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At least 1,405 records · Page 78

Inferring protein expression changes from mRNA in Alzheimer’s dementia using deep neural networks

Identifying the molecular systems and proteins that modify the progression of Alzheimer’s disease and related dementias (ADRD) is central to drug target selection. However, discordance between mRNA and protein abundance, and the scarcity of proteomic data, has limited our ability to advance candidate targets that are mainly based on gene expression. Therefore, by using a deep neural network that predicts protein abundance from mRNA expression, here we attempt to track the early protein drivers of ADRD. Specifically, by applying the clei2block deep learning model to 1192 brain RNA-seq samples, we identify protein modules and disease-associated expression changes that were not directly observed at the mRNA level. Moreover, pseudo-temporal trajectory inference based on the predicted proteome became more closely correlated with cognitive decline and hippocampal atrophy compared to RNA-based trajectories. This suggests that the predicted changes in protein expression could provide a better molecular representation of ADRD progression. Furthermore, overlaying clinical traits on protein pseudotime trajectory identifies protein modules altered before cognitive impairment. These results demonstrate how our method can be used to identify potential early protein drivers and possible drug targets for treating and/or preventing ADRD.

60 APPLIED LIFE SCIENCES↗

An adaptive approach to machine learning for compact particle accelerators

Abstract Machine learning (ML) tools are able to learn relationships between the inputs and outputs of large complex systems directly from data. However, for time-varying systems, the predictive capabilities of ML tools degrade if the systems are no longer accurately represented by the data with which the ML models were trained. For complex systems, re-training is only possible if the changes are slow relative to the rate at which large numbers of new input-output training data can be non-invasively recorded. In this work, we present an approach to deep learning for time-varying systems that does not require re-training, but uses instead an adaptive feedback in the architecture of deep convolutional neural networks (CNN). The feedback is based only on available system output measurements and is applied in the encoded low-dimensional dense layers of the encoder-decoder CNNs. First, we develop an inverse model of a complex accelerator system to map output beam measurements to input beam distributions, while both the accelerator components and the unknown input beam distribution vary rapidly with time. We then demonstrate our method on experimental measurements of the input and output beam distributions of the HiRES ultra-fast electron diffraction (UED) beam line at Lawrence Berkeley National Laboratory, and showcase its ability for automatic tracking of the time varying photocathode quantum efficiency map. Our method can be successfully used to aid both physics and ML-based surrogate online models to provide non-invasive beam diagnostics.

97 MATHEMATICS AND COMPUTING↗

Deep reinforcement learning for predicting kinetic pathways to surface reconstruction in a ternary alloy

Abstract The majority of computational catalyst design focuses on the screening of material components and alloy composition to optimize selectivity and activity for a given reaction. However, predicting the metastability of the alloy catalyst surface at realistic operating conditions requires an extensive sampling of possible surface reconstructions and their associated kinetic pathways. We present CatGym, a deep reinforcement learning (DRL) environment for predicting the thermal surface reconstruction pathways and their associated kinetic barriers in crystalline solids under reaction conditions. The DRL agent iteratively changes the positions of atoms in the near-surface region to generate kinetic pathways to accessible local minima involving changes in the surface compositions. We showcase our agent by predicting the surface reconstruction pathways of a ternary Ni 3 Pd 3 Au 2 (111) alloy catalyst. Our results show that the DRL agent can not only explore more diverse surface compositions than the conventional minima hopping method, but also generate the kinetic surface reconstruction pathways. We further demonstrate that the kinetic pathway to a global minimum energy surface composition and its associated transition state predicted by our agent is in good agreement with the minimum energy path predicted by nudged elastic band calculations.

