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Yet Another Discriminant Analysis (YADA): A Probabilistic Model for Machine Learning Applications

This paper presents a probabilistic model for various machine learning (ML) applications. While deep learning (DL) has produced state-of-the-art results in many domains, DL models are complex and over-parameterized, which leads to high uncertainty about what the model has learned, as well as its decision process. Further, DL models are not probabilistic, making reasoning about their output challenging. In contrast, the proposed model, referred to as Yet Another Discriminate Analysis(YADA), is less complex than other methods, is based on a mathematically rigorous foundation, and can be utilized for a wide variety of ML tasks including classification, explainability, and uncertainty quantification. YADA is thus competitive in most cases with many state-of-the-art DL models. Ideally, a probabilistic model would represent the full joint probability distribution of its features, but doing so is often computationally expensive and intractable. Hence, many probabilistic models assume that the features are either normally distributed, mutually independent, or both, which can severely limit their performance. YADA is an intermediate model that (1) captures the marginal distributions of each variable and the pairwise correlations between variables and (2) explicitly maps features to the space of multivariate Gaussian variables. Numerous mathematical properties of the YADA model can be derived, thereby improving the theoretic underpinnings of ML. Validation of the model can be statistically verified on new or held-out data using native properties of YADA. However, there are some engineering and practical challenges that we enumerate to make YADA more useful.

97 MATHEMATICS AND COMPUTING↗

Using Neural Architecture Search for Improving Software Flaw Detection in Multimodal Deep Learning Models

Software flaw detection using multimodal deep learning models has been demonstrated as a very competitive approach on benchmark problems. In this work, we demonstrate that even better performance can be achieved using neural architecture search (NAS) combined with multimodal learning models. We adapt a NAS framework aimed at investigating image classification to the problem of software flaw detection and demonstrate improved results on the Juliet Test Suite, a popular benchmarking data set for measuring performance of machine learning models in this problem domain.

97 MATHEMATICS AND COMPUTING↗

Using Neural Architecture Search for Improving Software Flaw Detection in Multimodal Deep Learning Models

Software flaw detection using multimodal deep learning models has been demonstrated as a very competitive approach on benchmark problems. In this work, we demonstrate that even better performance can be achieved using neural architecture search (NAS) combined with multimodal learning models. We adapt a NAS framework aimed at investigating image classification to the problem of software flaw detection and demonstrate improved results on the Juliet Test Suite, a popular benchmarking data set for measuring performance of machine learning models in this problem domain.

97 MATHEMATICS AND COMPUTING↗

Uncertainty quantification in multivariable regression for material property prediction with Bayesian neural networks

With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including multi-scale and multi-physics nature of materials, intricate interactions between numerous factors, limited availability of large curated datasets, etc. In this work, we introduce a physics-informed Bayesian Neural Networks (BNNs) approach for UQ, which integrates knowledge from governing laws in materials to guide the models toward physically consistent predictions. To evaluate the approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of creep tests demonstrates that this method produces point predictions and uncertainty estimations that are competitive or exceed the performance of conventional UQ methods such as Gaussian Process Regression. Additionally, we evaluate the suitability of employing UQ in an active learning scenario and report competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs.

36 MATERIALS SCIENCE↗

Machine learning-based interatomic potential development and phase transition analysis of ferroelectric hafnium dioxide

