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546 records · Page 31

AI Meets Exascale Computing: Advancing Cancer Research With Large-Scale High Performance Computing

The application of data science in cancer research has been boosted by major advances in three primary areas: (1) Data: diversity, amount, and availability of biomedical data; (2) Advances in Artificial Intelligence (AI) and Machine Learning (ML) algorithms that enable learning from complex, large-scale data; and (3) Advances in computer architectures allowing unprecedented acceleration of simulation and machine learning algorithms. These advances help build in silico ML models that can provide transformative insights from data including: molecular dynamics simulations, next-generation sequencing, omics, imaging, and unstructured clinical text documents. Unique challenges persist, however, in building ML models related to cancer, including: (1) access, sharing, labeling, and integration of multimodal and multi-institutional data across different cancer types; (2) developing AI models for cancer research capable of scaling on next generation high performance computers; and (3) assessing robustness and reliability in the AI models. In this paper, we review the National Cancer Institute (NCI) -Department of Energy (DOE) collaboration, Joint Design of Advanced Computing Solutions for Cancer (JDACS4C), a multi-institution collaborative effort focused on advancing computing and data technologies to accelerate cancer research on three levels: molecular, cellular, and population. This collaboration integrates various types of generated data, pre-exascale compute resources, and advances in ML models to increase understanding of basic cancer biology, identify promising new treatment options, predict outcomes, and eventually prescribe specialized treatments for patients with cancer.

60 APPLIED LIFE SCIENCES↗

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↗

Machine-Learning-Based Mapping and Modeling of Solar Energy with Ultra-High Spatiotemporal Granularity

Despite the rapid growth of solar energy, we still lack a dynamic, high-fidelity database that tracks the spatiotemporal variations of solar PVs and their associated infrastructures across different places at a spatially resolved scale. The absence of such data presents a barrier to various applications such as solar PV growth projection, solar energy integration, solar incentive design, and climate risk assessment. In this project, we aim to bridge this gap by developing AI-based algorithms to extract granular information about solar PV installations and their associated infrastructures (i.e., distribution grids) from widely available unstructured data like remote sensing images and street views. As a result, we have built the Solar Energy Atlas, a fine-grained, large-scale geospatial overlay of distributed solar PVs and distribution grids. On top of it, we have advanced the understanding of solar adoption and distribution grid vulnerability to climate-induced extremes. Our major contributions can be summarized as follow: (1) By developing new AI algorithms, we have built the most comprehensive solar PV spatiotemporal database covering the entire US. This is the first time we obtained the exact GPS locations, size, subtype, and installation year information for rooftop solar PVs across the US. This database can be used for solar PV growth projection, solar energy integration, solar energy policy analysis and design, and spatially-resolved climate risk assessment. (2) Leveraging this database, we have uncovered the socioeconomic driving factors that are correlated with earlier onset of solar adoption and higher saturated adoption levels. We have identified the heterogeneity in the effects of different types of financial incentives on solar adoption and provided implications for tailoring incentive design based on local income levels to promote equitable solar adoption. (3) We have developed a distribution grid GIS mapping algorithm which can obtain granular geospatial and topology information about distribution grids using multi-modal open data, reducing the dependency on hard-to-obtain smart meter data of conventional approaches. It shows effectiveness in both the U.S. and Sub-Saharan Africa. Using this algorithm, we have uncovered the non-uniform vulnerability of distribution grids to wildfires in California in the aspects of undergrounding protection and Distributed Energy Resources (DER) preparedness. This has provided important implications for improving the affordability and equity of grid adaptation approaches. (3) We have made our produced database publicly available and provided user-friendly interface to enable various stakeholders and the general public to interact with the data. We have also integrated the produced data into the Data Commons platform to enable the public to access the data and correlate it with other location-specific characteristics simply using natural language as queries. The impact of our project is three-fold: (1) New algorithms for mapping solar PVs and distribution grids across space and time, which are open source to facilitate researchers and industry; (2) New databases of solar PVs and distribution grids that have been made publicly available for engineering, social, and policy applications; (3) New understandings and actionable insights on the potential approaches to promoting solar adoption and reducing energy infrastructure vulnerabilities. In this report, we start by discussing the project background and motivation (section 5), followed by the overview of project objectives (section 6). Results and discussion for each task are presented in section 7. Significant accomplishments are summarized in section 8. This report will be concluded by discussing the paths forwards (section 9), products (section 10), and team roles (section 11).

14 SOLAR ENERGY↗

The Accelerator Neutrino Neutron InteractionExperiment: Design, Construction and Preparationfor First Physics

