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At least 1,423 records · Page 79

Trainable Gene Regulation Networks with Applications to Drosophila Pattern Formation

This chapter will very briefly introduce and review some computational experiments in using trainable gene regulation network models to simulate and understand selected episodes in the development of the fruit fly, Drosophila melanogaster. For details the reader is referred to the papers introduced below. It will then introduce a new gene regulation network model which can describe promoter-level substructure in gene regulation. As described in chapter 2, gene regulation may be thought of as a combination of cis-acting regulation by the extended promoter of a gene (including all regulatory sequences) by way of the transcription complex, and of trans-acting regulation by the transcription factor products of other genes. If we simplify the cis-action by using a phenomenological model which can be tuned to data, such as a unit or other small portion of an artificial neural network, then the full transacting interaction between multiple genes during development can be modelled as a larger network which can again be tuned or trained to data. The larger network will in general need to have recurrent (feedback) connections since at least some real gene regulation networks do. This is the basic modeling approach taken, which describes how a set of recurrent neural networks can be used as a modeling language for multiple developmental processes including gene regulation within a single cell, cell-cell communication, and cell division. Such network models have been called "gene circuits", "gene regulation networks", or "genetic regulatory networks", sometimes without distinguishing the models from the actual modeled systems.

Mjolsness, Eric↗

Aerosol-Radiation-Cloud Interactions in the South-East Atlantic: Model-Relevant Observations and the Beneficiary Modeling Efforts in the Realm of the EVS-2 Project ORACLES

Globally, aerosols remain a major contributor to uncertainties in assessments of anthropogenically-induced changes to the Earth climate system, despite concerted efforts using satellite and suborbital observations and increasingly sophisticated models. The quantification of direct and indirect aerosol radiative effects, as well as cloud adjustments thereto, even at regional scales, continues to elude our capabilities. Some of our limitations are due to insufficient sampling and accuracy of the relevant observables, under an appropriate range of conditions to provide useful constraints for modeling efforts at various climate scales. In this talk, I will describe (1) the efforts of our group at NASA Ames to develop new airborne instrumentation to address some of the data insufficiencies mentioned above; (2) the efforts by the EVS-2 ORACLES project to address aerosol-cloud-climate interactions in the SE Atlantic and (3) time permitting, recent results from a synergistic use of A-Train aerosol data to test climate model simulations of present-day direct radiative effects in some of the AEROCOM phase II global climate models.

Redemann, Jens↗

Deep learning-driven super-resolution in Raman hyperspectral imaging: Efficient high-resolution reconstruction from low-resolution data

Deep learning (DL) has become an indispensable tool in hyperspectral data analysis, automatically extracting valuable features from complex, high-dimensional datasets. Super-resolution reconstruction, an essential aspect of hyperspectral data, involves enhancing spatial resolution, particularly relevant to low-resolution hyperspectral data. Yet, the pursuit of super-resolution in hyperspectral analysis is fraught with challenges, including acquiring ground truth high-resolution data for training, generalization, and scalability. The pressing issue of extended spectral acquisition times, notably for high-resolution scans, is a significant roadblock in hyperspectral imaging. Super-resolution methods offer a promising solution by providing higher spatial resolution data to expedite data collection and yield more efficient outcomes. This paper delves into a practical application of these concepts using Raman imaging, where spectral acquisition times can be prohibitively long. In this context, DL-based super-resolution models demonstrate their efficacy by predicting and reconstructing high-resolution Raman data from low-resolution input, eliminating the need for resource-intensive high-resolution scans. While previous work often relied on substantial high-resolution datasets, this study showcases the ability to achieve similar outcomes even with limited data, presenting a more practical and cost-effective approach. In conclusion, the results offer a glimpse into the transformative potential of this technology to streamline hyperspectral imaging applications by saving valuable time and resources through the successful generation of high-resolution data from low-resolution inputs.

42 ENGINEERING↗

Multi-discipline resource inventory of soils, vegetation and geology

The author has identified the following significant results. Computer classification of natural vegetation, in the vicinity of Big Summit Prairie, Crook County, Oregon was carried out using MSS digital data. Impure training sets, representing eleven vegetation types plus water, were selected from within the area to be classified. Close correlations were visually observed between vegetation types mapped from the large scale photographs and the computer classification of the ERTS data (Frame 1021-18151, 13 August 1972).