The ferroelectric phase (𝑃⁢𝑐⁢𝑎⁢2 1 , which is in orthorhombic symmetry) of hafnium dioxide (HfO 2 ) has gained much attention due to its potential applications in nanoelectronics and advanced memory devices. However, its complex phase behavior under external stimuli, such as pressure and temperature, remains a subject of intense investigation. This study focuses on developing a machine learning-based interatomic potential (MLIP) that is trained with data from density-functional theory (DFT) calculations to simulate phase transitions and mechanical properties of HfO 2 . The developed MLIP predicts lattice parameters, equations of state, bulk and shear moduli, and elastic constants that closely align with DFT predictions for several phases and at various pressures. Once validated, the MLIP is used to investigate the phase transitions of ferroelectric HfO 2 (𝑃⁢𝑐⁢𝑎⁢2 1 ) under both isobaric and constant stress conditions at elevated temperatures ranging from 200 to 2500 K. We used several complementary methods, including local symmetry identification, radial distribution function, and x-ray diffraction characterization, to identify interesting phase transitions among several competitive hafnia phases predicted from our simulations. The suggested methods uniformly reveal that under pure deviatoric condition, the system favors a transition from the orthorhombic 𝑃⁢𝑐⁢𝑎⁢2 1 phase to a tetragonal (𝑃⁢4 2 /𝑛⁢𝑚⁢𝑐) phase, whereas a zero stress condition drives the system from the 𝑃⁢𝑐⁢𝑎⁢2 1 phase to another orthorhombic (𝑃⁢𝑏⁢𝑐⁢𝑛) phase. These findings provide crucial insights into stress and temperature-induced phase behavior of hafnia, guiding future experimental and theoretical studies for optimizing hafnia-based ferroelectric devices.

Ferroelectric HfO2↗

Learning Coagulation Processes With Combinatorial Neural Networks

Abstract Simulating the evolution of a coagulating aerosol or cloud of droplets in a key problem in atmospheric science. We present a proof of concept for modeling coagulation processes using a novel combinatorial neural network (CombNN) architecture. Using two types of data from a high‐detail particle‐resolved aerosol simulation, we show that CombNN models outperform standard neural networks and are competitive in accuracy with traditional state‐of‐the‐art sectional models. These CombNN models could have application in learning coarse‐grained coagulation models for multi‐species aerosols and for learning coagulation models from observed size‐distribution data.

54 ENVIRONMENTAL SCIENCES↗

Subseasonal Forecasting and MJO Teleconnections in Machine Learning Weather Prediction Models

Abstract In recent years, machine‐learning (ML) models trained on reanalysis data have rivaled physics‐based forecast models in terms of performance skill for global weather forecasting. With increased rollout stability, the question of how these models perform for subseasonal to seasonal (S2S, week 3–8) forecasting has emerged. In this study we run a large set of subseasonal hindcasts over 2004–2023 to evaluate two ML weather forecast models at the S2S time scale, SFNO‐HENS (Nvidia, fully ML) and NeuralGCM (Google Research, hybrid). Corresponding hindcasts from the European Centre for Medium‐Range Weather Forecasts (ECMWF) are used as a baseline for comparison to a physics‐based model. Because our focus is on predicting moisture transport over the Western United States between October and March, we evaluate the models' prediction skill for the Madden‐Julian Oscillation (MJO) and its associated teleconnections in the North Pacific. We find that both ML models are competitive with the ECWMF model, with comparable skill in predicting the North Pacific large‐scale circulation and the MJO at week 3 and beyond. Even though overall the mid‐latitude subseasonal prediction skill remains low, the ML models exhibit interesting behavior such as a realistic propagation of the MJO across the Maritime Continent and realistic teleconnections. A SFNO‐HENS sensitivity experiment with altered initial conditions in the tropics demonstrates the stability of the model, and it illustrates the capability of ML models to represent important physical processes of the atmosphere at the S2S time scale. Plain Language Summary Predicting weather patterns and precipitation a few weeks in advance (subseasonal time scale) is of great interest for stakeholders such as water managers in the Southwest United States (US), where arid conditions prevail. Subseasonal forecasts from traditional weather forecast models exhibit low skill in the region, limiting their applicability. Here we examine whether the recent breakthrough in weather forecasting made with machine learning/artificial intelligence models can translate to improved subseasonal forecasts. Recently‐developed machine learning models exhibit comparable skill to a state‐of‐the‐art physics‐based model for predicting weather patterns in the North Pacific/North America region, and associated moisture transport. The same applies to their skill in predicting the tropical pattern, the Madden‐Julian Oscillation, and its important remote perturbations over the midlatitude East Pacific and Southwest US. Additionally, a perturbation experiment carried out with one of the machine learning models illustrates their ability to not only predict the evolution of atmospheric fields, but also to learn and represent physical processes such as tropics‐extratropics Rossby wave propagation. Key Points Two machine learning weather forecast models exhibit state‐of‐the‐art prediction skill at the subseasonal time scale in the Pacific sector The models equal ECWMF in terms of Madden‐Julian oscillation (MJO) prediction skill, and they accurately predict the MJO propagation and associated teleconnections The two machine‐learning models represent key physical processes for subseasonal prediction, despite being trained for weather forecasting

