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At least 91 records · Page 5

Decoding diffraction and spectroscopy data with machine learning: A tutorial

This Tutorial provides a step-by-step guide on how to apply supervised machine-learning techniques to analyze diffraction and spectroscopy data. This Tutorial details four models—a reconstruction-focused model, a regression-focused model, a hybrid reconstruction/regression model, and a multimodal model—that use x-ray diffraction profiles and vibrational density of states spectra to predict various microstructural descriptors. In this Tutorial, we cover data pre-processing steps, constructions of the models via dimensionality reduction and regression, training, and analysis of these models. Comparisons of the model’s performance are provided, highlighting the strength and weakness of the various approaches utilized.

36 MATERIALS SCIENCE↗

Viterbi decoding of CRES signals in Project 8

Abstract Cyclotron radiation emission spectroscopy (CRES) is a modern approach for determining charged particle energies via high-precision frequency measurements of the emitted cyclotron radiation. For CRES experiments with gas within the fiducial volume, signal and noise dynamics can be modelled by a hidden Markov model. We introduce a novel application of the Viterbi algorithm in order to derive informational limits on the optimal detection of cyclotron radiation signals in this class of gas-filled CRES experiments, thereby providing concrete limits from which future reconstruction algorithms, as well as detector designs, can be constrained. The validity of the resultant decision rules is confirmed using both Monte Carlo and Project 8 data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Active causal learning for decoding chemical complexities with targeted interventions

Abstract Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have become standard for predictions, but they face challenges when applied across different datasets due to reliance on correlations between molecular representation and target properties. These approaches typically depend on large datasets to capture the diversity within the chemical space, facilitating a more accurate approximation, interpolation, or extrapolation of the chemical behavior of molecules. In our research, we introduce an active learning approach that discerns underlying cause-effect relationships through strategic sampling with the use of a graph loss function. This method identifies the smallest subset of the dataset capable of encoding the most information representative of a much larger chemical space. The identified causal relations are then leveraged to conduct systematic interventions, optimizing the design task within a chemical space that the models have not encountered previously. While our implementation focused on the QM9 quantum-chemical dataset for a specific design task—finding molecules with a large dipole moment—our active causal learning approach, driven by intelligent sampling and interventions, holds potential for broader applications in molecular, materials design and discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Decoding crops one cell at a time: from cell atlases to single-cell genetics

Understanding the mechanisms underlying key agricultural traits remains a central challenge in crop research, but recent advances in technologies are providing powerful tools to address this issue. Among these, single-cell and spatial transcriptomics have revealed tissue heterogeneity and spatial organization, offering unique insights into cellular gene expression dynamics and the coordinated activity of multiple cell types. These approaches help uncover how specific cell types contribute to agricultural traits and refine candidate loci lists through integration with trait-associated loci. Additionally, single-cell and spatial transcriptomics have the potential to serve as cell-level readout platforms integrating cellular perturbations, enabling high-throughput discovery of causal relationships between genotype and gene expression at the cellular level in plants. Successful implementation will accelerate the identification of key genetic variants for crop improvement. Furthermore we review lessons learned from application of single-cell screening in mammalian cells, highlight major technical and biological barriers to its use in plants, and outline potential strategies to overcome these challenges. Together, the widespread application and integration of single-cell and spatial transcriptomics with other technologies enable not only the descriptive cataloging of cell states but also the causal interrogation of sequence functions and regulatory networks at cell type resolution, ultimately advancing gene function studies and accelerating crop improvement.

Cellular heterogeneity↗

Decoding the star forming properties of gas-rich galaxy pairs

Here we extend the analysis of Bok et al. (2020) in which the H i content of isolated galaxies from the AMIGA (Analysis of the interstellar Medium in Isolated GAlaxies) sample and selected paired galaxies from ALFALFA (Arecibo Legacy Fast ALFA) were examined as a potential driver of galaxy location on the WISE (Wide-field Infrared Survey Explorer) mid-infrared SFR–M * sequence. By further characterizing the isolated and pair galaxy samples, i.e. in terms of optical galaxy morphology, a more detailed and quantitative description of local galaxy environment by way of the local number density (η) and tidal strength (Q) parameters, star formation efficiency (SFE HI ), and H i integrated profile asymmetries, we present plausible pathways for the broadening of the pair sample H i deficiency distribution towards both high and low deficiencies compared to the narrower isolated galaxy sample distribution (i.e. σ PAIRS = 0.34 versus σ AMIGA = 0.28). We associate the gas-rich tail of the pair deficiency distribution with the highest Q values, large profile asymmetries, and low SFEs. From this, we infer that merger activity is enhancing gas supplies, as well as disrupting the efficiency of star formation, via strong gravitational torques. The gas-poor wing of the deficiency distribution appears to be populated with galaxies in denser environments (with larger η values on average), more akin to groups. Despite our gas-rich selection criterion, there is a small population of early-type galaxies in the pair sample, which primarily fall in the positive deficiency wing of the distribution. These results suggest that a combination of a denser galaxy environment, early-type morphology, and higher stellar mass is contributing to the broadening of the deficiency distribution towards larger deficiencies.

