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At least 253 records · Page 14

OC7 Project Phase II: Code Comparison and Experimental Validation of Hydroelastic Effects and Member-Level Loads in Floating Structures

This paper presents results from Phase II of the OC7 project, focusing on hydroelastic modeling and member-level load prediction for a flexible floating offshore structure. Numerical predictions from 11 academic and industrial partners are validated against experimental measurements obtained from a 1:70-scale test of the VolturnUS-S semisubmersible platform. A comprehensive set of verification and validation cases is examined. The results demonstrate that hydrodynamic added mass has a significant impact on predicted elastic natural frequencies. Under regular wave excitation, the numerical models reproduce platform motions and mooring line tensions with good accuracy. Member-level loads are also predicted with reasonable accuracy. Some discrepancies are observed for potential-flow models not accounting for higher-order effects associated with the instantaneous wetted surface.

17 WIND ENERGY↗

Paired autoencoders for likelihood-free estimation in inverse problems

Abstract We consider the solution of nonlinear inverse problems where the forward problem is a discretization of a partial differential equation. Such problems are notoriously difficult to solve in practice and require minimizing a combination of a data-fit term and a regularization term. The main computational bottleneck of typical algorithms is the direct estimation of the data misfit. Therefore, likelihood-free approaches have become appealing alternatives. Nonetheless, difficulties in generalization and limitations in accuracy have hindered their broader utility and applicability. In this work, we use a paired autoencoder framework as a likelihood-free estimator (LFE) for inverse problems. We show that the use of such an architecture allows us to construct a solution efficiently and to overcome some known open problems when using LFEs. In particular, our framework can assess the quality of the solution and improve on it if needed. We demonstrate the viability of our approach using examples from full waveform inversion and inverse electromagnetic imaging.

Chung, Matthias (ORCID:0000000178224539)↗

SymbolNet: neural symbolic regression with adaptive dynamic pruning for compression

Abstract Compact symbolic expressions have been shown to be more efficient than neural network (NN) models in terms of resource consumption and inference speed when implemented on custom hardware such as field-programmable gate arrays (FPGAs), while maintaining comparable accuracy (Tsoi et al 2024 EPJ Web Conf. 295 09036). These capabilities are highly valuable in environments with stringent computational resource constraints, such as high-energy physics experiments at the CERN Large Hadron Collider. However, finding compact expressions for high-dimensional datasets remains challenging due to the inherent limitations of genetic programming (GP), the search algorithm of most symbolic regression (SR) methods. Contrary to GP, the NN approach to SR offers scalability to high-dimensional inputs and leverages gradient methods for faster equation searching. Common ways of constraining expression complexity often involve multistage pruning with fine-tuning, which can result in significant performance loss. In this work, we propose S y m b o l N e t , a NN approach to SR specifically designed as a model compression technique, aimed at enabling low-latency inference for high-dimensional inputs on custom hardware such as FPGAs. This framework allows dynamic pruning of model weights, input features, and mathematical operators in a single training process, where both training loss and expression complexity are optimized simultaneously. We introduce a sparsity regularization term for each pruning type, which can adaptively adjust its strength, leading to convergence at a target sparsity ratio. Unlike most existing SR methods that struggle with datasets containing more than O ( 10 ) inputs, we demonstrate the effectiveness of our model on the LHC jet tagging task (16 inputs), MNIST (784 inputs), and SVHN (3072 inputs).

Tsoi, Ho Fung (ORCID:0000000225502184)↗

Overcoming sparse datasets with multi-task learning as applied to high entropy alloys

Abstract The design of novel High Entropy Alloys for use in high-temperature applications is an area of active interest due to their potential to provide exceptional properties compared to conventional alloys. Since the increased popularity of machine learning, an important cog in the design process has been training surrogate models on alloy properties. However, these Single-Task models are trained on individual mechanical properties and do not take advantage of the relatedness between properties. Multi-Task models can capture the interdependencies between tasks, leading to potentially more accurate predictions for all tasks. In this paper, we investigate if Multi-Task models can show improvement over Single-Task models when used for predicting the mechanical properties of these alloys. To ensure fair evaluation between the models, we apply L 0 regularization and skip connections to the models, which allows them to adjust the number of model parameters and depth for optimal performance. We find that the Multi-Task models can leverage task relationships to perform better than Single-Task models, especially for high amounts of missing data in the tasks. Furthermore, adding simple auxiliary targets can boost Multi-Task performance even further despite not being effective as input descriptors to single-task models themselves. We anticipate that the proposed strategies can achieve more accurate predictions and consequently enable better design capabilities for such data-constrained domains without incurring much additional computational cost.