Peings, Yannick↗

Analysis and Benchmarking of feature reduction for classification under computational constraints

Abstract Machine learning is most often expensive in terms of computational and memory costs due to training with large volumes of data. Current computational limitations of many computing systems motivate us to investigate practical approaches, such as feature selection and reduction, to reduce the time and memory costs while not sacrificing the accuracy of classification algorithms. In this work, we carefully review, analyze, and identify the feature reduction methods that have low costs/overheads in terms of time and memory. Then, we evaluate the identified reduction methods in terms of their impact on the accuracy, precision, time, and memory costs of traditional classification algorithms. Specifically, we focus on the least resource intensive feature reduction methods that are available in Scikit-Learn library. Since our goal is to identify the best performing low-cost reduction methods, we do not consider complex expensive reduction algorithms in this study. In our evaluation, we find that at quadratic-scale feature reduction, the classification algorithms achieve the best trade-off among competitive performance metrics. Results show that the overall training times are reduced 61%, the model sizes are reduced 6×, and accuracy scores increase 25% compared to the baselines on average with quadratic scale reduction.

97 MATHEMATICS AND COMPUTING↗

Performance Evaluations of Noisy Approximate Quantum Fourier Arithmetic

The Quantum Fourier Transform (QFT) grants competitive advantages, especially in resource usage and circuit approximation, for performing arithmetic operations on quantum computers, and offers a potential route towards a numerical quantum-computational paradigm. In this paper, we utilize efficient techniques to implement QFT-based integer addition and multiplications. These operations are fundamental to various quantum applications including Shor’s algorithm, weighted sum optimization problems in data processing and machine learning and quantum algorithms requiring inner products. We carry out performance evaluations of these implementations based on IBM’s superconducting qubit architecture using different compatible noise models. We isolate the sensitivity of the component quantum circuits on both one-/two-qubit gate error rates, and the number of the arithmetic operands’ superposed integer states. We analyze performance, and identify the most effective approximation depths for quantum add and quantum multiply within the given context. We observe significant dependency of the optimal approximation depth on the degree of machine noise and the number of superposed states in certain performance regimes. Finally, we elaborate on the algorithmic challenges - relevant to signed, unsigned, modular and non-modular versions - that could also be applied to current implementations of QFT-based subtraction, division, exponentiation, and their potential tensor extensions. Here, we analyze performance trends in our results and speculate on possible future development within this computational paradigm.

97 MATHEMATICS AND COMPUTING↗

Information Content of JWST NIRSpec Transmission Spectra of Warm Neptunes

Warm Neptunes offer a rich opportunity for understanding exo-atmospheric chemistry. With the upcoming James Webb Space Telescope (JWST), there is a need to elucidate the balance between investments in telescope time versus scientific yield. We use the supervised machine-learning method of the random forest to perform an information content (IC) analysis on a 11-parameter model of transmission spectra from the various NIRSpec modes. The three bluest medium-resolution NIRSpec modes (0.7–1.27 μm, 0.97–1.84 μm, 1.66–3.07 μm) are insensitive to the presence of CO. The reddest medium-resolution mode (2.87–5.10 μm) is sensitive to all of the molecules assumed in our model: CO, CO{sub 2}, CH{sub 4}, C{sub 2}H{sub 2}, H{sub 2}O, HCN, and NH{sub 3}. It competes effectively with the three bluest modes on the information encoded on cloud abundance and particle size. It is also competitive with the low-resolution prism mode (0.6–5.3 μm) on the inference of every parameter except for the temperature and ammonia abundance. We recommend astronomers to use the reddest medium-resolution NIRSpec mode for studying the atmospheric chemistry of 800–1200 K warm Neptunes; its corresponding high-resolution counterpart offers diminishing returns. We compare our findings to previous JWST IC analyses that favor the blue orders and suggest that the reliance on chemical equilibrium could lead to biased outcomes if this assumption does not apply. A simple, pressure-independent diagnostic for identifying chemical disequilibrium is proposed based on measuring the abundances of H{sub 2}O, CO, and CO{sub 2}.

