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Knowledge-guided learning with curated prior genetic biomarkers for robust model interpretation

Abstract Motivation Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conventional deep learning approaches rely purely on data-driven learning, which can limit robust model interpretability, particularly in high-dimensional settings with limited size samples. In computational biology, knowledge-guided learning has primarily leveraged network- and structural-based knowledge, leading to biologically interpretable representations and enhanced predictive performance compared to conventional approaches. However, curated biomarkers, one of the most accessible forms of biological knowledge, remain largely unexplored within knowledge-guided paradigms. Results In this study, we propose a model-agnostic training paradigm, Biomarker-driven Explainable Prior-guided Learning (BioExPL), that can be applied to any neural networks that incorporates curated prior knowledge. BioExPL enforces neural networks to reflect curated biomarker priors in their latent representations through a novel knowledge-alignment loss. BioExPL consistently demonstrated significantly improved predictive performance and enhanced model interpretability with minimized computational overhead in simulation studies and intensive experiments on multiple cancer datasets. BioExPL not only integrates prior curated knowledge into the model but also accurately identifies unknown associated signals additionally. BioExPL is model-agnostic and domain-independent, enabling its integration into diverse neural network architectures. Availability and implementation The open-source is publicly available at: https://github.com/datax-lab/BioExPL.

Baek, Beomsu [Department of Computer Science, Univ

MAPIT User's Guide: v1.4.6-beta

The purpose of this guide is to serve as an introduction to practical usage of MAPIT and it’s underlying principles. This guide is not intended to be an comprehensive guide to safeguards or material accountancy. The reader is encouraged to review suggestions for additional reading in the theory guide for further understanding.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS

Threat Hunt Guide for BESS Environments

The rapid digitalization of the electric grid - driven by the integration of inverter-based resources (IBRs), battery energy storage systems (BESS), and advanced grid control platforms - has significantly enhanced grid efficiency, visibility, and flexibility. However, this evolution also introduces new cybersecurity risks, particularly through supply chain dependencies and operational blind spots at the grid edge. To address these challenges, Idaho National Laboratory (INL), through the Department of Energy (DOE) Office of Cybersecurity, Energy Security, and Emergency Response (CESER) Rapid Risk initiative, conducted a series of rapid risk assessment engagements with energy organizations across the United States. Drawing on lessons learned from these engagements, INL developed the following threat hunting guide for asset owners and operators (AOOs) to enhance their cybersecurity visibility within BESS and IBR systems. The guide demonstrates how to use passive network monitoring to baseline device behavior, detect adversarial activity, and investigate anomalies without disrupting operations. By implementing these practices, energy sector stakeholders can improve coordination between cybersecurity and operations teams and strengthen the resilience of distributed energy resources (DERs) within the modern power grid. Prior to implementing any network monitoring, packet capture, or threat hunting activity described in this guide, AOOs are strongly advised to review applicable governance frameworks, legal requirements, and organizational policies. This guide is intended for informational and educational purposes only. It does not replace compliance with any federal, state, or local cybersecurity mandates or industry standards. Implementation of described configurations, technologies, or analytic workflows is performed at the discretion and responsibility of the asset owner and operator.

25 - ENERGY STORAGE

Malcolm Deployment Guide for Solar Power Generation Plants

This guide provides detailed instructions for deploying Malcolm in Solar Power Generation systems. It covers the deployment process, from understanding the network architecture of these systems to configuring network switches and Switched Port Analyzer (SPAN) ports or mirror ports or TAPs. The guide also includes best practices for deploying Hedgehog sensors, another critical component in these systems. Following this guide, users can enhance network visibility, improve their system’s security, and effectively troubleshoot common issues.