36 MATERIALS SCIENCE↗

QSO photometric redshifts using machine learning and neural networks

ABSTRACT The scientific value of the next generation of large continuum surveys would be greatly increased if the redshifts of the newly detected sources could be rapidly and reliably estimated. Given the observational expense of obtaining spectroscopic redshifts for the large number of new detections expected, there has been substantial recent work on using machine learning techniques to obtain photometric redshifts. Here, we compare the accuracy of the predicted photometric redshifts obtained from deep learning (DL) with the k-nearest neighbour (kNN) and the decision tree regression (DTR) algorithms. We find using a combination of near-infrared, visible, and ultraviolet magnitudes, trained upon a sample of Sloan Digital Sky Survey quasi-stellar objects, that the kNN and DL algorithms produce the best self-validation result with a standard deviation of σΔz = 0.24 (σΔz(norm) = 0.11). Testing on various subsamples, we find that the DL algorithm generally has lower values of σΔz, in addition to exhibiting a better performance in other measures. Our DL method, which uses an easy to implement off-the-shelf algorithm with neither filtering nor removal of outliers, performs similarly to other, more complex, algorithms, resulting in an accuracy of Δz < 0.1 up to z ∼ 2.5. Applying the DL algorithm trained on our 70 000 strong sample to other independent (radio-selected) data sets, we find σΔz ≤ 0.36 (σΔz(norm) ≤ 0.17) over a wide range of radio flux densities. This indicates much potential in using this method to determine photometric redshifts of quasars detected with the Square Kilometre Array.

Curran, S. J.↗

Development of a Full-Scale Connected U-Net for Reflectivity Inpainting in Spaceborne Radar Blind Zones

CloudSat’s Cloud Profiling Radar is a valuable tool for remotely monitoring high-latitude snowfall, but its ability to observe hydrometeor activity near the Earth’s surface is limited by a radar blind zone caused by ground clutter contamination. This study presents the development of a deeply supervised U-Net-style convolutional neural network to predict cold season reflectivity profiles within the blind zone at two Arctic locations. The network learns to predict the presence and intensity of near-surface hydrometeors by coupling latent features encoded in blind zone-aloft clouds with additional context from collocated atmospheric state variables (i.e., temperature, specific humidity, and wind speed). Results show that the U-Net predictions outperform traditional linear extrapolation methods, with low mean absolute error, a 38% higher Sørensen–Dice coefficient, and vertical reflectivity distributions 60% closer to observed values. The U-Net is also able to detect the presence of near-surface cloud with a critical success index (CSI) of 72% and cases of shallow cumuliform snowfall and virga with 18% higher CSI values compared to linear methods. An explainability analysis shows that reflectivity information throughout the scene, especially at cloud edges and at the 1.2-km blind zone threshold, along with atmospheric state variables near the tropopause, are the most significant contributors to model skill. This surface-trained generative inpainting technique has the potential to enhance current and future remote sensing precipitation missions by providing a better understanding of the nonlinear relationship between blind zone reflectivity values and the surrounding atmospheric state.

54 ENVIRONMENTAL SCIENCES↗

NLML: A Deep Neural Network Emulator for the Exact Nonlinear Interactions in a Wind Wave Model

Nonlinear wave interactions describe the resonant energy transfer between wave components, playing a fundamental role in the evolution of ocean wave spectra. Nonlinear wave interactions significantly influence wave growth and development, making them essential for accurate wave modeling. However, resolving the full six-dimensional Boltzmann integral of the exact nonlinear wave interactions (Webb-Resio-Tracy method, WRT) is computationally expensive, limiting its application in real-time operational wave forecasting and for research purposes. Current approximations, such as the Discrete Interaction Approximation (DIA), prioritize computational speed over accuracy, resulting in significant errors in wave mean parameters. Here, we introduce NLML, a machine learning (ML) emulator designed to approximate the exact nonlinear wave interactions within WAVEWATCH III (WW3), with the goal of achieving the accuracy of WRT while maintaining the stability and computational speed of DIA. By leveraging GPU capabilities such as half precision inference, we achieved substantial speedups, up to 136x mathematical equation faster than the WRT and only a modest 1.04x mathematical equation slowdown relative to DIA, while achieving 2x mathematical equation the accuracy of DIA in global wave spectral energy and mean wave parameters, with up to 7x mathematical equation higher accuracy in some regions. Unlike previous ML approaches, NLML maintained inherent stability throughout model integration in a standalone, year-long WW3 simulation, without requiring additional constraints. Our new ML parameterization bridges the gap between accuracy and efficiency, offering a promising alternative for improving wave modeling in operational settings and research purposes.

