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At least 199 records · Page 11

Leveraging interpolation models and error bounds for verifiable scientific machine learning

Effective verification and validation techniques for modern scientific machine learning workflows are challenging to devise. Statistical methods are abundant and easily deployed, but often rely on speculative assumptions about the data and methods involved. Error bounds for classical interpolation techniques can provide mathematically rigorous estimates of accuracy, but often are difficult or impractical to determine computationally. Here, in this work, we present a best-of-both-worlds approach to verifiable scientific machine learning by demonstrating that (1) multiple standard interpolation techniques have informative error bounds that can be computed or estimated efficiently; (2) comparative performance among distinct interpolants can aid in validation goals; (3) deploying interpolation methods on latent spaces generated by deep learning techniques enables some interpretability for black-box models. We present a detailed case study of our approach for predicting lift-drag ratios from airfoil images. Code developed for this work is available in a public Github repository.

97 MATHEMATICS AND COMPUTING↗

Development of Machine Learning Algorithms to Segment and Study Images of Astromaterial Samples

Introduction: Micrometer-scale chemical analyses of chondritic meteorites and mission-returned asteroid samples can reveal details of the physical and chemical processes operating in the early solar system, including processes that gave rise to planets, moons, and minor bodies. These primitive astromaterials are comprised of chondrules, calcium- and aluminum-rich inclusions (CAI), and many other silicates, oxides, metals, sulfides, and fine-grained materials. The chemical and mineralogical complexity of these samples, vast populations of different components, and heterogeneity across mm to km scales, all limit our understanding of the origin and evolution of these materials. Here, we describe recent efforts to use machine learning techniques to automate the segmentation of chemical maps of chondritic meteorites, designed to aid studies of asteroid samples returned by spacecraft. By automating the task of segmentation it will become possible to rapidly analyze and interpret the sizes, shapes, mineralogy, chemistry, and other properties of every chondrule, calcium- and aluminum-rich inclusion (CAI) and other clast within and between asteroid samples. Sample return missions significantly accelerate and heighten the need to develop such new data analysis techniques, and associated data repositories. Techniques: Neural networks require abundant training data, i.e. images which have been segmented by a human user. We have manually segmented data available from previous petrologic and chemical work at NASA Johnson Space Center and the American Museum of Natural History [1-4]. These data were derived from energy- and wavelength-dispersive X-ray spectroscopy (EDS, WDS) mapping of samples from many chondrite groups. The Deeplabv3+ [5] neural network architecture was trained on human-labeled masks and used to create machine-labeled masks. Several different algorithms were investigated, with inputs ranging from common RGB image formats through to hyperspectral datasets, with raw data comprising greyscale maps of Mg, Ca, and Al, with or without Si, Fe, Ti for both EDS and WDS data, and extending to other elements in EDS only. Each greyscale image was paired with a binary mask for each labelled particle type. Results: The trained algorithms can segment (Fig 1), classify, and measure the dimensions of thousands of particles in chemical maps of a standard 1-inch round petrographic section in seconds to minutes, rather than many hours needed by a human. Accuracy of the algorithms varied from chondrite to chondrite and across particle types. Further results and details of the algorithms will be presented at the workshop. Future directions: Machine learning has the potential to revolutionize our understanding of complex particle populations contained within primitive astromaterial, with segmentation being a critical first step. Example applications include better understanding of particle transport, nebular reservoirs, parent body accretion, and a deeper understanding of the relationships between particle populations and bulk rock elemental and isotopic compositions. In addition to benefits that machine learning can bring to individual researchers, building a community data repository of thousands to millions of particles across hundreds of samples will open up many other possibilities. For example, with a large enough dataset it will be possible to search for exceptionally closely matching particles across disparate samples. Such a capability would enable a single CAI from OSIRISREx or Hayabusa/II samples to be matched to chondritic CAIs that exhibit near-identical size, texture, and mineralogy, down to the level of similar core phenocrysts, zonation, and rim sequences. Such comparative analyses will help to disentangle precursor chemistry, chronology, gas/dust reservoirs during heating, and accretion. Such an endeavor would be impossible without machine learning and a large community data repository of astromaterial chemical/mineralogic maps.

