among redundant gene pairs, but a predictive model of genetic redundancy incorporating a wide variety of features derived from accumulating omics and mutant phenotype data is yet to be established. In addition, the relative importance of these features for genetic redundancy remains largely unclear. Here, we establish machine learning models for predicting whether a gene pair is likely redundant or not in the model plant Arabidopsis thaliana based on six feature categories: functional annotations, evolutionary conservation including duplication patterns and mechanisms, epigenetic marks, protein properties including posttranslational modifications, gene expression, and gene network properties. The definition of redundancy, data transformations, feature subsets, and machine learning algorithms used significantly affected model performance based on holdout, testing phenotype data. Among the most important features in predicting gene pairs as redundant were having a paralog(s) from recent duplication events, annotation as a transcription factor, downregulation during stress conditions, and having similar expression patterns under stress conditions. We also explored the potential reasons underlying mispredictions and limitations of our studies. This genetic redundancy model sheds light on characteristics that may contribute to long-term maintenance of paralogs, and will ultimately allow for more targeted generation of functionally informative double mutants, advancing functional genomic studies.

59 BASIC BIOLOGICAL SCIENCES↗

Properties of giant dipole resonances within an extended pairing model with a focus on spectral statistics

In this paper, we report on a study of the spectral features associated with dipole resonances in medium mass nuclei (E ≤ 12 MeV), as revealed in the framework of the spd-interacting boson model. The effect of pairing correlations on the theory follows from solutions obtained through an application of the Bethe Ansatz Equation. In general, calculated spectra around the critical point of the vibrational to γ-soft transitions appears to approach that of a Gaussian Orthogonal Ensemble, while near the rotational and vibrational limits of the theory the spectra show more regular behavior. Specifically, the results reveal that the statistical features of the spectra are sensitive to the vector boson pairing strength, c p , in the transition region; that is, when c p is zero, or when the system approaches one of its dynamical symmetries limits the spectrum display regular features, while for stronger c p values, or when near to the critical phase transition region, the spectral feature show more chaotic behavior. Overall, our results indicate that the statistical features are governed by the interplay between dipole resonant energies, pairing correlations, and interactions between and among the single and vector bosons modes of the theory. As part of this work we also found out that chaoticity occurs when results were fit to a Berry-Robnik distribution. Throughout our analyses, we used experimentally known information about both positive and negative parity states. Our findings suggest that dipole resonances appear to be best-described by Poisson statistics for A ≈ 32-138 nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Chemical and steric effects in simulating noncontact atomic force microscopy images of organic molecules on a Cu (111) substrate

Noncontact mode of atomic force microscopy (nc-AFM) employing a CO-functionalized tip is a very powerful tool for studying molecular structures. However, interpreting nc-AFM images for nonplanar molecules can sometimes be problematic. To illustrate and resolve the nature of such problematic systems, we employ real-space pseudopotentials constructed within density functional theory to simulate nc-AFM images. In this work, we focus on several representative nonplanar organic molecules (pentacene, naphthanthrone, olympicene, and 6-phenylhexa-1,3,5-triynybenzene (PHTB)) on a typical substrate: the Cu (111) surface. This substrate results in significant distortions in the molecular geometries of pentacene and naphthanthrone. Including these distortions in simulated nc-AFM imaging notably improves the agreement between the simulated and measured images. In naphthanthrone, the relatively large interaction between the O atom and the Cu substrate offers a straightforward explanation for the absence of the C = O bond in the measured image. Nonplanar features such as tilting or twisting are also apparent in olympicene and PHTB. A “triangular” bright feature associated with the –CH 2 group in olympicene appears in simulated and measured nc-AFM images. This feature is directly related to the tilting angle of the molecule with respect to the Cu substrate. The “defective” benzene ring feature and the faint ellipsoidal C ≡ C feature in PHTB can be ascribed to its twisted nature. The ability to simulate such subatomic images in nc-AFM reflects the accuracy and efficiency of calculating quantum forces in real space.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Novel Fault Location Method for Power Systems Based on Attention Mechanism and Double Structure GRU Neural Network

