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At least 271 records · Page 15

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗

The axis ratio distribution of faint galaxies: Evidence for a populatin of dwarfgalaxies at I approximately 20.5

The axis ratio distribution of faint galaxies observed by the Hubble Space Telescope (HST) as part of the Medium Deep Survey (MDS) key project suggests that a very large fraction of the total population at magnitudes I greater than or equal to 20 mag consists of a class of galaxies with luminosity profile, axis ratio distribution, angular size, and color that resemble local dwarfs. We find that galaxies with exponential light profiles and small angular sizes (half-light radius less than 0.6 sec) have an axis ratio distribution that is incompatible with their being intrinsically flattened objects and is instead consistent with local elliptical galaxies. We call these objects 'Small Exponential Ellipticals.' They are most likely dwarf galaxies, and they are numerous enough that, together with irregular galaxies, they can account for most if not all of the excess in the number counts at I approximately 20-21 mag with respect to the standard no-evolution models. This may suggest that the excess number counts are best explained by dwarf-rich models with strong luminosity evolution of the dwarf galaxies. Our data also supports a very mild luminosity evolution of the giant galaxy populations, which contributes little to the excess number counts.

Im, Myungshin↗

Development of a broadband hard x-ray radiography platform for pulsed-power experiments

In this article, we develop and demonstrate a broadband hard x-ray radiography platform at the Zebra Pulsed Power Laboratory that integrates point-projection radiography, bremsstrahlung measurements, and hard x-ray pinhole imaging, designed to diagnose current-driven, cylindrically compressed matter. Initial laser-pulsed-power coupled experiments revealed that intense background radiation generated during 1 MA Zebra current shots overwhelmed laser-produced hard x-rays, obscuring radiographic images. Using combined spectral and spatial diagnostics, we identify energetic electrons accelerated by return currents as the dominant source of background hard x-rays, with electron energies inferred to be 3–4 MeV based on Monte Carlo simulations, and demonstrate mitigation through modifications to the radiation shielding and return-current configuration. The diagnostic platform was validated using a wire-pinch hard x-ray source, allowing radiographs of static 1-mm-diameter aluminum wires to be obtained while simultaneously measuring x-ray source spectra and spatial emission distributions within a single shot. Measured wire transmission profiles were quantitatively reconstructed using radiation transport simulations that incorporate an experimentally inferred two-temperature exponential x-ray spectrum from bremsstrahlung signal analysis and spatially distributed emission sources identified by pinhole imaging. Agreement between measured and simulated transmission profiles demonstrates the validity of the radiographic and x-ray source characterization approach, establishing this diagnostic platform as a promising tool for diagnosing magnetically driven, high-density plasmas relevant to warm dense matter and inertial fusion energy research.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

The reproduction number and its probability distribution for stochastic viral dynamics

We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.

59 BASIC BIOLOGICAL SCIENCES↗

Finite Control in Underdamped Distributed Parameter Systems

Specifically, a class of distributed parameter systems is defined using Hilbert space methods based on a partial differential equation model of a structure. In this space a simple, easy to check definition of underdamping is constructed based on the well known single degree of freedom concept of critical damping. It is then shown that if a given distributed parameter system satisfies this definition, each mode of the modal expansion of the solution is in fact an underdamped function of time. It is noted that a distributed parameter system which is underdamped is also uniformly exponentially stable. By appealing to the work of Gibson, a finite dimensional model of the system will yield satisfactory control laws. Furthermore, it is shown that the assumption of the underdamping also allows straightforward computation of rough bounds on the magnitude of the unmodeled or residual modes for a modal truncation scheme. Hence, underdamped systems are precisely that class of distributed parameter systems which are not likely to have spillover problems and which will yield convergence of finite dimensional control laws to control laws which are optimal for the full distributed parameter model of the system.

Inman, D. J.↗

Non-linear dynamics of jet quenching

We develop a comprehensive analytic framework for jet quenching in QCD media, based on a medium-induced parton cascade sourced by collinear virtual splittings. We show that the energy flow out of the jet cone, driven by turbulent gluon cascades, is governed by a non-linear rate equation that resums gluon splittings at arbitrary angles and is enhanced by the medium length, L. The solution of this equation sets the initial condition for a non-linear DGLAP-like evolution equation, which describes the collinear early vacuum cascade resolved by the medium at angles exceeding the medium resolution angle, θ c . For asymptotic jet energies, the medium-induced cascade displays an exponential behavior that generalizes the Poisson-like distribution of parton energy loss. This formulation enables the resummation of leading contributions in α s ln(1/R), and α s ln(R/θ c ), and powers of α s L. We briefly explore the limit of strong quenching, where analytic treatments are feasible, offering insights into the impact of parton cascades on jet quenching. These results provide guidance for future numerical simulations and analytical investigations.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Origin of medium-range atomic correlation in simple liquids: Density wave theory