Machine Learning↗

Integration of the Biot–Gassmann Fluid Substitution Method and Machine Learning-Based Velocity–Stress Relationship for Estimating In Situ Stresses

Recent advancements have shown that in situ stresses can be reliably estimated through an integrated machine/deep learning (ML/DL)-based framework, which relies on models trained and validated using true triaxial ultrasonic velocity (TUV) experimental data that involve measurements of ultrasonic velocity in saturated rocks under varying stress configurations. However, when the goal is to interpret lower frequency measurements, it may be more appropriate to run experiments on dry rocks and then obtain Biot–Gassmann-derived equivalent saturated velocities (low-frequency approximation) and employ these quantities for training ML/DL models to predict in situ stress. Whether the dispersion effect of frequency on the velocity–stress relationship substantially impacts in situ stress prediction is an important and unresolved question. This work presents an enhancement of ML/DL-based workflow by training and implementing ML/DL models using equivalent saturated acoustic velocities (low-frequency) obtained by applying Biot–Gassmann fluid substitution on the ultrasonic velocities of dry cores. The models were trained on TUV data sets derived from three subsurface cores extracted from the geothermal well 16B(78)-32 at the Utah FORGE site. Each core was subjected to 75 unique stress configurations for velocity measurement in the dry state. The ML/DL trained on the TUV data set with equivalent saturated velocities demonstrated promising performance to predict in situ stress in subsurface geological rocks using velocity–stress relationships with R 2 of 0.86, 0.971, and 0.975 and root mean squared error (RMSE) of 2.59, 1.92, and 1.80 for validation/testing phases of vertical, minimum horizontal, and maximum horizontal stress models, respectively. Additionally, interpretation and explanation by Shapley additive explanations (SHAP) analysis further improved scientific validation and model reliability for estimating in situ stresses.

colloids↗

Path Sampling for Rare Events Boosted by Machine Learning

The study by Jung et al. introduced Artificial Intelligence for Molecular Mechanism Discovery (AIMMD), a novel sampling algorithm that integrates machine learning to enhance the efficiency of transition path sampling (TPS). By enabling on-the-fly estimation of the committor probability and simultaneously deriving a human-interpretable reaction coordinate, AIMMD offers a robust framework for elucidating the mechanistic pathways of complex molecular processes. Here, this commentary provides a discussion and critical analysis of the core AIMMD framework, explores its recent extensions, and offers an assessment of the method’s potential impact and limitations.

Minh, Porhouy [Univ. of Minnesota, Minneapolis, MN↗

Repurposing Drilling Control Diagnostics for Subsurface Edge Detection and Boundary Advisement During Planetary Drilling

Informed decision-making during lunar drilling and sampling missions will require data monitoring tools and specialized ground data systems. Accurate and updated situational awareness, with ongoing data monitoring, is critical for timely responses by to incoming science data. Traverse plans and scheduled activities may need to be flexibly changed in order to react to unexpected data or situations. Unlike (for example) Mars missions, the relative lightspeed closeness of the Moon allows for near-real-time ground processing of incoming mission and instrument data. An Apollo-class lunar regolith drill will in a sense “travel” a meter or two vertically at a given subsurface characterization site. As the drill penetrates into lunar regolith, it is likely to encounter a range of material densities, orientations, fracture toughness, and (perhaps) ice percentages. Lunar drill telemetry can provide science teams with a valuable first look into the subsurface structure, the regolith bulk properties, and constituents at each drilled site. Real-time AI-based recognition and reaction to downhole situations has been developed for automated deeper drilling on Mars and beyond. We can leverage the same knowledge bases and pattern-matching as areal-time interpreter of the subsurface, a situational awareness tool during drilling operations. We recently (Sept. 2019) demonstrated this AI drilling monitoring and analysis capability, in control of in-situ drilling and sampling operations, mounted on a KREX-2 rover in Chile’s Atacama Desert. Terrestrial automated drilling log analyses in oil exploration have used similar machine learning techniques in classifying and identifying features in drilling logs –but these typically are designed assuming a drilling fluid influencing downhole measurements and data (permeability, resistivity). Drilling models and existing AI software designed to detect and respond to drilling faults and hard materials can be repurposed, for near-real-time (ground-based) interpretation of drilling telemetry –a potentially valuable advisory tool for strata boundaries and changes in drilling parameters. On the Moon, this approach could be used to study the structure and to some extent the composition of lunar regolith vs. borehole depth, based on recognizable variations in fracture hardness, drilling energy and penetration rates while actively drilling. Since the early 2000s, a series of increasingly-capable real-time drilling telemetry interpretation and characterization software tools have been developed. These subsurface models and software tools have monitored the real-time drilling data received, and automatically identified changes in drill behavior (e.g., encountering a harder target layer, bit inclusions, drill choking due to infall downhole, and others) correlating these with subsurface structures and features. We discuss the mappings between drill borehole parameters, faults or events detected, and modeled changes in rock layer boundaries, in examples drawn from field testing at analog sites in an Arctic impact crater, Rio Tinto, and Chile’s Atacama Desert. These demonstrate how subsurface structural boundaries led to fault detections and responses by the software.