79 ASTRONOMY AND ASTROPHYSICS↗

Performance evaluations of signed and unsigned noisy approximate quantum Fourier arithmetic

The Quantum Fourier Transform (QFT) grants competitive advantages, especially in resource usage and circuit approximation, for performing arithmetic operations on quantum computers, and offers a potential route toward a numerical quantum-computational paradigm. In this paper, we utilize efficient techniques to implement QFT-based integer addition and multiplications. These operations are fundamental to various quantum applications including Shor’s algorithm, weighted-sum optimization problems in data processing and machine learning, and quantum algorithms requiring inner products. We carry out performance evaluations of these implementations based on IBM’s superconducting-qubit architecture using different compatible noise models. We isolate the sensitivity of the component quantum circuits on both one-/two-qubit gate error rates, and the number of the arithmetic operands’ superposed integer states. We analyze performance and identify the most effective approximation depths for unsigned quantum addition and quantum multiplication within the given context. We then perform a similar analysis of signed addition and compare to the unsigned results. We observe significant dependency of the optimal approximation depth on the degree of machine noise and the number of superposed states in certain performance regimes. Finally, we elaborate on the algorithmic challenges—relevant to signed, unsigned, modular and non-modular versions—that could also be applied to current implementations of QFT-based subtraction, division, exponentiation, and their potential tensor extensions. Here, we analyze the performance trends in our results and speculate on possible future developments within this computational paradigm.

Computational models↗

Bayesian Adaptive Polynomial Chaos Expansions

Polynomial chaos expansions (PCEs) are widely used for uncertainty quantification (UQ) tasks, particularly in the applied mathematics community. However, PCE has received comparatively less attention in the statistics literature, and fully Bayesian formulations remain rare—especially with implementations in R. Motivated by the success of adaptive Bayesian machine learning models such as BART, BASS and BPPR, we develop a new fully Bayesian adaptive PCE method with an efficient and accessible R implementation: khaos. Our approach includes a novel proposal distribution that enables data-driven interaction selection and supports a modified g-prior tailored to PCE structure. Through simulation studies and real-world UQ applications, we demonstrate that the Bayesian adaptive PCE provides competitive performance for surrogate modeling, global sensitivity analysis and ordinal regression tasks.

97 MATHEMATICS AND COMPUTING↗

Integrated Research Infrastructure Architecture Blueprint Activity (Final Report 2023)

The complexity of scientific pursuits is increasing rapidly with aspects that require dynamic integration of experiment, observation, theory, modeling, simulation, visualization, machine learning (ML), artificial intelligence (AI), and analysis. Research projects across the Department of Energy (DOE) are increasingly data and compute intensive. Innovative research teams are accelerating the pace of discovery by using high-performance computational and data tools in their research workflows and leveraging multiple research infrastructures. Additionally, several recent high-level U.S. government reports underscore the necessity of a new advanced computing ecosystem for international competitiveness and national security. International competitors are moving forward with major research infrastructure integration efforts that seek to capture a competitive advantage in the global innovation race. Owing to its unparalleled constellation of world-class experimental and observational facilities and high-performance and extreme-scale computational, data, and networking infrastructure, DOE is positioned to be a global leader in this new era of integrated science. However, this new integration paradigm will demand continuing evolution to ensure the U.S. remains a global leader in research and innovation. The DOE Office of Science (SC) has seized on the strategic importance of integration and has adopted a vision for Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation. To respond to the evolving computational requirements of research and the competitive international innovation landscape, experimental facilities could be connected with high performance computing resources for near real-time analysis, and resources should be provided for merging enormous and diverse data for AI/ML techniques and analysis.

