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Evaluation of the Self Retrieval Augmented Generation Technique on Common Security Advisory Framework Data

This small experimental report evaluates a variation of Retrieval Augmented Generation (RAG), called Self-RAG. This method uses a generative language model that incorporates retrieved facts into its generation and is explicitly trained to be able to determine whether retrieved information is enough to answer the input query, with a user-defined threshold for confidence. We performed an experiment using data from the publicly available CISA Common Security Advisory Framework (CSAF) repository (https://github.com/cisagov/CSAF) as the database of facts to be used in retrieval. Qualitative results from the experiment demonstrate that the Self-RAG method has some ability to provide reasonable answers to queries that are in the dataset and will often ignore irrelevant information when asked outside of domain questions (e.g., general facts). In settings with deliberately confusing questions (the question is within domain, but asks about a fabricated advisory), it was able to refuse 40% of the time without further adjustments to the original framework. While this performance is not sufficient for current practical use, further improvements to data formatting, disambiguating results, and leveraging threshold values could improve performance significantly. However, evaluating this will require more extensive evaluations on larger datasets and potentially better models.

97 MATHEMATICS AND COMPUTING↗

AI Model Benchmarking for Nonproliferation Applications: Steel Thread Benchmarking Task Force Technical Report (Rev. 2)

Steel Thread is a NA-22 venture that seeks to build trustworthy, reliable AI models that can be used in a wide variety of nonproliferation tasks. A key aspect of building these models is developing appropriate benchmarks and evaluation methods, which will enable the venture to identify and adapt models to provide the most value in the nonproliferation domain. Benchmarks must be relevant to key tasks in this domain, such as question answering, information retrieval, document summarization and classification, consensus analysis, and image and data analysis. This report 1) provides an overview of benchmark design, evaluation, and challenges; 2) reviews a variety of open benchmarks, with a focus on language models and tasks; and 3) identifies benchmarks that are most relevant to Steel Thread. This report is intended to serve as a basis for further efforts to classify and evaluate benchmarks and their correlation with success on nonproliferation-specific tasks. The Steel Thread venture has defined benchmarks to be a particular combination of a dataset (or datasets) and a metric (or metrics) conceptualized as representing one or more specific tasks or sets of abilities for a specific modality. It is adopted by a research community as a shared framework for comparing methods.1 It includes 1) Data: Labeled (a designated subset not used for training, which could be all the data), 2) Metric: A way to quantify performance, 3) Task/Ability: What the benchmark is testing, 4) Protocol: A structured and repeatable evaluation process, 5) Baseline/Reference Model: For comparison; could be statistical, rule-based, SME-derived, or another model, and 6) Maintenance Plan: to update with new information over time; important for long-term utility. For further clarity, the definition includes what a benchmark, in this context, is not. It is not a corpus of training data, specific to a model (it is intended to apply to a range of models), a universal evaluation of performance, a guarantee that the ‘top’ model on the leaderboard will be the best fit for every specific use case, an all-encompassing proof of a model’s universal quality, nor is it a one-size-fits-all measure of success. It does not cover every real-world constraint (like operational, ethical, or cost considerations), a systems integration test, or a unit test. This definition was inspired by and resulted from discussions within the Steel Thread Benchmarking Task Force. This group was formed to define what we would mean as a benchmark within Steel Thread but persisted as the need to develop a thorough understanding of the large and expanding existing benchmarking space. This technical report is a result of the group’s divide and conquer approach to exploring this space. The release of benchmarks might not be progressing as quickly as model development, but it is moving very fast, as many benchmarks quickly become saturated, when state-of-the-art models score so close to the benchmark’s ceiling that their results are virtually indistinguishable. At that point, the test no longer differentiates between new systems, so researchers usually stop reporting scores as the benchmark no longer informs about improvements from the next generation of models. In the OpenAI announcement of GPT-5, they reported results on six flagship public benchmarks (AIME 2025, SWE-bench Verified, Aider Polyglot, MMMU, HealthBench Hard, GPQA) but the full system-card covers roughly thirty-five separate evaluations, comprising hundreds of test task items in total. There have been some efforts to summarize benchmarks in specific fields, like for text-to-image generation, but these surveys have had a narrow methodology scope. Therefore, a comprehensive survey of all benchmarks or even all benchmarks that could be relevant to Steel Thread is outside of the scope of this report. We chose some specific benchmarks to investigate in detail.

