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At least 109 records · Page 6

Agilent AgileBioFoundry CRADA (Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.

97 MATHEMATICS AND COMPUTING↗

Chemistry Informed Machine Learning-Based Heat Capacity Prediction of Solid Mixed Oxides

Knowing heat capacity is crucial for modeling temperature changes with the absorption and release of heat and for calculating the thermal energy storage capacity of oxide mixtures with energy applications. The current prediction methods (ab initio simulations, computational thermodynamics, and the Neumann–Kopp rule) are computationally expensive, not fully generalizable, or inaccurate. Machine learning has the potential of being fast, accurate, and generalizable, but it has been scarcely used to predict mixture properties, particularly for mixed oxides. Here, we demonstrate a method for the generalizable prediction of heat capacity of solid oxide pseudobinary mixtures using heat capacity data obtained from computational thermodynamics and descriptors from ab initio databases. Further, models trained through this workflow achieved an error (mean absolute error of 0.43 J mol –1 K –1 ) lower than the uncertainty in differential scanning calorimetry measurements, and the workflow can be extended to predict other properties derived from the Gibbs free energy and for higher-order oxide mixtures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development and implementation of high-throughput proteomic and metabolomics assays by using advanced chromatographic and mass spectrometric systems (CRADA Final Report)

The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOFMS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Overall, the project advanced rapid metabolomics by combining liquid chromatography, ion mobility spectrometry, and data-independent mass spectrometry with machine learning. This multidimensional approach uses retention time, collision cross-section, precursor mass, and fragment-ion information to distinguish chemically similar metabolites that can be difficult to resolve using conventional liquid- or gas-chromatography methods. The resulting workflow also provided automated metabolite-identification error estimates, addressing a recognized need for statistical confidence measures in metabolomics.

Petzold, Christopher [Lawrence Berkeley National L↗

Review of Solar Energetic Particle Models

Solar Energetic Particle (SEP) events are interesting from a scientific perspective as they are the product of a broad set of physical processes from the corona out through the extent of the heliosphere, and provide insight into processes of particle acceleration and transport that are widely applicable in astrophysics. From the operations perspective, SEP events pose a radiation hazard for aviation, electronics in space, and human space exploration, in particular for missions outside of the Earth’s protective magnetosphere including to the Moon and Mars. Thus, it is critical to improve the scientific understanding of SEP events and use this understanding to develop and improve SEP forecasting capabilities to support operations. Many SEP models exist or are in development using a wide variety of approaches and with differing goals. These include computationally intensive physics-based models, fast and light empirical models, machine learning-based models, and mixed-model approaches. The aim of this paper is to summarize all of the SEP models currently developed in the scientific community, including a description of model approach, inputs and outputs, free parameters, and any published validations or comparisons with data.

Kathryn Whitman↗

Refining fast calorimeter simulations with a Schrödinger Bridge

Machine learning-based simulations, especially calorimeter simulations, are promising tools for approximating the precision of classical high energy physics simulations with a fraction of the generation time. Nearly all methods proposed so far learn neural networks that map a random variable with a known probability density, like a Gaussian, to realistic-looking events. In many cases, physics events are not close to Gaussian and so these neural networks have to learn a highly complex function. We study an alternative approach: Schrödinger bridge Quality Improvement via Refinement of Existing Lightweight Simulations (SQuIRELS). SQuIRELS leverages the power of diffusion-based neural networks and Schrödinger bridges to map between samples where the probability density is not known explicitly. We apply SQuIRELS to the task of refining a classical fast simulation to approximate a full classical simulation. On simulated calorimeter events, we find that SQuIRELS is able to reproduce highly non-trivial features of the full simulation with a fraction of the generation time.