79 ASTRONOMY AND ASTROPHYSICS↗

Decoding the age–chemical structure of the Milky Way disc: an application of copulas and elicitable maps

In the Milky Way, the distribution of stars in the [α/Fe] versus [Fe/H] and [Fe/H] versus age planes holds essential information about the history of star formation, accretion, and dynamical evolution of the Galactic disc. We investigate these planes by applying novel statistical methods called copulas and elicitable maps to the ages and abundances of red giants in the Apache Point Observatory Galactic Evolution Experiment survey. We find that the high- and low-α disc stars have a clean separation in copula space and use this to provide an automated separation of the α sequences using a purely statistical approach. This separation reveals that the high-α disc ends at the same [α/Fe] and age at high [Fe/H] as the low-[Fe/H] start of the low-α disc, thus supporting a sequential formation scenario for the high- and low-α discs. We then combine copulas with elicitable maps to precisely obtain the correlation between stellar age τ and metallicity [Fe/H] conditional on Galactocentric radius R and height z in the range 0 < R < 20 kpc and |z| < 2 kpc. The resulting trends in the age–metallicity correlation with radius, height, and [α/Fe] demonstrate a ≈0 correlation wherever kinematically cold orbits dominate, while the naively expected negative correlation is present where kinematically hot orbits dominate. This is consistent with the effects of spiral-driven radial migration, which must be strong enough to completely flatten the age–metallicity structure of the low-α disc.

79 ASTRONOMY AND ASTROPHYSICS↗

Decoding the B → K ν ν excess at Belle II: Kinematics, operators, and masses

An excess in the branching fraction for B + → K + ν ν recently measured at Belle II may be a hint of new physics. We perform thorough likelihood analyses for different new physics scenarios such as B → K X with a new invisible particle X , or B → K χ χ through a scalar, vector, or tensor current with χ being a new invisible particle or a neutrino. We find that vector-current three-body decay with m X ≃ 0.6 GeV—which may be dark matter—is most favored, while two-body decay with m X ≃ 2 GeV is also competitive. The best-fit branching fractions for the scalar and tensor cases are a few times larger than for the two-body and vector cases. Past measurements provide further discrimination, although the best-fit parameters stay similar. Published by the American Physical Society 2024

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Decoding polymer self-dynamics using a two-step approach

The self-correlation function and corresponding self-intermediate scattering function in Fourier space are important quantities for describing the molecular motions of liquids. This work draws attention to a largely overlooked issue concerning the analysis of these space-time density-density correlation functions of polymers. Here, we show that the interpretation of non-Gaussian behavior of polymers is generally complicated by intrachain averaging of distinct self-dynamics of different segments. By the very nature of the mathematics involved, the averaging process not only conceals critical dynamical information, but also contributes to the observed non-Gaussian dynamics. To fully expose this issue and provide a thorough benchmark of polymer self-dynamics, we perform analyses of coarse-grained molecular dynamics simulations of linear and ring polymer melts as well as several theoretical models using a “two-step” approach, where interchain and intrachain averagings of segmental self-dynamics are separated. While past investigations primarily focused on the average behavior, our results indicate that a more nuanced approach to polymer self-dynamics is clearly required.

36 MATERIALS SCIENCE↗

Decoding structure-spectrum relationships with physically organized latent spaces

Here, a semisupervised machine learning method for the discovery of structure-spectrum relationships is developed and then demonstrated using the specific example of interpreting x-ray absorption near-edge structure (XANES) spectra. This method constructs a one-to-one mapping between individual structure descriptors and spectral trends. Specifically, an adversarial autoencoder is augmented with a rank constraint (RankAAE). The RankAAE methodology produces a continuous and interpretable latent space, where each dimension can track an individual structure descriptor. As a part of this process, the model provides a robust and quantitative measure of the structure-spectrum relationship by decoupling intertwined spectral contributions from multiple structural characteristics. This makes it ideal for spectral interpretation and the discovery of descriptors. The capability of this procedure is showcased by considering five local structure descriptors and a database of >50 000 simulated XANES spectra across eight first-row transition metal oxide families. The resulting structure-spectrum relationships not only reproduce known trends in the literature but also reveal unintuitive ones that are visually indiscernible in large datasets. The results suggest that the RankAAE methodology has great potential to assist researchers in interpreting complex scientific data, testing physical hypotheses, and revealing patterns that extend scientific insight.