97 MATHEMATICS AND COMPUTING↗

Predicting Search Task Difficulty through a Discrete‐Time Action Log Representation on Spectrum Kernel

ABSTRACT Predicting perceived difficulty on a web search task is an open problem in the interactive information retrieval field. A common approach to tackle it, is through features obtained from full search sessions, which are then used to train classification models. In this poster we attempt to predict perceived task difficulty at different stages of the search process. To do so, we use the spectrum kernel for support vector machine (SVM) classification. Our preliminary results suggest that by using behavioral data from the first query segment, it is possible to provide timely classifications of whether a search task is perceived as hard or easy.

Gacitúa, Daniel↗

Neuronal Plasma Membranes as Supramolecular Assemblies for Biological Memory

Biological memory is the ability to develop, retain, and retrieve information over time. Currently, it is widely accepted that memories are stored in synapses (i.e., connections between brain cells throughout the brain) through a process known as synaptic plasticity, which leads to either long-term potentiation (LTP) or long-term depression (LTD). However, the strengthening (LTP) and weakening (LTD) of synapses involve post-translational modifications to neural networks requiring de novo gene expression, a lengthy and energetically expensive process. Recently, we observed that lipid bilayers in the absence of peptides/proteins are capable of LTP, not unlike what has been observed in mammals and birds. As such, this finding has prompted us to postulate that the lipid bilayer provides a good model for understanding the molecular basis of biological memory. Here, in this article, we discuss the status, challenges, and opportunities of neuronal plasma membranes as structures for biological memory and learning, therapeutic targets for various brain disorders, and platforms for neural network developments.

59 BASIC BIOLOGICAL SCIENCES↗

Developing a Chemical and Structural Understanding of the Surface Oxide in a Niobium Superconducting Qubit

We report superconducting thin films of niobium have been extensively employed in transmon qubit architectures. Although these architectures have demonstrated remarkable improvements in recent years, further improvements in performance through materials engineering will aid in large-scale deployment. Here, we use information retrieved from secondary ion mass spectrometry and electron microscopy to conduct a detailed assessment of the surface oxide that forms in ambient conditions for transmon test qubit devices patterned from a niobium film. We observe that this oxide exhibits a varying stoichiometry with NbO and NbO 2 found closer to the niobium film and Nb 2 O 5 found closer to the surface. In terms of structural analysis, we find that the Nb 2 O 5 region is semicrystalline in nature and exhibits randomly oriented grains on the order of 1-2 nm corresponding to monoclinic N-Nb 2 O 5 that are dispersed throughout an amorphous matrix. Using fluctuation electron microscopy, we are able to map the relative crystallinity in the Nb 2 O 5 region with nanometer spatial resolution. Through this correlative method, we observe that amorphous regions are more likely to contain oxygen vacancies and exhibit weaker bonds between the niobium and oxygen atoms. Based on these findings, we expect that oxygen vacancies likely serve as a decoherence mechanism in quantum systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Impacts of Degradation on Water, Energy, and Carbon Cycling of the Amazon Tropical Forests

Selective logging, fragmentation, and understory fires directly degrade forest structure and composition. However, studies addressing the effects of forest degradation on carbon, water, and energy cycles are scarce. Here, we integrate field observations and high-resolution remote sensing from airborne lidar to provide realistic initial conditions to the Ecosystem Demography Model (ED-2.2) and investigate how disturbances from forest degradation affect gross primary production (GPP), evapotranspiration (ET), and sensible heat flux (H). We used forest structural information retrieved from airborne lidar samples (13,500 ha) and calibrated with 817 inventory plots (0.25 ha) across precipitation and degradation gradients in the eastern Amazon as initial conditions to ED-2.2 model. Our results show that the magnitude and seasonality of fluxes were modulated by changes in forest structure caused by degradation. During the dry season and under typical conditions, severely degraded forests (biomass loss ≥66%) experienced water stress with declines in ET (up to 34%) and GPP (up to 35%) and increases of H (up to 43%) and daily mean ground temperatures (up to 6.5°C) relative to intact forests. In contrast, the relative impact of forest degradation on energy, water, and carbon cycles markedly diminishes under extreme, multiyear droughts, as a consequence of severe stress experienced by intact forests. Our results highlight that the water and energy cycles in the Amazon are driven by not only climate and deforestation but also the past disturbance and changes of forest structure from degradation, suggesting a much broader influence of human land use activities on the tropical ecosystems.