Calorimeter methods↗

Multiresolution classification of turbulence features in image data through machine learning

During large-scale simulations, intermediate data products such as image databases have become popular due to their low relative storage cost and fast in-situ analysis. Serving as a form of data reduction, these image databases have become more acceptable to perform data analysis on. In this work, we present an image-space detection and classification system for extracting vortices at multiple scales through wavelet-based filtering. A custom image-space descriptor is used to encode a large variety of vortex-types and a machine learning system is trained for fast classification of vortex regions. By combining a radial-based histogram descriptor, a bag of visual words feature descriptor, and a support vector machine, our results show that we are able to detect and classify vortex features at various sizes at multiple scales. Once trained, our framework enables the fast extraction of vortices on new, unknown image datasets for flow analysis.

97 MATHEMATICS AND COMPUTING↗

A Workflow to Optimize Fast Neutron Irradiation in A Thermal Neutron Spectrum Test Reactor Leveraging Open-Source Tools

The Advanced Test Reactor (ATR) located at Idaho National Laboratory (INL) is one of the key nuclear engineering research and testing facilities within the US Department of Energy (DOE). The ATR is one of few high-power research reactors in the world with different application including accelerated testing of nuclear fuel, materials irradiation in a very high neutron flux environment, and medical radioisotope production [1]. Also, the ATR offers opportunities for testing fast spectrum fission and fusion reactor materials. The key challenges in this area are in further detailing and optimizing a fast spectrum environment within a thermal test reactor. This challenge involves researching, developing, and testing novel concepts for the multiplying of neutron populations into ever higher energy spectra in high flux test reactors like ATR. The main objective of this work is to investigate candidate materials for establishing a fast neutron experiment irradiation in thermal neutron spectrum test reactors which can be accomplished by filtering thermal and epithermal neutrons and boosting fast neutrons at designated irradiation positions. However, adding these filters will render the neutron spectrum and the criticality of the system. The selection of the thickness and material layers should be accomplished by developing an optimization design algorithm that is applicable for ATR to enhance the fast neutron spectrum irradiation utilizing high-fidelity Monte Carlo methods along with advanced machine learning capabilities. This paper presents workflow for design optimization to enhance fast neutron irradiation in the ATR. The workflow leverages open-source tools to develop an algorithm that is viable to ATR and can be leveraged in other reactors. The following sections discuss the development of the experiment design optimization workflow and its application to ATR irradiation positions.

42 - ENGINEERING↗

ML-Based Power System Stability Assessment Considering Network Topology Changes: WECC 20,000+ Bus System Case Study

Modern power grids are fast-changing and thus require real-time monitoring and online stability assessment. With the rapid development of machine learning (ML) techniques, using data-driven models to provide fast and accurate estimations of power system stability marginal information, such as frequency nadir for frequency stability and critical clearing time (CCT) for transient stability, have become possible. However, despite the numerous research on ML-based methods for frequency nadir and CCT prediction, there is limited work on the impact of different network topology changes. Furthermore, most previous studies only focused on small or synthetic systems, and there is a lack of research on actual large power system models. In this paper, the above issues are addressed by studying the actual U.S. Western Electricity Coordinating Council (WECC) system model with more than 20,000 buses. Massive simulations are conducted in PowerWorld Simulator to study the impact of various topology change scenarios on both frequency stability and transient stability. System operating information is extracted from the success dispatch cases of various network topologies to generate a comprehensive dataset for ML-based models. Two ML methods, random forest (RF) and multilayer perceptron (MLP) neural network, are trained and tested for both frequency nadir prediction and CCT prediction. Test results have proven the models are capable of online stability assessment for large power networks such as the WECC system with sufficient accuracy.

critical clearing time↗

A review on recent machine learning applications for imaging mass spectrometry studies