The atomic pair-distribution function of simple liquid and glass shows exponentially decaying oscillations beyond the first peak, representing the medium-range order (MRO). The structural coherence length that characterizes the exponential decay increases with decreasing temperature and freezes at the glass transition. Conventionally, the structure of liquid and glass is elucidated by focusing on a center atom and its neighboring atom shell characterized by the short-range order (SRO) and describing the global structure in terms of overlapping local clusters of atoms as building units. However, this local bottom-up approach fails to explain the strong drive to form the MRO, which is different in nature from the SRO. We propose to add an alternative top-down approach based upon the density wave theory. In this approach, one starts with a high-density gas state and seeks to minimize the global potential energy in reciprocal space through density waves using the pseudopotential. The local bottom-up and global top-down driving forces are not mutually compatible, and the competition and compromise between them result in a final structure with the MRO. This even-handed approach provides a more intuitive explanation of the structure of simple liquid and glass.

42 ENGINEERING↗

Theory and modeling of molecular modes in the NMR relaxation of fluids

Traditional theories of the nuclear magnetic resonance (NMR) autocorrelation function for intra-molecular dipole pairs assume a single-exponential decay, yet the calculated autocorrelation of realistic systems displays a rich, multi-exponential behavior, resulting in anomalous NMR relaxation dispersion (i.e., frequency dependence). We develop an approach to model and interpret the multi-exponential intra-molecular autocorrelation using simple, physical models within a rigorous statistical mechanical development that encompasses both rotational diffusion and translational diffusion in the same framework. Here, we recast the problem of evaluating the autocorrelation in terms of averaging over a diffusion propagator whose evolution is described by a Fokker–Planck equation. The time-independent part admits an eigenfunction expansion, allowing us to write the propagator as a sum over modes. Each mode has a spatial part that depends on the specified eigenfunction and a temporal part that depends on the corresponding eigenvalue (i.e., correlation time) with a simple, exponential decay. The spatial part is a probability distribution of the dipole pair, analogous to the stationary states of a quantum harmonic oscillator. Drawing inspiration from the idea of inherent structures in liquids, we interpret each of the spatial contributions as a specific molecular mode. These modes can be used to model and predict the NMR dipole–dipole relaxation dispersion of fluids by incorporating phenomena on the molecular level. We validate our statistical mechanical description of the distribution in molecular modes with molecular dynamics simulations interpreted without any relaxation models or adjustable parameters: the most important poles in the Padé–Laplace transform of the simulated autocorrelation agree with the eigenvalues predicted by the theory

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

C/2014 UN 271 (Bernardinelli-Bernstein): The Nearly Spherical Cow of Comets

Abstract Comet C/2014 UN 271 (Bernardinelli-Bernstein), incoming from the Oort cloud, is remarkable in having the brightest (and presumably largest) nucleus of any well-measured comet and having been discovered at the heliocentric distance r h ≈ 29 au, farther than any Oort cloud comet. In this work, we describe the discovery process and observations and the properties that can be inferred from images recorded until the first reports of activity in 2021 June. The orbit has i = 95°, with a perihelion of 10.97 au to be reached in 2031 and a previous aphelion at 40,400 ± 260 au. Backward integration of the orbit under a standard Galactic tidal model and known stellar encounters suggests a perihelion of q ≈ 18 au on its previous perihelion passage 3.5 Myr ago; hence, the current data could be the first ever obtained of a comet that has not been inside Uranus’s orbit in 4 Gyr. The photometric data show an unresolved nucleus with absolute magnitude H r = 8.0, colors that are typical of comet nuclei or Damocloids, and no secular trend as it traversed the range 34–23 au. For the r -band geometric albedo p r , this implies a diameter of 150 ( p r / 0.04 ) − 0.5 km. There is strong evidence of brightness fluctuations at the ±0.2 mag level, but no rotation period can be discerned. A coma, nominally consistent with a “stationary” 1/ ρ surface brightness distribution, grew in scattering cross section at an exponential rate from A f ρ ≈ 1 to ≈150 m as the comet approached from 28 to 20 au. The activity rate is consistent with a very simple model of sublimation of a surface species in radiative equilibrium with the Sun. The inferred enthalpy of sublimation matches those of CO 2 and NH 3 . More volatile species, such as N 2 , CH 4 , and CO, must be far less abundant on the sublimating surfaces.

