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At least 919 records · Page 51

Feature engineering descriptors, transforms, and machine learning for grain boundaries and variable-sized atom clusters

Abstract Obtaining microscopic structure-property relationships for grain boundaries is challenging due to their complex atomic structures. Recent efforts use machine learning to derive these relationships, but the way the atomic grain boundary structure is represented can have a significant impact on the predictions. Key steps for property prediction common to grain boundaries and other variable-sized atom clustered structures include: (1) describing the atomic structure as a feature matrix, (2) transforming the variable-sized feature matrix to a fixed length common to all structures, and (3) applying a machine learning algorithm to predict properties from the transformed matrices. We examine how these steps and different combinations of engineered features impact the accuracy of grain boundary energy predictions using a database of over 7000 grain boundaries. Additionally, we assess how different engineered features support interpretability, offering insights into the physics of the structure-property relationships.

36 MATERIALS SCIENCE↗

Accelerating error correction in tomographic reconstruction

Abstract Spurred by recent advances in detector technology and X-ray optics, upgrades to scanning-probe-based tomographic imaging have led to an exponential growth in the amount and complexity of experimental data and have created a clear opportunity for tomographic imaging to approach single-atom sensitivity. The improved spatial resolution, however, is highly susceptible to systematic and random experimental errors, such as center of rotation drifts, which may lead to imaging artifacts and prevent reliable data extraction. Here, we present a model-based approach that simultaneously optimizes the reconstructed specimen and sinogram alignment as a single optimization problem for tomographic reconstruction with center of rotation error correction. Our algorithm utilizes an adaptive regularizer that is dynamically adjusted at each alternating iteration step. Furthermore, we describe its implementation in a software package targeting high-throughput workflows for execution on distributed-memory clusters. We demonstrate the performance of our solver on large-scale synthetic problems and show that it is robust to a wide range of noise and experimental drifts with near-ideal throughput.

Ali, Sajid (ORCID:0000000321864636)↗

The structural information filtered features (SIFF) potential: Maximizing information stored in machine-learning descriptors for materials prediction

Machine learning inspired potentials continue to improve the ability for predicting structures of materials. However, many challenges still exist, particularly when calculating structures of disordered systems. These challenges are primarily due to the rapidly increasing dimensionality of the feature-vector space which in most machine-learning algorithms is dependent on the size of the structure. In this article, we present a feature-engineered approach that establishes a set of principles for representing potentials of physical structures (crystals, molecules, and clusters) in a feature space rather than a physically motivated space. Our goal in this work is to define guiding principles that optimize information storage of the physical parameters within the feature representations. In this manner, we focus on keeping the dimensionality of the feature space independent of the number of atoms in the structure. Our Structural Information Filtered Features (SIFF) potential represents structures by utilizing a feature vector of low-correlated descriptors, which correspondingly maximizes information within the descriptor. We present results of our SIFF potential on datasets composed of disordered (carbon and carbon–oxygen) clusters, molecules with C 7 O 2 H 2 stoichiometry in the GDB9-14B dataset, and crystal structures of the form (Al x Ga y In z ) 2 O 3 as proposed in the NOMAD Kaggle competition. Our potential's performance is at least comparable, sometimes significantly more accurate, and often more efficient than other well-known machine-learning potentials for structure prediction. However, primarily, we offer a different perspective on how researchers should consider opportunities in maximizing information storage for features.