drilling advisor↗

Machine learning-guided design of direct methanol fuel cells with a platinum group metal-free cathode

Direct methanol fuel cells (DMFCs) offer a promising solution for clean electricity generation, particularly in small electronics and remote auxiliary power units. However, optimizing their efficiency and performance is challenging due to the complex interactions between various factors. Here, we present a novel approach that integrates experiments with machine learning to model and predict the performance of these fuel cells using atomically dispersed platinum group metal (PGM)-free catalysts at the cathode. Further, our machine learning models, trained on diverse input parameters, allow for the comprehensive optimization of DMFC performance prior to fabrication and testing. Through extensive experimental validation, we demonstrate that this data-driven approach accurately predicts key performance metrics, such as maximum power output and polarization curves. By combining our models with interpretable game-theory methods, we provide deep insights into the factors governing fuel cell performance, ultimately paving the way for the design of scalable and efficient DMFC technologies.

25 ENERGY STORAGE↗

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↗

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↗

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↗

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)↗

PIXLISE-C: Exploring The Data Analysis Needs of NASA Scientists for Mineral Identification

NASA JPL scientists working on the micro x-ray fluorescence (microXRF) spectroscopy data collected from Mars surface perform data analysis to look for signs of past microbial life on Mars. Their data analysis workflow mainly involves identifying mineral com- pounds through the element abundance in spatially distributed data points. Working with the NASA JPL team, we identified pain points and needs to further develop their existing data visualization and analysis tool. Specifically, the team desired improvements for the process of creating and interpreting mineral composition groups. To address this problem, we developed an interactive tool that enables scientists to (1) cluster the data using either manual lasso-tool selection or through various machine learning clustering algorithms, and (2) compare the clusters and individual data points to make informed decisions about mineral compositions. Our preliminary tool supports a hybrid data analysis workflow where the user can manually refine the machine-generated clusters.

Davidoff, Scott↗

Increasing the Scale of the Mass Spectrometry Query Language Compendium with Explainable AI

A significant bottleneck in metabolomics data interpretation is the effective use of domain knowledge to assign structural information based on fragmentation patterns. The mass spectrometry query language (MassQL) aims to make this process accessible and applicable across multiple analysis platforms. While advanced computational methods are capable of predicting compound structures from fragmentation data, AI/ML approaches often rely on complex, opaque criteria that are difficult to interpret or modify. As a result, their predictive patterns cannot be readily translated into human-readable rules, such as those used in MassQL. Here, in this study, we introduce ChemEcho, a machine learning embedding method that converts tandem mass spectrometry data into sparse feature vectors containing peak and neutral mass subformulae to enhance explainable AI/ML-based methods. An advantage of this approach is that decision trees trained using these feature vectors can be directly translated to MassQL. Using a battery of decision trees trained using ChemEcho embeddings to predict molecular attributes, we generated over 1500 MassQL queries for 765 molecular features and evaluated their precision and recall. From these queries, the 50 highest-performing queries were integrated into the MassQL compendium. This set of generated MassQL queries included environmentally and biologically relevant classes such as PFAS and molecules containing phosphate or sulfate substructures. To illustrate the impact these queries would have on a typical metabolomics experiment, these MassQL queries were applied to a public metabolomics data set─resulting in a marked increase in the structural information derived from tandem mass spectra. Access and reuse of these queries is expected to enhance structural annotation in untargeted experiments, leading to more specific claims and advancing many applications in metabolomics.

Harwood, Thomas V. [USDOE Joint Genome Institute (↗

Sparse distributed memory

Sparse distributed memory was proposed be Pentti Kanerva as a realizable architecture that could store large patterns and retrieve them based on partial matches with patterns representing current sensory inputs. This memory exhibits behaviors, both in theory and in experiment, that resemble those previously unapproached by machines - e.g., rapid recognition of faces or odors, discovery of new connections between seemingly unrelated ideas, continuation of a sequence of events when given a cue from the middle, knowing that one doesn't know, or getting stuck with an answer on the tip of one's tongue. These behaviors are now within reach of machines that can be incorporated into the computing systems of robots capable of seeing, talking, and manipulating. Kanerva's theory is a break with the Western rationalistic tradition, allowing a new interpretation of learning and cognition that respects biology and the mysteries of individual human beings.