79 ASTRONOMY AND ASTROPHYSICS↗

Minimum distortion quantizers

The well-known algorithm of Max is used to determine the minimum distortion quantizers for normal, two-sided exponential, and specialized two-sided gamma input distributions and for mean-square, magnitude, and relative magnitude error distortion criteria. The optimum equally-spaced and unequally-spaced quantizers are found, with the resulting quantizer distortion and entropy. The quantizers, and the quantizers with entropy coding, are compared to the rate distortion bounds for mean-square and magnitude error.

Jones, H. W., Jr.↗

Gamma-ray bursts and neutron star field decay

Assuming a Galactic origin of gamma-ray bursts, we use pulsar data to calculate the spatial distribution of neutron stars and determine the sampling depths of current detectors. Based on these distance limits, we calculate the corresponding age distribution of Galactic neutron stars and apply an exponential field decay model to test whether the observed high incidence rate of cyclotron lines is consistent with suggested field decay time scales of order 10 exp 7 years. We find that the properties of the observed population of gamma-ray bursts are inconsistent with the idea that bursts originate at arbitrary times on neutron stars whose fields decay on time scales shorter than about 10 exp 9 years. Possible interpretations of this inconsistency are discussed.

Hartmann, Dieter↗

NGC 4314. II - Hubble Space Telescope I-band surface photometry of the nuclear region

We present an HST I-band Planetary Camera image of the nuclear region of NGC 4314, an anemic barred galaxy with recent star formation confined to a nuclear ring. These data resolve the nuclear ring into multiple sites of new star formation and resolve associated dust lanes into discrete clouds. Deconvolution results in at least 0.13 arcsec resolution, as demonstrated by the de Vaucouleurs r exp 1/4 law. Contrasted with similar studies of M87 and NGC 7457, we find no photometric evidence for an extreme concentration of stars in the center of NGC 4314. We identify an oval distortion of length 8 arcsec in the nuclear region, using ellipse-fitting routines and the unsharp masked frame. This nuclear bar has newer stars near its ends. We catalog 14 star clusters associated with H II regions in the nuclear ring. As an additional demonstration of the resolution achieved, the integral size distribution of these clusters is described by an exponential relationship which prevails down to 0.14 arcsec.

Benedict, G. F.↗

Geology of the Gusec cratered plains from the Spirit rover transverse

The cratered plains of Gusev traversed by Spirit are generally low-relief rocky plains dominated by impact and eolian processes. Ubiquitous shallow, soil-filled, circular depressions, called hollows, are modified impact craters. Rocks are dark, fine-grained basalts, and the upper 10 m of the cratered plains appears to be an impact-generated regolith developed over intact basalt flows. Systematic field observations across the cratered plains identified vesicular clasts and rare scoria similar to original lava flow tops, consistent with an upper inflated surface of lava flows with adjacent collapse depressions. Crater and hollow morphometry are consistent with most being secondaries. The size frequency distribution of rocks >0.1 m diameter generally follows exponential functions similar to other landing sites for total rock abundances of 5-35%. Systematic clast counts show that areas with higher rock abundance and more large rocks have higher thermal inertia. Plains with lower thermal inertia have fewer rocks and substantially more pebbles that are well sorted and evenly spaced, similar to a desert pavement or lag. Eolian bed forms (ripples and wind tails) have coarse surface lags, and many are dust covered and thus likely inactive. Deflation of the surface _5-25 cm likely exposed two-toned rocks and elevated ventifacts and transported fines into craters creating the hollows. This observed redistribution yields extremely slow average erosion rates of _0.03 nm/yr and argues for very little long-term net change of the surface and a dry and desiccating environment similar to today's since the Hesperian (or _3 Ga).

Spirit↗

Emperical Tests of Acceptance Sampling Plans

Acceptance sampling is a quality control procedure applied as an alternative to 100% inspection. A random sample of items is drawn from a lot to determine the fraction of items which have a required quality characteristic. Both the number of items to be inspected and the criterion for determining conformance of the lot to the requirement are given by an appropriate sampling plan with specified risks of Type I and Type II sampling errors. In this paper, we present the results of empirical tests of the accuracy of selected sampling plans reported in the literature. These plans are for measureable quality characteristics which are known have either binomial, exponential, normal, gamma, Weibull, inverse Gaussian, or Poisson distributions. In the main, results support the accepted wisdom that variables acceptance plans are superior to attributes (binomial) acceptance plans, in the sense that these provide comparable protection against risks at reduced sampling cost. For the Gaussian and Weibull plans, however, there are ranges of the shape parameters for which the required sample sizes are in fact larger than the corresponding attributes plans, dramatically so for instances of large skew. Tests further confirm that the published inverse-Gaussian (IG) plan is flawed, as reported by White and Johnson (2011).