Simonson, G. H.↗

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗

PMU Data Quality and Sensor Health Monitoring

Phasor Measurement Units (PMUs) play a critical role in the evolution of the electric power industry by providing high-precision, real-time monitoring of essential power system metrics. However, effectively detecting abnormalities and critical events from PMU data is a complex task, complicated by intricate temporal patterns, a scarcity of labeled data for training algo- rithms, and constraints on online computational power. In this study, we apply TranAD, an innovative algorithm that combines transformer architectures with the refinement of adversarial learning, to both synthetic and real-world PMU datasets for developing a data quality and sensor online health monitoring platform for utilities. Our findings reveal that TranAD not only provides efficient detection and localization but also enhances the detail with which abnormalities are detected, marking a a significant step forward in the field of clean data acquisition processes for power system monitoring

deep neural network, machine learning (ML)↗

Development of the Senseiver for efficient field reconstruction from sparse observations

Abstract The reconstruction of complex time-evolving fields from sensor observations is a grand challenge. Frequently, sensors have extremely sparse coverage and low-resource computing capacity for measuring highly nonlinear phenomena. While numerical simulations can model some of these phenomena using partial differential equations, the reconstruction problem is ill-posed. Data-driven-strategies provide crucial disambiguation, but these suffer in cases with small amounts of data, and struggle to handle large domains. Here we present the Senseiver, an attention-based framework that excels in reconstructing complex spatial fields from few observations with low overhead. The Senseiver reconstructs n -dimensional fields by encoding arbitrarily sized sparse sets of inputs into a latent space using cross-attention, producing uniform-sized outputs regardless of the number of observations. This allows efficient inference by decoding only a sparse set of output observations, while a dense set of observations is needed to train. This framework enables training of data with complex boundary conditions and extremely large fine-scale simulations. We build on the Perceiver IO by enabling training models with fewer parameters, which facilitates field deployment, and a training framework that allows a flexible number of sensors as input, which is critical for real-world applications. We show that the Senseiver advances the state-of-the-art of field reconstruction in many applications.

97 MATHEMATICS AND COMPUTING↗

An Efficient 1-D Thermal Stratification Model for Pool-Type Sodium-Cooled Fast Reactors

Investigating thermal stratification in the upper plenum of a sodium fast reactor (SFR) is presently a technology gap in SFR safety analysis. Understanding thermal stratification will promote safe operation of the SFR before its commercial deployment. Stratified layers of liquid sodium with a large vertical temperature gradient could be established in the upper plenum of an SFR during a down-power or a loss-of-flow transient. These stratified layers are unstable and could result in uncertainties for the core safety of an SFR. In order to predict the occurrence of the thermal stratification efficiently, we developed a one-dimensional (1-D) transport model to estimate the temperature profile of the ambient fluid in the upper plenum. This model demands much less computational effort than computational fluid dynamics (CFD) codes and provides calculations with higher fidelity than historical system-level codes. Two flow conditions were considered separately in the current study depending on if in-vessel components are presented in the upper plenum. For the condition where in-vessel components, specifically the upper internal structure, are presented, we assumed that the impinging sodium was evenly dispersed in the ambient fluid within the distance between the bottom of the in-vessel component and the jet inlet surface. For the condition where no in-vessel components are presented, we assumed that the impinging sodium was evenly dispersed in the ambient fluid within the jet length, which was determined through data-driven trainings. The newly developed 1-D model showed similar performance with the CFD model in both cases. However, due to the assumption of flat profiles of the impinging jet axial dispersion rate, nonnegligible discrepancies between the 1-D prediction and the measured data were observed.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Dataset for 'Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning', Water 2022

This data package presents forcing data, model code, and model output for classical machine learning models that predict monthly stream water temperature as presented in the manuscript ‘Stream Temperature Predictions for River Basin Management in the Pacific Northwest and Mid-Atlantic Regions Using Machine Learning’, Water (Weierbach et al., 2022). Specifically, for input forcing datasets we include two files each generated using the BASIN-3D data integration tool (Varadharajan et al., 2022) for stations in the Pacific Northwest and Mid Atlantic Hydrologic regions. Model code (written in python with the use of jupyter notebooks) includes codes for data preprocessing, training Multiple Linear Regression, Support Vector Regression, and Extreme Gradient Boosted Tree models, and additional notebooks for analysis of model output. We include specific model output files which represent modeling configurations presented in the manuscript also presented in an hdf5 format. Together, these data make up the workflow for predictions across three scenarios (single station, regional, and predictions in unmonitored basins) presented in the manuscript and allow for reproducibility of modeling procedures.

