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Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection. Here, we characterized the variation in resistance to ROS across the ancient yeast subphylum Saccharomycotina and used machine learning (ML) to identify gene families whose sizes were predictive of ROS resistance.
A combination of machine learned interatomic potentials (MLIPs) and enhanced sampling simulations is used to investigate the activation of methane on a Ni(111) surface. The work entails the development and iterative refinement of MLIPs, initially trained on a dataset constructed via ab initio molecular dynamics (AIMD) simulations, supplemented by adaptive biasing forces, to enrich the sampling of catalytically relevant configurations. Our results reveal that by incorporating collective variables that capture the behavior of the reactant molecule, as well as additional frames that describe the dynamic response of the catalytic surface, it is possible to enhance considerably the accuracy of predicted energies and forces. By employing enhanced sampling schemes in the refinement of the MLIP, we systematically explore the potential energy surface, leading to a refined MLIP capable of predicting DFT-level energies and forces and replicating key geometric characteristics of the catalytic system. The resulting free energy landscapes at several temperatures provide a detailed view of the thermodynamics and dynamics of methane activation. Specifically, as methane approaches and dissociates on the catalytic surface, the process involves the dynamic interplay of CH 4 and the Ni catalyst that includes both enthalpic and entropic contributions. The progression towards the transition state involves an CH 4 moiety that is increasingly restrained in its ability to rotate or translate, while the stage following the transition state is characterized by a notable rise of the Ni atom that interacts with the cleaved C–H bond. Furthermore, this leads to an increase in the mobility of the adsorbed species, a feature that becomes more pronounced at higher temperatures.
The use of machine learning (ML) to refine low-level theoretical calculations to achieve higher accuracy is a promising and actively evolving approach known as Δ-ML. The density matrix renormalization group (DMRG) is a powerful variational approach widely used for studying strongly correlated quantum systems. High computational efficiency can be achieved without compromising accuracy. Here, we demonstrate the potential of a simple ML model to significantly enhance the performance of the quantum chemical DMRG method.
We use deep machine learning (ML) combined with first-principles calculations to search for energetically favorable ternary magnetic zirconium–iron borides. We show that an iterative ML approach enables efficient screening of vast structural libraries, effectively selecting promising candidates for subsequent first-principles investigations. Twenty-two new Fe-rich ternary compounds with formation energies within 60 meV atom −1 above the known ternary convex hull and with magnetic polarization larger than 0.6 T are identified, among which ten structures exhibit significant uniaxial anisotropy with magnetocrystalline anisotropy constant K 1 ⩾ 0.8 MJ m −3 , including a Zr 2 Fe 14 B phase. Such an ML-guided approach dramatically accelerates the discovery of rare-earth-free permanent magnetic materials.
Machine learning (ML) models were developed to predict process various conditions and compositions by creating a model from a database with approximately 1000 entries and 24 independent variables.
Quantifying uncertainties for machine learning (ML) models is a foundational challenge in modern data analysis. This challenge is compounded by at least two key aspects of the field: (a) inconsistent terminology surrounding uncertainty and estimation across disciplines, and (b) the varying technical requirements for establishing trustworthy uncertainties in diverse problem contexts. In this position paper, we aim to clarify the depth of these challenges by identifying these inconsistencies and articulating how different contexts impose distinct epistemic demands. We examine the current landscape of estimation targets (e.g., prediction, inference, simulation-based inference), uncertainty constructs (e.g., frequentist, Bayesian, fiducial), and the approaches used to map between them. Drawing on the literature, we highlight and explain examples of problematic mappings. To help address these issues, we advocate for standards that promote alignment between the \textit{intent} and \textit{implementation} of uncertainty quantification (UQ) approaches. We discuss several axes of trustworthiness that are necessary (if not sufficient) for reliable UQ in ML models, and show how these axes can inform the design and evaluation of uncertainty-aware ML systems. Our practical recommendations focus on scientific ML, offering illustrative cases and use scenarios, particularly in the context of simulation-based inference (SBI).
- Machine Learning (ML) has enabled models that can improve efficiency and decrease computational cost - ML models are crucial in enabling Integrated Computational Materials Engineering (ICME) - Large data sets require robust means of storing ML data and models
Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have used strings, fingerprints, global features and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a new approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects, enhancing expressivity and interpretability. Learning to predict the stereoelectronics-infused representation with a tailored double graph neural network workflow enables its application to any downstream molecular machine learning task without expensive quantum-chemical calculations. We show that the explicit addition of stereoelectronic information substantially improves the performance of message-passing two-dimensional machine learning models for molecular property prediction. We show that the learned representations trained on small molecules can accurately extrapolate to much larger molecular structures, yielding chemical insight into orbital interactions for previously intractable systems, such as entire proteins, opening new avenues of molecular design. Finally, we have developed a web application (simg.cheme.cmu.edu) where users can rapidly explore stereoelectronic information for their own molecular systems.
