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Description of the TCERT Vetting Reports for Data Release 25

This document, the Kepler Instrument Handbook (KIH), is for Kepler and K2 observers, which includes the Kepler Science Team, Guest Observers (GOs), and astronomers doing archival research on Kepler and K2 data in NASAs Astrophysics Data Analysis Program (ADAP). The KIH provides information about the design, performance, and operational constraints of the Kepler flight hardware and software, and an overview of the pixel data sets available. The KIH is meant to be read with these companion documents:1. Kepler Data Processing Handbook (KSCI-19081) or KDPH (Jenkins et al., 2016). The KDPH describes how pixels downlinked from the spacecraft are converted by the Kepler Data Processing Pipeline (henceforth just the pipeline) into the data products delivered to the MAST archive. 2. Kepler Archive Manual (KDMC-10008) or KAM (Thompson et al., 2016). The KAM describes the format and content of the data products, and how to search for them.3. Kepler Data Characteristics Handbook (KSCI-19040) or KDCH (Christiansen et al., 2016). The KDCH describes recurring non-astrophysical features of the Kepler data due to instrument signatures, spacecraft events, or solar activity, and explains how these characteristics are handled by the pipeline.4. Kepler Data Release Notes 25 (KSCI-19065) or DRN 25 (Thompson et al., 2015). DRN 25 describes signatures and events peculiar to individual quarters, and the pipeline software changes between a data release and the one preceding it.Together, these documents supply the information necessary for obtaining and understanding Kepler results, given the real properties of the hardware and the data analysis methods used, and for an independent evaluation of the methods used if so desired.

Instrument↗

Towards AI-assisted neutrino flavor theory design

Particle physics theories, such as those which explain neutrino flavor mixing, arise from a vast landscape of model-building possibilities. A model’s construction typically relies on the intuition of theorists. It also requires considerable effort to identify appropriate symmetry groups, assign field representations, and extract predictions for comparison with experimental data. We develop Autonomous Model Builder (AMBer), a framework in which a reinforcement learning agent interacts with a streamlined physics software pipeline to search these spaces efficiently. AMBer selects symmetry groups, particle content, and group representation assignments to construct models while minimizing the number of free parameters introduced. We validate our approach in well-studied regions of theory space and extend the exploration to a previously unexamined symmetry group. While demonstrated in the context of neutrino flavor theories, this approach of reinforcement learning with physics software feedback may be extended to other theoretical model-building problems in the future.

Baretz, Jason Benjamin↗

LDM-151: Data Management Science Pipelines Design

The LSST Science Requirements Document (the LSST SRD) specifies a set of data product guidelines, designed to support science goals envisioned to be enabled by the LSST observing program. Following these guidelines, the details of these data products have been described in the LSST Data Products Definition Document (DPDD), and captured in a formal flow-down from the SRD via the LSST System Requirements (LSR), Observatory System Specifications (OSS), to the Data Management System Requirements (DMSR). The LSST Data Management subsystem's responsibilities include the design, implementation, deployment and execution of software pipelines necessary to generate these data products. This document describes the design of the scientific aspects of those pipelines.

79 ASTRONOMY AND ASTROPHYSICS↗

Investigating Scientific Data Change with User Research Methods

Scientific datasets are continually expanding and changing due to fluctuations with instruments, quality assessment and quality control processes, and modifications to software pipelines. Datasets include minimal information about these changes or their effects requiring scientists manually assess modifications through a number of labor intensive and ad-hoc steps. The Deduce project is investigating data change to develop metrics, methods, and tools that will help scientists systematically identify and make decisions around data changes. Currently, there is a lack of understanding, and common practices, for identifying and evaluating changes in datasets since systematically measuring and managing data change is under explored in scientific work. We are conducting user research to address this need by exploring scientist's conceptualizations, behaviors, needs, and motivations when dealing with changing datasets. Our user research utilizes multiple methods to produce foundational, generative insights and evaluate research products produced by our team. In this paper, we detail our user research process and outline our findings about data change that emerge from our studies. Our work illustrates how scientific software teams can push beyond just usability testing user interfaces or tools to better probe the underlying ideas they are developing solutions to address.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

