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At least 1,567 records · Page 87

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗

Microgrid Assisted Design for Remote Areas

In this work, we present a three-stage multiobjective mixed-integer linear programming (MILP) for the optimal expansion planning and operation of isolated multienergy microgrids in remote areas. By selecting the optimal distributed generators (DGs) and energy storage systems (ESSs) mix selection, siting, sizing, and scheduling in the remote microgrid, the proposed model is targeted to minimize the annualized total cost of microgrids while enhancing the performance of the system, i.e., minimizing the voltage deviations and line power loss. To represent the electricity and heat flow between generation resources and various electrical, heating, and cooling loads in the isolated microgrid, linearized power flow, and heat flow constraints are employed in the proposed optimization model. The available capacity of DGs and ESSs are modeled as discrete constants instead of continuous variables for practical purpose. Numerical simulation results on a remote microgrid consisting of DGs, ESSs, and various loads validate the proposed method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

The Heuristic Dynamic Programming Approach in Boost Converters

In this study, a heuristic dynamic programming controller is proposed to control a boost converter. Conventional controllers such as proportional-integral-derivative (PID) or proportional-integral (PI) are designed based on the linearized small-signal model near the operating point. Therefore, the performance of the controller during the start-up, the load change, or the input voltage variation is not optimal since the system model changes by varying the operating point. The heuristic dynamic programming controller optimally controls the boost converter by following the approximate dynamic programming. The advantage of the HDP is that the neural network-based characteristic of the proposed controller enables boost converters to easily cope with large disturbances. An HDP with a well-trained critic and action networks can perform as an optimal controller for the boost converter. To compare the effectiveness of the traditional PI-based and the HDP boost converter, the simulation results are provided.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Quantifying the Multi-Objective Cost of Uncertainty

Various real-world applications involve modeling complex systems with immense uncertainty and optimizing multiple objectives based on the uncertain model. Quantifying the impact of the model uncertainty on the given operational objectives is critical for designing optimal experiments that can most effectively reduce the uncertainty that affect the objectives pertinent to the application at hand. In this paper, we propose the concept of mean multi-objective cost of uncertainty (multi-objective MOCU) that can be used for objective-based quantification of uncertainty for complex uncertain systems considering multiple operational objectives. We provide several illustrative examples that demonstrate the concept and strengths of the proposed multi-objective MOCU. Furthermore, we present a real-world example based on the mammalian cell cycle network to demonstrate how the multi-objective MOCU can be used for quantifying the operational impact of model uncertainty when there are multiple, possibly competing, objectives.

42 ENGINEERING↗

Design Optimization of A generic Fissile Solution for Mo99 production using Electron Beam-based Neutron Generator using MCNP+CFD

Molybdenum-99 ( 99 Mo) is a medical isotope used in 80% of all medical imaging procedures today. However, 99 Mo is not directly administered to patients for imaging; its decay product, technetium-99m ( 99 mTc), is a metastable isotope with a half-life of ~6 hours. Such a short half-life does not allow for production, separation, and application to a patient before decaying further. Therefore, the solution is to produce the precursor to 99 mTc, 99 Mo. 99 Mo has a half-life of 66 hours, long enough to produce the material and send it to the desired location before it fully decays. Under National Nuclear Security Administration’s (NNSA) highly enriched uranium (HEU) minimization mission, the Material Management and Minimization (M3) office leads the Molybdenum-99 (Mo-99) program. A major goal of the Mo-99 program is to develop methods of producing 99 Mo using low enriched uranium (LEU) opposed to the traditionally used HEU domestically in the U.S. Internationally, LEU is the new standard for use in research reactors and isotope production facility. In this study, we introduce a generic fissile solution system for 99 Mo production facility meeting the design requirement of 1) LEU usage as fissile material and 2) subcritical fissile system coupled with a horizontal electron beam (E-beam) accelerator. The focus of this research is to optimize a fissile solution configuration for maximum 99 Mo production yield using MCNP model, and ultimately implement the optimized design with computational fluid dynamics (CFD) model to understand thermal hydraulic behavior and solution convection characteristic. The report consists of two parts: 1) isotope yield calculation and criticality analysis with a wide range of parametric test matrix, and 2) thermal hydraulic analysis for solution mixing and cooling assessment.