14 SOLAR ENERGY

Uncertainty guided online ensemble for non-stationary data streams in fusion science

Machine Learning (ML) is poised to play a pivotal role in the development and operation of next-generation fusion devices. Fusion data shows non-stationary behavior with distribution drifts, resulted by both experimental evolution and machine wear-and-tear. ML models assume stationary distribution and fail to maintain performance when encountered with such non-stationary data streams. Online learning techniques have been leveraged in other domains, however it has been largely unexplored for fusion applications. In this paper, we investigate online learning for continuous adaptation to drifting data streams in the prediction of Toroidal Field (TF) coils deflection at the DIII-D fusion facility. We further address the short-term performance degradation inherent to standard online learning, which arises because ground truth is unavailable at prediction time. To mitigate this issue, we propose an uncertainty-guided online ensemble framework. The method leverages the Deep Gaussian Process Approximation (DGPA) for calibrated uncertainty estimation and uses these uncertainty measures to guide a meta-algorithm that aggregates predictions from learners trained over different historical horizons. Our results show that online learning reduces prediction error by 80% compared to a static model. The online ensemble and the proposed uncertainty-guided ensemble further reduce error by approximately 6%, and 10% respectively, relative to standard single-model online learning, while also providing calibrated uncertainty estimates to support operational decision-making.

AI

Optimized matching conditions for self-guided laser wakefield accelerators

We revisit the matching conditions for self-guided laser pulse propagation in plasma and refine their formulation to maximize the energy of electrons produced via laser wakefield acceleration. Bayesian optimization, combined with particle-in-cell simulations carried out in a quasi-three-dimensional geometry and a Lorentz-boosted frame, is employed. The optimization identifies the maximum electron energy that a self-guided laser wakefield accelerator, driven by a laser of a given energy, can produce, together with the corresponding acceleration distance. Our results further demonstrate that electrons with energies close to the maximum value can be obtained across a relatively wide range of input parameters and without the need for their precise tuning. This provides substantial flexibility for experimental implementation and significantly relaxes the operational constraints associated with self-guided laser wakefield accelerators.

43 PARTICLE ACCELERATORS

Nonperturbative Guiding Center Model for Magnetized Plasmas

Perturbative guiding center theory adequately describes the slow drift motion of charged particles in the strongly magnetized regime characteristic of thermal particle populations in various magnetic fusion devices. However, it breaks down for particles with large-enough energy. Here, we report on a data-driven method for learning a nonperturbative guiding center model from full-orbit particle simulation data. We show the data-driven model significantly outperforms traditional asymptotic theory in magnetization regimes appropriate for fusion-born α particles in stellarators, thus opening the door to nonperturbative guiding center calculations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY

Structure-guided discovery of ancestral CRISPR-Cas13 ribonucleases

The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation in heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral systems. Here, to address this, we developed an automated structural-search pipeline to identify an ancestral clade of Cas13 (Cas13an) and further trace Cas13 origins to defense-associated ribonucleases. Despite being one-third the size of other Cas13s, Cas13an mediates robust programmable RNA depletion and defense against diverse bacteriophages. However, unlike its larger counterparts, Cas13an uses a single active site for both CRISPR RNA processing and RNA-guided cleavage, revealing that the ancestral nuclease domain has two modes of activity. Discovery of Cas13an deepens our understanding of CRISPR-Cas evolution and expands opportunities for precision RNA editing, showcasing the promise of structure-guided genome mining.

59 BASIC BIOLOGICAL SCIENCES

Machine learning model inputs, outputs, and scripts associated with “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions”

