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At least 19 records

Dataset for Top Model Decision Tree: Selecting Segmentation Models for Reliable Quantitative Analysis in Low- and Ultralow-Dose CryoEM

Motivation Multiple deep learning model architectures can be used to segment bacterial membranes in cryoEM images. However, an AI-based tool advancement is often presented with only a single segmentation model for broad use, and this single model may show inconsistent results across datasets from different users. Here, we present the Top Model Decision Tree, a model screening framework to screen for the best model to generate bacterial inner and outer membrane masks based on user priorities. We use pre-trained segmentation models from YOLOv11, YOLO26, U-Net, Detectron2 and SAM3 fine-tuned on bacterial inner and outer membranes imaged with cryoEM. Run the Framework This notebook must be opened in Google Colab. Mount Google Drive and run with a GPU-based runtime. Open the notebook and follow steps to git clone in folders and files within this repository. There will be a repeating top_model_decision_tree.ipynb (notebook clone) that will not be used. Save your .png binary mask files and .csv table outputs within your Google Drive or download before closing the notebook. The models and all analysis/training scripts are available at [GitHub: https://github.com/Lynnicia/CryoEM_membranes_top_model_decision_tree and https://github.com/Sireesiru/Semantic-Segmentation-of-bacterial-cell-envelope-using-U-Nets.

59 BASIC BIOLOGICAL SCIENCES↗

Linear model decision trees as surrogates in optimization of engineering applications

Machine learning models are promising as surrogates in optimization when replacing difficult to solve equations or black-box type models. This work demonstrates the viability of linear model decision trees as piecewise-linear surrogates in decision-making problems. Linear model decision trees can be represented exactly in mixed-integer linear programming (MILP) and mixed-integer quadratic constrained programming (MIQCP) formulations. Furthermore, they can represent discontinuous functions, bringing advantages over neural networks in some cases. We present several formulations using transformations from Generalized Disjunctive Programming (GDP) formulations and modifications of MILP formulations for gradient boosted decision trees (GBDT). We then compare the computational performance of these different MILP and MIQCP representations in an optimization problem and illustrate their use on engineering applications. Importantly, we observe faster solution times for optimization problems with linear model decision tree surrogates when compared with GBDT surrogates using the Optimization and Machine Learning Toolkit (OMLT).

42 ENGINEERING↗

Optimality versus reality: Closing the gap between renewable energy decision models and government deployment in the United States

Energy decision models are widely used to evaluate the technical and economic feasibility of renewable energy, as well as to help inform the deployment of these technologies. However, a gap exists between the optimal model solutions and what is deployed. This paper explores why these gaps exist in the public sector using the results of interviews with 20 federal, state, and city government agencies that have used the Renewable Energy Integration and Optimization (REopt™) model to inform energy decisions. We then propose adaptations to technical modeling capabilities, and communication of results, which may help increase clean energy deployment. This research may be useful to both analytical modelers and the organizations using such decision tools to inform policy, regulation, planning, and deployment of clean energy systems.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Characterization and Valuation of the Uncertainty of Calibrated Parameters in Microsimulation Decision Models

We evaluated the implications of different approaches to characterize the uncertainty of calibrated parameters of microsimulation decision models (DMs) and quantified the value of such uncertainty in decision making. We calibrated the natural history model of CRC to simulated epidemiological data with different degrees of uncertainty and obtained the joint posterior distribution of the parameters using a Bayesian approach. We conducted a probabilistic sensitivity analysis (PSA) on all the model parameters with different characterizations of the uncertainty of the calibrated parameters. We estimated the value of uncertainty of the various characterizations with a value of information analysis. We conducted all analyses using high-performance computing resources running the Extreme-scale Model Exploration with Swift (EMEWS) framework. The posterior distribution had a high correlation among some parameters. The parameters of the Weibull hazard function for the age of onset of adenomas had the highest posterior correlation of -0.958. When comparing full posterior distributions and the maximum-a-posteriori estimate of the calibrated parameters, there is little difference in the spread of the distribution of the CEA outcomes with a similar expected value of perfect information (EVPI) of $\$$653 and $\$$685, respectively, at a willingness-to-pay (WTP) threshold of $\$$66,000 per quality-adjusted life year (QALY). Ignoring correlation on the calibrated parameters’ posterior distribution produced the broadest distribution of CEA outcomes and the highest EVPI of $\$$809 at the same WTP threshold. Different characterizations of the uncertainty of calibrated parameters affect the expected value of eliminating parametric uncertainty on the CEA. Ignoring inherent correlation among calibrated parameters on a PSA overestimates the value of uncertainty.