White, K. Preston, Jr.↗

CLEAR: Boosted Ly alpha Transmission of the Intergalactic Medium in UV-bright Galaxies

Reionization is an inhomogeneous process, thought to begin in small ionized bubbles of the intergalacticmedium (IGM) around overdense regions of galaxies. Recent Lyman-alpha (Lyα) studies during the epochof reionization show growing evidence that ionized bubbles formed earlier around brighter galaxies, suggest-ing higher IGM transmission of Lyαfrom these galaxies. We investigate this problem using IR slitless spec-troscopy from the Hubble Space Telescope (HST) Wide-Field Camera 3 (WFC3) G102 grism observations of148 galaxies selected via photometric redshifts at6.0< z <8.2. These galaxies have spectra extracted fromthe CANDELS LyαEmission at Reionization (CLEAR) survey. We combine the CLEAR data for 275 galaxieswith the Keck/DEIMOS+MOSFIRE dataset from the Texas Spectroscopic Search for LyαEmission at the Endof Reionization Survey. We then constrain the Lyαequivalent-width (EW) distribution at6.0< z <8.2, whichis described by an exponential form,dN/dEW∝exp(-EW)/W0, with the characteristice-folding scale width(W0). We confirm a significant drop of the Lyαstrength (orW0) atz >6. Furthermore, we compare the redshiftevolution ofW0between galaxies at different UV luminosities. The UV-bright (MUV<−21, orLUV> L∗)galaxies show weaker evolution with a decrease of 0.4 (±0.2) dex inW0atz >6while UV-faint (MUV>−21,orLUV< L∗) galaxies exhibit a significant drop by a factor of 0.7-0.8 (±0.2) dex inW0fromz <6toz >6.Our results add to the accumulating evidence that UV-bright galaxies exhibit boosted Lyαtransmission in theIGM, suggesting that reionization completes sooner in regions proximate to galaxies of higher UV luminosity.

Intae Jung↗

Disk plus halo models of gamma-ray burst sources

The present consideration of Gaussian halo, exponential halo, and standard 'dark matter' halo forms for the distribution of Galactic halo sources indicates that about 70 percent of the gamma-ray bursts observed by the BATSE program can come from local Galactic disk neutron stars, with the rest lying in an extended Galactic halo. Two specific disk-halo combinations are considered as examples which use an exponential disk; in the first case, this is combined with a Gaussian halo, and in the second, with a dark matter halo.

Smith, I. A.↗

Modulation of lens cell adhesion molecules by particle beams

Cell adhesion molecules (CAMs) are proteins which anchor cells to each other and to the extracellular matrix (ECM), but whose functions also include signal transduction, differentiation, and apoptosis. We are testing a hypothesis that particle radiations modulate CAM expression and this contributes to radiation-induced lens opacification. We observed dose-dependent changes in the expression of beta 1-integrin and ICAM-1 in exponentially-growing and confluent cells of a differentiating human lens epithelial cell model after exposure to particle beams. Human lens epithelial (HLE) cells, less than 10 passages after their initial culture from fetal tissue, were grown on bovine corneal endothelial cell-derived ECM in medium containing 15% fetal bovine serum and supplemented with 5 ng/ml basic fibroblast growth factor (FGF-2). Multiple cell populations at three different stages of differentiation were prepared for experiment: cells in exponential growth, and cells at 5 and 10 days post-confluence. The differentiation status of cells was characterized morphologically by digital image analysis, and biochemically by Western blotting using lens epithelial and fiber cell-specific markers. Cultures were irradiated with single doses (4, 8 or 12 Gy) of 55 MeV protons and, along with unirradiated control samples, were fixed using -20 degrees C methanol at 6 hours after exposure. Replicate experiments and similar experiments with helium ions are in progress. The intracellular localization of beta 1-integrin and ICAM-1 was detected by immunofluorescence using monoclonal antibodies specific for each CAM. Cells known to express each CAM were also processed as positive controls. Both exponentially-growing and confluent, differentiating cells demonstrated a dramatic proton-dose-dependent modulation (upregulation for exponential cells, downregulation for confluent cells) and a change in the intracellular distribution of the beta 1-integrin, compared to unirradiated controls. In contrast, there was a dose-dependent increase in ICAM-1 immunofluorescence in confluent, but not exponentially-growing cells. These results suggest that proton irradiation downregulates beta 1-integrin and upregulates ICAM-1, potentially contributing to cell death or to aberrant differentiation via modulation of anchorage and/or signal transduction functions. Quantification of the expression levels of the CAMs by Western analysis is in progress.

NASA Discipline Radiation Health↗