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DOE OSTI2023

QES-Plume v1.0: a Lagrangian dispersion model

Low-cost simulations providing accurate predictions of transport of airborne material in urban areas, vegetative canopies, and complex terrain are demanding because of the small-scale heterogeneity of the features influencing the mean flow and turbulence fields. Common models used to predict turbulent transport of passive scalars are based on the Lagrangian stochastic dispersion model. The Quick Environmental Simulation (QES) tool is a low-computational-cost framework developed to provide high-resolution wind and concentration fields in a variety of complex atmospheric-boundary-layer environments. Part of the framework, QES-Plume, is a Lagrangian dispersion code that uses a time-implicit integration scheme to solve the generalized Langevin equations which require mean flow and turbulence fields. Here, QES-Plume is driven by QES-Winds, a 3D fast-response model that computes mass-consistent wind fields around buildings, vegetation, and hills using empirical parameterizations, and QES-Turb, a local-mixing-length turbulence model. In this paper, the particle dispersion model is presented and validated against analytical solutions to examine QES-Plume’s performance under idealized conditions. In particular, QES-Plume is evaluated against a classical Gaussian plume model for an elevated continuous point-source release in uniform flow, the Lagrangian scaling of dispersion in isotropic turbulence, and a non-Gaussian plume model for an elevated continuous point-source release in a power-law boundary-layer flow. In these cases, QES-Plume yields a maximum relative error below 6 % when compared with analytical solutions. In addition, the model is tested against wind-tunnel data for a uniform array of cubical buildings. QES-Plume exhibits good agreement with the experiment with 99 % of matched zeros and 59 % of the predicted concentrations falling within a factor of 2 of the experimental concentrations. Furthermore, results also emphasize the importance of using high-quality turbulence models for particle dispersion in complex environments. Finally, QES-Plume demonstrates excellent computational performance.

58 GEOSCIENCES↗

DOE OSTI2026

Deployment of Traditional and Hybrid Machine Learning for Critical Heat Flux Prediction in the CTF Thermal-Hydraulics Code

Critical heat flux (CHF) marks the transition from nucleate to film boiling, where heat transfer to the working fluid can rapidly deteriorate. Accurate CHF prediction is essential for efficiency, safety, and preventing equipment damage, particularly in nuclear reactors. Although widely used, empirical correlations frequently exhibit discrepancies when compared to experimental data, limiting their reliability in diverse operational conditions. Traditional machine learning (ML) approaches have demonstrated potential for CHF prediction but often suffer from limited interpretability, data scarcity, and insufficient knowledge of physical principles. Hybrid model approaches, which combine data-driven ML with base models, mitigate these concerns by incorporating prior knowledge of the domain. This study integrates an externally trained purely data-driven ML model and two hybrid models (using the Biasi and Bowring CHF correlations) within the CTF subchannel code via a custom Fortran framework. Performance was evaluated using two validation cases: a subset of the Nuclear Regulatory Commission (NRC) CHF database and the Bennett dryout experiments. In both cases, the hybrid models demonstrated significantly lower error metrics compared to conventional empirical correlations, with the best models often reducing relative error by about 5 percentage points. The pure ML model achieved comparable accuracy, outperforming the hybrid Biasi model in the NRC test case (3.3% versus 5.5% relative error) but exhibiting slightly higher error against the hybrid Bowring model in the Bennett test case (7.7% versus 6.1%). Trend analysis of error parity indicated that ML-based models reduced the tendency for CHF overprediction, improving overall accuracy. These results demonstrate that ML-based CHF models can be effectively integrated into subchannel codes and could potentially increase performance compared to conventional methods.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Dynamics and growth rate implications of ribosomes and mRNAs interaction in E. coli