60 APPLIED LIFE SCIENCES↗

A Stochastic Charging Station Deployment Model for Electrified Taxi Fleets in Coupled Urban Transportation and Power Distribution Networks

Metropolitansworldwide are increasingly adopting electric taxis (ET) to address concerns about transportation-related emissions. However, the widespread deployment of electric taxis presents challenges in terms of increased electricity demand and changing demand profiles. This transition impacts both the urban transportation network (TN) and the electricity power distribution network (PDN), highlighting the interdependence between these two systems. Here, in this paper, we propose a two-stage stochastic programming planning model that aims to optimize both the TN and PDN, enabling efficient deployment of charging stations and grid upgrades. Our model seeks to strike a balance between meeting ET drivers' charging preferences, minimizing the costs associated with infrastructure deployment and grid expansion, and harmonizing the coordination between the TN and PDN. Additionally, we explore the potential benefits of utilizing an autonomous ET fleet to enhance overall system performance.

33 ADVANCED PROPULSION SYSTEMS↗

Optimizing Distributed Training on Frontier for Large Language Models

Large language models (LLMs) have demonstrated remarkable success as foundational models, benefiting various downstream applications through fine-tuning. Loss scaling studies have demonstrated the superior performance of larger LLMs compared to their smaller counterparts. Nevertheless, training LLMs with billions of parameters poses significant challenges and requires considerable computational resources. For example, training a one trillion parameter GPT-style model on 20 trillion tokens requires a staggering 120 million exaflops. This research explores efficient distributed training strategies to extract this computation from Frontier, the world's first exascale supercomputer. We enable and investigate various model and data parallel training techniques, such as tensor parallelism, pipeline parallelism, and sharded data parallelism, to facilitate training a trillion-parameter model on Frontier. We empirically assess these techniques and their associated parameters to determine their impact on memory footprint, communication latency, and GPU's computational efficiency. We analyze the complex interplay among these techniques and find a strategy to combine them to achieve high throughput through hyperparameter tuning. We have identified efficient strategies for training large LLMs of varying sizes through empirical analysis and hyperparameter tuning. For 22 Billion, 175 Billion, and 1 Trillion parameters, we achieved GPU throughputs of 38.38%, 36.14%, and 31.96%, respectively. For the training of the 175 Billion parameter model and the 1 Trillion parameter model, we achieved 100% weak scaling efficiency on 1024 and 3072 Mi250X GPUs, respectively. We also achieved strong scaling efficiencies of 89% and 87% for these two models. We trained these models only tens of iterations instead of training till completion.

Yin, Junqi↗

Spatial distributions of X CO 2 seasonal cycle amplitude and phase over northern high-latitude regions

Satellite-based observations of atmospheric carbon dioxide (CO 2 ) provide measurements in remote regions, such as the biologically sensitive but undersampled northern high latitudes, and are progressing toward true global data coverage. Recent improvements in satellite retrievals of total column-averaged dry air mole fractions of CO 2 (X CO 2 ) from the NASA Orbiting Carbon Observatory 2 (OCO-2) have allowed for unprecedented data coverage of northern high-latitude regions, while maintaining acceptable accuracy and consistency relative to ground-based observations, and finally providing sufficient data in spring and autumn for analysis of satellite-observed X CO 2 seasonal cycles across a majority of terrestrial northern high-latitude regions. Here, we present an analysis of X CO 2 seasonal cycles calculated from OCO-2 data for temperate, boreal, and tundra regions, subdivided into 5° latitude by 20° longitude zones. We quantify the seasonal cycle amplitudes (SCAs) and the annual half drawdown day (HDD). OCO-2 SCAs are in good agreement with ground-based observations at five high-latitude sites, and OCO-2 SCAs show very close agreement with SCAs calculated for model estimates of X CO 2 from the Copernicus Atmosphere Monitoring Services (CAMS) global inversion-optimized greenhouse gas flux model v19r1 and the CarbonTracker2019 model (CT2019B). Model estimates of X CO 2 from the GEOS-Chem CO 2 simulation version 12.7.2 with underlying biospheric fluxes from CarbonTracker2019 (GC-CT2019) yield SCAs of larger magnitude and spread over a larger range than those from CAMS, CT2019B, or OCO-2; however, GC-CT2019 SCAs still exhibit a very similar spatial distribution across northern high-latitude regions to that from CAMS, CT2019B, and OCO-2. Zones in the Asian boreal forest were found to have exceptionally large SCA and early HDD, and both OCO-2 data and model estimates yield a distinct longitudinal gradient of increasing SCA from west to east across the Eurasian continent. In northern high-latitude regions, spanning latitudes from 47 to 72° N, longitudinal gradients in both SCA and HDD are at least as pronounced as latitudinal gradients, suggesting a role for global atmospheric transport patterns in defining spatial distributions of X CO2 seasonality across these regions. GEOS-Chem surface contact tracers show that the largest X CO 2 SCAs occur in areas with the greatest contact with land surfaces, integrated over 15–30d. The correlation of X CO 2 SCA with these land surface contact tracers is stronger than the correlation of X CO 2 SCA with the SCA of CO 2 fluxes or the total annual CO 2 flux within each 5° latitude by 20° longitude zone. This indicates that accumulation of terrestrial CO 2 flux during atmospheric transport is a major driver of regional variations in X CO 2 SCA.