97 MATHEMATICS AND COMPUTING↗

SPECs Early-Stage Decision Model: User Manual

The SPECs Early-Stage Decision (ESD) model is central to the SPECs procurement solutions toolkit. The ESD model is an Excel-based spreadsheet model, which provides information about the economic and strategic value of a proposed battery-storage project or solar-plus-storage (solar-plus) project. The model can be used to explore combinations of storage-related project value streams in order to define a potential project, while educating co-op decision-makers about project benefits and costs. A sensitivity analysis function speeds the development of "what-if" scenarios. A gap analysis function solves for top-priority metrics and supports the inclusion of hard-to-monetize strategic values, such as the value of storage to defer costly system upgrades in light of increasing distributed solar and other distributed energy resources (DERs). Model outputs include the utility data, assumptions, and use-case scenarios that are recommended content for the requests for proposals (RFPs). The model may also provide an initial "sanity check" for RFP responses, supporting further discussions among utility staff, vendors and stakeholders. The ESD is not a "finance-grade" modeling tool, and users are cautioned to be mindful of its limitations, but the model has been reviewed by users, who recommend it as a way to drive faster and better project design and planning, as well as to facilitate better communications with vendors, grid partners, and stakeholders.

14 SOLAR ENERGY↗

Core Modeling & Decision Support Capabilities: FASTSim, RouteE, T3CO & OpenPATH

These are the slides on NREL's Core Modeling and Decision Support Capabilities project for presentation at the 2023 Annual Merit Review for the U.S. Department of Energy, Vehicle Technologies Office. The project is funded by the Energy-Efficient Mobility Systems program to support four core tools: the Future Automotive Systems Technology Simulator (FASTSim), the Route Energy Prediction Model (RouteE), the Transportation Technology Total Cost of Ownership (T3CO) tool, and the Open Platform for Agile Trip Heuristics (OpenPATH).

ADVANCED PROPULSION SYSTEMS↗

Effects of random forest modeling decisions on biogeochemical time series predictions

Abstract Random forests (RF) are an increasingly popular machine learning approach used to model biogeochemical processes in the Earth system. While RF models are robust to many assumptions that complicate deterministic models, there are several important parameterization decisions for appropriate use and optimal model fit. We explored the role that parameter decisions, including training/testing data splitting strategies, variable selection, and hyperparameters play on RF goodness‐of‐fit by constructing models using 1296 unique parameter combinations to predict concentrations of nitrate, a key nutrient for biogeochemical cycling in aquatic ecosystems. Models were built on long‐term, publicly available water quality and meteorology time series collected by the National Estuarine Research Reserve monitoring network for two contrasting ecosystems representing freshwater and brackish estuaries. We found that accounting for temporal dependence when splitting data into training and testing subsets was key for avoiding over‐estimation of model predictive power. In addition, variable selection, the ratio of training to testing data, and to a lesser degree, variables per split and number of trees, were significant parameters for optimizing RF goodness‐of‐fit. We also explored how model parameter decisions influenced interpretation of the relative importance of predictors to the model, and model predictor‐dependent variable relationships, with results suggesting that both data structure and model parameterization influence these factors. Because much of the current RF literature is written for the computational and statistical science communities, the primary goal of this study is to provide guidelines for aquatic scientists new to machine learning to apply RF techniques appropriately to aquatic biogeochemical datasets.