54 ENVIRONMENTAL SCIENCES↗

Automated electrosynthesis reaction mining with multimodal large language models (MLLMs)

Leveraging the chemical data available in legacy formats such as publications and patents is a significant challenge for the community. Automated reaction mining offers a promising solution to unleash this knowledge into a learnable digital form and therefore help expedite materials and reaction discovery. However, existing reaction mining toolkits are limited to single input modalities (text or images) and cannot effectively integrate heterogeneous data that is scattered across text, tables, and figures. In this work, we go beyond single input modalities and explore multimodal large language models (MLLMs) for the analysis of diverse data inputs for automated electrosynthesis reaction mining. We compiled a test dataset of 65 articles (MERMES-T24 set) and employed it to benchmark five prominent MLLMs against two critical tasks: (i) reaction diagram parsing and (ii) resolving cross-modality data interdependencies. The frontrunner MLLM achieved ≥96% accuracy in both tasks, with the strategic integration of single-shot visual prompts and image pre-processing techniques. We integrate this capability into a toolkit named MERMES (multimodal reaction mining pipeline for electrosynthesis). Our toolkit functions as an end-to-end MLLM-powered pipeline that integrates article retrieval, information extraction and multimodal analysis for streamlining and automating knowledge extraction. This work lays the groundwork for the increased utilization of MLLMs to accelerate the digitization of chemistry knowledge for data-driven research.

Leong, Shi Xuan↗

PhysBERT: A text embedding model for physics scientific literature

The specialized language and complex concepts in physics pose significant challenges for information extraction through Natural Language Processing (NLP). Central to effective NLP applications is the text embedding model, which converts text into dense vector representations for efficient information retrieval and semantic analysis. In this work, we introduce PhysBERT, the first physics-specific text embedding model. Pre-trained on a curated corpus of 1.2 × 106 arXiv physics papers and fine-tuned with supervised data, PhysBERT outperforms leading general-purpose models on physics-specific tasks, including the effectiveness in fine-tuning for specific physics subdomains.

Hellert, Thorsten (ORCID:0000000227970926)↗

Efficient numerical methods to solve sparse linear equations with application to PageRank

Over the last two decades, the PageRank problem has received increased interest from the academic community as an efficient tool to estimate web-page importance in information retrieval. Despite numerous developments, the design of efficient optimization algorithms for the PageRank problem is still a challenge. Here, we propose three new algorithms with a linear time complexity for solving the problem over a bounded-degree graph. The idea behind them is to set up the PageRank as a convex minimization problem over a unit simplex, and then solve it using iterative methods with small iteration complexity. Our theoretical results are supported by an extensive empirical justification using real-world and simulated data.

97 MATHEMATICS AND COMPUTING↗

BioADAPT-MRC: adversarial learning-based domain adaptation improves biomedical machine reading comprehension task

ABSTRACT Motivation Biomedical machine reading comprehension (biomedical-MRC) aims to comprehend complex biomedical narratives and assist healthcare professionals in retrieving information from them. The high performance of modern neural network-based MRC systems depends on high-quality, large-scale, human-annotated training datasets. In the biomedical domain, a crucial challenge in creating such datasets is the requirement for domain knowledge, inducing the scarcity of labeled data and the need for transfer learning from the labeled general-purpose (source) domain to the biomedical (target) domain. However, there is a discrepancy in marginal distributions between the general-purpose and biomedical domains due to the variances in topics. Therefore, direct-transferring of learned representations from a model trained on a general-purpose domain to the biomedical domain can hurt the model’s performance. Results We present an adversarial learning-based domain adaptation framework for the biomedical machine reading comprehension task (BioADAPT-MRC), a neural network-based method to address the discrepancies in the marginal distributions between the general and biomedical domain datasets. BioADAPT-MRC relaxes the need for generating pseudo labels for training a well-performing biomedical-MRC model. We extensively evaluate the performance of BioADAPT-MRC by comparing it with the best existing methods on three widely used benchmark biomedical-MRC datasets—BioASQ-7b, BioASQ-8b and BioASQ-9b. Our results suggest that without using any synthetic or human-annotated data from the biomedical domain, BioADAPT-MRC can achieve state-of-the-art performance on these datasets. Availability and implementation BioADAPT-MRC is freely available as an open-source project at https://github.com/mmahbub/BioADAPT-MRC. Supplementary information Supplementary data are available at Bioinformatics online.