Imaging mass spectrometry (IMS) is a powerful analytical technique widely used in biology, chemistry, and materials science fields that continue to expand. IMS provides a qualitative compositional analysis and spatial mapping with high chemical specificity. The spatial mapping information can be 2D or 3D depending on the analysis technique employed. Due to the combination of complex mass spectra coupled with spatial information, large high-dimensional datasets (hyperspectral) are often produced. Therefore, the use of automated computational methods for an exploratory analysis is highly beneficial. The fast-paced development of artificial intelligence (AI) and machine learning (ML) tools has received significant attention in recent years. These tools, in principle, can enable the unification of data collection and analysis into a single pipeline to make sampling and analysis decisions on the go. There are various ML approaches that have been applied to IMS data over the last decade. Here, in this review, we discuss recent examples of the common unsupervised (principal component analysis, non-negative matrix factorization, k-means clustering, uniform manifold approximation and projection), supervised (random forest, logistic regression, XGboost, support vector machine), and other methods applied to various IMS datasets in the past five years. The information from this review will be useful for specialists from both IMS and ML fields since it summarizes current and representative studies of computational ML-based exploratory methods for IMS.

47 OTHER INSTRUMENTATION↗

Safe Reinforcement Learning for Emergency Load Shedding of Power Systems

The paradigm shift in the electric power grid necessitates a revisit of existing control methods to ensure the grid’s security and resilience. In particular, the increased uncertainties and rapidly changing operational conditions in power systems have revealed outstanding issues in terms of either speed, adaptiveness, or scalability of the existing control methods for power systems. On the other hand, the availability of massive real-time data can provide a clearer picture of what is happening in the grid. Recently, deep reinforcement learning (RL) has been regarded and adopted as a promising approach leveraging massive data for fast and adaptive grid control. However, like most existing machine learning (ML)- based control techniques, RL control usually cannot guarantee the safety of the power systems. In this paper, we introduce a novel method for safe RL-based load shedding of power systems that can enhance the safe voltage recovery of the electric power grid after experiencing faults. Numerical simulation on the IEEE 39-bus testcase is performed to demonstrate the effectiveness of the proposed safe RL emergency control, as well as its adaptive capability to faults not seen in the training.

reinforcement learning, emergency control, power g↗

Optimizing Performance on Trinity Utilizing Machine Learning, Proxy Applications and Scheduling Priorities

The sheer number of nodes continues to increase in today’s supercomputers, the first half of Trinity alone contains more than 9400 compute nodes. Since the speed of today’s clusters are limited by the slowest nodes, it more important than ever to identify slow nodes, improve their performance if it can be done, and assure minimal usage of slower nodes during performance critical runs. This is an ongoing maintenance task that occurs on a regular basis and, therefore, it is important to minimize the impact upon its users by assessing and addressing slow performing nodes and mitigating their consequences while minimizing down time. These issues can be solved, in large part, through a systematic application of fast running hardware assessment tests, the application of Machine Learning, and making use of performance data to increase efficiency of large clusters. Proxy applications utilizing both MPI and OpenMP were developed to produce data as a substitute for long runtime applications to evaluate node performance. Machine learning is applied to identify underperforming nodes, and policies are being discussed to both minimize the impact of underperforming nodes and increase the efficiency of the system. In this paper, I will describe the process used to produce quickly performing proxy tests, consider various methods to isolate the outliers, and produce ordered lists for use in scheduling to accomplish this task.

97 MATHEMATICS AND COMPUTING↗

A Gaussian Process Enhancement to Linear Parameter Varying Models

Simulation and analysis for modern engineering systems now routinely requires the merging of multiple disciplines, physical-domains, time-scales, and data sets — all at ever increasing levels. These capabilities are especially needed in the domain of Advanced Air Mobility, where rapidly emerging vehicle designs are significantly more complex, while having to be both cost-effective and safe. To meet these engineering challenges, machine learning methods are an attractive option for merging models and data across multiple areas while providing uncertainty quantification and maintaining computational efficiency. This paper examines the use of Gaussian process machine learning to generalize and enhance the commonly used class of quasi-Linear Parameter Varying models for fast full-envelope simulation while also supporting control system design and analysis with model uncertainty. Gaussian process machine learning is selected because it: can fuse multiple data sets, enables an easy trade-off between data fitting and smoothing, provides model uncertainty quantification, scales well with increasing complexity, and does not generally require starting from a large training data set. To demonstrate the benefits of the approach, a robust stability analysis with Gaussian process uncertainty is shown for a NASA reference design of an electric quad-rotor air-taxi concept vehicle with motor parameter uncertainty.