The Eighteenth Data Release of the Sloan Digital Sky Surveys: Targeting and First Spectra from SDSS-V

The eighteenth data release (DR18) of the Sloan Digital Sky Survey (SDSS) is the first one for SDSS-V, the fifth generation of the survey. SDSS-V comprises three primary scientific programs or “Mappers”: the Milky Way Mapper (MWM), the Black Hole Mapper (BHM), and the Local Volume Mapper. This data release contains extensive targeting information for the two multiobject spectroscopy programs (MWM and BHM), including input catalogs and selection functions for their numerous scientific objectives. We describe the production of the targeting databases and their calibration and scientifically focused components. DR18 also includes ~25,000 new SDSS spectra and supplemental information for X-ray sources identified by eROSITA in its eFEDS field. We present updates to some of the SDSS software pipelines and preview changes anticipated for DR19. We also describe three value-added catalogs (VACs) based on SDSS-IV data that have been published since DR17, and one VAC based on the SDSS-V data in the eFEDS field.

79 ASTRONOMY AND ASTROPHYSICS↗

The Future of a Myriad of Accelerated Biodiscoveries Lies in AI‐Powered Mass Spectrometry and Multiomics Integration

The intersection of modern artificial intelligence (AI) and mass spectrometry (MS) is set to transform the MS‐based “omics” research fields, particularly proteomics, metabolomics, lipidomics, and glycomics, enabling advancements across a wide range of domains, from health to environment and industrial biotechnology. Beginning with an overview of key challenges inherent in MS software pipelines, this personal perspective explores how AI‐driven solutions can address them to enhance data processing, integration and interpretation. It proposes a paradigm shift in molecular identification and quantitation algorithms, leveraging AI to enable holistic interpretation of MS‐based multiomics data. While centered on MS‐based omics, this holistic AI‐driven paradigm is also critical for connecting dynamic biochemical changes to genomics and transcriptomics contexts, reinforcing the integrative value of MS in multiomics research. Ultimately, this AI‐driven approach could enhance efficiency, accuracy, and molecular breadth of coverage, deepening our systems‐level understanding of biological processes and accelerating a myriad of biodiscoveries.

47 OTHER INSTRUMENTATION↗

Rapid Annotation of Photosynthetic Systems (RAPS): automated algorithm to generate genome-scale metabolic networks from algal genomes

Algae have mounting potential to serve as platform strains for engineering efforts, but tools for these species lag behind traditional model systems like E. coli and yeast. Metabolic models are one such tool that would enhance our ability to rationally engineer algae but current automated algorithms to build models do not perform well for algal genomes. We introduce a novel software pipeline, Rapid Annotation of Photosynthetic Systems (RAPS), which leverages manual curation efforts of published models to create high quality first draft metabolic networks for new species. We compared models produced by our pipeline to published models and found that these models are able to capture more genes than the published models and are more predictive of experimentally determined growth rate. We used RAPS to automate the creation of 8 first draft metabolic models of new species to enable the further study of metabolism in these species.

09 BIOMASS FUELS↗

Inductive predictions of hydrologic events using a Long Short-Term Memory network and the Soil and Water Assessment Tool

We present machine learning methods to predict hydrologic features such as streamflow and soil moisture from spatially and temporally varying hydrological and meteorological data. Here, we used a temporal reduction technique to reduce computation and memory requirements and trained a Long Short-Term Memory (LSTM) network to predict soil moisture and streamflow over multiple watersheds. We show LSTM networks can be trained in a fraction of the time required by complex process-based and attention-based models such as Soil and Water Assessment Tool (SWAT) and GeoMAN without sacrificing accuracy. We also demonstrate that outside data - sourced from a watershed other than the target - can be used to train LSTM to comparable or even superior prediction accuracy. The success of LSTM in such spatially-inductive settings shows hydrologic features can be predicted with minimal prior knowledge of the watershed in question. Finally, we make all methodologies of this work publicly available as an end-to-end software pipeline that facilitates rapid prototyping of hydrologic learners.