Understanding how cells grow and adapt under various nutrient conditions is pivotal in the study of biological stoichiometry. Recent studies provide empirical evidence that cells use multiple strategies to maintain an optimal protein production rate under different nutrient conditions. Mathematical models can provide a solid theoretical foundation that can explain experimental observations and generate testable hypotheses to further our understanding of the growth process. In this study, we generalize a modeling framework that centers on the translation process and study its asymptotic behaviors to validate algebraic manipulations involving the steady states. Using experimental results on the growth of E. coli under C-, N-, and P-limited environments, we simulate the expected quantitative measurements to show the feasibility of using the model to explain empirical evidence. Our results support the findings that cells employ multiple strategies to maintain a similar protein production rate across different nutrient limitations. Moreover, we find that the previous study underestimates the significance of certain biological rates, such as the binding rate of ribosomes to mRNA and the transition rate between different ribosomal stages. Furthermore, our simulation shows that the strategies used by cells under C- and P-limitations result in a faster overall growth dynamics than under N-limitation. In conclusion, the general modeling framework provides a valuable platform to study cell growth under different nutrient supply conditions, which also allows straightforward extensions to the coupling of transcription, translation, and energetics to deepen our understanding of the growth process.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

BrickQA: Bridging the Semantic Gap in Building Operations with Dynamic Graph Exploration

While standardized ontologies like the Brick schema address data heterogeneity in Building Automation Systems (BAS), accessing this semantic data remains a challenge as domain experts often lack the expertise to formulate complex SPARQL queries. To bridge this gap, we present BrickQA, a Large Language Model (LLM)-based framework that translates natural language into executable SPARQL queries through structured query decomposition, dynamic schema exploration, and inline validation. BrickQA utilizes an iterative reasoning agent to actively navigate graph topology through dynamic exploration actions without requiring exhaustive context injection or model fine-tuning. This approach effectively mitigates hallucinations, particularly in large-scale building knowledge graphs. Empirical evaluation on BuildingQA, a standardized benchmark, demonstrates that BrickQA significantly outperforms ReAct baselines, delivering a 0.291–0.355 absolute F1 improvement while achieving 3 × –12.7 × higher token cost-efficiency. Beyond these metrics, the framework maintains structural fidelity across heterogeneous buildings and remains resilient to ambiguous queries without requiring site-specific fine-tuning. Furthermore, a case study on operational analytics validates the framework’s capability to handle temporal and aggregation constraints, effectively transforming abstract semantic models into actionable facility management insights.1

Ko, Yun-Dam↗

DOE OSTI2023

Ground Motion Models (GMMs) Improvements Using Earthquake Simulations on High Performance Computers

A computationally efficient simulation platform was developed that can provide representative synthetic ground motions from crustal earthquakes in the Stable Continental Regions of Central and Eastern US (CEUS), using 3D modeling and high-performance computing. The main objective was to use synthetic ground motion to provide constrains to refinements of exiting ergodic Ground Motion Models (GMMs), for large magnitude earthquakes and near-fault distances, for which these models are less reliable. Physics-based broadband (0-5Hz) ground motion simulations were used to estimate the near-fault ground motion amplitudes and within event and between-event variabilities associated with fault rupture characteristics. As part of a strategy for selecting a reginal velocity model and validation of developed rupture modeling technique, ground motions from the moment magnitude Mw5.0 November 7, 2016, Cushing Oklahoma, and Mw5.8 September 3, 2016, Pawnee Oklahoma earthquakes were simulated. In our simulations we used a 3D regional velocity model that was based on Saikia’s 1D velocity model. Saikia’s model demonstrated better performance in modelling high frequency regional wave propagation for CEUS region. The proposed 3D model includes lateral variations added to the 1D background model using the stochastic scheme of Pitarka and Mellors. Comparisons of the simulations with recordings of both earthquakes demonstrated the reliability of our deterministic simulation approach while emphasizing the importance of including small-scale variability in the regional velocity model needed to reproduce the observed high-frequency wave scattering effects. As part of validation analysis, comparisons with different GMMs for a Mw6.5 earthquake in the CESUS region resulted in a very good match between the simulated and empirical ground motion models. Initial investigations of within-event and between-event ground motion variabilities for Mw6.5 scenario earthquakes on a strike-slip fault, suggest that they are strongly related to spatial slip and slip rate variations, average rupture velocity, rupture area and rupture initiation location. For certain scenarios we found that the ground motion variability observed at near-fault distances (< 5 km) also persists at longer distances. Regardless of the rupture scenario, the simulated ground motion tends to fully saturate at short distances and for all periods. The near-fault saturation has to do with the attenuation of waves propagating along the fault and local rupture radiation pattern that also contribute to stronger ground motion variation at such distances. Analysis of effects of rupture initiation location suggest that the peak ground motion (PGV) and spectral acceleration (SA) can be quite variable due to rupture directivity effects. Such effects are stronger at periods longer than 1s. The effect of the 1D velocity models and surface topography on simulated ground motion were investigated by comparing three component synthetic seismograms computed at selected sites. Effect of surface topography was considered using the ratio between spectral accelerations simulated for two 1D models with flat surface topography and realistic model with surface topography. Overall, the topography slightly amplifies (by ~30%) the ground motion amplitude in the frequency range 1-3Hz. The effect of topography is more visible in the surface and coda waves portion of the seismograms.