54 ENVIRONMENTAL SCIENCES↗

NLR Core Modeling & Decision Support Capabilities: FASTSim, RouteE, T3CO & OpenPATH

This project is part of the program area to develop and improve core capabilities for the Energy-Efficient Mobility Systems (EEMS) program that enable research, development and deployment of advanced mobility solutions and enhance the EEMS Program's ability to address system-level transportation challenges. Advancements to the Future Automotive Systems Technology Simulator (FASTSim), Route Energy Prediction Model (RouteE), Transportation Technology Total Cost of Ownership (T3CO) and Open Platform for Agile Trip Heuristics (OpenPATH) core capabilities under this project supports the overall EEMS Program goals to effectively evaluate energy and mobility impacts of future transportation technologies and services, and to identify the most promising pathways to reduce transportation costs and environmental harms, and to improve mobility access. This presentation was prepared for the 2026 Annual Merit Review of this project.

33 ADVANCED PROPULSION SYSTEMS↗

Decision-Model Supported Algal Cultivation Process Enhancement (DMSACPE) (Final Technical Report)

This project was proposed in response to the FY19 Bioenergy Technologies Office Multi-Topic Funding Opportunity Announcement DE-FOA-0002029, Area of Interest Subtopic 1 (AOI1): Cultivation Intensification Processes for Algae. The main challenge identified by the FOA was “in translating results between laboratory research systems and larger-scale outdoor (or mass culture) systems. These difficulties limit reliable experimental durations, adequate and representative experimental volumes of material, and results that can be reproduced reliably. By overcoming the challenge in translating results between laboratory and mass cultures, the objective of AOI 1 is to increase the harvest yield, robustness, and quality of algae cultivation for biofuels and bioproducts”. This report marks the final technical deliverable of this project and reviews all the major findings of the research program.

09 BIOMASS FUELS↗

A forecast-driven decision-making model for long-term operation of a hydro-wind-photovoltaic hybrid system

Hydro-wind-photovoltaic (PV) hybrid system has the potential to increase the integration of renewable energy sources into an existing grid. For the long-term operation of the system, due to the non-storable nature of wind and PV power, it is essentially to decide the optimal long-term carryover storage of cascade reservoirs. However, it remains a challenge due to high uncertainties of long-term forecasts and complicated hydraulic/electrical relationships between cascade reservoirs. Here in this study, a forecast-driven decision-making model is proposed for the hybrid system, which converts the multi-stage long-term operation process into a two-stage operation problem (including current stage and carryover stage) to avoid using longer-horizon forecast information with lower accuracy. First, the carryover stage energy surfaces (CESs) considering the forecast uncertainties of wind, solar and hydro resources are proposed to characterize carryover stage benefit quantitatively. Then a CESs-based forward decision-making optimization model is developed to guide the long-term operation of a hydro-wind-photovoltaic hybrid system. The applications in a hydro-wind-PV hybrid system of Yalong River basin results show that: compared with conventional operation, 1) power generation increases 9.03%; 2) in terms of the carryover storages control, the reservoir impounding and drawdown timing are delayed, and the drawdown depth is increased, which can be used to formulate better reservoir operation rules.

13 HYDRO ENERGY↗

Navigating Uncertainty: Challenges in Visualizing Ensemble Data and Surrogate Models for Decision Systems

Uncertainty visualization plays a critical role in transforming ensemble simulation data into actionable insights by effectively communicating various dimensions of uncertainty within a system. The emergence of artificial intelligence-driven surrogate models trained on multirun ensemble data offers a transformative opportunity to replace computationally intensive simulations with fast estimates, enabling users to explore data spaces with unprecedented depth and interactivity. However, integrating ensemble data and surrogate models into decision-making workflows and tools introduces novel challenges for uncertainty visualization. These include reconciling and clearly communicating the unique uncertainties associated with ensembles and their surrogate model estimates, and leveraging these approximations to inform actionable decisions. This work explores these challenges in the context of high-dimensional data visualization, bridging discrete datasets with their continuous representations and addressing the complexities of systems that support iterative navigation between input and output spaces. We evaluate the role of uncertainty visualization in fostering intuitive, actionable interactions and identify critical hurdles in advancing this frontier of computational simulation.

97 MATHEMATICS AND COMPUTING↗