Fault location is one of the most essential techniques to maintain the stable operation of power systems. A fast and accurate fault location allows operators to restore power grids faster and avoid economic losses. Conventional methods rely on expert knowledge to extract the necessary features (e.g. DWT, DFT). For large systems, more coupling effects of transmission lines require more complex feature engineering, and incomplete features can easily introduce large errors. To overcome this, a deep learning approach without manual feature extraction is introduced to the fault location model under big data application. Towards this end, in the proposed method, the attention mechanism, the Bi-GRU and a dual structure network are applied to analyze the current data from different perspectives. Complete information for the fault features is extracted for the fault location. Based on a time series model and benefit from the ability to internally acquire the information architecture of faulty line, the established model is adaptive to the power grids with very complex topologies. Simulation results indicate that the proposed double-structure model reduces the maximum error and is less affected by noise. In comparison with different structures and different models, the proposed method shows better performance in IEEE 39-bus system.

42 ENGINEERING↗

AutoAtlas: Neural Network for 3D Unsupervised Partitioning and Representation Learning

Here we present a novel neural network architecture called AutoAtlas for fully unsupervised partitioning and representation learning of 3D brain Magnetic Resonance Imaging (MRI) volumes. AutoAtlas consists of two neural network components: one neural network to perform multi-label partitioning based on local texture in the volume, and a second neural network to compress the information contained within each partition. We train both of these components simultaneously by optimizing a loss function that is designed to promote accurate reconstruction of each partition, while encouraging spatially smooth and contiguous partitioning, and discouraging relatively small partitions. We show that the partitions adapt to the subject specific structural variations of brain tissue while consistently appearing at similar spatial locations across subjects. AutoAtlas also produces very low dimensional features that represent local texture of each partition. We demonstrate prediction of metadata associated with each subject using the derived feature representations and compare the results to prediction using features derived from FreeSurfer anatomical parcellation. Since our features are intrinsically linked to distinct partitions, we can then map values of interest, such as partition-specific feature importance scores onto the brain for visualization.

42 ENGINEERING↗

Assessment of Machine Learning Wall Modeling Approaches for Large Eddy Simulation of Gas Turbine Film Cooling Flows: An a Priori Study

Here, in this work, a priori analysis of machine learning (ML) strategies is carried out with the goal of data-driven wall modeling for large eddy simulation (LES) of gas turbine film cooling flows. High-fidelity flow datasets are extracted from wall-resolved LES (WRLES) of flow over a flat plate interacting with the coolant flow supplied by a single row of 7-7-7 shaped cooling holes inclined at 30 degrees with the flat plate at different blowing ratios (BR). The WRLES are performed using the high-order Nek5000 spectral element computational fluid dynamics (CFD) solver. Light gradient boosting machine (LightGBM) is employed as the ML algorithm for the data-driven wall model. Parametric tests are conducted to systematically assess the influence of a wide range of input flow features (velocity components, velocity gradients, pressure gradients, and fluid properties) on the accuracy of ML wall model with respect to prediction of wall shear stress. In addition, the use of spatial stencil and time delay is also explored within the ML wall modeling framework. It is shown that features associated with gradients of the streamwise and spanwise velocity components have a major impact on the prediction fidelity of wall model, while the effect of gradients of wall-normal velocity component is found to be negligible. Moreover, adding flow feature information from an x-y-z spatial stencil significantly improves the ML model accuracy and generalizability compared to just using local flow features from the matching location. Overall, highest prediction accuracy is achieved when both spatial stencil and time delay features are incorporated within the data-driven wall modeling paradigm.

33 ADVANCED PROPULSION SYSTEMS↗

Design of a Novel Information System for Semi-Automated Management of Cybersecurity in Industrial Control Systems

There is an urgent need in many critical infrastructure sectors, including the energy sector, for attaining detailed insights into cybersecurity features and compliance with cybersecurity requirements related to their Operational Technology (OT) deployments. Frequent feature changes of OT devices interfere with this need, posing a great risk to customers. One effective way to address this challenge is via a semi-automated cyber-physical security assurance approach, which enables verification and validation of the OT device cybersecurity claims against actual capabilities, both pre- and post-deployment. To realize this approach, this paper presents new methodology and algorithms to automatically identify cybersecurity-related claims expressed in natural language form in ICS device documents. Here, we developed an identification process that employs natural language processing (NLP) techniques with the goal of semi-automated vetting of detected claims against their device implementation. We also present our novel NLP components for verifying feature claims against relevant cybersecurity requirements. The verification pipeline includes components such as automated vendor identification, device document curation, feature claim identification utilizing sentiment analysis for conflict resolution, and reporting of features that are claimed to be supported or indicated as unsupported. Our novel matching engine represents the first automated information system available in the cybersecurity domain that directly aids the generation of ICS compliance reports.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Is Knowledge about Running Applications Helping Improve Runtime Prediction of HPC Jobs?

High-performance computing systems rely upon scheduling algorithms to achieve high utilization. These schedulers rely upon user estimates of job resource requirements, such as runtime, to determine optimal scheduling of incoming jobs. These user estimates, however, are prone to error. To mitigate this error, significant research has been directed at providing better estimates of job runtime, usually employing machine learning techniques. These techniques are dependent upon the input features selected. Among the possible features is the primary application used by the job. In a survey of more than 20 papers directed at improving runtime prediction, only four included primary application as an input feature. We focus this investigation specifically on the value of adding primary application as an input feature, and find that it does improve model performance, especially for jobs with longer runtimes, though this improvement varies based on the application used. We recommend further research to determine the cause of this variability as well as an optimal strategy for employing a mixture of models both including and not including primary application as a feature.

MATHEMATICS AND COMPUTING↗

Topological Interpretability for Deep Learning

With the growing adoption of AI-based systems across everyday life, the need to understand their decision-making mechanisms is correspondingly increasing. The level at which we can trust the statistical inferences made from AI-based decision systems is an increasing concern, especially in high-risk systems such as criminal justice or medical diagnosis, where incorrect inferences may have tragic consequences. Despite their successes in providing solutions to problems involving real-world data, deep learning (DL) models cannot quantify the certainty of their predictions. These models are frequently quite confident, even when their solutions are incorrect. This work presents a method to infer prominent features in two DL classification models trained on clinical and non-clinical text by employing techniques from topological and geometric data analysis. We create a graph of a model's feature space and cluster the inputs into the graph's vertices by the similarity of features and prediction statistics. We then extract subgraphs demonstrating high-predictive accuracy for a given label. These subgraphs contain a wealth of information about features that the DL model has recognized as relevant to its decisions. We infer these features for a given label using a distance metric between probability measures, and demonstrate the stability of our method compared to the LIME and SHAP interpretability methods. This work establishes that we may gain insights into the decision mechanism of a DL model. This method allows us to ascertain if the model is making its decisions based on information germane to the problem or identifies extraneous patterns within the data.

Spannaus, Adam↗

Taking the MPI standard and the open MPI library to exascale

The Open MPI for Exascale (OMPI-X) project was one of two in the Exascale Computing Project (ECP) focused on advancing the MPI ecosystem. The OMPI-X team worked with other MPI Forum members to champion several important features for inclusion in the MPI 4.0, 4.1, and upcoming 5.0 MPI standard versions, in support of the needs of exascale applications and systems. The team also worked with the larger Open MPI community to bring implementations of these new features and other enhancements into Open MPI, one of the leading open-source implementations of the MPI interface. Here, this paper describes the motivation for the work of the OMPI-X project in the context of exascale computing needs, the nature of the resulting new capabilities in the MPI standard, and how they were implemented in the Open MPI library. Features include improved support for “MPI + X” programming models through partitioned communications and support for user-level threading, sessions, fault tolerance through the user-level fault mitigation (ULFM) and Reinit models, and other features. We also discuss enhancements to Open MPI providing improved performance and scalability for existing features, such as collective operations, one-sided operations, support for the Slingshot-11 interconnect of the initial exascale systems, and how the OMPI-X team worked to improve quality assurance for the Open MPI library, particularly on platforms of interest to the Department of Energy community.

97 MATHEMATICS AND COMPUTING↗