97 MATHEMATICS AND COMPUTING↗

Coupling flux balance analysis with reactive transport modeling through machine learning for rapid and stable simulation of microbial metabolic switching

Integrating genome-scale metabolic networks with reactive transport models (RTMs) provides a detailed description of the dynamic changes in microbial growth and metabolism. Despite promising demonstrations in the past, computational inefficiency has been pointed out as a critical issue to overcome because it requires repeated application of linear programming (LP) to obtain flux balance analysis (FBA) solutions in every time step and spatial grid. To address this challenge, we propose a new simulation method where we train and validate artificial neural networks (ANNs) using randomly sampled FBA solutions and incorporate the resulting surrogate FBA model (represented as algebraic equations) into RTMs as source/sink terms. We demonstrate the efficiency of our method via a case study of Shewanella oneidensis MR-1. During aerobic growth on lactate, S. oneidensis produces metabolic byproducts (such as pyruvate and acetate), which are subsequently consumed as alternative carbon sources when the preferred nutrients are depleted. To effectively simulate these complex dynamics, we used a cybernetic approach that models metabolic switches as the outcome of dynamic competition among multiple growth options. In both zero-dimensional batch and one-dimensional column configurations, the ANN-based surrogate models achieved substantial reduction of computational time by several orders of magnitude compared to the original LP-based FBA models. Moreover, the ANN models produced robust solutions without any special measures to prevent numerical instability. These developments significantly promote our ability to utilize genome-scale networks in complex, multi-physics, and multi-dimensional ecosystem modeling.

59 BASIC BIOLOGICAL SCIENCES↗

Protein-ligand binding affinity prediction using multi-instance learning with docking structures

Recent advances in 3D structure-based deep learning approaches demonstrate improved accuracy in predicting protein-ligand binding affinity in drug discovery. These methods complement physics-based computational modeling such as molecular docking for virtual high-throughput screening. Despite recent advances and improved predictive performance, most methods in this category primarily rely on utilizing co-crystal complex structures and experimentally measured binding affinities as both input and output data for model training. Nevertheless, co-crystal complex structures are not readily available and the inaccurate predicted structures from molecular docking can degrade the accuracy of the machine learning methods. We introduce a novel structure-based inference method utilizing multiple molecular docking poses for each complex entity. Our proposed method employs multi-instance learning with an attention network to predict binding affinity from a collection of docking poses. We validate our method using multiple datasets, including PDBbind and compounds targeting the main protease of SARS-CoV-2. The results demonstrate that our method leveraging docking poses is competitive with other state-of-the-art inference models that depend on co-crystal structures. This method offers binding affinity prediction without requiring co-crystal structures, thereby increasing its applicability to protein targets lacking such data.

97 MATHEMATICS AND COMPUTING↗

Uranium Oxide Synthetic Pathway Discernment through Unsupervised Morphological Analysis

We present a novel unsupervised machine learning method for quantitative representation of scanning electron micrographs and its applications and performance for nuclear forensic analysis of uranium ore concentrates. The method uses a vector quantizing variational autoencoder followed by a histogram operation to encode a micrograph into a single dimensional representation, called the latent vector. The method requires no extant labeling of the data and can be applied over large datasets of micrographs with minimal human interaction. The representations generated are broadly descriptive of each micrograph and the microstructure of the material imaged. In the case of uranium ore concentrate analysis, the representations were amenable to processing reagent and ore concentrate species classification with accuracy of 81:8%, which is competitive with state-of-the-art supervised networks. The representations were also used to classify previously unseen processing routes, were able to classify imaging parameters such as magnification (to 76:0% accuracy), were able to classify fine grained process parameters such as calcining temperature (to 74:4% accuracy), and their informatic properties indicate that they are generally descriptive of the image represented. This method can be applied across microstructure analysis fields to perform quantitative analysis without the need for labor intensive and possibly biased human analysis.