This research paper explores the use of machine learning to relate images of flame structure and luminosity to measured NOx emissions. Images of reactions produced by 16 aero-engine derived injectors for a ground-based turbine operated on a range of fuel compositions, air pressure drops, preheat temperatures and adiabatic flame temperatures were captured and postprocessed. The experimental investigations were conducted under atmospheric conditions, capturing CO, NO and NOx emissions data and OH* chemiluminescence images from 27 test conditions. The injector geometry and test conditions were based on a statistically designed test plan. These results were first analyzed using the traditional analysis approach of analysis of variance (ANOVA). The statistically based test plan yielded 432 data points, leading to a correlation for NOx emissions as a function of injector geometry, test conditions and imaging responses, with 70.2% accuracy. As an alternative approach to predicting emissions using imaging diagnostics as well as injector geometry and test conditions, a random forest machine learning algorithm was also applied to the data and was able to achieve an accuracy of 82.6%. This study offers insights into the factors influencing emissions in ground-based turbines while emphasizing the potential of machine learning algorithms in constructing predictive models for complex systems.
Recent theoretical results in quantum machine learning have demonstrated a general trade-off between the expressive power of quantum neural networks (QNNs) and their trainability; as a corollary of these results, practical exponential separations in expressive power over classical machine learning models are believed to be infeasible as such QNNs take a time to train that is exponential in the model size. We here circumvent these negative results by constructing a hierarchy of efficiently trainable QNNs that exhibit unconditionally provable, polynomial memory separations of arbitrary constant degree over classical neural networks—including state-of-the-art models, such as Transformers—in performing a classical sequence modeling task. This construction is also computationally efficient, as each unit cell of the introduced class of QNNs only has constant gate complexity. We show that contextuality—informally, a quantitative notion of semantic ambiguity—is the source of the expressivity separation, suggesting that other learning tasks with this property may be a natural setting for the use of quantum learning algorithms.
The Multiscale Machine-Learned Modeling Infrastructure (MuMMI) is a multiscale workflow management infrastructure that can concurrently orchestrate thousands of molecular dynamics (MD) simulations operating at different time and/or length scales, spanning nanoseconds to seconds and nanometers to micrometers. MuMMI uses machine learning (backed by biology experiments) to guide a massive ensemble of MD simulations that capture biologically relevant time and length scales with unprecedented resolution. MuMMI supports multiple MD codes such as GROMACS and ddcMD and can be fully deployed using the HPC package manager Spack. MuMMI has been used in many publications to run hundreds of thousands simulations, leading to significant biology breakthroughs.
Five paradigms are described for machine learning: connectionist (neural network) methods, genetic algorithms and classifier systems, empirical methods for inducing rules and decision trees, analytic learning methods, and case-based approaches. Some dimensions are considered along with these paradigms vary in their approach to learning, and the basic methods are reviewed that are used within each framework, together with open research issues. It is argued that the similarities among the paradigms are more important than their differences, and that future work should attempt to bridge the existing boundaries. Finally, some recent developments in the field of machine learning are discussed, and their impact on both research and applications is examined.
The OVERFLOW Machine Learning Airfoil Performance (PALMO) database has been created to enable robust modeling of airfoil performance in a variety of applications. The database uses OVERFLOW simulation data second-order accurate in time and fourth-order accurate in space with Spalart-Allmaras turbulence closure. The foundation of the in-development PALMO database is the airfoil base cube. Each base cube includes simulation data parametrized over a range of Mach numbers, Reynolds numbers, and angles-of-attack. This first release of the database includes the NACA 4-series airfoils, with parametrization in airfoil thickness and camber from an NACA 0006 to an NACA 4424. In total, 52,480 NACA 4-series calculations were run on the NASA High-End Compute Capability (HECC) supercomputer and the corresponding airfoil performance coefficients are embedded in the Appendix of this document for public distribution. This provides high-order-accurate simulation data covering a wide range of aerospace design applications, which enables users to develop OVERFLOW-quality airfoil performance look-up tables without additional high-performance computing. In addition to engineering design and analysis of aerospace vehicles, PALMO is well suited to be a benchmark dataset for the development and testing of machine learning methods in aerospace engineering. Downstream surrogate models enable OVERFLOW- quality airfoil performance predictions for any arbitrary combination of camber, thickness, Mach number, Reynolds number, and angle-of-attack within the bounds of the database.
To enable autonomy in space, machine-learning and computer vision applications become invaluable for sensor processing. However, these algorithms are computationally complex and unfeasible for many embedded central processing units (CPUs) and usually require external coprocessors, such as graphics processing units (GPUs) or accelerators specific to the application, including application specific integrated circuits (ASICs). In power-constrained systems, GPUs tend to consume more power than is acceptable (>40W), so lower-power accelerators have shown promise to provide the performance needed under spacecraft constraints. For radiation engineers, developing methodologies that can properly test CPUs, GPUs, and accelerators, and enable comparisons between them remains a necessary complication to solve as the devices become more complex. The methodology in this test aims to be a start in developing a baseline single-event effect (SEE) test for client-device machine learning accelerators. This category of devices do not host their own operating system. This testing campaign is a continuation of a previous 200 MeV proton test performed in January 2024. This report covers two heavy ion tests of the SAKURA-I card: one in April 2024, and one in June 2024. Additional data was needed after the April test due to ion-range issues experienced at higher linear-energy transfers (LETs). These range issues are described in more detail in Section 8. This experiment characterizes SEEs and data error susceptibility of the EdgeCortix SAKURA-I machine-learning accelerator under heavy ions. The device was monitored for single event upsets (SEUs) and single event functional interrupts (SEFIs) at the Lawrence Berkeley National Laboratory’s 88-inch cyclotron. The SAKURA-I board accelerates machine-learning inference applications on a host computer through a PCIex16 connection. For the purposes of devising an end to end automated analysis workflow for this experiment, the YOLO-V5 and SSD300 objection-detection models, and the ResNet-50, EfficientNet, and MobileNetV2 image classification models were used as a representative suite of analytical machine-learning models.
We demonstrate transfer learning capabilities in a machine-learned algorithm trained for particle-flow reconstruction in high energy particle colliders. This paper presents a cross-detector fine-tuning study, where we initially pretrain the model on a large full simulation dataset from one detector design, and subsequently fine-tune the model on a sample with a different collider and detector design. Specifically, we use the Compact Linear Collider detector (CLICdet) model for the initial training set and demonstrate successful knowledge transfer to the CLIC-like detector (CLD) proposed for the Future Circular Collider in electron-positron mode. We show that with an order of magnitude less samples from the second dataset, we can achieve the same performance as a costly training from scratch, across particle-level and event-level performance metrics, including jet and missing transverse momentum resolution. Furthermore, we find that the fine-tuned model achieves comparable performance to the traditional rule-based particle-flow approach on event-level metrics after training on 100,000 CLD events, whereas a model trained from scratch requires at least 1 million CLD events to achieve similar reconstruction performance. To our knowledge, this represents the first full-simulation cross-detector transfer learning study for particle-flow reconstruction. These findings offer valuable insights towards building large foundation models that can be fine-tuned across different detector designs and geometries, helping to accelerate the development cycle for new detectors and opening the door to rapid detector design and optimization using machine learning.
ABSTRACT In this study, we consider three different machine‐learning methods—a three‐hidden‐layer neural network, support vector regression, and Gaussian process regression—and compare how well they can learn from a synthetic data set for proton acceleration in the Target Normal Sheath Acceleration regime. The synthetic data set was generated from a previously published theoretical model by Fuchs et al. 2005 that we modified. Once trained, these machine‐learning methods can assist with efforts to maximize the peak proton energy, or with the more general problem of configuring the laser system to produce a proton energy spectrum with desired characteristics. In our study, we focus on both the accuracy of the machine‐learning methods and the performance on one GPU including memory consumption. Although it is arguably the least sophisticated machine‐learning model we considered, support vector regression performed very well in our tests.
Machine learning techniques have emerged as a useful tool for identifying complex patterns and correlations in large datasets, such as associating catalyst performance to its physicochemical properties. In the heterogeneous catalysis communities, machine learning models have mostly been developed using high-throughput quantum chemistry calculations, with only a few case studies resulting in experimentally validated catalyst improvements. This limited success may be due to the use of simplified catalyst structures in computational studies and the lack of comprehensive experimental datasets. In this Review, we bring together studies integrating high-throughput approaches and machine learning for the advancement of solid heterogeneous catalysis, leveraging both experimental and computational data. We systematically analyze trends in the field, based on the descriptors used as model input and output; the materials, devices, or reactions investigated; the dataset size; and the overall achievements. Furthermore, for models reporting unitless R 2 values, we compare the performances based on these mentioned trends.
Scientific machine learning (SciML) has emerged as a versatile approach to address complex computational science and engineering problems. Within this field, physics-informed neural networks (PINNs) and deep operator networks (DeepONets) stand out as the leading techniques for solving partial differential equations by incorporating both physical equations and experimental data. However, training PINNs and DeepONets require significant computational resources, including long computational times and large amounts of memory. In search of computational efficiency, training neural networks using half precision (float16) rather than the conventional single (float32) or double (float64) precision has gained substantial interest, given the inherent benefits of reduced computational time and memory consumed. However, we find that float16 cannot be applied to SciML methods, because of gradient divergence at the start of training, weight updates going to zero, and the inability to converge to a local minima. To overcome these limitations, we explore mixed precision, which is an approach that combines the float16 and float32 numerical formats to reduce memory usage and increase computational speed. Our experiments showcase that mixed precision training not only substantially decreases training times and memory demands but also maintains model accuracy. Here, we also reinforce our empirical observations with a theoretical analysis. The research has broad implications for SciML in various computational applications.