Denning, Peter J.↗

Rare Lepton Decays and Differentiable Hadronization Models - From Signatures of New Physics to Data-driven Event Generation

This dissertation is partitioned into two parts: phenomenological studies focused on rare lepton decays as probes of heavy and light new physics, and the development of differentiable, data-driven hadronization models. Part I develops the phenomenology of new physics signatures stemming from rare charged lepton flavor violating decays probed by experiments at the intensity frontier. These include interactions mediated by both high-scale effective operators and light new physics, manifesting in multi-lepton final states ($\mu \to 5e$), elastic nuclear transitions ($\mu \to e$ conversion), baryon-number-violating muon capture, and time-dependent signals from ultralight dark matter ($\mu \to e \phi, \tau \to \ell \phi$). Part II develops two distinct strategies for advancing differentiable and data-driven hadronization models. One involves comprehensive reweighting frameworks for hadronization that enable efficient uncertainty estimation, facilitate parameter tuning, and interface naturally with differentiable programming paradigms. The other introduces machine-learning-based methods for extracting microscopic fragmentation dynamics directly from macroscopic observables through the deformation of existing models -- effectively providing solutions to the inverse problem of hadronization. Altogether, these studies advance the interpretability, flexibility, and precision of theoretical predictions for both high-intensity and high-energy experiments.

Menzo, Tony [Cincinnati U.] (ORCID:000000022013457↗

Evidential Deep Learning: Enhancing Predictive Uncertainty Estimation for Earth System Science Applications

Abstract Robust quantification of predictive uncertainty is a critical addition needed for machine learning applied to weather and climate problems to improve the understanding of what is driving prediction sensitivity. Ensembles of machine learning models provide predictive uncertainty estimates in a conceptually simple way but require multiple models for training and prediction, increasing computational cost and latency. Parametric deep learning can estimate uncertainty with one model by predicting the parameters of a probability distribution but does not account for epistemic uncertainty. Evidential deep learning, a technique that extends parametric deep learning to higher-order distributions, can account for both aleatoric and epistemic uncertainties with one model. This study compares the uncertainty derived from evidential neural networks to that obtained from ensembles. Through applications of the classification of winter precipitation type and regression of surface-layer fluxes, we show evidential deep learning models attaining predictive accuracy rivaling standard methods while robustly quantifying both sources of uncertainty. We evaluate the uncertainty in terms of how well the predictions are calibrated and how well the uncertainty correlates with prediction error. Analyses of uncertainty in the context of the inputs reveal sensitivities to underlying meteorological processes, facilitating interpretation of the models. The conceptual simplicity, interpretability, and computational efficiency of evidential neural networks make them highly extensible, offering a promising approach for reliable and practical uncertainty quantification in Earth system science modeling. To encourage broader adoption of evidential deep learning, we have developed a new Python package, Machine Integration and Learning for Earth Systems (MILES) group Generalized Uncertainty for Earth System Science (GUESS) (MILES-GUESS) ( https://github.com/ai2es/miles-guess ), that enables users to train and evaluate both evidential and ensemble deep learning. Significance Statement This study demonstrates a new technique, evidential deep learning, for robust and computationally efficient uncertainty quantification in modeling the Earth system. The method integrates probabilistic principles into deep neural networks, enabling the estimation of both aleatoric uncertainty from noisy data and epistemic uncertainty from model limitations using a single model. Our analyses reveal how decomposing these uncertainties provides valuable insights into reliability, accuracy, and model shortcomings. We show that the approach can rival standard methods in classification and regression tasks within atmospheric science while offering practical advantages such as computational efficiency. With further advances, evidential networks have the potential to enhance risk assessment and decision-making across meteorology by improving uncertainty quantification, a longstanding challenge. This work establishes a strong foundation and motivation for the broader adoption of evidential learning, where properly quantifying uncertainties is critical yet lacking.

Schreck, John S.↗

Applications of visualization technology in the structural sciences

The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data—particularly from cryo-electron microscopy and x-ray crystallography—are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.

Eng, Edward T. [New York Structural Biology Center↗