58 GEOSCIENCES↗

DOE OSTI2022

Evaluating the Performance of Random Forest and Iterative Random Forest Based Methods when Applied to Gene Expression Data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3. We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

iRF-Loop, expression network, Populus Trichocarpa↗

DOE OSTI2024

Calibration verification for stochastic agent-based disease spread models

Accurate disease spread modeling is crucial for identifying the severity of outbreaks and planning effective mitigation efforts. To be reliable when applied to new outbreaks, model calibration techniques must be robust. However, current methods frequently forgo calibration verification (a stand-alone process evaluating the calibration procedure) and instead use overall model validation (a process comparing calibrated model results to data) to check calibration processes, which may conceal errors in calibration. In this work, we develop a stochastic agent-based disease spread model to act as a testing environment as we test two calibration methods using simulation-based calibration, which is a synthetic data calibration verification method. The first calibration method is a Bayesian inference approach using an empirically-constructed likelihood and Markov chain Monte Carlo (MCMC) sampling, while the second method is a likelihood-free approach using approximate Bayesian computation (ABC). Simulation-based calibration suggests that there are challenges with the empirical likelihood calculation used in the first calibration method in this context. These issues are alleviated in the ABC approach. Despite these challenges, we note that the first calibration method performs well in a synthetic data model validation test similar to those common in disease spread modeling literature. We conclude that stand-alone calibration verification using synthetic data may benefit epidemiological researchers in identifying model calibration challenges that may be difficult to identify with other commonly used model validation techniques.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Polyhedral Relaxations for Optimal Pump Scheduling of Potable Water Distribution Networks

The classic pump scheduling or optimal water flow (OWF) problem for water distribution networks (WDNs) minimizes the cost of power consumption for a given WDN over a fixed time horizon. In its exact form, the OWF is a computationally challenging mixed-integer nonlinear program (MINLP). It is complicated by nonlinear equality constraints that model network physics, discrete variables that model operational controls, and intertemporal constraints that model changes to storage devices. To address the computational challenges of the OWF, this paper develops tight polyhedral relaxations of the original MINLP, derives novel valid inequalities (or cuts) using duality theory, and implements novel optimization-based bound tightening and cut generation procedures. The efficacy of each new method is rigorously evaluated by measuring empirical improvements in OWF primal and dual bounds over 45 literature instances. The evaluation suggests that our relaxation improvements, model strengthening techniques, and a thoughtfully selected polyhedral relaxation partitioning scheme can substantially improve OWF primal and dual bounds, especially when compared with similar relaxation-based techniques that do not leverage these new methods.

bound tightening↗

DOE OSTI2020

Validation of Thermal Scattering Laws for Light Water at Elevated Temperatures with Diffusion Experiments

Light water is the most important neutron moderator in many reactor applications. Thermal neutron scattering kernels for H bound in H 2 O are represented by ENDF-format thermal scattering laws (TSLs) evaluated at discrete temperatures T . Nuclear data evaluations are conventionally validated utilizing a combination of critical benchmarks and experimental cross section data. Existing public critical benchmarks may be inadequate for testing water TSLs over the full range of T of interest in reactor applications, and experimental thermal scattering cross section data for water is sparse at elevated T . In this work, MC21 is used to simulate the decay of the equilibrium thermal neutron flux in light-water spheres of several radii. The fundamental-mode time eigenvalue $\mathcal{a}$ is calculated at 22 °C and 227 °C (at saturation pressure) for each sphere using three different H-H 2 O TSLs. Fitting $\mathcal{a}$ to a polynomial function of geometric buckling allows calculation of the thermal neutron diffusion length L . Extrapolation lengths are treated as a function of the transport mean free path and geometry. Experimental L data from 25 publications at 49 temperatures (from 10 °C to 295 °C), computed by several different time-dependent and space-dependent decay methods, is used to develop an empirical fit of L vs. T . The MC21-calculated L for the TSLs tested are within ±1% of the predicted values at 22 °C and 227 °C. This validation approach, which may be repeated at arbitrary T , constitutes an integral benchmark specific to and characterizing the detailed physics of the thermal scattering kernel applied.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Empirically verified analysis of dual pre-cooling system for hydrogen refuelling station