NOTE: The manuscript associated with this data package is currently in review. The data may be revised based on reviewer feedback. Upon manuscript acceptance, this data package will be updated with the final dataset and additional metadata. This data package is associated with the manuscript “Artificial intelligence-guided iterations between observations and modeling significantly improve environmental predictions” (Malhotra et al., in prep). This effort was designed following ICON (integrated, coordinated, open, and networked) principles to facilitate a model-experiment (ModEx) iteration approach, leveraging crowdsourced sampling across the contiguous United States (CONUS). New machine learning models were created every month to guide sampling locations. Data from the resulting samples were used to test and rebuild the machine learning models for the next round of sampling guidance. Associated sediment and water geochemistry and in situ sensor data can be found at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1923689, https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1729719, and https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1603775. This data package is associated with two GitHub repositories found at https://github.com/parallelworks/dynamic-learning-rivers and https://github.com/WHONDRS-Hub/ICON-ModEx_Open_Manuscript. In addition to this readme, this data package also includes two file-level metadata (FLMD) files that describes each file and two data dictionaries (DD) that describe all column/row headers and variable definitions. This data package consists of two main folders (1) dynamic-learning-rivers and (2) ICON-ModEx_Open_Manuscript which contain snapshots of the associated GitHub repositories. The input data, output data, and machine learning models used to guide sampling locations are within dynamic-learning-rivers. The folder is organized into five top-level directories: (1) “input_data” holds the training data for the ML models; (2) “ml_models” holds machine learning (ML) models trained on the data in “input_data”; (3) “examples” contains files for direct experimentation with the machine learning model, including scripts for setting up “hindcast” run; (4) “scripts” contains data preprocessing and postprocessing scripts and intermediate results specific to this data set that bookend the ML workflow; and (5) “output_data” holds the overall results of the ML model on that branch. Each trained ML model resides on its own branch in the repository; this means that inputs and outputs can be different branch-to-branch. There is also one hidden directory “.github/workflows”. This hidden directory contains information for how to run the ML workflow as an end-to-end automated GitHub Action but it is not needed for reusing the ML models archived here. Please see the top-level README.md in the GitHub repository for more details on the automation. The scripts and data used to create figures in the manuscript are within ICON-ModEx_Open_Manuscript. The folder is organized into four folders which contain the scripts, data, and pdf for each figure. Within the “fig-model-score-evolution” folder, there is a folder called “intermediate_branch_data” which contains some intermediate files pulled from dynamic-learning-rivers and reorganized to easily integrate into the workflows. NOTE: THIS FOLDER INCLUDES THE FILES AT THE POINT OF PAPER SUBMISSION. IT WILL BE UPDATED ONCE THE PAPER IS ACCEPTED WITH ANY REVISIONS AND WILL INCLUDE A DD/FLMD AT THAT POINT. We thank the United States Forest Service, Washington Department of Fish and Wildlife, Washington Department of Natural Resources, Cowiche Canyon Conservatory, Washington State Parks and Recreation Commission (Scientific Research Permit #210901), and the Confederated Tribes and Bands of the Yakama Nation for access to field locations where the samples labeled “SSS” were collected. We also thank the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview. WHONDRS consortium members were asked to provide any acknowledgments for the collection of samples labeled “CM” and the following is a list of acknowledgments that were submitted with their corresponding Site IDs: (MART) Research activities were conducted in part on the Wind River Experimental Forest within the Gifford Pinchot National Forest; (MP- 100379) Philadelphia is part of Lenapehoking, the ancestral homelands of the Lenape peoples; (MP-102398) Land surveyed is the ancestral homelands of the Nookhose'iinenno (Arapaho), Tsis tsis'tas (Cheyenne), and Nuuchu (Ute); (MP-100749 and MP- 100747) Georgia Coastal Ecosystem LTER, OCE-1832178; (SP-70 and SP-72) Eastern Shoshone, Shoshone-Bannock; (MP- 102944) Funded by Oregon Watershed Enhancement Board. On the traditional lands of the Confederated Tribes of the Siletz, Confederated Tribes of the Grand Rhonde, and the Clatsop-Nehalem Confederated Tribe; (MP- 100607) Holiday Creek is located on the traditional territory of the Monacan Indian Nation; (SP-45) Lafayette Blue Springs State Park; (MP-102420) NSF DEB-2016749; (MP-100019) New Hampshire Agriculture Experiment Station; (SP-35) Rayonier (land owner; https://www.rayonier.com/); (MP- 101276) US Department of Energy, Office of Science, Biological and Environmental Research, Subsurface Biogeochemical Research, Watershed Dynamics and Evolution SFA at ORNL; (MP- 103224) Watershed Dynamics and Evolution SFA at ORNL; (MP- 101584) Traditional lands of the Oceti Sakowin (Dakota, Lakota, Nakoda) and Anishinaabe Peoples.