Gaussian Process↗

OLCF’s Advanced Computing Ecosystem (ACE): FY25 Update for Ongoing Efforts

The advent of widespread use of artificial intelligence (AI) and machine learning (ML) models in science, coupled with fast data production rates of scientific instruments strain the traditional batch-oriented high-performance computing (HPC) environment. As scientific exploration continues to require more data and faster processing and analysis, new emerging technologies and capabilities to enable cross-facility and time-sensitive workflows are required for seamless integration of HPC and experimental facilities. The Advanced Computing Ecosystem (ACE) is a strategic initiative within the Oak Ridge Leadership Computing Facility (OLCF) established in 2024 to support the development of cutting-edge technologies to advance computational research and infrastructure at OLCF and across the Department of Energy (DOE). Several DOE initiatives are spearheading the evolution of the scientific landscape by blurring facility boundaries and connecting the user facilities to advance scientific capabilities and ensure energy dominance. The DOE Integrated Research Infrastructure (IRI) program is one example that is laying a foundation to support complex cross-facility workflows. The IRI program aims to integrate diverse computational resources, data infrastructures, and scientific instruments to facilitate collaboration and accelerate scientific discovery. The Interconnected Science Ecosystem (INTERSECT) initiative at Oak Ridge National Laboratory (ORNL) is another example that aims to revolutionize scientific research through AI-driven, interconnected autonomous laboratories and research facilities. Finally, the American Science Cloud (AmSC), recently announced in the “One Big Beautiful Bill”, aims to leverage prior infrastructure efforts of the IRI and automation and AI efforts of INTERSECT (and others) to build a federated, AI-augmented AmSC platform to unify the DOE’s computing, experimental, and data resources to catalyze scientific innovation.

97 MATHEMATICS AND COMPUTING↗

Understanding Mixed Precision GEMM with MPGemmFI: Insights into Fault Resilience

Emerging deep learning workloads urgently need fast general matrix multiplication (GEMM). Thus, one of the critical features of machine-learning-specific accelerators such as NVIDIA Tensor Cores, AMD Matrix Cores, and Google TPUs is the support of mixed-precision enabled GEMM. For DNN models, lower-precision FP data formats and computation offer acceptable correctness but significant performance, area, and memory footprint improvement. While promising, the mixed-precision computation on error resilience remains unexplored. To this end, we develop a fault injection framework that systematically injects fault into the mixed-precision computation results. We investigate how the faults affect the accuracy of machine learning applications. Based on the characteristics of error resilience, we offer lightweight error detection and correction solutions that significantly improve the overall model accuracy by 75% if the models experience hardware faults. The solutions can be efficiently integrated into the accelerator's pipelines.

Fang, Bo↗

AutoReP: Automatic ReLU Replacement for Fast Private Network Inference

The proliferation of the Machine-Learning-As-A-Service (MLaaS) market has brought to light a number of clients’ data privacy and security concerns. One promising solution is private inference (PI) techniques using cryptographic primitives. These techniques often come with high computation and communication overhead associated with the non-linear operator such as ReLU. Several approaches have been developed in reducing the number of ReLU operations, however, they either require a heuristic threshold selection or introduce significant accuracy drop. This work presents AutoReP, a gradient-based framework for non-linear operators reduction that aims to mitigate these concerns from a systematic perspective. AutoReP automates the process of discrete selection of ReLU and polynomial functions on neurons to accelerate PI applications. We also introduce distribution-aware polynomial approximation (DaPa) to accurately approximate ReLUs under given distribution, preserving model expressivity. Our experimental results demonstrate significant accuracy improvements of 6.12% (94.31%, 12.9K ReLU budget, CIFAR-10), 8.39% (74.92%, 12.9K ReLU budget, CIFAR-100), and 9.45% (63.69%, 55K ReLU budget, Tiny-ImageNet) over current state-of-the-art methods, e.g., SNL. Morever, AutoReP is applied to EfficientNet-B2 on ImageNet dataset, and achieved 75.55% accuracy with 176.1 × ReLU budget reduction.

