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At least 955 records · Page 53

Analyzing and Exploring Training Recipes for Large-Scale Transformer-Based Weather Prediction

Abstract The rapid rise of deep learning (DL) in numerical weather prediction (NWP) has led to a proliferation of models which forecast atmospheric variables with comparable or superior skill than traditional physics-based NWP. However, among these leading DL models, there is a wide variance in both the training settings and architecture used. Further, the lack of thorough ablation studies makes it hard to discern which components are most critical to success. In this work, we show that it is possible to attain high forecast skill even with relatively off-the-shelf architectures, simple training procedures, and moderate compute budgets. Specifically, we train a minimally modified Swin Transformer V2 (SwinV2) on ERA5 data and find that it attains superior skill in terms of mean-square errors of deterministic forecasts when compared against the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS). Almost all DL–NWP systems share a core set of hyperparameters and design decisions. To aid and expedite future DL–NWP research, we present an in-depth, systematic exploration of different loss functions, model sizes and depths, patch sizes, and multistep training objectives. We also examine the model performance with metrics beyond the typical accuracy (ACC) and RMSE and investigate how the performance scales with model size. Through our open-source code, scoring pipelines, and models, we share our findings on key aspects of the training pipeline. These ablations reduce the necessity for expensive hyperparameter tuning and lower the barrier to entry for future DL–NWP research. Significance Statement This study investigates the potential of using large-scale transformer-based models for weather prediction, showing that it is possible to achieve high forecast accuracy with simpler, off-the-shelf architectures. By training a minimally modified SwinV2 transformer on ERA5 data, we show that the model achieves competitive forecast skill in terms of mean-square error for key variables, outperforming the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS) at all lead times. Our findings suggest that effective training strategies, such as multistep fine-tuning and channel-weighted losses, significantly enhance the model’s performance. However, we also highlight that these improvements come with trade-offs in other areas, such as ensemble spread and high-frequency spatial detail. This work highlights the promise of deep learning in improving weather forecasts, which could lead to better preparedness and response to weather events, ultimately benefiting society by providing more reliable weather predictions.

Willard, Jared D. [Lawrence Berkeley National Labo↗

Optimizing a magnitude-limited spectroscopic training sample for photometric classification of supernovae

ABSTRACT In preparation for photometric classification of transients from the Legacy Survey of Space and Time (LSST) we run tests with different training data sets. Using estimates of the depth to which the 4-m Multi-Object Spectroscopic Telescope (4MOST) Time Domain Extragalactic Survey (TiDES) can classify transients, we simulate a magnitude-limited sample reaching rAB ≈ 22.5 mag. We run our simulations with the software snmachine, a photometric classification pipeline using machine learning. The machine-learning algorithms struggle to classify supernovae when the training sample is magnitude limited, in contrast to representative training samples. Classification performance noticeably improves when we combine the magnitude-limited training sample with a simulated realistic sample of faint high-redshift supernovae observed from larger spectroscopic facilities; the algorithms’ range of average area under receiver operator characteristic curve (AUC) scores over 10 runs increases from 0.547–0.628 to 0.946–0.969 and purity of the classified sample reaches 95 per cent in all runs for two of the four algorithms. By creating new, artificial light curves using the augmentation software avocado, we achieve a purity in our classified sample of 95 per cent in all 10 runs performed for all machine-learning algorithms considered. We also reach a highest average AUC score of 0.986 with the artificial neural network algorithm. Having ‘true’ faint supernovae to complement our magnitude-limited sample is a crucial requirement in optimization of a 4MOST spectroscopic sample. However, our results are a proof of concept that augmentation is also necessary to achieve the best classification results.

79 ASTRONOMY AND ASTROPHYSICS↗

The Pristine dwarf galaxy survey – IV. Probing the outskirts of the dwarf galaxy Boötes I

ABSTRACT We present a new spectroscopic study of the dwarf galaxy Boötes I (Boo I) with data from the Anglo-Australian Telescope and its AAOmega spectrograph together with the Two Degree Field multi-object system. We observed 36 high-probability Boo I stars selected using Gaia Early Data Release 3 proper motions and photometric metallicities from the Pristine survey. Out of those, 27 are found to be Boo I stars, resulting in an excellent success rate of 75 per cent at finding new members. Our analysis uses a new pipeline developed to estimate radial velocities and equivalent widths of the calcium triplet lines from Gaussian and Voigt line profile fits. The metallicities of 16 members are derived, including 3 extremely metal-poor stars ([Fe/H] < −3.0), which translates into a success rate of 25 per cent at finding them with the combination of Pristine and Gaia. Using the large spatial extent of our new members that spans up to 4.1 half-light radii and spectroscopy from the literature, we find a systemic velocity gradient of 0.40 ± 0.10 km s−1 arcmin−1 and a small but resolved metallicity gradient of −0.008 ± 0.003 dex arcmin−1. Finally, we show that Boo I is more elongated than previously thought with an ellipticity of ϵ = 0.68 ± 0.15. Its velocity and metallicity gradients as well as its elongation suggest that Boo I may have been affected by tides, a result supported by direct dynamical modelling.

Longeard, Nicolas↗

A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project

Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. Here we describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.

59 BASIC BIOLOGICAL SCIENCES↗

Watermarks in stream processing systems: semantics and comparative analysis of Apache Flink and Google cloud dataflow

Streaming data processing is an exercise in taming disorder: from oftentimes huge torrents of information, we hope to extract powerful and timely analyses. But when dealing with streaming data, the unbounded and temporally disordered nature of real-world streams introduces a critical challenge: how does one reason about the completeness of a stream that never ends? In this paper, we present a comprehensive definition and analysis of watermarks, a key tool for reasoning about temporal completeness in infinite streams.First, we describe what watermarks are and why they are important, highlighting how they address a suite of stream processing needs that are poorly served by eventually-consistent approaches:• Computing a single correct answer, as in notifications.• Reasoning about a lack of data, as in dip detection.• Performing non-incremental processing over temporal subsets of an infinite stream, as in statistical anomaly detection with cubic spline models.• Safely and punctually garbage collecting obsolete inputs and intermediate state.• Surfacing a reliable signal of overall pipeline health.Second, we describe, evaluate, and compare the semantically equivalent, but starkly different, watermark implementations in two modern stream processing engines: Apache Flink and Google Cloud Dataflow.

Akidau, Tyler↗

microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes

Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait , a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.

Karaoz, Ulas↗

Label Assist: Personalized Travel Models for Longitudinal Data Collection

Understanding travel behavior is crucial to transportation decarbonization. OpenPATH is an open-source mobility platform which collects and analyzes human travel behavior at the individual level. The mobile application passively senses trips and prompts users to label them. However, users find the labeling process burdensome; less than half the trips are typically labeled, making much of the data unusable in aggregate analyses of mobility patterns. Prior work has addressed the response fatigue challenge through automated mode inference using sensor data, but sensors cannot capture all aspects of travel behavior. We explore an alternative approach in which we leverage prior user input to predict travel choices in novel trips. We first explore trip clustering methods and develop a novel two-step pipeline using DBSCAN and SVMs to extract realistic geospatial clusters. We then propose two strategies to predict trip labels: (i) clustering trips and extrapolating labels for similar trips, and (ii) random forest classification. The random forest approach is able to achieve - $70-80% accuracy (purpose: 72%, mode: 79%, replaced mode: 81%). These novel approaches to trip classification allow us to increase the rate of user labeling by suggesting predicted labels to be verified by the user. Unlabeled trips can also contribute to aggregate analyses, using label predictions and their associated confidences as a substitute. While there exist other travel survey apps with the ability to infer travel choices, to our knowledge, this is the first paper to describe such a supervised system and rigorously evaluate it.

ADVANCED PROPULSION SYSTEMS,ENERGY PLANNING, POLIC↗

The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes

The OSU/PNNL Superfund Research Program represents a longstanding collaboration to quantify Polycyclic Aromatic Hydrocarbons (PAHs) at various superfund sites in the Pacific Northwest and assess their potential impact on human health. To link the chemical measurements to biological activity, we describe the use of the zebrafish as a high-throughput developmental model of human exposure that provides quantitative measurements of the biological ramifications of exposure to toxicants. Toward this end, we have linked over 150 PAHs found at Superfund sites to the effect of these same chemicals in zebrafish, creating a rich dataset that links environmental exposure to biological response. To quantify this response, we have implemented a dose-response modelling pipeline to calculate benchmark dose parameters which enable potency comparison across over 500 chemicals and 10 zebrafish-specific phenotypes. Our portal provides public access to this dataset via an interactive web site designed to support exploration and re-use of these data by the scientific community at http://srp.pnnl.gov.

Gosline, Sara JC↗

Data for "High-resolution microCT reveals relationships between stomata and interior leaf anatomy in Sorghum"

Includes three different types of stacks, in two folders: "REC_RAW_STACKS.zip" contains: (1) Raw gray-scale reconstructed microCT x-ray scans, in the form of individual stacks per sample. "ML_STACKS.zip" contains: (2) Stacks that have been labeled using a machine-learning mask-RCNN pipeline identifying epidermis, mesophyll, airspace, vascular bundle, and background. (3) Stacks that have stomata locations labeled using a small point. The three types of stacks were used to calculate a variety of anatomical and physiological traits, using ImageJ Macros provided on Github: https://github.com/leakey-lab/microCT-Macros-Fischer. Young leaves from WT and transgenic Sorghum plants. CSV "microCT_REC2_META.csv" contains metadata, including sample/sub-sample labels.

3D↗

Cosmic shear in harmonic space from the Dark Energy Survey Year 1 Data: compatibility with configuration space results

ABSTRACT We perform a cosmic shear analysis in harmonic space using the first year of data collected by the Dark Energy Survey (DES-Y1). We measure the cosmic weak lensing shear power spectra using the metacalibration catalogue and perform a likelihood analysis within the framework of CosmoSIS. We set scale cuts based on baryonic effects contamination and model redshift and shear calibration uncertainties as well as intrinsic alignments. We adopt as fiducial covariance matrix an analytical computation accounting for the mask geometry in the Gaussian term, including non-Gaussian contributions. A suite of 1200 lognormal simulations is used to validate the harmonic space pipeline and the covariance matrix. We perform a series of stress tests to gauge the robustness of the harmonic space analysis. Finally, we use the DES-Y1 pipeline in configuration space to perform a similar likelihood analysis and compare both results, demonstrating their compatibility in estimating the cosmological parameters S8, σ8, and Ωm. We use the DES-Y1 metacalibration shape catalogue, with photometric redshifts estimates in the range of 0.2−1.3, divided in four tomographic bins finding σ8(Ωm/0.3)0.5 = 0.766 ± 0.033 at 68 per cent CL. The methods implemented and validated in this paper will allow us to perform a consistent harmonic space analysis in the upcoming DES data.

79 ASTRONOMY AND ASTROPHYSICS↗

Graph Identification of Proteins in Tomograms (GRIP-Tomo) 2.0: Topologically aware classification for proteins

Cryo-electron tomography (cryo-ET) enables structural characterization of biomolecules under near-native conditions. Existing approaches for interpreting the resulting three-dimensional volumes are computationally expensive and have difficulty interpreting density associated with small proteins/complexes. To explore alternate approaches for identifying proteins in cryo-ET data we pursued a Graph Network and topologically invariant approach. Here, we report on a fast algorithm that classifies particles by searching for nuances of evolutionarily conversed motifs and the geometrical characteristics of protein structure. GRIP-Tomo 2.0 is a machine-learning pipeline that extracts interpretable topological features of protein structures within noisy experimental backgrounds. Compared to version 1.0, the new pipeline includes three upgrades that significantly improve performance including synthetic tomogram generation simulating realistic noise, graph-based persistent feature extraction as protein fingerprints, and high-performance computing acceleration. GRIP-Tomo 2.0 achieves over 90% accuracy in classifying between proteins and noise using both real and synthetic datasets which represents a foundational step toward advancing cryo-ET workflows and empowering automated visual proteomics.

Li, Chengxuan↗

Search of strong lens systems in the Dark Energy Survey using convolutional neural networks

We present our search for strong lens, galaxy-scale systems in the first data release of the Dark Energy Survey (DES), based on a color-selected parent sample of 18 745 029 luminous red galaxies (LRGs). We used a convolutional neural network (CNN) to grade this LRG sample with values between 0 (non-lens) and 1 (lens). Our training set of mock lenses is data-driven, that is, it uses lensed sources taken from HST-COSMOS images and lensing galaxies from DES images of our LRG sample. A total of 76 582 cutouts were obtained with a score above 0.9, which were then visually inspected and classified into two catalogs. The first one contains 405 lens candidates, of which 90 present clear lensing features and counterparts, while the other 315 require more evidence, such as higher resolution imaging or spectra, to be conclusive. A total of 186 candidates are newly identified by our search, of which 16 are among the 90 most promising (best) candidates. The second catalog includes 539 ring galaxy candidates. This catalog will be a useful false positive sample for training future CNNs. For the 90 best lens candidates we carry out color-based deblending of the lens and source light without fitting any analytical profile to the data. This method is shown to be very efficient in the deblending, even for very compact objects and for objects with a complex morphology. Finally, from the 90 best lens candidates, we selected 52 systems with one single deflector to test an automated modeling pipeline that has the capacity to successfully model 79% of the sample within an acceptable computing runtime.

79 ASTRONOMY AND ASTROPHYSICS↗

The Impact of Time-Aware Design Choices in ICS Anomaly Detection

Industrial control systems (ICS) remain vulnerable to increasingly sophisticated cyberattacks, yet evaluating anomaly detection models in these environments is challenging due to temporal dependencies, missing-not-at-random patterns, and extremely imbalanced datasets. These factors make common practices—especially random data splits and na¨ıve imputation— prone to severe temporal leakage, which can inflate reported performance and obscure real-world limitations. In this work, we systematically examine classical machine learning models, temporal deep learning architecture, and tensordecomposition– based methods on a gas-pipeline dataset using a fully temporally separated evaluation pipeline designed to mimic realistic deployment conditions. Our findings show that proper temporal handling and MNAR-aware preprocessing significantly alter the relative performance of popular anomaly-detection methods, providing practical guidance for designing reliable, leakage-resistant ICS intrusion-detection systems.

97 MATHEMATICS AND COMPUTING↗

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we, in this study, generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology.

59 BASIC BIOLOGICAL SCIENCES↗

HyRAM+ (Hydrogen Plus Other Alternative Fuels Risk Assessment Models) v.4.0

HyRAM+ is a software toolkit for conducting quantitative risk assessment (QRA) and consequence modeling for hydrogen and other alternative fuels infrastructure and transportation systems. HyRAM+ contains validated, simplified release behavior models, a standardized QRA approach, and engineering models and generic data relevant to hydrogen installations. HyRAM (hydrogen-only) versions 1.0 to 3.1 were developed by Sandia for the U.S. Department of Energy (DOE) Hydrogen and Fuel Cell Technologies Office (HFTO). The U.S. DOE Vehicle Technologies Office (VTO) and U.S. Department of Transportation (DOT) Pipeline and Hazardous Material Safety Administration (PHMSA) contributed to the development of HyRAM+ version 4.0 regarding the addition of methane (natural gas) and propane models. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-10862 O

Groth, Katrina↗

HyRAM+ (Hydrogen Plus Other Alternative Fuels Risk Assessment Models) v.4.1.1

HyRAM+ is a software toolkit for conducting quantitative risk assessment (QRA) and consequence modeling for hydrogen and other alternative fuels infrastructure and transportation systems. HyRAM+ contains validated, simplified release behavior models, a standardized QRA approach, and engineering models and generic data relevant to hydrogen installations. HyRAM (hydrogen-only) versions 1.0 to 3.1 were developed by Sandia for the U.S. Department of Energy (DOE) Hydrogen and Fuel Cell Technologies Office (HFTO). The U.S. DOE Vehicle Technologies Office (VTO) and U.S. Department of Transportation (DOT) Pipeline and Hazardous Material Safety Administration (PHMSA) contributed to the development of HyRAM+ version 4.0 regarding the addition of methane (natural gas) and propane models. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-10862 O

Groth, Katrina↗

HyRAM+ (Hydrogen Plus Other Alternative Fuels Risk Assessment Models) v.5.1.1

HyRAM+ is a software toolkit for conducting quantitative risk assessment (QRA) and consequence modeling for hydrogen and other alternative fuels infrastructure and transportation systems. HyRAM+ contains validated, simplified release behavior models, a standardized QRA approach, and engineering models and generic data relevant to hydrogen installations. HyRAM (hydrogen-only) versions 1.0 to 3.1 were developed by Sandia for the U.S. Department of Energy (DOE) Hydrogen and Fuel Cell Technologies Office (HFTO). The U.S. DOE Vehicle Technologies Office (VTO) and U.S. Department of Transportation (DOT) Pipeline and Hazardous Material Safety Administration (PHMSA) contributed to the development of HyRAM+ version 4.0 regarding the addition of methane (natural gas) and propane models. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525. SAND2021-10862 O

Groth, Katrina↗

GOOML - Finding Optimization Opportunities for Geothermal Operations: Preprint

Geothermal Operational Optimization with Machine Learning (GOOML) is a transferable and extensible component-based geothermal asset modeling framework that considers complex steamfield relationships and identifies optimization prospects using a data-driven approach. We have used this framework to develop digital twins that provide steamfield operators with an operational environment to analyze and understand historical and forecasted power production, explore new steamfield configuration possibilities, and seek optimal asset management for real world applications. The GOOML modeling software is built on a generic component-based systems framework that allows for both historical and forecast analysis. A GOOML model can perform historical data-assimilation using first-principal thermodynamics to create a meaningful data model. Historical production data can then be coupled with a forecast framework to train machine-learning models of steamfield components to predict future outputs. This modeling environment enables digital exploration of steamfield design configurations and operational scenarios. GOOML digital twins have been developed for steamfields in New Zealand and the United States representing differing power generation and field conditions. These digital twins have been validated by comparing hindcast predictions against historical production data. Reinforcement learning experiments were conducted to demonstrate the ability to programmatically explore the operations space using machine learning agents. Our initial results are compelling; two to five percent increases in annual energy production were demonstrated by the GOOML models with no additional infrastructure build required. GOOML offers a new approach to geothermal operations by applying state-of-the-art machine learning algorithms, comprehensive data analytics, and interaction with digital twins. Through application of these tools, operators will realize greater availability and higher net generation which will increase the cost effectiveness of geothermal energy projects.

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