97 MATHEMATICS AND COMPUTING↗

Progress in end-to-end optimization of fundamental physics experimental apparata with differentiable programming

In this article we examine recent developments in the research area concerning the creation of end-to-end models for the complete optimization of measuring instruments. The models we consider rely on differentiable programming methods and on the specification of a software pipeline including all factors impacting performance — from the data-generating processes to their reconstruction and the inference on the parameters of interest — along with the careful specification of a utility function well aligned with the end goals of the experiment. Building on previous studies originated within the MODE Collaboration, we focus specifically on applications involving instruments for particle physics experimentation, as well as industrial and medical applications that share the detection of radiation as their data-generating mechanism. This report illustrates the most recent advancements in the area, and outlines, for each of the discussed applications as well as for automatic differentiation itself, ongoing and future work.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Constructing Self-Labeled Materials Imaging Datasets from Open Access Scientific Journals with EXSCLAIM!

Due to recent improvements in image resolution and acquisition speeds, materials microscopy is experiencing an explosion in imaging data. Yet, despite the volume of images generated, the overall accessibility landscape is highly fragmented, as researchers who do release images to the public, often only do so as snapshots of their larger private dataset in context of scientific journal publications. The effort to automatically consolidate images and descriptive information from web-based platforms has garnered broad attention from the computer vision, language technologies, and chemistry/materials informatics communities. However, these methods are problematic for scientific figures because over 30% of figures are compound in nature, and it is the individual images themselves, paired with relevant context, that are necessary for construction a proper labeled dataset. To this end, we outline in this paper the design of a software pipeline for the automatic EXtraction, Separation, and Caption-based natural Language Annotation of IMages from scientific figures (EXSCLAIM!). Successful consolidation of materials imaging across literature sources will enhance navigation and searchability of materials microscopy images for both novice and experienced researchers, as well as establish the framework necessary for users to search by images, text, or some combination of both.

36 MATERIALS SCIENCE↗

Optical emissivity dataset of multi-material heterogeneous designs generated with automated figure extraction

Optical device design is typically an iterative optimization process based on a good initial guess from prior reports. Optical properties databases are useful in this process but difficult to compile because their parsing requires finding relevant papers and manually converting graphical emissivity curves to data tables. Here, we present two contributions: one is a dataset of thermal emissivity records with design-related parameters, and the other is a software tool for automated colored curve data extraction from scientific plots. We manually collected 64 papers with 176 figures reporting thermal emissivity and automatically retrieved 153 colored curve data records. The automated figure analysis software pipeline uses Faster R-CNN for axes and legend object detection, EasyOCR for axes numbering recognition, and k-means clustering for colored curve retrieval. Additionally, we manually extracted geometry, materials, and method information from the text to add necessary metadata to each emissivity curve. Finally, we analyzed the dataset to determine the dominant classes of emissivity curves and determine the underlying design parameters leading to a type of emissivity profile.

47 OTHER INSTRUMENTATION↗

Boosting RDataFrame performance with transparent bulk event processing

RDataFrame is ROOT’s high-level interface for Python and C++ data analysis. Since it first became available, RDataFrame adoption has grown steadily and it is now poised to be a major component of analysis software pipelines for LHC Run 3 and beyond. Thanks to its design inspired by declarative programming principles, RDataFrame enables the development of highperformance, highly parallel analyses without requiring expert knowledge of multi-threading and I/O: user logic is expressed in terms of self-contained, small computation kernels tied together by a high-level API. This design completely decouples analysis logic from its actual execution, and opens several interesting avenues for workflow optimization. In particular, in this work we explore the benefits of moving internal data processing from an event-by-event to a bulkby-bulk loop. This refactoring dramatically reduces the framework’s runtime overheads; in collaboration with the I/O layer it improves data access patterns; it exposes information that optimizing compilers might use to auto-vectorize the invocation of user-defined computations; finally, while existing user-facing interfaces remain unaffected, it becomes possible to additionally offer interfaces that explicitly expose bulks of events, useful e.g. for the injection of GPU kernels into the analysis workflow. In order to inform similar future R&D, design challenges will be presented, as well as an investigation of the relevant timememory trade-off backed by novel performance benchmarks.