Peng, Hongwu↗

Automatic Loss Factor Modeling and Attribution on Unlabeled PV Energy Data

We present a novel approach for modeling the loss factors of photovoltaic power generation systems (PV systems). This method is a white-box machine learning model built on convex optimization that is fast, interpretable, and auditable. It takes as an input the measured daily energy produced by the system, over a multi-year period, and returns a multiplicative decomposition model of the daily energy signal and full attribution of the total energy loss to each feature. The methods section of this paper has two major components: (1) the description of the signal decomposition (SD) model, expressed in the SD framework, and (2) the attribution of total energy losses via Shapley values. We validate the method on synthetic and open-source data sets and compare to similar methods from the literature.

artificial intelligence↗

SMALE: Enhancing Scalability of Machine Learning Algorithms on Extreme-Scale Computing Platforms

Deployment and execution of machine learning tasks on extreme-scale computing platforms face several significant technical challenges: 1) High computing cost incurred by dense networks – The computing workload of deep networks with densely-connected topology increases rapidly with the network size, imposing a non-scalable computing model of extreme-scale computing platforms; 2) Non-optimized workload distribution – Many advanced deep learning algorithms, e.g., sparsification and irregular net-work topology, produce very unbalanced workload distribution on extreme-scale computing platforms. The computation efficiency is greatly hindered by the incurred data and computation redundancies as well as long tails of the node with extensive workload; 3) Constraints in data movement and I/O bottle-neck – Inter-node data movement in extreme-scale computing platforms are associated with high energy and latency costs, and subject to the constraints of I/O bandwidth; and 4) Generalization of algorithm realization and acceleration on computing platforms – The large varieties of machine learning algorithms and structures of extreme-scale computing platforms make the derivation of a generalized algorithm realization and acceleration method very challenging, which, however, is the requirement by domain scientists and interested users. We call the above challenges Smale’s Problems in Machine Learning and Understanding for High-Performance Computing Scientific Discovery. The objective of our three-year research project is to develop a holistic innovation set at structure, assembly, and acceleration layers of machine learning algorithms to address the above challenges in algorithm deployment and execution. Three tasks are particularly performed, including: At the algorithm structure level, we investigate the techniques that can structurally sparsify on the topology of deep networks for computing workload reduction. We also study clustering and pruning techniques that can optimize the workload distributions over the extreme-scale computing platforms; At the algorithm assembly level, we derive a unified learning framework for unsupervised transfer learning and dynamic growing capabilities. Novel training methods are also exploited to enhance the training efficiency of the proposed framework; At the algorithm acceleration level, we will develop a series of techniques that can accelerate the computation of sparse matrix operations, which are one of the core executions in deep learning and optimize memory access of the concerned platforms. Our proposed techniques attack the fundamental problems in machine learning algorithms running on extreme-scale computing platforms by vertically integrating the solutions at three closely entangled layers, paving the long-term scaling path of machine learning applications under DOE context. Three tasks corresponding to the above respective research orientations are performed during the three-year project period with our collaborators at ORNL. The outcome of the proposed project is anticipated to form a holistic solution set of novel algorithms and network topologies, efficient training techniques, and fast acceleration methods to promote the computing scalability of the machine learning applications of particular interest to DOE.

97 MATHEMATICS AND COMPUTING↗