60 APPLIED LIFE SCIENCES↗

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

When ChatGPT Meets Vulnerability Management: The Good, the Bad, and the Ugly

Vulnerability management is a very challenging and time-consuming task. For many organizations, security operators need to learn about the properties of vulnerabilities to prioritize and mitigate them. Due to the lack of automated tools for vulnerability assessment, operators usually manually search for and read related information from sources online. Recent advances in large language models, like ChatGPT, open up an opportunity for time savings and may prompt operators to use these models as vulnerability information sources. In this work, we evaluate the ability of ChatGPT and several of its siblings to accurately answer user questions about vulnerability properties as well as to provide information for how to mitigate a vulnerability. We also explore their summarization capabilities when multiple vulnerability advisory documents are provided. We find that the models perform poorly on information retrieval tasks, but they perform quite well on summarization.

McClanahan, Kylie↗

Attention-based Aspect Reasoning for Knowledge Base Question Answering on Clinical Notes

Question Answering (QA) in clinical notes has gained a lot of attention in the past few years. Existing machine reading comprehension approaches in clinical domain can only handle questions about a single block of clinical texts and fail to retrieve information about different patients and clinical notes. To handle more complex questions, we aim at creating knowledge base from clinical notes to link different patients and clinical notes, and performing knowledge base question answering (KBQA). Based on the expert annotations in n2c2, we first created the ClinicalKBQA dataset that includes 8,952 QA pairs and covers questions about seven medical topics through 322 question templates. Then, we proposed an attention-based aspect reasoning (AAR) method for KBQA and investigated the impact of different aspects of answers (e.g., entity, type, path, and context) for prediction. The AAR method achieves better performance due to the well-designed encoder and attention mechanism. In the experiments, we find that both aspects, type and path, enable the model to identify answers satisfying the general conditions and produce lower precision and higher recall. On the other hand, the aspects, entity and context, limit the answers by node-specific information and lead to higher precision and lower recall.

Wang, Ping↗

Python HITMIX

SAND2024-10158O Python HITMIX is a software package for computing hitting time moments of vertices in a graph. Hitting time moments can be used to rank the strengths of relationships between vertices in a graph. Examples are provided for computing and using hitting time moments on generic graphs and similarity graphs arising from the analysis of text documents in information retrieval applications. 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.

Dunlavy, Daniel↗

Integrating LEO and GEO Observations: Toward Optimal Summertime Satellite Precipitation Retrieval

Abstract Reliable quantitative precipitation estimation with a rich spatiotemporal resolution is vital for understanding the Earth’s hydrological cycle. Precipitation estimation over land and coastal regions is necessary for addressing the high degree of spatial heterogeneity of water availability and demand, and for resolving the extremes that modulate and amplify hazards such as flooding and landslides. Advancements in computation power along with unique high spatiotemporal and spectral resolution data streams from passive meteorological sensors aboard geosynchronous Earth-orbiting (GEO) and low Earth-orbiting (LEO) satellites offer exciting opportunities to retrieve information about surface precipitation phenomena using data-driven machine learning techniques. In this study, the capabilities of U-Net–like architecture are investigated to map instantaneous, summertime surface precipitation intensity at the spatial resolution of 2 km. The calibrated brightness temperature products from the Global Precipitation Measurement (GPM) Microwave Imager (GMI) radiometer are combined with multispectral images (visible, near-infrared, and infrared bands) from the Advanced Baseline Imager (ABI) aboard the GOES-R satellites as main inputs to the U-Net–like precipitation algorithm. Total precipitable water and 2-m temperature from the Global Forecast System (GFS) model are also used as auxiliary inputs to the model. The results show that the U-Net–like algorithm can capture fine-scale patterns and intensity of surface precipitation at high spatial resolution over stratiform and convective precipitation regimes. The evaluations reveal the potential of extracting relevant, high spatial features over complex surface types such as mountainous regions and coastlines. The algorithm allows users to interpret the inputs’ importance and can serve as a starting point for further exploration of precipitation systems within the field of hydrometeorology.