Debnath, Arindam (ORCID:0000000194274499)↗

Physics-guided dual implicit neural representations for source separation

Significant challenges exist in efficient data analysis of most advanced experimental and observational techniques because the collected signals often include unwanted contributions, such as background and signal distortions, that can obscure the physically relevant information of interest. To address this, we have developed a self-supervised machine-learning approach for source separation using a dual implicit neural representation framework that jointly trains two neural networks: one for approximating distortions of the physical signal of interest and the other for learning the effective background contribution. Our method learns directly from the raw data by minimizing a reconstruction-based loss function without requiring labeled data or pre-defined dictionaries. We demonstrate the effectiveness of our framework by considering a challenging case study involving large-scale simulated, as well as experimental, momentum-energy-dependent inelastic neutron scattering data in a four-dimensional parameter space, characterized by heterogeneous background contributions and unknown distortions to the target signal. The method is found to successfully separate physically meaningful signals from a complex or structured background even when the signal characteristics vary across all four dimensions of the parameter space. An analytical approach that informs the choice of the regularization parameter is presented. Our method offers a versatile framework for addressing source separation problems across diverse domains, ranging from superimposed signals in astronomical measurements to structural features in biomedical image reconstructions.

47 OTHER INSTRUMENTATION↗

Data imbalance in drug response prediction: multi-objective optimization approach in deep learning setting

Abstract Drug response prediction (DRP) methods tackle the complex task of associating the effectiveness of small molecules with the specific genetic makeup of the patient. Anti-cancer DRP is a particularly challenging task requiring costly experiments as underlying pathogenic mechanisms are broad and associated with multiple genomic pathways. The scientific community has exerted significant efforts to generate public drug screening datasets, giving a path to various machine learning models that attempt to reason over complex data space of small compounds and biological characteristics of tumors. However, the data depth is still lacking compared to application domains like computer vision or natural language processing domains, limiting current learning capabilities. To combat this issue and improves the generalizability of the DRP models, we are exploring strategies that explicitly address the imbalance in the DRP datasets. We reframe the problem as a multi-objective optimization across multiple drugs to maximize deep learning model performance. We implement this approach by constructing Multi-Objective Optimization Regularized by Loss Entropy loss function and plugging it into a Deep Learning model. We demonstrate the utility of proposed drug discovery methods and make suggestions for further potential application of the work to achieve desirable outcomes in the healthcare field.

Biochemistry & Molecular Biology↗

LATTE: open-source, high-performance traveltime computation, tomography and source location in acoustic and elastic media

Traveltime-based tomography and source location are fundamental approaches for imaging subsurface structures and understanding the spatiotemporal distribution of seismicity from local to global scales. We present an open-source, high-performance framework integrating eikonal equation solvers and adjoint-state theory for traveltime computation, velocity tomography, source location and joint tomography-location in 2-D/3-D acoustic and elastic media. We introduce novel regularization schemes based on total generalized p-variation, structural similarity and multitask machine learning to enhance the fidelity and interpretability of inverted models and source locations. Key features of our implementation also include the ability to leverage both absolute-difference and double-difference traveltime misfits for high-fidelity velocity tomography and source parameter estimation; support for traveltime computation and inversion in diverse 2-D/3-D scenarios with arbitrary source and receiver distributions; and a perturbation-based optimal step-size estimation method to reduce computational costs. In addition, our implementation employs shared-memory and distributed-memory parallelization to provide an efficient solution for traveltime computation, tomography, and source location. In conclusion, we validate the efficacy and accuracy of our approach through multiple synthetic data examples.

58 GEOSCIENCES↗

Random Forest Prediction of Crystal Structure from Electron Diffraction Patterns

Transmission electron microscopy (TEM) diffraction patterns are regularly used to determine the structure of crystalline materials. Electron diffraction is the most common method to solve for unknown or partially known crystal structures, as it provides direct and interpretable feedback on the orientation of crystal grains under the beam [1]. However, it remains a challenge to determine the crystal structure of a new material or even a new phase of an existing material. Analysis of such materials commonly requires manual exploration and comparison with simulated diffraction patterns. This is often a time consuming process with no obvious start point when many similar structures are possible, and this method cannot be used to determine crystal structure or orientation from structures not included in the diffraction libraries. Therefore, we have developed a machine learning model to determine the crystal structure of a material from its electron diffraction pattern.