The dual cooling system at the California State University Los Angeles Hydrogen Research and Fueling Facility is analysed to predict the output hydrogen temperature in different ambient conditions. Initially, the facility was built with a coil chiller T20 cooling, sufficient for occasional fuelings. A flat plate evaporator system was added in series to resolve any issues for multiple fuelings even in the hottest weather. This study was commenced to verify the set points and determine the control requirements for the dual setup in order to inform future designs. A numerical-empirical model of the cooling system was developed by reverse engineering, using the station experimental measurements and database records. The subsystems are characterized separately but validated as a whole system imposing specific and standard operating conditions. The cooling model is tested with different inputs to validate the pre-set parameter variation of the cooling components. Ten scenarios were investigated to evaluate the fueling output parameters, testing two hydrogen temperature input trends (according to the facility initial conditions) and five ambient temperatures (from 15 °C to 35 °C). In closing, the simulation results have confirmed that the hydrogen output temperature remains within the range imposed by the SAE J2601 for each scenario studied, around -22 °C and -25 °C.

08 HYDROGEN↗

DOE OSTI2022

The global spectrum of plant form and function: enhanced species-level trait dataset

Here we provide the ‘Global Spectrum of Plant Form and Function Dataset’, containing species mean values for six vascular plant traits. Together, these traits –plant height, stem specific density, leaf area, leaf mass per area, leaf nitrogen content per dry mass, and diaspore (seed or spore) mass – define the primary axes of variation in plant form and function. The dataset is based on ca. 1 million trait records received via the TRY database (representing ca. 2,500 original publications) and additional unpublished data. It provides 92,159 species mean values for the six traits, covering 46,047 species. The data are complemented by higher-level taxonomic classification and six categorical traits (woodiness, growth form, succulence, adaptation to terrestrial or aquatic habitats, nutrition type and leaf type). Data quality management is based on a probabilistic approach combined with comprehensive validation against expert knowledge and external information. Intense data acquisition and thorough quality control produced the largest and, to our knowledge, most accurate compilation of empirically observed vascular plant species mean traits to date.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Validation and Verification for INL Modelica-based TEDS models Via Experimental Results

This report provides an overview on the verification and validation (V&V) of the Thermal Energy Distribution System (TEDS) model developed in the Modelica process modeling ecosystem using experimental data. Model development has led to the creation of a dynamic process model of the experimental TEDS facility housed within the Energy Systems Laboratory (ESL) at Idaho National Laboratory (INL). The model was then used during the preconstruction phase of the experimental effort to inform experimental design (e.g., insulation requirements, bypass line placement, expected performance of components) and to test innovative control schemes prior to the initial operation. The TEDS model developed in Modelica includes the primary components of the TEDS experimental unit: a 200kW Chromalox heater; a single-tank packed-bed thermal energy storage system filled with 0.125-inch alumina (Al2O3) beads; an ethylene-glycol-to-Therminol-66 heat exchanger; system piping; five control valves; and all associated temperature, pressure, and volumetric flow sensors. Using the Institute of Electrical and Electronics Engineers (IEEE) V&V methodologies, considered the gold standard in the engineering field, the model was verified using a combination of static analysis, spatial convergence, and regression tests. Then using dynamic time warping (DTW) initial runs to validate and tune the TEDS model versus the experiment were conducted. This tuning method was accomplished using the INL Risk Analysis Virtual ENvironment (RAVEN) software package. Tuning is required to account for physical phenomena that are less understood within the empirical heat transfer correlations. Through the commencement of this work, a systems-level model of TEDS with associated control systems, sensors, piping diameters, and component capabilities has been created. This model was utilized in the pre-experimental phase to inform system design, insulation thicknesses, and potential control schemes to operate the system effectively and safely. Then, initial experimental startup and operational data were used to demonstrate the validation and tuning methodology. This process demonstrates the classical two-step approach of a model informing experimental design followed by the experiment validation and tuning the model.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2026