54 ENVIRONMENTAL SCIENCES

Best Practices Guide for Energy-Efficient Data Center Design

This guide provides an overview of best practices for energy-efficient data center design which spans the categories of information technology (IT) systems and their environmental conditions, data center air management, cooling and electrical systems, and heat recovery. IT system energy efficiency and environmental conditions are presented first because measures taken in these areas have a cascading effect of secondary energy savings for the mechanical and electrical systems. This guide concludes with a section on metrics and benchmarking values by which a data center and its systems energy efficiency can be evaluated. No design guide can offer “the most energy-efficient” data center design but the guidelines that follow offer suggestions that provide efficiency benefits for a wide variety of data center scenarios.

29 ENERGY PLANNING, POLICY, AND ECONOMY

BeyondFingerprinting: AI-guided discovery of robust materials & processes

BeyondFingerprinting was a 2021-2024 Sandia Grand Challenge LDRD exploring the potential to develop new resilient materials and manufacturing processes by taking an artificial-intelligence (AI)-guided approach that integrates human-subject-matter expertise with algorithms enriched with physics-based constraints to unearth process-structure-property correlations. Such algorithms, trained on high-throughput experiments and simulations, are shown to serve as surrogate models that efficiently detect key “fingerprints” in materials data, prognose material performance, and guide effective process improvements. To accelerate broader adoption across mission areas, this AI-guided approach was demonstrated with three complex process-centric exemplars: electroplating, physical vapor deposition, and laser powder bed fusion. Together, these exemplars impact nearly every hardware component relevant to DOE and NNSA national security missions.

36 MATERIALS SCIENCE

Best Practices in Integrated Resource Planning: A guide for planners developing the electricity resource mix of the future

Most states today require regulated electric utilities to file an IRP every 1 to 5 years, and some utilities voluntarily prepare these plans. Planning needs have changed in recent years due to emerging load growth, plant retirements, rising costs, and more extreme weather events – among other factors. In response, Synapse Energy Economics and Lawrence Berkeley National Laboratory produced a joint report, Best Practices in Integrated Resource Planning: A guide for planners developing the electricity resource mix of the future. The guide offers best planning practices for electricity systems undergoing a major transition, but also contains a wealth of practical guidance to develop technically sophisticated, clearer, more effective, and state-of-the-art electric utility resource plans. The guide is for resource planning professionals and stakeholders involved in resource planning processes. This diverse group includes utility personnel tasked with conducting resource planning and making investment decisions, state regulatory commissions that develop planning guidance and oversee the resource planning process, and stakeholders that represent a wide range of interests—utility consumer advocates, environmental groups, industrial customers, local governments, independent power producers, and many other

29 ENERGY PLANNING, POLICY, AND ECONOMY

Federal Home-to-Work Electric Vehicle Program Guide

This document serves as a comprehensive resource for Federal agencies in developing their own program resources that promote the efficient and effective use of electric vehicles (EVs) for home-to-work travel while ensuring compliance with Federal regulations and sustainability objectives. One mission of the U.S. Department of Energy's Federal Energy Management Program (FEMP) Fleet program is to help federal fleet managers meet or exceed statutory requirements related to energy and environmental performance while improving overall fleet efficiency, reducing costs, and meeting mission requirements. To further this mission, FEMP provides resources to support Federal agencies with increasing alternative fuel vehicle (AFV) acquisitions and reducing petroleum use. EVs are AFVs and help agencies meet federal fleet requirements. Federal fleets include government-owned EVs used for home-to-work travel. The purpose of this document is to serve as a guide for Federal agencies in developing their own internal program documents to manage government-owned EVs used for home-to-work travel. Federal agencies should consult their counsel and consider their own policies and authorities in the implementation of any policies or best practices regarding government-owned EVs used for home-to-work travel. The guide provides key considerations for agencies, including launching a pilot program to fine-tune best practices, conducting a cost-benefit analysis to compare home versus public charging, and exploring cost-effective solutions, such as installing standard outlets instead of dedicated charging stations. The guide underscores the importance of legal and financial considerations, such as verifying agency authority to install home charging infrastructure at an employee's home, ensuring the availability and appropriateness of using agency funds for home charging infrastructure, and understanding the tax implications of reimbursements.