36 MATERIALS SCIENCE↗

Improved Three-Dimensional Reconstructions in Electron Ptychography through Defocus Series Measurements

A detailed analysis of ptychography for three-dimensional (3D) phase reconstructions of thick specimens is performed. Here, we introduce multi-focus ptychography, which incorporates a 4D-STEM defocus series to enhance the quality of 3D reconstructions along the beam direction through a higher overdetermination ratio. This method is compared with established multi-slice ptychography techniques, such as conventional ptychography, regularized ptychography, and multi-mode ptychography. Additionally, we contrast multi-focus ptychography with an alternative method that uses virtual optical sectioning through a reconstructed scattering matrix (S-matrix), which offers more precise 3D structure information compared to conventional ptychography. Our findings from multiple 3D reconstructions based on simulated and experimental data demonstrate that multi-focus ptychography surpasses other techniques, particularly in accurately reconstructing the surfaces and interface regions of thick specimens.

3D reconstruction↗

Fate of supernova progenitors in massive binary systems

ABSTRACT How massive stars end their lives depends on the core mass, core angular momentum, and hydrogen envelopes at death. However, these key physical facets of stellar evolution can be severely affected by binary interactions. In turn, the effectiveness of binary interactions itself varies greatly depending on the initial conditions of the binaries, making the situation much more complex. We investigate systematically how binary interactions influence core–collapse progenitors and their fates. Binary evolution simulations are performed to survey the parameter space of supernova progenitors in solar metallicity binary systems and to delineate major evolutionary paths. We first study fixed binary mass ratios ($q=M_2/M_1$ = 0.5, 0.7, and 0.9) to elucidate the impacts of initial mass and initial separation on the outcomes, treating separately Type Ibc supernova, Type II supernova, accretion-induced collapse (AIC), rapidly rotating supernova (Ibc-R), black hole formation, and long gamma ray burst (long GRB). We then conduct 12 binary population synthesis model calculations, varying the initial condition distributions and binary evolution parameters, to estimate various supernova fractions. We obtain a Milky Way supernova rate $R_{\rm SN} = (1.78$–$2.47) \times 10^{-2} \, {\rm yr}^{-1}$ which is consistent with observations. We find the rates of AIC, Ibc-R, and long GRB to be $\sim 1/100$ the rate of regular supernovae. Our estimated long GRB rates are higher than the observed long GRB rate and close to the low luminosity GRB rate, although care must be taken considering our models are computed with solar metallicity. Furthering binary modelling and improving the inputs one by one will enable more detailed studies of these and other transients associated with massive stars.

Astronomy & Astrophysics↗

The variability structure function of the highest luminosity quasars on short time-scales

ABSTRACT The stochastic photometric variability of quasars is known to follow a random-walk phenomenology on emission time-scales of months to years. Some high-cadence rest-frame optical monitoring in the past has hinted at a suppression of variability amplitudes on shorter time-scales of a few days or weeks, opening the question of what drives the suppression and how it might scale with quasar properties. Here, we study a few thousand of the highest luminosity quasars in the sky, mostly in the luminosity range of $L_{\rm bol}$$=[46.4, 47.3]$ and redshift range of $z=[0.7, 2.4]$. We use a data set from the NASA/Asteroid Terrestrial-impact Last Alert System facility with nightly cadence, weather permitting, which has been used before to quantify strong regularity in longer term rest-frame-UV variability. As we focus on a careful treatment of short time-scales across the sample, we find that a linear function is sufficient to describe the UV variability structure function. Although the result can not rule out the existence of breaks in some groups completely, a simpler model is usually favoured under this circumstance. In conclusion, the data are consistent with a single-slope random walk across rest-frame time-scales of $\Delta t=[10, 250]$ d.

Tang, Ji-Jia (ORCID:0000000218600886)↗

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗

Second-order renormalized Hamiltonian of Yukawa theory

Using the renormalization group procedure for effective particles we calculate the effective Hamiltonians in the theory of a fermion field coupled to a scalar field via the Yukawa interaction. The theory is renormalized by the addition of counterterms. Necessary counterterms are determined by computing matrix elements of the effective Hamiltonian. All calculations are performed up to the second order in the expansion in powers of the coupling constant. Renormalized effective Hamiltonians are well-defined symmetric forms acting in the Fock space as opposed to the renormalized bare Hamiltonian, which is not well defined without regularization. We introduce computational techniques that should streamline higher-order calculations and may be of independent interest.