54 ENVIRONMENTAL SCIENCES↗

Accelerating massively parallel hemodynamic models of coarctation of the aorta using neural networks

Comorbidities such as anemia or hypertension and physiological factors related to exertion can influence a patient’s hemodynamics and increase the severity of many cardiovascular diseases. Observing and quantifying associations between these factors and hemodynamics can be difficult due to the multitude of co-existing conditions and blood flow parameters in real patient data. Machine learning-driven, physics-based simulations provide a means to understand how potentially correlated conditions may affect a particular patient. Here, we use a combination of machine learning and massively parallel computing to predict the effects of physiological factors on hemodynamics in patients with coarctation of the aorta. We first validated blood flow simulations against in vitro measurements in 3D-printed phantoms representing the patient’s vasculature. We then investigated the effects of varying the degree of stenosis, blood flow rate, and viscosity on two diagnostic metrics – pressure gradient across the stenosis (ΔP) and wall shear stress (WSS) - by performing the largest simulation study to date of coarctation of the aorta (over 70 million compute hours). Using machine learning models trained on data from the simulations and validated on two independent datasets, we developed a framework to identify the minimal training set required to build a predictive model on a per-patient basis. We then used this model to accurately predict ΔP (mean absolute error within 1.18 mmHg) and WSS (mean absolute error within 0.99 Pa) for patients with this disease.

59 BASIC BIOLOGICAL SCIENCES↗

The HEP.TrkX Project: deep neural networks for HL-LHC online and offline tracking

Particle track reconstruction in dense environments such as the detectors of the High Luminosity Large Hadron Collider (HL-LHC) is a challenging pattern recognition problem. Traditional tracking algorithms such as the combinatorial Kalman Filter have been used with great success in LHC experiments for years. However, these state-of-the-art techniques are inherently sequential and scale poorly with the expected increases in detector occupancy in the HL-LHC conditions. The HEP.TrkX project is a pilot project with the aim to identify and develop cross-experiment solutions based on machine learning algorithms for track reconstruction. Machine learning algorithms bring a lot of potential to this problem thanks to their capability to model complex non-linear data dependencies, to learn effective representations of high-dimensional data through training, and to parallelize easily on high-throughput architectures such as GPUs. This contribution will describe our initial explorations into this relatively unexplored idea space. Furthermore, we will discuss the use of recurrent (LSTM) and convolutional neural networks to find and fit tracks in toy detector data.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A Short-Term and High-Resolution System Load Forecasting Approach Using Support Vector Regression with Hybrid Parameters Optimization

This work proposes an approach for distribution system load forecasting, which aims to provide highly accurate short-term load forecasting with high resolution utilizing a support vector regression (SVR) based forecaster and a two-step hybrid parameters optimization method. Specifically, because the load profiles in distribution systems contain abrupt deviations, a data normalization is designed as the pretreatment for the collected historical load data. Then an SVR model is trained by the load data to forecast the future load. For better performance of SVR, a two-step hybrid optimization algorithm is proposed to determine the best parameters. In the first step of the hybrid optimization algorithm, a designed grid traverse algorithm (GTA) is used to narrow the parameters searching area from a global to local space. In the second step, based on the result of the GTA, particle swarm optimization (PSO) is used to determine the best parameters in the local parameter space. After the best parameters are determined, the SVR model is used to forecast the short-term load deviation in the distribution system.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Towards Trust-Augmented Visual Analytics for Data-Driven Energy Modeling

The promise of data-driven predictive modeling is being increasingly realized in various science and engineering disciplines, where experts are used to the more conventional, simulation-driven modeling practices. However, trust remains a bottleneck for greater adoption of machine learning-based models for domain experts, who might not be necessarily trained in data science. In this paper, we focus on the building energy domain, where physics-based simulations are being complemented or replaced by machine learning-based methods for forecasting energy supply and demand at various spatio-temporal scales. We study the trust problem in close collaboration with energy scientists and engineers and describe how visual analytics can be leveraged for alleviating this trust bottleneck for stakeholders with varying degrees of expertise and analytics goals in this domain.