This thesis covers work performed for the Accelerator Neutrino Neutron Interaction Experiment (ANNIE) between 2015 and 2020. ANNIE is a beamline neutrino experiment located at the Fermi National Accelerator Laboratory in Chicago. Its primary physics goals are the measurement of neutrino interaction cross-sections on oxygen, and a measurement of the multiplicity of final state neutrons from these interactions, both as functions of final state kinematics. In order to achieve these goals ANNIE will be pioneering the use of Large Area Picosecond Photodetectors and the use of gadolinium doping to enhance neutron visibility in a water Cherenkov detector. Over the time period of this thesis the ANNIE detector was constructed, an initial 'Phase I' background run was completed, the detector was decommissioned and then substantially upgraded in preparation for the main 'Phase II' physics run. At the time of writing ANNIE is being re-commissioned, with Phase II data taking anticipated to begin in 2021. During this time I spent 21/2 years on-site contributing to almost all aspects of hardware work, while performing software development for the simulation and analysis frameworks. As my first software task I developed Monte Carlo simulations of the detector response, based on the WCSim framework. While thismore » framework provided a starting point for the tank simulation significant modifications were required to implement the complete ANNIE detector system. This included a rewrite of the geometry, along with modifications to the photosensor definitions, hit collections, digitization, triggering, input and output interfaces, etc. To take advantage of improved modelling of neutrons in Geant4.10 the physics lists were also reimplemented in the new version format. As part of this work I determined performance metrics based on the output files, calculating kinematic acceptance, detector efficiency and expected event rates. My contributions on reconstruction focused primarily on the MRD, for which I implemented two track reconstruction algorithms, specialised for high and low energy muons. The high energy algorithm achieves >90% efficiency for tracks with at least 8 hits, and is robust against dead paddles and unrelated hits. The low energy algorithm performs a search in combination with tank information to provide sensitivity down to a single MRD hit. Early data handling work for the Phase I background run included writing the code for handling TDC hits and performing studies on neutron detection without the requirement of multi-hit coincidence. As the collaboration moved to a new framework for the Phase II analysis I performed a substantial amount of work to develop the codebase, implementing tools to perform tasks such as file IO, data parsing, waveform processing, event building, timestamp alignment, time clustering, hit residual calculation, event visualisation etc. I helped develop the python API for integrating multi-language tools, and ported the framework into a Singularity container to provide a self-contained environment that…« less

43 PARTICLE ACCELERATORS↗

ARCH: Large-scale knowledge graph via aggregated narrative codified health records analysis

Objective: Electronic health record (EHR) systems contain a wealth of clinical data stored as both codified data and free-text narrative notes (NLP). The complexity of EHR presents challenges in feature representation, information extraction, and uncertainty quantification. Here, to address these challenges, we proposed an efficient Aggregated naRrative Codified Health (ARCH) records analysis to generate a large-scale knowledge graph (KG) for a comprehensive set of EHR codified and narrative features. Methods: Using data from 12.5 million Veterans Affairs patients, ARCH first derives embedding vectors and generates similarities along with associated p-values to measure the strength of relatedness between clinical features with statistical certainty quantification. Next, ARCH performs a sparse embedding regression to remove indirect linkage between features to build a sparse KG. Finally, ARCH was validated on various clinical tasks, including detecting known relationships between entity pairs, predicting drug side effects, disease phenotyping, as well as sub-typing Alzheimer’s disease patients. Results: ARCH produces high-quality clinical embeddings and KG for over 60,000 codified and narrative EHR concepts. The KG and embeddings are visualized in the R-shiny powered web-API.3 ARCH achieved high accuracy in detecting EHR concept relationships, with AUCs of 0.926 (codified) and 0.861 (NLP) for similar EHR concepts, and 0.810 (codified) and 0.843 (NLP) for related pairs. It detected drug side effects with a 0.723 AUC, which improved to 0.826 after fine-tuning. Using both codified and NLP features, the detection power increased significantly. Compared to other methods, ARCH has superior accuracy and enhances weakly supervised phenotyping algorithms’ performance. Notably, it successfully categorized Alzheimer’s patients into two subgroups with varying mortality rates. Conclusion: The proposed ARCH algorithm generates large-scale high-quality semantic representations and knowledge graph for both codified and NLP EHR features, useful for a wide range of predictive modeling tasks.

Electronic health records↗

Distributions of the Mean for Lognormally Distributed Data - 19427

In environmental sciences, a distribution of the mean is often needed for right-skewed data. For example, risk assessments are often based on distributions of the mean to obtain upper confidence limits (UCLs) for analyte concentrations, and, in probabilistic performance assessment (PPA) models, parameters are given distributions rather than deterministic values, and they are usually given distributions of their mean rather than the population distributions to account for the large spatial and temporal domains to which they are applied. How this distribution of the mean is developed depends on the characteristics of the parameter's full distribution and how the parameter relates to its use. In this presentation, I will discuss the implications of a right skew in distribution development. Parameters may vary over orders of magnitude and/or may be right-skewed. The material property of saturated hydraulic conductivity, Ks, is a prime example of such a parameter. Right-skewed parameters are often assumed to follow lognormal distributions. If X follows a lognormal distribution, then log(X) follows a normal distribution. For some right-skewed parameters, practitioners go back and forth between the two forms of the data depending on their needs. For example, it may be preferred to use the untransformed version of X in a model or equation, but it is easier to visualize the parameter values on a logarithmic scale. However, distribution development for the average value of the parameter will differ depending on whether X or log(X) is modeled. This difference is due to Jensen's Inequality, a theorem which states that the expected value of a concave function of a variable is less than or equal to the same function of the expected value of the variable; a logarithm is a concave function. In other words, the mean of log(X) is always less than or equal to the log of the mean of X and therefore the mean estimated from a distribution based on log(X) is less than or equal to the mean estimated from a distribution based on X. If a parameter is naturally considered on a log scale by subject matter experts, then distributions developed for the mean of log(X) may be more consistent with the use of the parameters in the literature than distributions developed for X. The statistical decisions of distribution development will be discussed within the context of right-skewed, lognormal data. These issues include method-of-moments versus maximum likelihood estimation of the distribution parameters and the use of bootstrapping to aid in the visualization of a distribution of the mean. The details surrounding Jensen's Inequality will be explained and visualized within the context of distribution development of a right-skewed parameter such as saturated hydraulic conductivity. (authors)

54 ENVIRONMENTAL SCIENCES↗