36 MATERIALS SCIENCE↗

DaYu: Optimizing Distributed Scientific Workflows by Decoding Dataflow Semantics and Dynamics

The combination of ever-growing scientific datasets and distributed workflow complexity creates I/O performance bottlenecks due to data volume, velocity, and variety. Although the increasing use of descriptive data formats (e.g., HDF5, netCDF) helps organize these datasets, it also creates obscure bottlenecks due to the need to translate high level operations into file addresses and then into low-level I/O operations. To address this challenge, we introduce DaYu, a method and toolset for analyzing (a) semantic relationships between logical datasets and file addresses, (b) how dataset operations translate into I/O, and (c) the combination across entire workflows. DaYu's analysis and visualization enables identification of critical bottlenecks and reasoning about remediation. We describe our methodology and propose optimization guidelines. Evaluation on scientific workflows demonstrates up to 3.7x performance improvements in I/O time for obscure bottlenecks. The time and storage overhead for DaYu's time-ordered data is typically under 0.2% of runtime and 0.25% of data volume, respectively.

Tang, Meng↗

Decoding Ethiopian Abodes: Towards Classifying Buildings by Occupancy Type Using Footprint Morphology

Building occupancy classification plays a crucial role in urban planning, disaster management, and population modeling. Traditional methods often require extensive field surveys or detailed datasets, which can be time-consuming, expensive, and may yield incomplete or erroneous data. In this paper, we present a novel approach for classifying buildings as residential or non-residential using only building footprint data. By extracting geometric shape derivatives that characterize building morphology, we developed a high-accuracy classification model employing a combination of unsupervised and supervised learning methods. We utilized open-source data from Open Street Map, aggregating it to create binary labels for buildings based on their respective human use type. Our approach demonstrates the potential for scalability without the need for additional data sources other than building footprints and labels, offering a more efficient solution for building occupancy classification.

Adams, Daniel↗

Decoding Resilience by Modeling Outage and Restoration Processes in Distribution Grids: A Pittsburgh Case Study

Climate-induced extreme weather events, such as floods and heatwaves, pose significant challenges to the resilience of urban power distribution grids. This paper examines the outage and restoration dynamics of Pittsburgh's power grid during the flood event in April 2024 and three heatwaves in June, July, and August 2024. We introduce a comprehensive modeling framework that integrates outage and restoration processes, enabling the quantification of resilience metrics, including total customer-hours of power outage, maximum residual values, and restoration durations across various ZIP codes. Our analysis highlights spatial disparities in outage impacts and restoration efficiencies, with ZIP Code 15222 experiencing the highest cumulative disruptions, while ZIP Code 15217 shows lower susceptibility. By linking statistical trends with weather events, this study underscores the critical need for targeted infrastructure upgrades and advanced restoration strategies. Furthermore, the proposed framework offers valuable insights for planning and managing resilient power systems in the face of increasing climate stress.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Hidden Allies: Decoding the Core Endohyphal Bacteriome of Aspergillus fumigatus

ABSTRACT Bacterial–fungal interactions that influence the behaviour of one or both organisms are common in nature. Well‐studied systems include endosymbiotic relationships that range from transient to long‐term associations. Diverse endohyphal bacteria associate with fungal hosts, emphasising the need to better comprehend the fungal bacteriome. We evaluated the hypothesis thatAspergillus fumigatusharbours an endohyphal community of bacteria that influence the host phenotype. We analysed whether 38A. fumigatusstrains show stable association with diverse endohyphal bacteria; all derived from single‐conidium cultures that were subjected to antibiotic and heat treatments. The fungal bacteriome, inferred through analysis of bacterial diversity within the fungal strains (short‐ and long‐ read sequencing methods), revealed the presence of core endohyphal bacterial genera. Microscopic analysis further confirmed the presence of endohyphal bacteria. The fungal strains exhibited high genetic diversity and phenotypic heterogeneity in drug susceptibility and in vivo virulence. No correlations were observed between genomic or functional traits and bacteriome diversity, but the abundance of some bacterial genera correlated with fungal virulence or posaconazole susceptibility. The observed endobacteriome may play functional roles, for example, nitrogen fixation. Our study emphasises the existence of complex interactions between fungi and endohyphal bacteria, possibly impacting the phenotype of the fungal host, including virulence.

Environmental Sciences & Ecology↗

Decoding the interstitial/vacancy nature of dislocation loops with their morphological fingerprints in face-centered cubic structure

Dislocation loops are critical defects inducing detrimental effects like embrittlement and swelling in materials under irradiation. Distinguishing their nature (interstitial- or vacancy-type) is a long-standing challenge with great implications for understanding radiation damage. Here, we demonstrate that the morphology of radiation-induced Frank loops can unveil their nature in face-centered cubic (fcc) structure: Circular loops are interstitial-type in all fcc materials, while segmented loops are vacancy-type in high stacking fault energy (SFE) alloys but varied-type in low SFE and high-entropy alloys. The polygonal shape is attributed to the dissociation of an a 0 /3<111> dislocation into an a 0 /6<112> Shockley partial and an a 0 /6<110> stair-rod dislocation. The dissociation of vacancy loops is energetically favorable, whereas interstitial loops require external stimuli to promote dislocation propagation. This “morphology-nature” correlation not only highlights the asymmetry of vacancy/interstitial loops but also offers an efficient way to distinguish loop nature for a wide range of materials.

Ma, Kan [City Univ. of Hong Kong, Kowloon (Hong Ko↗