Wasserstein Normalized Autoencoder for Anomaly Detection in ProtoDUNE Vertical-Drift Detector

ProtoDUNE Vertical Drift needs a selective triggering algorithm. The detector sits on Earth's surface, so cosmic activity dominates its data. Our goal in this paper is to trigger on neutrino events more robustly than the current deployed Analog-to-Digital Converter Simple Window (ADCSW) model and, eventually, search for signals of Beyond Standard Model (BSM) physics at DUNE as our ultimate North Star objective. As a step towards this goal, we evaluate a Wasserstein Normalized Autoencoder (WNAE) on simulated collection-plane only windows of shape $1\times10\times10$ where Neutrinos act as our BSM-proxy and Cosmic-ray Muons serve as our learned background. The network parameters are fitted using only cosmic-ray muon events as background in order to maintain an unsupervised pipeline. Training uses finite-step Langevin $x^-$ samples, positive-sample reconstruction energy, and an empirical sliced $2$-Wasserstein objective to learn a normalized Boltzmann energy model. We then calibrate on a nominal $5\,\mathrm{Hz}$ operating threshold calculated from cosmic validation data. Both WNAE and ADCSW accept 311 of 194,083 held-out cosmic background events at this $5\,\mathrm{Hz}$ threshold. We found that WNAE accepts 9,677 of 34,634 neutrino-proxy events $(27.9\pm0.24)\%$, compared with 10,076 $(29.1\pm0.24)\%$ for ADCSW, an observed WNAE-minus-ADCSW difference of $-1.15\%$. At another nominal $2\,\mathrm{Hz}$ target threshold, the corresponding efficiencies are $(20.5\pm0.22)\%$ and $(22.6\pm0.22)\%$, respectively. Of the WNAE-selected neutrino proxies at $5\,\mathrm{Hz}$, $(20.8\pm0.4)\%$ of the classified neutrino-proxy events are unique to WNAE, where the uncertainty is an absolute binomial standard error of $0.4\%$.

Zheng, Jake [U. Chicago (main)] (ORCID:00090002189↗

DOE OSTI2026

Wasserstein Normalized Autoencoder for Anomaly Detection in ProtoDUNE Vertical-Drift Detector

Zheng, Jake [Chicago U.] (ORCID:0009000218901379)↗

DOE OSTI2022

AI-Enabled Discovery and Physics-Based Optimization of Energy Efficient Processing Strategies for Advanced Turbine Alloys (Final Technical Report)

In this project, the multi-organizational team of academic and industrial researchers from the University of Kentucky an aerospace and energy generation OEM partner has leveraged novel Digital Process Twin (DPT) models of process/structure interactions (i.e., process-induced surface integrity) to advance a paradigm of fully integrated computational materials engineering (ICME). Using efficient process models as the core of a digital process simulator for a reinforcement learning algorithm, the team has integrated industrial data and metrics of structure/performance/energy relationships and manufacturing-related energy metrics to optimize dynamic processing parameters for significantly improved life-cycle energy efficiency of advanced γ-TiAl low-pressure turbine (LPT) alloys, as indicated by a set of design relevant parameters (e.g., residual stresses and scrap rate). The key objective and anticipated outcome of the project was at least a 10% reduction in life-cycle embodied energy for a recently developed, γ-TiAl low-pressure turbine (LPT) alloy and nickel-based superalloy Inconel 718, through the adoption of the proposed AI-enabled process optimization approach. The final project outcomes significantly exceeded this original target, realizing manufacturing-related energy efficiency improvements of more than 130% for TiAl and up to 80% for Inconel 718. Rather than following the prevailing and highly inefficient empirical paradigm, the proposed study demonstrated the feasibility of adopting a digital, physics-based process design and optimization paradigm. The recurring need for manual intervention, rework, reinspection causes significant production bottlenecks and unnecessary expense associated with delivering the requisite component quality. The OEM partner, and turbine industry in general, expect to reap significant cost and resource savings if an AI-optimized set of parameters can be applied to specific machining operations. The technical scope of the proposed project involved the paving of a realistic path towards model-based and AI-enabled Integrated Computational Materials Engineering (ICME), and away from inefficient empirical process optimization and legacy manufacturing practices, which are no longer able to efficiently process novel high-performance turbine alloy materials. The project team will address the fundamental knowledge gap that currently exists within the ICME paradigm with respect to the process/structure/performance/energy impacts of finishing processes. While significant resources have been devoted to the ‘early stages’ of manufacturing, such as alloy design, primary and secondary processing, finishing processes have not been adequately integrated within ICME. To provide an actionable path towards model-based finishing process design (e.g., machining, burnishing, grinding, polishing), we will employ a novel AI-enabled process optimization paradigm, based on a computationally efficient, physics-based process simulator. Through limited experimental work to calibrate and validate our process simulator model via an advanced in-situ characterization technique and process optimization via reinforcement learning, the project will seek to demonstrate a viable alternative to the inefficient ‘legacy’ processing strategies, empirical testing and broad scope machining learning approaches, all of which fail to adequately consider complex process physics. The project team has identified an intermetallic γ-TiAl LPT alloy, which is currently being used as part of the OEM partner’s advanced gas turbine designs. This particular alloy poses significant manufacturing challenges during finishing operations, which limit the degree to which the current turbine design can be manufactured in an energy- and cost-efficient manner. Empirical testing and numerical modeling efforts to optimize processing parameters for γ-TiAl have not been able to resolve these manufacturing challenges, so the proposed physics-based AI-enabled optimization technology would offer a truly novel and transformative capability. The multi-organizational team of academic and industry experts from the UKY and the OEM partner will work together closely to demonstrate the analytical and experimental critical function and characteristic proof of concept of this novel approach.