Ab initio calculations↗

Quantum critical collapse abhors a naked singularity

Classical critical collapse yields naked singularities from smooth initial data, challenging cosmic censorship, and shaping the spectrum of primordial black holes. We show that one-loop vacuum polarization near the threshold qualitatively changes this outcome by dressing the singularity with a horizon within a controlled semiclassical regime. In analytically tractable Einstein-scalar critical spacetimes, a one-loop $s$-wave treatment linearized around self-similar backgrounds shows that regularity uniquely selects an asymptotically Minkowskian, vacuum-polarization state. Its renormalized stress tensor carries a universal quantum growing mode that competes with the classical unstable mode, shifts the critical point, and generates a trapped surface along with a finite mass gap at the new threshold, thereby enforcing horizon formation even under arbitrary fine-tuning. In primordial collapse, the threshold shift enters exponentially into the formation fraction, while the mass gap truncates the low-mass tail, suggesting potentially important consequences for the predicted mass spectrum. Furthermore, these results provide a self-consistent semiclassical treatment of critical collapse and yield sharp predictions within the one-loop, near-critical, linearized regime.

Anomalies↗

Quantum Ising model on (2+1)-dimensional anti–de Sitter space using tensor networks

We study the quantum Ising model on (2+1)-dimensional anti-de Sitter space using matrix product states (MPS) and matrix product operators (MPOs). We explore the bulk phase diagram of the theory on regular tessellations of hyperbolic space with coordination number seven and find disordered and ordered phases separated by a phase transition. We find that the boundary-boundary spin correlation function exhibits power law scaling deep in the disordered phase of the Ising model consistent with holography. At the critical point, we find the boundary entanglement entropy scales logarithmically with subsystem size but away from this, we see a linear scaling. In comparison, the full system exhibits a volume law scaling, which is expected in chaotic and/or highly connected systems. We also measure out of time ordered correlators (OTOCs) to explore the scrambling behavior of the theory.

Quantum spin models↗

Beyond fragmented dopant dynamics in quantum spin lattices: Robust localization and non-Gaussian diffusion

The motion of dopants in magnetic spin lattices has received tremendous attention for at least four decades due to its connection to high-temperature superconductivity. Despite these efforts, we lack a complete understanding of their behavior, especially out of the equilibrium and at nonzero temperatures. In this paper, we take a significant step towards a much deeper understanding based on state-of-the-art matrix-product-state calculations. In particular, we investigate the nonequilibrium dynamics of a dopant in two-leg 𝑡−𝐽 ladders with antiferromagnetic XXZ spin interactions. In the Ising limit, we find that the dopant is localized for all investigated nonzero temperatures due to an emergent disordered potential, with a localization length controlled by the underlying correlation length of the spin lattice, which increases exponentially with decreasing temperature. The dopant, hereby, only delocalizes asymptotically in the zero temperature limit. This greatly generalizes the localization effect discovered recently in Hilbert space fragmented models [Phys. Rev. Res. 6, 023325 (2024), SciPost Phys. Core 7, 054 (2024)]. In the presence of spin-exchange processes at rate 𝛼, the dopant diffuses with a diffusion coefficient, 𝐷 ℎ , depending nonmonotonically on 𝛼. It initially increases linearly as 𝐷 ℎ ∝ 𝛼 for 𝛼 ≪ 1 before dropping off as 𝛼 −1 for 𝛼 > 1. Moreover, we show that the underlying spin dynamics at infinite temperature behaves qualitatively the same, albeit with important quantitative differences. We substantiate these findings by showing that the dynamics features self-similar scaling behavior, which strongly deviates from the Gaussian behavior of regular diffusion, especially for weak spin exchange. Finally, we show that the diffusion coefficient 𝐷 ℎ follows an Arrhenius relation at high temperatures, whereby it is exponentially suppressed upon cooling.

Anomalous diffusion↗

Kinematic Flow and the Emergence of Time

Perhaps the most basic question we can ask about cosmological correlations is how their strength changes as we smoothly vary kinematic parameters. The answer is encoded in differential equations that govern this evolution in kinematic space. In this Letter, we introduce a new perspective on these differential equations. We show that, in the simplified setting of conformally coupled scalars in power-law Friedmann-Robertson-Walker spacetimes, the equations for arbitrary tree-level processes can be obtained from a small number of simple combinatorial rules. While this “kinematic flow” is defined purely in terms of boundary data, it reflects the physics of bulk time evolution. The unexpected regularity of the equations suggests the existence of an autonomously defined mathematical structure from which cosmological correlations and the time evolution of the associated spacetime emerge.

79 ASTRONOMY AND ASTROPHYSICS↗