Kandakatla, Akshith R.↗

Intra-hour Solar Irradiance Forecast in Multiple Locations using Deep Transfer Learning

In recent years, solar power system installation imposes several challenges on the operations of local and regional power grids due to the inherent variability of ground-level solar irradiance. This work proposes a novel real-time solar forecast methodology for intra-hour solar irradiance based on deep transfer learning from ground-based sky imager for time horizons ranging from 5-15 min. There are three unique aspects of the proposed methodology: (1) a Deep Learning based algorithm development which is modeled as a classification approach rather than a traditional regression approach; (2) the use of the Transfer Learning technique to show generalization capability, robustness, and portability of baseline model in the newly deployed location where availability of enough data for training is typically scarce, and (3) redefinition of point-based irradiation forecast error estimation technique with a window-based one that is more intuitive and user-friendly. The system is developed using multiple years of irradiance and sky image recording in New Jersey and one-year data from Colorado, USA. The method is validated against ground telemetry from these two locations of diverse geographic and climatic conditions. Results show that the forecasting method proposed in this work is robust and highly accurate (8% MAPE error) for multiple locations deployment.

Deep Learning, Convolution Neural Networks, transf↗

Physics-Informed Learning Machines for Multiscale and Multiphysics Problems (PHILMS) (Technical Report)

The research work at University of California Santa Barbara (UCSB) resulted in several new developments in the areas of scientific machine learning, numerical analysis, and practical methods for data-driven modeling, prediction, reductions, and simulation. Many of the projects were carried out in collaboration with members of the national laboratories at Sandia National Laboratories (SNL), Pacific Northwestern National Laboratories (PNNL), and other institutions. Results included developing new scientific machine learning methods, related theory and mathematical frameworks for analysis and training, data-driven numerical solvers, and related tools and software for scientific computation. During the support period, over 16+ papers were submitted for publication, and 4 open-source software packages were developed and released (available at http://atzberger.org/). In addition, 7+ students and 2 post-docs were mentored in collaboration with the laboratory staff for future careers in academia, government labs, and industry.

97 MATHEMATICS AND COMPUTING↗

Metrics and Methods for Radiation Detection Algorithm Characterization for Nuclear/Radiological Source Search

This report presents a series of recommendations for data to train and evaluate radiation detection algorithms and performance metrics to evaluate these algorithms. These recommendations were formed through a community consensus approach through the Detection Radiation Algorithms Group (DRAG), a multi-institution collaboration spanning eight Department of Energy laboratories and John Hopkins Applied Physics Laboratory. This report includes recommendations on background data variability, and metrics to quantify variability, sources and shielding configurations to include in data collection campaigns and detector response variability. In addition, this report describes several anomaly detection and identification algorithms and recommends metrics to report their performance. Finally, this report ends with a discussion on machine learning algorithms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Accelerating Multiphase Simulations With Denoising Diffusion Model Driven Initializations

This study introduces a hybrid fluid simulation approach that integrates generative diffusion models with physics‐based simulations, aiming at reducing the computational costs of flow simulations while still honoring all the physical properties of interest. Pore‐scale simulations enhance our understanding of applications such as assessing hydrogen and storage efficiency in underground reservoirs. Nevertheless, they are computationally expensive and the presence of non‐unique solutions can require multiple simulations within a single geometry. To overcome the computational cost hurdle, we propose a method that couples generative diffusion models and physics‐based simulations. While training the data‐driven model, we simultaneously generate initial conditions and perform physics‐based simulations using these. This integrated approach enables us to receive real‐time feedback on a single compute node equipped with both CPUs and GPUs. By efficiently managing these processes within a single compute node, we can continuously monitor performance and halt training once the model meets the specified criteria. To test our model, we generate realizations in a real Berea sandstone fracture which shows that our technique is up to 4.4 times faster than commonly used flow simulation initializations.

36 MATERIALS SCIENCE↗

NCSP Training and Education Program [Slides]

The mission of the Nuclear Criticality Safety Program is to provide sustainable expert leadership, direction and the technical infrastructure necessary to develop, maintain, and disseminate the essential technical tools, training, and data required to support safe, efficient fissionable material operations within DOE; the vision of the program is a Continually improving, adaptable, and transparent program that communicates and collaborates globally to incorporate technology, practices, and programs to be responsive to the essential technical needs of those responsible for developing, implementing, and maintaining nuclear criticality safety. Training and education topics for the program include a 1-week Manager/Criticality Safety Officer Course and a 2-week NCS Engineer Hands-on Training Course.

42 ENGINEERING↗