20 FOSSIL-FUELED POWER PLANTS↗

DOE OSTI2026

Ten questions concerning low-cost indoor air quality sensors: Perspectives from research and practice

Low-cost indoor air quality (IAQ) sensors are increasingly being used in homes and commercial and public buildings, driven by growing concerns about the impact of air on health, cognitive performance, and occupant wellbeing. These sensors offer a potentially transformative opportunity to increase spatial and temporal coverage of IAQ monitoring at a fraction of the cost of conventional reference instruments. However, their widespread use raises questions around accuracy, calibration, placement, data handling and interpretation, and integration into existing standards and workflows. This paper presents ten critical questions concerning the use of low-cost IAQ sensors in buildings, drawing on the latest empirical research, field deployments, and emerging practice. It discusses potential frameworks for deployment and evaluation, examines current sensor capabilities for measuring common pollutants, identifies methodological gaps in validation and uncertainty quantification, and outlines the extent to which existing IAQ standards can accommodate sensor-based evidence. The paper also explores how monitoring needs and deployment models vary by building type, the potential of real-time IAQ data to support building operations, and the ethical and legal implications of widespread sensor use. While significant challenges remain in ensuring data quality and building stakeholder trust, new applications are emerging through open data initiatives and advances in analytics and visualization. As the technology, science, and standards co-evolve, low-cost IAQ sensors are poised to become integral to routine building operation, building science, and environmental health research.

Parkinson, Thomas↗

DOE OSTI2022

Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data

Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Parameter extraction approaches for compact modeling of thermoelectric modules

Thermoelectric (TE) cooling has experienced rapid advancements with the foundational understanding of TE materials. TE modules, compact and lightweight devices, have become the prevalent approach for implementing TE technologies. Accurately quantifying TE physical parameters (Seebeck coefficient α, thermal conductivity κ, and thermal resistance ρ) is challenging due to the dynamic temperature changes in operation. Furthermore, extracting lumped property parameters is crucial for designing energy systems using TE modules. Existing research has several limitations, such as lack of comparative analysis between prevalent formulae, reliance on potentially inaccurate vendor-supplied data, disregard for fundamental assumptions, and absence of empirical measurements. Further, this study addresses these gaps by conducting TE material characterization, comparing three existing formulae using vendor datasheets, designing a laboratory test facility for model validation and refinement, and outlining a structured data extraction procedure. The study's novelty lies in multiple key contributions: (1) a detailed comparative analysis of existing formulae for extracting TE property parameter; (2) executing experimental work in a laboratory setting to validate the model and elucidate its limitations; (3) highlighting potential risks; (4) clarifying possible assumptions from both material and engineering perspectives; and (5) considering temperature differential impacts. This comprehensive approach addresses the current research gaps and provides valuable insights into the design and application of TE modules in various energy systems.

36 MATERIALS SCIENCE↗