16 TIDAL AND WAVE POWER↗

E(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials

Abstract This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cassini Distributed Instrument Operations: What We've Learned Since Saturn Orbit Insertion

The Cassini mission to Saturn is complex with 12 science teams conducting distributed operations across the United States and Europe. Each Team includes scientists from around the world who actively participate in operations, including observation design, instrument commanding, downlink processing, and archiving. This represents a change in how JPL complex deep-space missions have been operated. Since Saturn Orbit Insertion (SOI), the Cassini Project has spent 17 months conducting science operations and has gained real-world experience that has tested the assumptions and rationale for this approach. We have learned that many of the expected benefits have been realized, but there were numerous unexpected challenges as well. This paper will discuss the lessons learned from the Cassini Tour experience to date. It will revisit the assumptions and rationale behind the distributed instrument operations design and will describe the results, good and bad, of implementing this method of operations. We will describe how Instrument Teams are structured, their roles and responsibilities, what challenges they faced going into orbital operations (the 'tour') and what creative solutions were proposed when funding limitations and schedule milestones prevented optimum solutions. We will also discuss the problems that have been encountered both on the ground and with the instruments, how these problems and anomalies were overcome, and what was learned along the way about the characteristics of distributed instrument operations.

Cassini↗

A Neural Differential Equation Formulation for Modeling Atmospheric Effects in Hyperspectral Images

Atmospheric correction is the process for removing atmospheric effects from spectral data; a necessary step for recovering salient spectral properties. The complex interactions between the atmosphere and light are dominated by absorbance and scattering physics. Existing methods for modeling atmospheric interactions typically rely on deep knowledge of relevant environmental conditions and high-fidelity numerical simulations of the governing physics in order to obtain accurate estimates of these effects. Additionally, existing approaches often require a subject matter expert for pre/post-processing of the data. Model-based approaches for removing atmospheric effects struggle in situations where such domain expertise is not available, and require significant human effort and computational power even when that expertise is available. In contrast, we propose a data-driven approach the uses Neural Differential Equations (NDEs) to accurately learn the interactions between electromagnetic radiation and the atmospheric without access to location specific environmental information. Once trained, the NDE can be applied bi-directionally; to apply or remove atmospheric effects. We demonstrate the effectiveness and utility of these techniques on an example multi-spectral scene.

Koch, James V.↗

A Novel LDPP-MADDPG Approach for Distributed Power Allocation in mmWave Cellular Networks

This paper considers the problem of distributed beam scheduling and power allocation problem in millimeter- Wave (mmWave) cellular networks, in which multiple Base Stations (BSs) operate as individual operators over a shared spectrum. We propose a novel learning-aided approach that integrates the Lyapunov Drift-Plus-Penalty (LDPP) framework and Multi-agent Deep Deterministic Policy Gradient (MADDPG) reinforcement learning algorithms. This offers a powerful approach to learning stable and constraint-aware policies, reaping the joint benefit of both LDPP and MADDPG, in complex multiagent environments. The major challenge for this approach is to integrate these two approaches in a meaningful and effective manner. The key idea to solve this problem is to introduce a novel feature of local observation that incorporates potential negative value of the reward function due to the stochastic constraints introduced by the LDPP framework. Empirical results demonstrate that our proposed scheme outperforms the baseline methods under various conditions.

99 - GENERAL AND MISCELLANEOUS↗

Physics-informed latent neural operator for real-time predictions of time-dependent parametric PDEs

Deep operator network (DeepONet) has shown significant promise as surrogate models for systems governed by partial differential equations (PDEs), enabling accurate mappings between infinite-dimensional function spaces. However, when applied to systems with high-dimensional input-output mappings arising from large numbers of spatial and temporal collocation points, these models often require heavily overparameterized networks, leading to long training times. Latent DeepONet addresses some of these challenges by introducing a two-step approach: first learning a reduced latent space using a separate model, followed by operator learning within this latent space. While efficient, this method is inherently data-driven and lacks mechanisms for incorporating physical laws, limiting its robustness and generalizability in data-scarce settings. Here, in this work, we propose PI-Latent-NO, a physics-informed latent neural operator framework that integrates governing physics directly into the learning process. Our architecture features two coupled DeepONets trained end-to-end: a Latent-DeepONet that learns a low-dimensional representation of the solution, and a Reconstruction-DeepONet that maps this latent representation back to the physical space. By embedding PDE constraints into the training via automatic differentiation, our method eliminates the need for labeled training data and ensures physics-consistent predictions. The proposed framework is both memory and compute-efficient, exhibiting near-constant scaling with problem size and demonstrating significant speedups over traditional physics-informed operator models. We validate our approach on a range of parametric PDEs, showcasing its accuracy, scalability, and suitability for real-time prediction in complex physical systems.

Latent representations↗

Machine Learned Hückel Theory: Interfacing Physics and Deep Neural Networks

The Hückel Hamiltonian is an incredibly simple tight-binding model known for its ability to capture qualitative physics phenomena arising from electron interactions in molecules and materials. Part of its simplicity arises from using only two types of empirically fit physics-motivated parameters: the first describes the orbital energies on each atom and the second describes electronic interactions and bonding between atoms. By replacing these empirical parameters with machine-learned dynamic values, we vastly increase the accuracy of the extended Hückel model. The dynamic values are generated with a deep neural network, which is trained to reproduce orbital energies and densities derived from density functional theory. The resulting model retains interpretability, while the deep neural network parameterization is smooth and accurate and reproduces insightful features of the original empirical parameterization. Altogether, this work shows the promise of utilizing machine learning to formulate simple, accurate, and dynamically parameterized physics models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

End-to-end deep learning pipeline for real-time Bragg peak segmentation: from training to large-scale deployment

X-ray crystallography reconstruction, which transforms discrete X-ray diffraction patterns into three-dimensional molecular structures, relies critically on accurate Bragg peak finding for structure determination. As X-ray free electron laser (XFEL) facilities advance toward MHz data rates (1 million images per second), traditional peak finding algorithms that require manual parameter tuning or exhaustive grid searches across multiple experiments become increasingly impractical. While deep learning approaches offer promising solutions, their deployment in high-throughput environments presents significant challenges in automated dataset labeling, model scalability, edge deployment efficiency, and distributed inference capabilities. We present an end-to-end deep learning pipeline with three key components: (1) a data engine that combines traditional algorithms with our peak matching algorithm to generate high-quality training data at scale, (2) a modular architecture that scales from a few million to hundreds of million parameters, enabling us to train large expert-level models offline while deploying smaller, distilled models at the edge, and (3) a decoupled producer-consumer architecture that separates specialized data source layer from model inference, enabling flexible deployment across diverse computing environments. Using this integrated approach, our pipeline achieves accuracy comparable to traditional methods tuned by human experts while eliminating the need for experiment-specific parameter tuning. Although current throughput requires optimization for MHz facilities, our system's scalable architecture and demonstrated model compression capabilities provide a foundation for future high-throughput XFEL deployments.

Wang, Cong↗

DeepAstroUDA: semi-supervised universal domain adaptation for cross-survey galaxy morphology classification and anomaly detection