54 ENVIRONMENTAL SCIENCES↗

Optimal observing strategies for velocity-suppressed dark matter annihilation

Numerous particle models for the cosmological dark matter feature a pair-annihilation rate that scales with powers of the relative velocity between the annihilating particles. As a result, the annihilation rate in the central regions of a dark matter halo can be significantly lower than at the halo’s periphery for particular ambient gravitational potentials. While this might be offset by an increasing dark matter pair number density in the inner halo, it raises the question; what angular region for dark matter models with velocity-suppressed annihilation rates optimizes the signal to noise ratio? We consider simplified background models for galactic and extragalactic targets and demonstrate that the optimal observing strategy varies greatly case by case. Generally, a bright central source warrants an annular region of interest, while a flatter background warrants as large as possible an angular region, possibly including the central regions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Overcoming sparse datasets with multi-task learning as applied to high entropy alloys

Abstract The design of novel High Entropy Alloys for use in high-temperature applications is an area of active interest due to their potential to provide exceptional properties compared to conventional alloys. Since the increased popularity of machine learning, an important cog in the design process has been training surrogate models on alloy properties. However, these Single-Task models are trained on individual mechanical properties and do not take advantage of the relatedness between properties. Multi-Task models can capture the interdependencies between tasks, leading to potentially more accurate predictions for all tasks. In this paper, we investigate if Multi-Task models can show improvement over Single-Task models when used for predicting the mechanical properties of these alloys. To ensure fair evaluation between the models, we apply L 0 regularization and skip connections to the models, which allows them to adjust the number of model parameters and depth for optimal performance. We find that the Multi-Task models can leverage task relationships to perform better than Single-Task models, especially for high amounts of missing data in the tasks. Furthermore, adding simple auxiliary targets can boost Multi-Task performance even further despite not being effective as input descriptors to single-task models themselves. We anticipate that the proposed strategies can achieve more accurate predictions and consequently enable better design capabilities for such data-constrained domains without incurring much additional computational cost.

Debnath, Arindam (ORCID:0000000194274499)↗

Surrogate Optimization of Computationally Expensive Black-Box Problems with Hidden Constraints (SHEBO) v1.0

SHEBO (surrogate optimization of problems with hidden constraints and expensive black-box objectives) is an efficient optimization algorithm that employs surrogate models to solve computationally expensive black-box simulation optimization problems that have hidden constraints. Hidden constraints are encountered when the objective function evaluation does not return a value for a parameter vector. These constraints are often encountered in optimization problems in which the objective function is computed by a black-box simulation code. SHEBO uses a combination of local and global search strategies together with an evaluability prediction function and a dynamically adjusted evaluability threshold to iteratively select new sample points.

Mueller, Juliane↗

Western Interconnection Baseline Study

The purpose of the baseline study is to evaluate the degree to which current industry planning processes meet the national 2035 decarbonization goals for the Western Interconnection. This analysis serves as a comparative baseline for the scenario analysis conducted in the NTP Study using a Western Interconnection dataset that is readily available to industry. This baseline analysis differs from the production cost modeling analysis and power flow analysis in the main NTP Study report (forthcoming). In particular, the analysis presented in this report reflects a business-as-usual future with an optimistic build out of specific planned transmission projects and foreseeable generation. In contrast, the NTP Study models a future generation and transmission expansion based on optimization from a capacity expansion model. The analysis presented herein also reflects a 2030 timeframe, whereas the main NTP Study production cost modeling analysis and power flow analysis reflect a 2035 time frame. This baseline analysis utilizes industry’s most reliable data to account for future transmission projects across various stages of development, with a particular focus on those in the permitting stage. Additionally, it incorporates projections for changes in generation capacity (both additions and retirements). This baseline analysis outlines a probable trajectory, given current process and practice, for the future of the bulk power system with a horizon extending to 2030.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