29 ENERGY PLANNING, POLICY, AND ECONOMY

Cybersecurity Incident Response Guide for Wind

As wind energy systems become increasingly digitized and interconnected, they face a growing array of cyber threats that can disrupt operations, compromise safety, and trigger cascading impacts across the energy ecosystem. The Wind Incident Response Guide provides a structured, wind-specific framework for preparing for, detecting, responding to, and recovering from cyber incidents. Drawing on lessons from field demonstrations, cyber-physical testbeds, and stakeholder engagement across the wind sector, this guide integrates technical, operational, and regulatory considerations to support asset owners, operators, and responders. It outlines key roles and responsibilities, maps incident response phases to wind-specific scenarios, and highlights applicable laws, regulations, standards, and best practices. By tailoring general cybersecurity principles to the unique architectures and operational constraints of wind systems—including remote access, legacy components, and environmental interfaces—this guide aims to enhance resilience, reduce response time, and support coordinated action across public and private stakeholders. It is intended as a practical resource for utilities, developers, regulators, and emergency managers working to secure the future of wind energy.

17 - WIND ENERGY

A Guide for Creating a Building-Level Action Plan to Manage Refrigerants in Buildings

The Guide for Creating a Building-Level Action Plan to Manage Refrigerants in Buildings has been developed in response to stakeholder feedback and interest received during the Better Buildings Managing Refrigerants Working Group. This guide includes best practices and a step-by-step guide to create a plan to manage their organization's refrigerants. Stakeholders were interested in guidance for refrigerant management to help reduce costs and protect efficiency of equipment, to mitigate risk related to increased maintenance and operational budgets, and to manage costs of using legacy refrigerants.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI

Suppression of Collisionless Magnetic Reconnection in the High Ion β, Strong Guide Field Limit

Abstract In magnetic reconnection, the ion bulk outflow speed and ion heating have been shown to be set by the available reconnecting magnetic energy, i.e., the energy stored in the reconnecting magnetic field ( B r ). However, recent simulations, observations, and theoretical works have shown that the released magnetic energy is inhibited by upstream ion plasma beta β i —the relative ion thermal pressure normalized to magnetic pressure based on the reconnecting field—for antiparallel magnetic field configurations. Using kinetic theory and hybrid particle-in-cell simulations, we investigate the effects of β i on guide field reconnection. While previous works have suggested that guide field reconnection is uninfluenced by β i , we demonstrate that the reconnection process is modified and the outflow is reduced for sufficiently large β i > ( B r 2 + B g 2 ) / B r 2 . We develop a theoretical framework that shows that this reduction is consistent with an enhanced exhaust pressure gradient, which reduces the outflow speed as v out ∝ 1 / β i . These results apply to systems in which guide field reconnection is embedded in hot plasmas, such as reconnection at the boundary of eddies in fully developed turbulence like the solar wind or the magnetosheath as well as downstream of shocks such as the heliosheath or the mergers of galaxy clusters.

Giai, Carlos A.

Cyber Informed Engineering (CIE) Curriculum Guide

The Cyber-Informed Engineering (CIE) Curriculum Guide provides a framework, guidance, and resources for incorporating CIE into university-level engineering programs and related educational activities. A key goal of this guide is to help institutions deliver CIE focused education to produce future engineers and technicians who meet the nation’s infrastructure needs. To accommodate a broad range of educational goals and approaches, this guide outlines several practical integration strategies, links to resources that can accelerate CIE adoption, and offers perspectives from partner academic institutions on the various implementation strategies.

42 ENGINEERING

Verification of nonperturbative guiding center theory in symmetric fields

We verify a recently-developed nonperturbative guiding center formalism to charged particle dynamics in fields with two-parameter continuous symmetry groups. This entails finding exact constants of motion, valid in the nonperturbative regime, that agree with Kruskal’s adiabatic invariant series to all orders in the perturbative regime, when the field scale length is large compared with a typical gyroradius. We demonstrate that the nonperturbative guiding center model makes exact predictions in these cases, even though it eliminates the cyclotron timescale, thereby establishing a theoretical baseline for performance of the nonperturbative formalism.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY