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At least 469 records · Page 26

Machine learning for reparameterization of multi-scale closures

Scientific machine learning (ML) is becoming increasingly useful in learning closure models for multi-scale physics problems; however, many ML approaches require a vast array of training data and can struggle with generalization and interpretability. Here, rather than learning an entire closure operator, we adopt an existing reduced-dimension model of the microphysics and learn an optimal re-parameterization of the solver. We demonstrate two approaches for training the reduced dimension closure model (1) an a priori method that optimizes the closure parameterization and the neural network parameters separately and (2) an a posteriori method that simultaneously optimizes both. Using the simulation of biomass pyrolysis as a motivating example, we show that the a posteriori method achieves better target losses and is less dependent on training dataset size for generalizability. We then demonstrate the impact that implementing this reparameterization has at the macroscale, showing improved predictive performance with no modification to the underlying macroscale solvers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

CCUS 2024, Interpreting the strain tensor Larry Murdoch Interpreting strain tensor data to characterize and monitor reservoirs for CO2 storage and other applications

Recent advances in instrumentation have made it feasible to measure the transient strain tensor caused by small changes in fluid volume or pressure in the subsurface and this has opened the door to new opportunities for characterization and monitoring during CCUS. We have demonstrated this method by deploying strainmeters at shallow depths (30 to 40m) and then conducting injection well tests in an underlying reservoir at 530m depth. The resulting data indicated that the horizontal strain at shallow strainmeters was tensile and the vertical strain was compressive. The radial strain was less than the horizontal strain, and the strain rates decreased from 100 nanostrain/day to roughly 10 ne/d over a few days (1 nanostrain = 1 part per billion strain). We then used the strain data to estimate reservoir properties, geometry and pressure through inversion of poroelastic forward models using both numerical and novel analytical methods. The average horizontal strain in the caprock resembles the transient pressure in the underlying reservoir and classic type-curve methods from transient well testing can be used for preliminary interpretations of strain data. We have developed fast, closed-form analytical solutions to a pressurized poroelastic inclusion and inhomogeneity in a half-space. Numerical models developed using finite element methods allow more details of the subsurface to be included in the inversion, but they require much longer run times and this makes inversion cumbersome using standard methods. We have developed an inversion approach that uses a proxy model created using machine learning to do most of the forward calculations. This approach markedly reduces the computational requirements and makes it feasible to use Bayesian inversion with large numerical models. Bayesian inversion is important because it provides predictions with uncertainties, which makes the results useful for decision making. We have shown with field tests and simulations that the strain tensor in the caprock is sensitive to pressure in the reservoir, reservoir properties and boundaries, and pressure in the caprock caused by leaks. These results indicate that measuring and interpreting the shallow strain tensor could be a valuable tool for both initial reservoir characterization efforts and long-term monitoring during CCUS. Recent advances in instrumentation have made it feasible to measure the transient strain tensor caused by small changes in fluid volume or pressure in the subsurface and our objective was to evaluate opportunities for strain monitoring during characterization and monitoring for CCUS. Our approach was to deploy strainmeters at shallow depths (30 to 40m) and then conduct injection well tests in an underlying reservoir at 530m depth. The results indicate that the horizontal strain at shallow strainmeters was tensile and the vertical strain was compressive. The radial strain was less than the horizontal strain, and the strain rates decreased from 100 nanostrain/day to roughly 10 ne/d over a few days (1 nanostrain = 1 part per billion strain). We then used the strain data to estimate reservoir properties, geometry and pressure through inversion of poroelastic forward models using both numerical and novel analytical methods. The average horizontal strain in the caprock resembles the transient pressure in the underlying reservoir and classic type-curve methods from transient well testing can be used for preliminary interpretations of strain data. We have developed fast, closed-form analytical solutions to a pressurized poroelastic inclusion and inhomogeneity in a half-space. Numerical models developed using finite element methods allow more details of the subsurface to be included in the inversion, but they require much longer run times and this makes inversion cumbersome using standard methods. We have developed an inversion approach that uses a proxy model created using machine learning to do most of the forward calculations. This approach markedly reduces the computational requirements and makes it feasible to use Bayesian inversion with large numerical models. Bayesian inversion is important because it provides predictions with uncertainties, which makes the results useful for decision making. In conclusion, we have shown with field tests and simulations that the strain tensor in the caprock is sensitive to pressure in the reservoir, reservoir properties and boundaries, and pressure in the caprock caused by leaks. These results indicate that measuring and interpreting the shallow strain tensor could be a valuable tool for both initial reservoir characterization efforts and long-term monitoring during CCUS.

Murdoch, Larry↗

Machine-learning-assisted insight into spin ice Dy 2 Ti 2 O 7

Complex behavior poses challenges in extracting models from experiment. An example is spin liquid formation in frustrated magnets like Dy 2 Ti 2 O 7 . Understanding has been hindered by issues including disorder, glass formation, and interpretation of scattering data. Here, we use an automated capability to extract model Hamiltonians from data, and to identify different magnetic regimes. This involves training an autoencoder to learn a compressed representation of three-dimensional diffuse scattering, over a wide range of spin Hamiltonians. The autoencoder finds optimal matches according to scattering and heat capacity data and provides confidence intervals. Validation tests indicate that our optimal Hamiltonian accurately predicts temperature and field dependence of both magnetic structure and magnetization, as well as glass formation and irreversibility in Dy 2 Ti 2 O 7 . The autoencoder can also categorize different magnetic behaviors and eliminate background noise and artifacts in raw data. Our methodology is readily applicable to other materials and types of scattering problems.

36 MATERIALS SCIENCE↗

Role of physics in physics-informed machine learning

Physical systems are characterized by inherent symmetries, one of which is encapsulated in the units of their parameters and system states. These symmetries enable a lossless order-reduction, e.g., via dimensional analysis based on the Buckingham theorem. Despite the latter's benefits, machine learning (ML) strategies for the discovery of constitutive laws seldom subject experimental and/or numerical data to dimensional analysis. We demonstrate the potential of dimensional analysis to significantly enhance the interpretability and generalizability of ML-discovered secondary laws. Our numerical experiments with creeping fluid flow past solid ellipsoids show how dimensional analysis enable both deep neural networks and sparse regression reproduce old results, e.g., Stokes law for a sphere, and generate new ones, e.g., an expression for an ellipsoid misaligned with the flow direction. Furthermore, our results suggest the need to incorporate other physics-based symmetries and invariances into ML-based techniques for equation discovery.

97 MATHEMATICS AND COMPUTING↗

A materials-informatics based study of solid electrolytes and protective coatings for Li batteries

All-solid-state batteries with Li metal anode can address the safety issues surrounding traditional Li-ion batteries as well as the demand for higher energy densities. However, the development of solid electrolytes and protective coatings simultaneously possessing high ionic conductivity and wide electrochemical stability has proven to be a challenge. Here, we present a data-driven approach to explore the Li compound space for promising solid electrolytes and coatings. This is accomplished through the generation of a large database of battery-related materials properties of Li compounds by computing Li+ migration barriers using bond-valence-based pair potentials, and stability windows using density functional theory energies. Using this database, we implement machine learning models that can accurately predict migration barriers and electrochemical stability windows for any new Li compound. Through feature engineering, we ensure that our models are both accurate and interpretable. We perform feature importance analysis on our models to highlight materials properties that can be tuned for future design of coatings/electrolytes. Our database and informatics approach provide a valuable tool for the rapid discovery of new solid-state battery chemistries.

Solid state batteries↗

RX-ADS: Interpretable Anomaly Detection Using Adversarial ML for Electric Vehicle CAN Data

Recent year has brought considerable advancements in Electric Vehicles (EVs) and associated infrastructures/ communications. Intrusion Detection Systems (IDS) are widely deployed for anomaly detection in such critical infrastructures. This paper presents an Interpretable Anomaly Detection System (RX-ADS) for intrusion detection in CAN protocol communication in EVs. Contributions include: 1) window based feature extraction method; 2) deep Autoencoder based anomaly detection method; and 3) adversarial machine learning based explanation generation methodology. The presented approach was tested on two benchmark CAN datasets: OTIDS and Car Hacking. The anomaly detection performance of RX-ADS was compared against the state-of-the-art approaches on these datasets: HIDS and GIDS. The RX-ADS approach presented performance comparable to the HIDS approach (OTIDS dataset) and has outperformed HIDS and GIDS approaches (Car Hacking dataset). Further, the proposed approach was able to generate explanations for detected abnormal behaviors arising from various intrusions. Furthermore, these explanations were later validated by information used by domain experts to detect anomalies. Other advantages of RX-ADS include: 1) the method can be trained on unlabeled data; 2) explanations help experts in understanding anomalies and root course analysis, and also help with AI model debugging and diagnostics, ultimately improving user trust in AI systems.

42 ENGINEERING↗

Importance of Engineered and Learned Molecular Representations in Predicting Organic Reactivity, Selectivity, and Chemical Properties

Machine-readable chemical structure representations are foundational in all attempts to harness machine learning for the prediction of reactivities, selectivities, and chemical properties directly from molecular structure. The featurization of discrete chemical structures into a continuous vector space is a critical phase undertaken before model selection, and the development of new ways to quantitatively encode molecules is an active area of research. Here, we highlight the application and suitability of different representations, from expert-guided “engineered” descriptors to automatically “learned” features, in different prediction tasks relevant to organic and organometallic chemistry, where differing amounts of training data are available. These tasks include statistical models of stereo- and enantioselectivity, thermochemistry, and kinetics developed using experimental and quantum chemical data. The use of expert-guided molecular descriptors provides an opportunity to incorporate chemical knowledge, domain expertise, and physical constraints into statistical modeling. In applications to stereoselective organic and organometallic catalysis, where data sets may be relatively small and 3D-geometries and conformations play an important role, mechanistically informed features can be used successfully to obtain predictive statistical models that are also chemically interpretable. We provide an overview of several recent applications of this approach to obtain quantitative models for reactivity and selectivity, where topological descriptors, quantum mechanical calculations of electronic and steric properties, along with conformational ensembles, all feature as essential ingredients of the molecular representations used. Alternatively, more flexible, general-purpose molecular representations such as attributed molecular graphs can be used with machine learning approaches to learn the complex relationship between a structure and prediction target. This approach has the potential to out-perform more traditional representation methods such as “hand-crafted” molecular descriptors, particularly as data set sizes grow. One area where this is particularly relevant is in the use of large sets of quantum mechanical data to train quantitative structure–property relationships. A general approach toward curating useful data sets and training highly accurate graph neural network models is discussed in the context of organic bond dissociation enthalpies, where this strategy outperforms regression using precomputed descriptors. Finally, we describe how graph neural network predictions can be incorporated into mechanistically informed statistical models of chemical reactivity and selectivity. Once trained, this approach avoids the expensive computational overhead associated with quantum mechanical calculations, while maintaining chemical interpretability. We illustrate examples for which fast predictions of bond dissociation enthalpy and of the identities of radicals formed through cleavage of a molecule’s weakest bond are used in simple physical models of site-selectivity and reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ensuring thermodynamic consistency with invertible coarse-graining

Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insights by isolating the essential degrees of freedom that dictate the thermodynamic properties of a complex, condensed-phase system. The reduced complexity of the model typically leads to lower computational costs and more efficient sampling compared with atomistic models. Designing “good” coarse-grained models is an art. Generally, the mapping from fine-grained configurations to coarse-grained configurations itself is not optimized in any way; instead, the energy function associated with the mapped configurations is. In this work, we explore the consequences of optimizing the coarse-grained representation alongside its potential energy function. We use a graph machine learning framework to embed atomic configurations into a low-dimensional space to produce efficient representations of the original molecular system. Because the representation we obtain is no longer directly interpretable as a real-space representation of the atomic coordinates, we also introduce an inversion process and an associated thermodynamic consistency relation that allows us to rigorously sample fine-grained configurations conditioned on the coarse-grained sampling. We illustrate that this technique is robust, recovering the first two moments of the distribution of several observables in proteins such as chignolin and alanine dipeptide.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Small Molecule Evaluator

Using machine learning to score potential drug candidates may offer an advantage over traditional imprecise scoring functions because the parameters and model structure can be learned from the data. However, models may lack interpretability, are often overfit to the data, and are not generalizable to drug targets and chemotypes not in the training data. Benchmark datasets are prone to artificial enrichment and analogue bias due to the overrepresentation of certain scaffolds in experimentally determined active sets. Datasets can be evaluated using spatial statistics to quantify the dataset topology and better understand potential biases. Dataset clumping comprises a combination of self-similarity of actives and separation from decoys in chemical space and is associated with overoptimistic virtual screening results. This code explores methods of quantifying potential biases and examines some common benchmark datasets.

Ellingson, Sally↗

Budget Constrained Machine Learning for Early Prediction of Adverse Outcomes for COVID-19 Patients

Background: Machine learning (ML) based risk stratification models of Electronic Health records (EHR) data may help to optimize treatment of COVID-19 patients, but are often limited by their lack of clinical interpretability and cost of laboratory tests. We develop a ML based tool for predicting adverse outcomes based on EHR data to optimize clinical utility under a given cost structure. This cohort study was performed using deidentified EHR data from COVID-19 patients from ProMedica Healthcare in northwest Ohio and southeastern Michigan. Methods: We tested performance of various ML approaches for predicting either increasing ventilatory support or mortality and the set of model features under a budget constraint was optimized via exhaustive search across all combinations of features. Results: The optimal sets of features for predicting ventilation under any budget constraint included demographics and comorbidities (DCM), basic metabolic panel (BMP), D-dimer, lactate dehydrogenase (LDH), erythrocyte sedimentation rate (ESR), CRP, brain natriuretic peptide (BNP), and procalcitonin and for mortality included DCM, BMP, complete blood count, D-dimer, LDH, CRP, BNP, procalcitonin and ferritin. Conclusions: This study presents a quick, accurate and cost-effective method to evaluate risk of deterioration for patients with SARS-CoV-2 infection at the time of clinical evaluation.

Cadena Pico, JoseE.↗

Decoding substrate specificity determining factors in glycosyltransferase-B enzymes – insights from machine learning models

Substrate specificity is an essential characteristic of any enzyme's function and an understanding of the factors that determine this specificity is crucial for enzyme engineering. Unlike the structure of an enzyme which is directly impacted by its sequence, substrate specificity as an enzyme attribute involves a rather indirect relationship with sequence as it also depends on structural aspects that dictate substrate accessibility and active site dynamics. In this study, we explore the performance of classifier-based machine learning models trained on curated sequence and structural data for a class of glycosyltransferases (GTs), namely GT-Bs, to understand their substrate specificity determining factors. GTs enable the transfer of sugar moieties to other biomolecules such as oligosaccharides or proteins and are found in all kingdoms of life. In plants, GTs participate in the biosynthesis of plant cell wall biopolymers (e.g.: hemicelluloses and pectins) and are an integral part of the enzymatic machinery that enables the storage of carbon and energy as plant biomass. To elucidate the substrate specificity of uncharacterized GT-Bs, we constructed multi-label machine learning models (Support Vector Classifier, K-Nearest Neighbors, Gaussian Naïve-Bayes, Random Forest) that incorporate both sequence and structural features. These models achieve good predictive accuracies on test datasets. However, despite our use of structural information, we highlight that there is further scope for improvement in training these models to draw interpretable relationships between sequence, structure and substrate specificity determining motifs in GT-Bs.

97 MATHEMATICS AND COMPUTING↗

Characterizing Drought Behavior in the Colorado River Basin Using Unsupervised Machine Learning

Drought is a pressing issue for the Colorado River Basin (CRB) due to the social and economic value of water resources in the region and the significant uncertainty of future drought under climate change. Here, we use climate simulations from various Earth System Models (ESMs) to force the Variable Infiltration Capacity hydrologic model and project multiple drought indicators for the sub-watersheds within the CRB. We apply an unsupervised machine learning (ML) based on Non-Negative Matrix Factorization using K-means clustering (NMFk) to synthesize the simulated historical, future, and change in drought indicators. The unsupervised ML approach can identify sub-watersheds where key changes to drought indicator behavior occur, including shifts in snowpack, snowmelt timing, precipitation, and evapotranspiration. While changes in future precipitation vary across ESMs, the results indicate that the Upper CRB will experience increasing evaporative demand and surface-water scarcity, with some locations experiencing a shift from a radiation-limited to a water-limited evaporation regime in the summer. Large shifts in peak runoff are observed in snowmelt-dominant sub-watersheds, with complete disappearance of the snowmelt signal for some sub-watersheds. The work demonstrates the utility of the NMFk algorithm to efficiently identify behavioral changes of drought indicators across space and time and to quickly analyze and interpret hydro climate model results.

54 ENVIRONMENTAL SCIENCES↗

When less is more: How increasing the complexity of machine learning strategies for geothermal energy assessments may not lead toward better estimates

Previous moderate- and high-temperature geothermal resource assessments of the western United States utilized data-driven methods and expert decisions to estimate resource favorability. Although expert decisions can add confidence to the modeling process by ensuring reasonable models are employed, expert decisions also introduce human and, thereby, model bias. This bias can present a source of error that reduces the predictive performance of the models and confidence in the resulting resource estimates. Our study aims to develop robust data-driven methods with the goals of reducing bias and improving predictive ability. We present and compare nine favorability maps for geothermal resources in the western United States using data from the U.S. Geological Survey's 2008 geothermal resource assessment. Two favorability maps are created using the expert decision-dependent methods from the 2008 assessment (i.e., weight-of-evidence and logistic regression). With the same data, we then create six different favorability maps using logistic regression (without underlying expert decisions), XGBoost, and support-vector machines paired with two training strategies. The training strategies are customized to address the inherent challenges of applying machine learning to the geothermal training data, which have no negative examples and severe class imbalance. We also create another favorability map using an artificial neural network. We demonstrate that modern machine learning approaches can improve upon systems built with expert decisions. We also find that XGBoost, a non-linear algorithm, produces greater agreement with the 2008 results than linear logistic regression without expert decisions, because the expert decisions in the 2008 assessment rendered the otherwise linear approaches non-linear despite the fact that the 2008 assessment used only linear methods. The F1 scores for all approaches appear low (F1 score < 0.10), do not improve with increasing model complexity, and, therefore, indicate the fundamental limitations of the input features (i.e., training data). Until improved feature data are incorporated into the assessment process, simple non-linear algorithms (e.g., XGBoost) perform equally well or better than more complex methods (e.g., artificial neural networks) and remain easier to interpret.

15 GEOTHERMAL ENERGY↗

Latent-space time evolution of non-intrusive reduced-order models using Gaussian process emulation

Non-intrusive reduced-order models (ROMs) have recently generated considerable interest for constructing computationally efficient counterparts of nonlinear dynamical systems emerging from various domain sciences. They provide a low-dimensional emulation framework for systems that may be intrinsically high-dimensional. This is accomplished by utilizing a construction algorithm that is purely data-driven. It is no surprise, therefore, that the algorithmic advances of machine learning have led to non-intrusive ROMs with greater accuracy and computational gains. However, in bypassing the utilization of an equation-based evolution, it is often seen that the interpretability of the ROM framework suffers. This becomes more problematic when black-box deep learning methods are used which are notorious for lacking robustness outside the physical regime of the observed data. In this article, we propose the use of a novel latent-space interpolation algorithm based on Gaussian process regression. Notably, this reduced-order evolution of the system is parameterized by control parameters to allow for interpolation in space. The use of this procedure also allows for a continuous interpretation of time which allows for temporal interpolation. The latter aspect provides information, with quantified uncertainty, about full-state evolution at a finer resolution than that utilized for training the ROMs. This research assesses the viability of this algorithm for an advection-dominated system given by the inviscid shallow water equations.

97 MATHEMATICS AND COMPUTING↗

Subnanometer Substructures in Nanoassemblies Formed from Clusters under a Reactive Atmosphere Revealed Using Machine Learning

Size-selected clusters, soft-landed on an oxide substrate, is a promising and highly tunable material for heterogeneous catalysis. Agglomeration of the deposited clusters, however, leads to changes in the particle properties and structure. The latter for such cluster assemblies can also be different from that in self standing nanoparticles of similar sizes. To monitor the formation of such complex materials, in situ studies at different length scales are required. Toward that goal, we combined small-angle X-ray scattering (SAXS), X-ray absorption near-edge structure (XANES) spectroscopy, ab initio simulations, and machine learning (artificial neural network) techniques. We detected significant differences between the sizes of particle agglomerates, as probed by SAXS, and the sizes of locally ordered regions, as seen by XANES. We interpret these differences as an evidence for the fractal, grape-cluster-like structure of the agglomerates; thus, XANES and SAXS provide highly complementary structural information. This finding can have a profound effect on our understanding of particle sintering and assembly processes and of structure properties relationship in ultradispersed metal catalysts in reaction conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Accelerating the design of lattice structures using machine learning

Lattices remain an attractive class of structures due to their design versatility; however, rapidly designing lattice structures with tailored or optimal mechanical properties remains a significant challenge. With each added design variable, the design space quickly becomes intractable. To address this challenge, research efforts have sought to combine computational approaches with machine learning (ML)-based approaches to reduce the computational cost of the design process and accelerate mechanical design. While these efforts have made substantial progress, significant challenges remain in (1) building and interpreting the ML-based surrogate models and (2) iteratively and efficiently curating training datasets for optimization tasks. Here, we address the first challenge by combining ML-based surrogate modeling and Shapley additive explanation (SHAP) analysis to interpret the impact of each design variable. We find that our ML-based surrogate models achieve excellent prediction capabilities (R 2 > 0.95) and SHAP values aid in uncovering design variables influencing performance. We address the second challenge by utilizing active learning-based methods, such as Bayesian optimization, to explore the design space and report a 5 × reduction in simulations relative to grid-based search. Collectively, these results underscore the value of building intelligent design systems that leverage ML-based methods for uncovering key design variables and accelerating design.

36 MATERIALS SCIENCE↗

Continental-Scale Controls on Hyporheic Respiration Revealed by Knowledge-Guided Machine Learning

Hyporheic zone sediments regulate organic matter turnover and in-stream respiration, yet controls on sediment respiration remain poorly constrained across heterogeneous river networks, limiting prediction of stream metabolism and carbon processing at continental scales. Here, we integrate observations from ~90 river corridors across the United States in the WHONDRS consortium with a knowledge-guided machine learning (KGML) framework that couples thermodynamic rate theory with machine learning to identify dominant controls on hyporheic respiration. Diagnostic analyses show that organic matter concentration and thermodynamic favorability define an upper bound on respiration potential, whereas biological catalytic capacity and physical accessibility jointly govern realized respiration rates through interaction effects. To represent unmeasurable accessibility constraints, we use the mechanistic model as a scaffold for KGML, allowing machine learning to target residual structure not explained by process theory. This hybrid framework improves predictive skill relative to both the mechanistic model alone and fully data-driven models while preserving interpretability. These results indicate that variability in hyporheic respiration is largely mechanistically structured and demonstrate how integrating process theory with explainable AI enhances predictive performance while enabling scalable synthesis of river corridor observations.

Zheng, Jianqiu↗

Generalizable, fast, and accurate DeepQSPR with fastprop

Abstract Quantitative Structure–Property Relationship studies (QSPR), often referred to interchangeably as QSAR, seek to establish a mapping between molecular structure and an arbitrary target property. Historically this was done on a target-by-target basis with new descriptors being devised to specifically map to a given target. Today software packages exist that calculate thousands of these descriptors, enabling general modeling typically with classical and machine learning methods. Also present today are learned representation methods in which deep learning models generate a target-specific representation during training. The former requires less training data and offers improved speed and interpretability while the latter offers excellent generality, while the intersection of the two remains under-explored. This paper introduces , a software package and general Deep-QSPR framework that combines a cogent set of molecular descriptors with deep learning to achieve state-of-the-art performance on datasets ranging from tens to tens of thousands of molecules. provides both a user-friendly Command Line Interface and highly interoperable set of Python modules for the training and deployment of feedforward neural networks for property prediction. This approach yields improvements in speed and interpretability over existing methods while statistically equaling or exceeding their performance across most of the tested benchmarks. is designed with Research Software Engineering best practices and is free and open source, hosted at github.com/jacksonburns/fastprop.

Burns, Jackson W. (ORCID:0000000206579426)↗