Abstract Artificial intelligence methods show great promise in increasing the quality and speed of work with large astronomical datasets, but the high complexity of these methods leads to the extraction of dataset-specific, non-robust features. Therefore, such methods do not generalize well across multiple datasets. We present a universal domain adaptation method, DeepAstroUDA , as an approach to overcome this challenge. This algorithm performs semi-supervised domain adaptation (DA) and can be applied to datasets with different data distributions and class overlaps. Non-overlapping classes can be present in any of the two datasets (the labeled source domain, or the unlabeled target domain), and the method can even be used in the presence of unknown classes. We apply our method to three examples of galaxy morphology classification tasks of different complexities (three-class and ten-class problems), with anomaly detection: (1) datasets created after different numbers of observing years from a single survey (Legacy Survey of Space and Time mock data of one and ten years of observations); (2) data from different surveys (Sloan Digital Sky Survey (SDSS) and DECaLS); and (3) data from observing fields with different depths within one survey (wide field and Stripe 82 deep field of SDSS). For the first time, we demonstrate the successful use of DA between very discrepant observational datasets. DeepAstroUDA is capable of bridging the gap between two astronomical surveys, increasing classification accuracy in both domains (up to 40 % on the unlabeled data), and making model performance consistent across datasets. Furthermore, our method also performs well as an anomaly detection algorithm and successfully clusters unknown class samples even in the unlabeled target dataset.

79 ASTRONOMY AND ASTROPHYSICS↗

Modeling Nanoconfinement Effects Using Active Learning

Predicting the spatial configuration of gas in nanopores of is relevant in applications such as fluid flow forecasting and hydrocarbon reserves estimation. For example, shale reservoirs have suffered from computationally intractable multiscale problems, since fluid properties such as viscosity, density, and adsorption must be calculated by using expensive molecular dynamics (MD) simulations within each nanopore, whereas flow through these connected nanopores must be simulated at the micrometer scale. We utilize machine learning techniques to quickly and accurately model nanoscale confinement effects as an important step toward bridging the nano and micro scales. Our workflow is based on building and training physics-based deep-neural-networks models by learning from a database of MD calculations. The model accounts for the adsorption phenomenon by predicting the statistical distribution of gas inside nanopores. Because large databases of MD calculations are expensive to create, we investigate active learning (AL) as a data set construction strategy. In this workflow, new data are selected based on the model uncertainty via the query-by-committee approach. We show that our workflow obtains accurate models that generalize to real scanning electron microscopy geometries with 1/10th of the number of MD calculations required vs random data set generation. Our method enables the possibility of modeling nanoconfinement effects at the mesoscale, where complex connected sets of nanopores affect flow.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Open-Science Approach to Address Individual Response to Simulated GCR In Genetically Diverse Populations of Mice and Humans

This project addresses the challenge of understanding and predicting individual radiation sensitivity by integrating genetics, demographics and biomarker characteristics across species (mice and humans). We hypothesize that ex vivo DNA repair response to GCR components is a central determinant of cancer risk from space radiation and can serve as a biomarker of radiation risk in combination with genetics. Automated image quantification of 53BP1+ radiation-induced foci (RIF) during the first 4-48 h post-irradiation was performed as a function of dose and LET in non-immortalized primary skin fibroblasts derived from 76 mice across 15 strains (5 inbred reference strains and 10 collaborative-cross strains) exposed to X rays (0.1, 1 and 4 Gy), 350 MeV/n 40Ar and 600 MeV/n 56Fe (1.1 and 3 particles/100sq. μm), as well as in peripheral blood mononuclear cells (PBMCs) from 768 healthy donors (matched ethnicity, 50/50 male/female, 18-70 years old) exposed to gamma rays (0.1 and 1 Gy), 350 MeV/n 28Si, 350 MeV/n 40Ar and 600 MeV/n 56Fe (1.1 and 3 particles/100sq. μm). A genome-wide association study (GWAS) was performed on the mouse strains between DNA damage responses to space radiation and single nucleotide polymorphisms (SNPs). We found SNPs, which were significantly associated to the RIF phenotype, mapped to genes and pathways that are functionally linked to health hazards for deep space exploration (e.g. carcinogenesis, nervous system damage and immune dysfunction). Some of these SNPs were located within protein coding regions, potentially interfering with protein functions and providing promising genetic targets for countermeasures. We also found correlations between both spontaneous and radiation-induced DNA damage and SNPs mapped to pathways associated with cellular metabolism. GWAS is undergoing for the human data. All data have been made available via the NASA Space Biology Open-Science database (genelab.nasa.gov) and we will discuss how various genomic and transcriptomic datasets can be accessed for modeling and integrated using machine learning methods for discovering new radiation biology.

Sylvain V Costes↗

Deep Learning for Intelligent Bubble Size Detection in the Spallation Neutron Source Visual Target

The Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL) will undergo proton power upgrade (PPU), increasing the proton beam power from 1.4 MW to 2.8 MW. From 2.8 MW, 2.0 MW will go to the current First Target Station and the rest will go to the future Second Target Station (STS). The First Target Station uses a liquid mercury target that is contained in a 316L stainless steel vessel. The proton beam is pulsed at 60 Hz, with a pulse of about 0.7μs. When the proton beam hits the target, the intense energy deposition leads to a rapid rise in temperature in the mercury. This temperature rise creates pressure waves that propagate through the mercury and cause cavitation erosion. The power upgrade will cause stronger pressure waves that will further increase damage because of cavitation. Injecting small helium bubbles in the mercury has been an efficient method of mitigating the pressure wave at 1.4 MW. However, at higher power, additional mitigation is necessary. Therefore, the 2 MW target vessel will be equipped with swirl bubblers and an additional gas injection port near the nose to inject more gas in the target. To develop a gas injection strategy and design, flow visualization in water with a transparent prototypical target (“visual target”) was performed. Bubble sizes and their spatial distribution in the flow loop are crucial to understanding the effectiveness of the bubbles in mitigating pressure waves. Bubbles were generated in the visual target under varied conditions of input pressures with helium and air. Images were captured using a high-speed camera at varied frame rates at different positions away from the swirl bubbler and different depths in the flow loop under varying lighting conditions. Initially, methods such as circular Hough transforms were applied after a series of images processing to obtain a general distribution of bubble sizes. Bubbles smaller than 500 μm are preferred to effectively mitigate the effect of pressure waves, which demands an accurate bubble detection and sizing system. Intelligent detection and identification of bubble sizes alleviate misdetection and improves accuracies. Employing neural networks, intelligent detection of bubble sizes and their distribution was developed and provides a robust alternative to traditional techniques. Human intervention was employed to label in-focus and out-of-focus bubbles in the set of training images. An object detection network using a pretrained convolutional neural network was created that extracted the features from the training images. Data augmentation was used to improve network accuracy through a random transformation of the original data.

Rasheed, Fayaz↗

Improving radiograph analysis throughput through transfer learning and object detection

SIGN Fracture Care International partners with surgeons in low-resource hospitals worldwide to provide access to effective orthopedic care by donating educational materials and innovatively designed surgical implants. Over two decades, SIGN’s Online Surgical Database (SOSD) has grown to contain over 500,000 medical images, with radiographs holding the majority share. One challenge in working with hospitals worldwide is that both the radiographs uploaded to the SOSD and the data entry accompanying the uploads vary in quality. To improve the accuracy of data in the SOSD, we trained a model to detect surgical implants in radiographs. We first developed a tool to automatically detect radiographs, then trained an object detection model to determine the number and placement of surgical implants visible in the radiograph. Active learning was used to generate a training set containing 2,510 radiographs with screws, nails, and plates labeled by bounding boxes. Training a model to simultaneously recognize all three classes of implants gave a low average precision (AP) for the plate class, likely due to the low number of plate instances in our training set and the large variety of surgical plates used by SIGN-partnered surgeons. Applying standard image augmentation techniques to increase the plate count in our training set did not appreciably increase the AP of plate detection. To improve plate detection, we redrew the bounding boxes to account for correlations between the screw and plate classes. Training one model to detect nails and screws and a separate model to detect plates increased the AP of plate detection by 78.8 percentage points. The AP of each class was 80.7% for screws, 93.6% for nails, and 92.6% for plates; meanwhile, the sensitivity was 92% for screws, 86% for nails, and 81% for plates. We show that object detection methods can be used to detect surgical implants in radiographs of varying quality; however, the detection ability is dependent on the type of implant, and some implants, in our case plates, must be treated differently than others. Such tools can improve the throughput of radiograph analysis, assisting physicians and surgeons with the treatment of bone fractures.

60 APPLIED LIFE SCIENCES↗