Meteorology & Atmospheric Sciences↗

Deep Learning Denoising Applied to Regional Distance Seismic Data in Utah

Seismic waveform data are generally contaminated by noise from various sources. Suppressing this noise effectively so that the remaining signal of interest can be successfully exploited remains a fundamental problem for the seismological community. To date, the most common noise suppression methods have been based on frequency filtering. These methods, however, are less effective when the signal of interest and noise share similar frequency bands. Inspired by source separation studies in the field of music information retrieval (Jansson et al., 2017) and a recent study in seismology (Zhu et al., 2019), we implemented a seismic denoising method that uses a trained deep convolutional neural network (CNN) model to decompose an input waveform into a signal of interest and noise. In our approach, the CNN provides a signal mask and a noise mask for an input signal. The short-time Fourier transform (STFT) of the estimated signal is obtained by multiplying the signal mask with the STFT of the input signal. To build and test the denoiser, we used carefully compiled signal and noise datasets of seismograms recorded by the University of Utah Seismograph Stations network. Results of test runs involving more than 9000 constructed waveforms suggest that on average the denoiser improves the signal-to-noise ratios (SNRs) by ~5 db, and that most of the recovered signal waveforms have high similarity with respect to the target waveforms (average correlation coefficient of ~0.80) and suffer little distortion. Application to real data suggests that our denoiser achieves on average a factor of up to ~2-5 improvement in SNR over band-pass filtering and can suppress many types of noise that band-pass filtering cannot. For individual waveforms, the improvement can be as high as ~15 db.

58 GEOSCIENCES↗

AI-Ready Control System for the Fermilab Accelerator Complex

Reliable, high-intensity operation of the Fermilab Accelerator Complex is critical to the success of the Long-Baseline Neutrino Facility and Deep Underground Neutrino Experiment. We describe the requirements and infrastructure necessary to support routine use of artificial intelligence and machine learning (AI/ML) in the accelerator control system. Three capabilities are identified: a machine learning operations (MLOps) framework standardizing the lifecycle of AI/ML automation from data management through deployment and monitoring; a data quality framework defining and enforcing standards required to build trustworthy AI/ML applications; and workflow integration with large language models to assist physicists, engineers, and operators with information retrieval, code development, and routine analysis. Use cases spanning beam diagnostics, beam control, and support system automation illustrate the technical requirements across the complex.

43 PARTICLE ACCELERATORS↗

A Double-Edged Sword: The Role of Prior Knowledge in Memory Aging

People accumulate knowledge throughout their lifespan and the accumulated knowledge influences how we encode and retrieve information in memory processing. This study aims to investigate the role of knowledge in associative memory across the adult lifespan, and specifically examines the effects of two material properties that interact with prior knowledge: congruency – whether the material is congruent with people’s prior knowledge, and ambiguity – whether the material is ambiguous to interpret based on prior knowledge. 273 participants (aged 22–70 years old) completed an incidental memory task online. Participants were shown pictures depicting an object in a scene and judged if the object was likely or unlikely to be in the particular scene. Later, in the recognition test, participants were asked to identify if the exact picture was presented earlier. The pictures were manipulated to have varying levels of congruency, meaning that some depicted likely object–scene pairs and some unlikely. We also measured how different the likely/unlikely judgment for each object–scene pair was across all participants to determine the ambiguity level of the object–scene pair: some were more likely to receive diverse responses across people, whereas others are unambiguously consistent (or inconsistent) with common knowledge shared by most people. We used mixed-effects logistic regressions to predict memory outcome for each trial as a function of age, age 2 , congruency/ambiguity, and their interactions. The object–scene pairs perceived as congruent had higher hit rates than incongruent ones, as well as higher false alarm rates, especially in middle-aged and older people. Higher ambiguity was also related to both greater true and false memory, independent of age. Finally, the effect of ambiguity only emerged when the object–scene pair was perceived incongruent. The results suggest that people rely on prior knowledge to process new information and that this reliance improves hit responses, but also induces false memories particularly for middle-aged and older people, suggesting a double-edged role of knowledge in associative memory and its disproportionate influence on memory aging. Over-reliance on knowledge in older adults, which has been suspected in other cognitive processes, may be one of the mechanisms underlying associative memory decrease in aging.

60 APPLIED LIFE SCIENCES↗