Guiraud, Enrico↗

Agilent CRADA (Abstract)

The CRADA between Agilent Technologies Inc. and Battelle will focus on five software components as listed below: Prototype 4D Feature Finding functionality with a particular focus on recovering low level features and extending the bottom end dynamic range of IM-MS technology. Compare and contrast developments to current 4D Feature Finding capabilities. Highlight important algorithmic aspects employed. Implement the PNNL saturation correction algorithm. Agilent will give PNNL the needed data file access API and assistance in understanding it implementation and any needed instrumental aspects. Supported high resolution products to include Agilent’s TOF, QTOF and IM-QTOF mass spectrometers. PNNL will then work with Agilent to benchmark performance. Implementation of the PNNL Hadamard de-multiplexing algorithm. Agilent will give provide PNNL the needed date file access API access and as needed assistance in understanding the current Agilent multiplexed IM offering. PNNL will then work with Agilent on benchmark performance. Add ion mobility collision cross sections to existing and new metabolomic libraries for data analysis with Agilent’s informatics program MPP/ID Browser. PNNL will work with Agilent to create a software pipeline that takes data from chemical and metabolic standards and properly formats it for inclusion in MPP accessible libraries, using the collision cross section as a new separation dimension. Improvements of MPP multidimensional matching to identify metabolomic features using multiple characteristics beyond retention time and accurate mass. Most significantly matching will include analyte collision cross section with proposed support for sample fraction or RapidFire cartridge and fragmentation spectra. PNNL will work with Agilent to modify and improve the current MPP analysis pipeline to allow for creating, aligning, and identifying MS features defined by accurate mass, collision cross section and chromatographic retention time. As additional criteria such as fraction or RapidFire cartridge type are supported in the identification process, then they also will become part of the automation workflow. This includes the automation of said system to work with command line program (i.e. not a GUI) sufficient for programmatic execution in a pipeline.

97 MATHEMATICS AND COMPUTING↗

Scalable Truck Charging Demand Simulation for Cost-Optimized Infrastructure Planning

This project developed a scalable, high-resolution model to simulate medium- and heavy-duty (MHD) electric truck charging demand and assess its impact on grid infrastructure. Using generative modeling, simulation, and cost optimization, the project delivered an end-to-end software pipeline and a library of 96 real-world scenarios for the Dallas–Houston megaregion. We demonstrated a modular architecture for transportation and grid modeling, implemented cost-optimized infrastructure planning methods, and quantified grid capital, operational, and environmental costs across a wide range of truck electrification scenarios. The results have been adopted by major utility stakeholders and contributed to regional planning efforts.

24 POWER TRANSMISSION AND DISTRIBUTION↗

AI-Driven Detector Design for the EIC (Final Technical Report)

We developed an optimization workflow based on DNN-based fast-simulation and reconstruction algorithms. We used these methods to advance the design of calorimeter systems for the Electron-Ion Collider (EIC). This DNN-driven optimization provides a blueprint for integrating gradient-based methods into detector-design workflows. All software pipelines and methods have been released publicly and incorporated into the EIC collaboration’s physics studies, broadening their impact. Three journal articles detailing the methods developed here serve as a reference for the design and optimal use of next generation high-granularity calorimeter systems in nuclear and particle physics.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hybrid learning techniques for scientific data reduction with performance guarantees

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗

Pose Estimation for the Inspecta Project

In this addendum report we take the lessons learned from our initial generic object pose estimation research described in (Smartt, et al., 2025) and apply it to metal cup seals, which are attached to items after an international nuclear safeguards inspection (i.e., metal cup seals may be attached to containers of spent nuclear fuel after an inspector has measured and verified the material). We have also refined our software pipeline and training techniques since the final Inspecta report and will describe that process here. The objective of this task is to allow a robot to acquire images of the engraved seal characters to confirm that the correct seal is attached to the correct container. However, the seal may be attached in any orientation and therefore the robot manipulator arm with a camera needs to align with the normal face of the seal.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