36 MATERIALS SCIENCE↗

Covariance Shaping Over Riemannian Manifolds for Massive MIMO Communication

Acquiring accurate instantaneous channel state information (CSI) is a challenging aspect of massive multi-input multi-output (MIMO) communication. Utilizing statistical information, such as channel covariance matrix, to design statistical beamforming vectors is robust when compared to instantaneous CSI. In this paper, we propose a novel MIMO covariance shaping scheme over Riemannian manifolds. It serves as an effective statistical beamforming solution to a number of close proximity user equipment (UE) that are undergoing substantial channel correlation. Proposed algorithm exploits the Hermitian positive definite nature of covariance matrices lying over Riemannian manifold. We introduce Wasserstein distance function as a Riemannian metric to measure distances between channel covariance matrices. Furthermore, K-means clustering technique is utilized to effectively identify the optimal shape of effective optimal covariance matrices. Our findings suggest that maximizing the geodesic distance between covariance matrices ultimately leads to a corresponding increase in the network throughput, as determined by the beamforming vector used to shape the covariance matrices. Simulation results validate that the proposed solution converges faster than Euclidean-based state-of-the-art, while maintaining the same computational complexity. Finally, the sum rate performance asymptotically achieves full capacity for two-UE case and more than 96% of the upper bound exhaustive search benchmark for multi-UE scenario.

42 ENGINEERING↗

Fuzzy modeling based on generalized neural networks and fuzzy clustering objective functions

An approach to the formulation of fuzzy if-then rules based on clustering objective functions is proposed. The membership functions are then calibrated with the generalized neural networks technique to achieve a desired input-output mapping. The learning procedure is basically a gradient-descent algorithm. A Kalman filter algorithm is used to improve the overall performance.

Sun, Chuen-Tsai↗

BOREAS AFM-12 1-km AVHRR Seasonal Land Cover Classification

The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-12 team's efforts focused on regional scale Surface Vegetation and Atmosphere (SVAT) modeling to improve parameterization of the heterogeneous BOREAS landscape for use in larger scale Global Circulation Models (GCMs). This regional land cover data set was developed as part of a multitemporal one-kilometer Advanced Very High Resolution Radiometer (AVHRR) land cover analysis approach that was used as the basis for regional land cover mapping, fire disturbance-regeneration, and multiresolution land cover scaling studies in the boreal forest ecosystem of central Canada. This land cover classification was derived by using regional field observations from ground and low-level aircraft transits to analyze spectral-temporal clusters that were derived from an unsupervised cluster analysis of monthly Normalized Difference Vegetation Index (NDVI) image composites (April-September 1992). This regional data set was developed for use by BOREAS investigators, especially those involved in simulation modeling, remote sensing algorithm development, and aircraft flux studies. Based on regional field data verification, this multitemporal one-kilometer AVHRR land cover mapping approach was effective in characterizing the biome-level land cover structure, embedded spatially heterogeneous landscape patterns, and other types of key land cover information of interest to BOREAS modelers.The land cover mosaics in this classification include: (1) wet conifer mosaic (low, medium, and high tree stand density), (2) mixed coniferous-deciduous forest (80% coniferous, codominant, and 80% deciduous), (3) recent visible bum, vegetation regeneration, or rock outcrops-bare ground-sparsely vegetated slow regeneration bum (four classes), (4) open water and grassland marshes, and (5) general agricultural land use/ grasslands (three classes). This land cover mapping approach did not detect small subpixel-scale landscape features such as fens, bogs, and small water bodies. Field observations and comparisons with Landsat Thematic Mapper (TM) suggest a minimum effective resolution of these land cover classes in the range of three to four kilometers, in part, because of the daily to monthly compositing process. In general, potential accuracy limitations are mitigated by the use of conservative parameterization rules such as aggregation of predominant land cover classes within minimum horizontal grid cell sizes of ten kilometers. The AFM-12 one-kilometer AVHRR seasonal land cover classification data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

Steyaert, Lou↗

Machine Learning–Augmented Laser-Induced Breakdown Spectroscopy for Spectral Discrimination of Iron Oxalates

Enhanced characterization and phase identification of post-PUREX Pu Oxalates (PuOXA) are pivotal for nonproliferation and pre-detonation nuclear forensics. Despite significant advances in the characterization of PuO 2 samples, little is known about the impact of both the chemical structure and oxidation states of PuOXA (i.e., Pu(III) and Pu(IV)) have on optical emission signatures. Here, we demonstrate the analytical capabilities of laser-induced breakdown spectroscopy (LIBS) applied to Fe(II) and Fe(III) oxalate samples as surrogates for PuOXA, highlighting the discriminating features in the LIBS emission spectra arising from differences in the oxidation states within mixed FeOXA samples. We report the enhancement of spectral feature selection using Principal Component Analysis (PCA), which enables the analytical superiority of machine learning algorithms such as Linear Discriminant Analysis (LDA), Quadratic Discriminant Analysis (QDA), Partial Least Squares Regression (PLSR), Support Vector Regression (SVR), and Random Forest Regression (RFR) over conventional univariate techniques for phase discrimination and chemometric analysis. Cluster analysis revealed how both matrix effects and laser ablation influence cluster separability by introducing spectral artifacts that misdirect the maximization of variance. PCA-selected emission lines were used in the regression models, demonstrating that both univariate and multivariate linear regression models (i.e., PLSR and SVR) can achieve acceptable performance, with machine learning models outperforming conventional calibration regressions. Furthermore, the application of non-linearly activated PCA-selected emission lines illustrates how simplifying the data while retaining captured variance enables the use of less complex and more computationally efficient models. Furthermore, this is particularly evident in the underperformance of RFR, which suffers from increased computational costs and overfitting owing to its high complexity.

Oxalates↗

A glimpse into the fungal metabolomic abyss: Novel network analysis reveals relationships between exogenous compounds and their outputs

Fungal specialized metabolites are a major source of beneficial compounds that are routinely isolated, characterized, and manufactured as pharmaceuticals, agrochemical agents, and industrial chemicals. The production of these metabolites is encoded by biosynthetic gene clusters that are often silent under standard growth conditions. There are limited resources for characterizing the direct link between abiotic stimuli and metabolite production. Herein, we introduce a network analysis-based, data-driven algorithm comprising two routes to characterize the production of specialized fungal metabolites triggered by different exogenous compounds: the direct route and the auxiliary route. Both routes elucidate the influence of treatments on the production of specialized metabolites from experimental data. The direct route determines known and putative metabolites induced by treatments and provides additional insight over traditional comparison methods. The auxiliary route is specific for discovering unknown analytes, and further identification can be curated through online bioinformatic resources. We validated our algorithm by applying chitooligosaccharides and lipids at two different temperatures to the fungal pathogen Aspergillus fumigatus. After liquid chromatography–mass spectrometry quantification of significantly produced analytes, we used network centrality measures to rank the treatments’ ability to elucidate these analytes and confirmed their identity through fragmentation patterns or in silico spiking with commercially available standards. Later, we examined the transcriptional regulation of these metabolites through real-time quantitative polymerase chain reaction. Our data-driven techniques can complement existing metabolomic network analysis by providing an approach to track the influence of any exogenous stimuli on metabolite production. Our experimental-based algorithm can overcome the bottlenecks in elucidating novel fungal compounds used in drug discovery.

59 BASIC BIOLOGICAL SCIENCES↗

ADEPT: a domain independent sequence alignment strategy for gpu architectures

Bioinformatic workflows frequently make use of automated genome assembly and protein clustering tools. At the core of most of these tools, a significant portion of execution time is spent in determining optimal local alignment between two sequences. This task is performed with the Smith-Waterman algorithm, which is a dynamic programming based method. With the advent of modern sequencing technologies and increasing size of both genome and protein databases, a need for faster Smith-Waterman implementations has emerged. Multiple SIMD strategies for the Smith-Waterman algorithm are available for CPUs. However, with the move of HPC facilities towards accelerator based architectures, a need for an efficient GPU accelerated strategy has emerged. Existing GPU based strategies have either been optimized for a specific type of characters (Nucleotides or Amino Acids) or for only a handful of application use-cases. In this paper, we present ADEPT, a new sequence alignment strategy for GPU architectures that is domain independent, supporting alignment of sequences from both genomes and proteins. Our proposed strategy uses GPU specific optimizations that do not rely on the nature of sequence. We demonstrate the feasibility of this strategy by implementing the Smith-Waterman algorithm and comparing it to similar CPU strategies as well as the fastest known GPU methods for each domain. ADEPT’s driver enables it to scale across multiple GPUs and allows easy integration into software pipelines which utilize large scale computational systems. We have shown that the ADEPT based Smith-Waterman algorithm demonstrates a peak performance of 360 GCUPS and 497 GCUPs for protein based and DNA based datasets respectively on a single GPU node (8 GPUs) of the Cori Supercomputer. Overall ADEPT shows 10x faster performance in a node-to-node comparison against a corresponding SIMD CPU implementation. ADEPT demonstrates a performance that is either comparable or better than existing GPU strategies. We demonstrated the efficacy of ADEPT in supporting existing bionformatics software pipelines by integrating ADEPT in MetaHipMer a high-performance denovo metagenome assembler and PASTIS a high-performance protein similarity graph construction pipeline. Our results show 10% and 30% boost of performance in MetaHipMer and PASTIS respectively.

59 BASIC BIOLOGICAL SCIENCES↗

Generation of orthogonal grids by boundary grid relaxation

Two elliptic grid generation schemes that yield orthogonal grids are presented (FGBR and UBGR). With the UBGR scheme, the grid points on the flow boundaries are automatically determined by the algorithm, while the FBGR scheme at most one half of the boundary grid points may be prespecified and the remainder of boundary grid points are determined automatically. Numerical examples show their capability of easy stretching, clustering and shock fitting while maintaining orthogonality of grid. The present method can be implemented into existing elliptic grid generation programs with relatively minor modifications.

Nakamura, S.↗

In Situ Measurements of Angular-Dependent Light Scattering by Aerosols over the Contiguous United States

This work provides a synopsis of aerosol phase function (F (sub 11)) and polarized phase function (F (sub 12)) measurements made by the Polarized Imaging Nephelometer (PINeph) during the Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and the Deep Convection Clouds and Chemistry (DC3) field campaigns. In order to more easily explore this extensive dataset, an aerosol classification scheme is developed that identifies the different aerosol types measured during the deployments. This scheme makes use of ancillary data that include trace gases, chemical composition, aerodynamic particle size and geographic location, all independent of PI-Neph measurements. The PI-Neph measurements are then grouped according to their ancillary data classifications and the resulting scattering patterns are examined in detail. These results represent the first published airborne measurements of F (sub 11) and minus F (sub 12) divided by F (sub 11) for many common aerosol types. We then explore whether PI-Neph light-scattering measurements alone are sufficient to reconstruct the results of this ancillary data classification algorithm. Principal component analysis (PCA) is used to reduce the dimensionality of the multi-angle PI-Neph scattering data and the individual measurements are examined as a function of ancillary data classification. Clear clustering is observed in the PCA score space, corresponding to the ancillary classification results, suggesting that, indeed, a strong link exists between the angular scattering measurements and the aerosol type or composition. Two techniques are used to quantify the degree of clustering and it is found that in most cases the results of the ancillary data classification can be predicted from PI-Neph measurements alone with better than 85 percent recall. This result both emphasizes the validity of the ancillary data classification as well as the PI-Neph's ability to distinguish common aerosol types without additional information.

Aerosol phase function↗

Diurnal Variability of Vertical Structure from a TRMM Passive Microwave "Virtual Radar" Retrieval

Robust description of the diurnal cycle from TRMM observations is complicated by the limitations of Low Earth Orbit (LEO) sampling; from a 'climatological' perspective, sufficient sampling must exist to control for both spatial and seasonal variability, before tackling an additional diurnal component (e.g., with 8 additional 3-hourly or 24 1-hourly bins). For documentation of vertical structure, the narrow sample swath of the TRMM Precipitation Radar limits the resolution of any of these components. A neural-network based 'virtual radar" retrieval has been trained and internally validated, using multifrequency / multipolarization passive microwave(TM1) brightness temperatures and textures parameters and lightning (LIS) observations, as inputs, and PR volumetric reflectivity as targets (outputs). By training the algorithms (essentially highly multivariate, nonlinear regressions) on a very large sample of high-quality co-located data from the center of the TRMM swath, 3D radar reflectivity and derived parameters (VIL, IWC, Echo Tops, etc.) can be retrieved across the entire TMI swath, good to 8-9% over the dynamic range of parameters. As a step in the retrieval (and as an output of the process), each TMI multifrequency pixel (at 85 GHz resolution) is classified into one of the 25 archetypal radar profile vertical structure "types", previously identified using cluster analysis. The dynamic range of retrieved vertical structure appears to have higher fidelity than the current (Version 6) experimental GPROF hydrometeor vertical structure retrievals. This is attributable to correct representation of the prior probabilities of vertical structure variability in the neural network training data, unlike the GPROF cloud-resolving model training dataset used in the V6 algorithms. The LIS lightning inputs are supplementary inputs, and a separate offline neural network has been trained to impute (predict) LIS lightning from passive-microwave-only data. The virtual radar retrieval is thus, in principle, extensible to Aqua/AMSR-E and NPOESS/CMIS passive microwave instruments. The virtual radar approach yields a threefold increase in effective sampling from the mission, albeit of lower-quality "retrieved" data, reducing the variance of local estimates by one third (or the standard deviation by-0.57). In this talk, the variance reduction is leveraged to more finely resolve global diurnal variability in both space and time (local hour).

Boccippio, Dennis J.↗

Structures cluster

The objective of this program is to develop technology needed for structural evaluation of alternative space construction concepts. Those concepts are as follows: interactive effects on dynamic performance of various environment and self-generated disturbance; new materials concepts, failure mechanisms, and non-destructive evaluation/failure detection; develop stable control algorithms and design effective combination of hierarchical and adaptive controls; and assess control-structure integrated performance and stability.

Datta, Subhendu K.↗

Extracting structural motifs from pair distribution function data of nanostructures using explainable machine learning

Characterization of material structure with X-ray or neutron scattering using e.g. Pair Distribution Function (PDF) analysis most often rely on refining a structure model against an experimental dataset. However, identifying a suitable model is often a bottleneck. Recently, automated approaches have made it possible to test thousands of models for each dataset, but these methods are computationally expensive and analysing the output, i.e. extracting structural information from the resulting fits in a meaningful way, is challenging. Our Machine Learning based Motif Extractor (ML-MotEx) trains an ML algorithm on thousands of fits, and uses SHAP (SHapley Additive exPlanation) values to identify which model features are important for the fit quality. We use the method for 4 different chemical systems, including disordered nanomaterials and clusters. ML-MotEx opens for a type of modelling where each feature in a model is assigned an importance value for the fit quality based on explainable ML.

36 MATERIALS SCIENCE↗

Dark Energy Survey: Galaxy sample for the baryonic acoustic oscillation measurement from the final dataset

In this paper, we present and validate the galaxy sample used for the analysis of the baryon acoustic oscillation (BAO) signal in the Dark Energy Survey (DES) Y6 data. The definition is based on a color and redshift-dependent magnitude cut optimized to select galaxies at redshifts higher than 0.6, while ensuring a high-quality photo- z determination. The optimization is performed using a Fisher forecast algorithm, finding the optimal i -magnitude cut to be given by i < 19.64 + 2.894 z ph . For the optimal sample, we forecast an increase in precision in the BAO measurement of ∼ 25 % with respect to the Y3 analysis. Our BAO sample has a total of 15,937,556 galaxies in the redshift range 0.6 < z ph < 1.2 , and its angular mask covers 4 , 273.42 deg 2 to a depth of i = 22.5 . We validate its redshift distributions with three different methods: directional neighborhood fitting algorithm (DNF), which is our primary photo- z estimation; direct calibration with spectroscopic redshifts from VIPERS, which is a spectroscopic galaxy sample that overlaps with our BAO sample and is complete within our selection cuts; and clustering redshift using SDSS galaxies. The fiducial redshift distribution is a combination of these three techniques performed by modifying the mean and width of the DNF distributions to match those of VIPERS and clustering redshift. In this paper, we also describe the methodology used to mitigate the effect of observational systematics, which is analogous to the one used in the Y3 analysis. This paper is one of the two dedicated to the analysis of the BAO signal in DES Y6. In its companion paper, we present the angular diameter distance constraints obtained through the fitting to the BAO scale.

79 ASTRONOMY AND ASTROPHYSICS↗

A Global End-Member Approach to Derive aCDOM(440) from Near-Surface Optical Measurements

This study establishes an optical inversion scheme for deriving the absorption coefficient of colored (or chromophoric, depending on the literature) dissolved organic material (CDOM) at the 440 nm wavelength, which can be applied to global water masses with near-equal efficacy. The approach uses a ratio of diffuse attenuation coefficient spectral end members, i.e., a short and long wavelength pair. The global perspective is established by sampling "extremely" clear water plus a generalized extent in turbidity and optical properties that each span three decades of dynamic range. A unique data set was collected in oceanic, coastal, and inland waters (as shallow as 0.6 m) from the North Pacific Ocean, the Arctic Ocean, Hawaii, Japan, Puerto Rico, and the east and west coasts of the United States. The data were partitioned using subjective categorizations to define a validation quality subset of conservative water masses, i.e., the inflow and outflow of properties constrain the range in the gradient of a constituent, plus 15 subcategories of water masses that were not evolving conservatively. The dependence on subcategories was confirmed with an objective methodology based on cluster analysis techniques. The latter defined five distinct classes with validation quality data present in all classes, but which also decreased in percent composition as a function of increasing class number and optical complexity. Four different algorithms based on different validation quality end members were validated with accuracies of 1.–6.2 %, wherein pairs with the largest spectral span were most accurate. Although algorithm accuracy decreased with the inclusion of more subcategories containing non-conservative water masses, changes to the algorithm fit were small when a preponderance of subcategories were included. The high accuracy for all end-member algorithms was the result of data acquisition and data processing improvements, e.g., increased vertical sampling resolution to less than 1mm and a boundary constraint to mitigate wave focusing effects, respectively. An independent evaluation with a historical database confirmed the consistency of the algorithmic approach and its application to quality assurance, e.g., to flag data outside expected ranges, identify suspect spectra, and objectively determine the in-water extrapolation interval by converging agreement for all applicable end-member algorithms. The legacy data exhibit degraded performance (as 44 % uncertainty) due to a lack of high-quality near-surface observations, especially for clear waters wherein wave-focusing effects are problematic. The novel optical approach allows the in situ estimation of an in-water constituent in keeping with the accuracy obtained in the laboratory.

Stanford B Hooker↗

High-level coupled-cluster energetics by merging moment expansions with selected configuration interaction

Inspired by our earlier semi-stochastic work aimed at converging high-level coupled-cluster (CC) energetics, we propose a novel form of the CC(P; Q) theory in which the stochastic Quantum Monte Carlo propagations, used to identify dominant higher-than-doubly excited determinants, are replaced by the selected configuration interaction (CI) approach using the perturbative selection made iteratively (CIPSI) algorithm. The advantages of the resulting CIPSI-driven CC(P; Q) methodology are illustrated by a few molecular examples, including the dissociation of F 2 and the automerization of cyclobutadiene, where we recover the electronic energies corresponding to the CC calculations with a full treatment of singles, doubles, and triples based on the information extracted from compact CI wave functions originating from relatively inexpensive Hamiltonian diagonalizations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