Scanning Electron Microscopy, Vector Quantizing Va↗

2019 Budget Request for the DOE Computational Science Graduate Fellowship (CSGF) Grant

The Department of Energy Computational Science Graduate Fellowship (DOE CSGF) is necessary to meet the continual challenging national workforce needs that arise as computational science and engineering problems continue to grow in scope and complexity. Computational science and engineering (CSE) is a multidisciplinary approach that uses scientific computing to solve practical problems methods and to supply technical tools across the scientific discovery spectrum. In particular, the DOE CSGF emphasizes high-performance computing (HPC) that enables CSE that advances science and engineering in directions important to the DOE and the economy in general. Over the past half-century, HPC has been an essential tool for DOE’s success. During this period, important missions, such as nuclear stockpile stewardship, have turned to HPC as an essential technology. Entire science disciplines, such as biology and cosmology, have been transformed through the augmentation of scientific observation via HPC. At government laboratories and in industry, DOE CSGF alumni are helping push traditional HPC boundaries while contributing to discoveries in high-energy physics, renewable energy, fusion-reactor design, additive manufacturing, nanomaterials for next-generation batteries and transistors, and turbine and advanced nuclear reactor modeling. In addition, HPC is used to address national health needs that will eventually point to cures both by helping cancer researchers manage and analyze huge troves of data, by simulating biological mechanisms, and by accelerating drug development — including continuing to rise to the challenge of pandemic-related research. A 2023 report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR office, “Can the United States Maintain Its Leadership in High-Performance Computing?” says of the Program, “The CSGF program provides a barometer for disciplines that will be of interest to future DOE computing.” An explosion in scientific and technological data has driven the need for increasingly sophisticated HPC to transform those data into scientific understanding. With access to more and more data and the proliferation of HPC, Machine Learning and Artificial Intelligence are experiencing a renaissance, complementing the now well-established use of computational simulation. Indeed, in its September 2020 subcommittee report on “AI/ML, Data Intensive Science and High-Performance Computing”, the DOE Advanced Scientific Computing Advisory Committee (ASCAC) explicitly called for a fellowship program to train computational and data scientists to tackle exascale and data-intensive computing challenges. This collaboration of empirical and theory-based modeling will increasingly inform federal policymakers whose decisions affect American society and future generations, and it requires highly skilled and intellectually agile computational scientists who can support the fast-moving DOE National Laboratory research environment. In fact, the DOE CSGF program has explicitly and consistently addressed this need.

97 MATHEMATICS AND COMPUTING↗

Buyers Collusion in Incentivized Forwarding Networks: A Multi-Agent Reinforcement Learning Study

We present the issue of monetarily incentivized forwarding in a multi-hop mesh network architecture from an economic perspective. It is anticipated that credit-incentivized forwarding and relaying will be a simple method of exchanging transmission power and spectrum for connectivity. However, gateways and forwarding nodes, like any other free market, may create an oligopolistic market for the users they serve. In this study, a coalition scheme between buyers aims to address price control by gateways or nodes closer to gateways. In a Stackelberg competition game, buyer agents (users) and sellers (gateways) make decisions using reinforcement learning (RL), with decentralized Deep Q-Networks to buy and sell forwarding resources. We allow communication links between the buyers with a limited messaging space, without defining a collusion mechanism. The idea is to demonstrate that through messaging, and RL tacit collusion can emerge between agents in a decentralized setup. The multi-agent reinforcement learning (MARL) system is presented and analyzed from a machine-learning perspective. Moreover, MARL dynamics are discussed via mean field analysis to better understand divergence causes and make implementation recommendations for such systems. Finally, the simulation results show the results of coordination among the users.

42 ENGINEERING↗