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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Evolution of the Peridynamics Co-Authorship Network

We report peridynamics is a relatively new field in continuum mechanics that has developed over the past 20 years. This paper studies the evolution of collaborations in the field of peridynamics since its inception using social network analysis. For this purpose, we construct a network for each year from 2000 to 2019 describing co-authorship between scientists in peridynamics. In these networks, each node represents a scientist and each link connects two co-authoring scientists with a link weight representing the frequency and strength of their collaboration; each network as a whole can be thought of as a graph representation of the peridynamics community for the given year. By constructing a network for each year, we are able to analyze the evolution of the network in time and discuss the implications of this evolution for the peridynamics community. Our study demonstrates that the peridynamics community has been growing exponentially in size in recent years. Centrality metrics are also used to identify the most collaborative scientists in the community. Moreover, we compute link recommendations based on both elevating a scientist’s position in the network with respect to certain centrality metrics or closing structural holes in the network identified with persistent homology. We further extend the analysis to higher-order networks whose nodes represent groups of scientists in the community and whose links connect collaborating groups. In some sense, our work studies the past, present, and future of the peridynamics community.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Harnessing Machine Learning and Data Fusion for Accurate Undocumented Well Identification in Satellite Images

This study utilizes satellite data to detect undocumented oil and gas wells, which pose significant environmental concerns, including greenhouse gas emissions. Three key findings emerge from the study. Firstly, the problem of imbalanced data is addressed by recommending oversampling techniques like Rotation–GaussianBlur–Solarization data augmentation (RGS), the Synthetic Minority Over-Sampling Technique (SMOTE), or ADASYN (an extension of SMOTE) over undersampling techniques. The performance of borderline SMOTE is less effective than that of the rest of the oversampling techniques, as its performance relies heavily on the quality and distribution of data near the decision boundary. Secondly, incorporating pre-trained models trained on large-scale datasets enhances the models’ generalization ability, with models trained on one county’s dataset demonstrating high overall accuracy, recall, and F1 scores that can be extended to other areas. This transferability of models allows for wider application. Lastly, including persistent homology (PH) as an additional input improves performance for in-distribution testing but may affect the model’s generalization for out-of-distribution testing. A careful consideration of PH’s impact on overall performance and generalizability is recommended. Overall, this study provides a robust approach to identifying undocumented oil and gas wells, contributing to the acceleration of a net-zero economy and supporting environmental sustainability efforts.

SMOTE↗
DOE OSTI2020

Topological Regularization via Persistence-Sensitive Optimization

Optimization, a key tool in machine learning and statistics, relies on regularization to reduce overfitting. Traditional regularization methods control a norm of the solution to ensure its smoothness. Recently, topological methods have emerged as a way to provide a more precise and expressive control over the solution, relying on persistent homology to quantify and reduce its roughness. All such existing techniques back-propagate gradients through the persistence diagram, which is a summary of the topological features of a function. Their downside is that they provide information only at the critical points of the function. We propose a method that instead builds on persistence-sensitive simplification and translates the required changes to the persistence diagram into changes on large subsets of the domain, including both critical and regular points. This approach enables a faster and more precise topological regularization, the benefits of which we illustrate with experimental evidence.

Nigmetov, Arnur↗
DOE OSTI2022

A Topological Approach for Motion Track Discrimination

Detecting small targets at range is difficult because there is not enough spatial information present in an image sub-region containing the target to use correlation-based methods to differentiate it from dynamic confusers present in the scene. Moreover, this lack of spatial information also disqualifies the use of most state-of-the-art deep learning image-based classifiers. Here, we use characteristics of target tracks extracted from video sequences as data from which to derive distinguishing topological features that help robustly differentiate targets of interest from confusers. In particular, we calculate persistent homology from time-delayed embeddings of dynamic statistics calculated from motion tracks extracted from a wide field-of-view video stream. In short, we use topological methods to extract features related to target motion dynamics that are useful for classification and disambiguation and show that small targets can be detected at range with high probability.

Emerson, Tegan H.↗
DOE OSTI2021

Amphiphile conformation impacts aggregate morphology and solution structure across multiple lengthscales

Although the self-assembly of amphiphiles is well-studied in aqueous solutions, much less is understood about the fundamental driving forces and structure property relationships in non-polar media. In recent work [Journal of Physical Chemistry B, 2020, 124, 10822.] the authors have studied a series of malonomide-based amphiphiles that are relevant to liquid-liquid extraction. That work demonstrated that aggregation is largely driven by local dipole-dipole interactions between molecules. Here, we build upon this observation to develop a more detailed understanding of how the balance of dipole-dipole interactions (controlled by conformation) and molecular architecture influences the morphology of the aggregates across lengthscales. Using constrained molecular dynamics about key degrees of freedom, we demonstrate that the conformation of N,N-dimethyl,N,N-dioctylhexylethoxy malonamide (DMDOHEMA) and N,N-dimethyl,N,N-dibutyltetradecyl malonamide (DMDBTDMA) has a significant impact upon self-association - where appropriate conformational sampling is essential. To quantify the aggregate morphology, several graph theoretic and persistent homology based properties are determined. The former examines the patterns of intermolecular interactions within clusters, while the latter examines the 3-dimensional spatial distribution. Based upon these analyses, we find that the morphology of aggregates, particularly at higher malonamide concentration, depends on a balance of dipole alignment and alkyl tail sterics. Dipole alignment encourages linear patterns of the intermolecular interactions within aggregates, while the alkyl tail steric interactions between the malonamide result in noticeably less linear aggregates for DMDOHEMA than DMDBTDMA. This is reflected in the spatial distribution, where more holes or voids exist between extractants within the DMDOHEMA that distribute within the solution in more of a "swiss cheese" arrangement as opposed to the more filamentous distribution of DMBDTDMA. This study links conformation and molecular structure to the morphology of amphiphile assemblies, and serves as a basis for ongoing study of multicomponent amphiphile solutions with polar and other solutes, and how these impact aggregation phenomena.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Two-Dimensional Energy Histograms as Features for Machine Learning to Predict Adsorption in Diverse Nanoporous Materials

A major obstacle for machine learning (ML) in chemical science is the lack of physically informed feature representations that provide both accurate prediction and easy interpretability of the ML model. In this work, we describe adsorption systems using novel two-dimensional energy histogram (2D-EH) features, which are obtained from the probe-adsorbent energies and energy gradients at grid points located throughout the adsorbent. The 2D-EH features encode both energetic and structural information of the material and lead to highly accurate ML models (coefficient of determination R2 ~ 0.94–0.99) for predicting single-component adsorption capacity in metal–organic frameworks (MOFs). Here, we consider the adsorption of spherical molecules (Kr and Xe), linear alkanes with a wide range of aspect ratios (ethane, propane, n-butane, and n-hexane), and a branched alkane (2,2-dimethylbutane) over a wide range of temperatures and pressures. The interpretable 2D-EH features enable the ML model to learn the basic physics of adsorption in pores from the training data. We show that these MOF-data-trained ML models are transferrable to different families of amorphous nanoporous materials. We also identify several adsorption systems where capillary condensation occurs, and ML predictions are more challenging. Nevertheless, our 2D-EH features still outperform structural features including those derived from persistent homology. The novel 2D-EH features may help accelerate the discovery and design of advanced nanoporous materials using ML for gas storage and separation in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Structure and properties of densified silica glass: characterizing the order within disorder

The broken symmetry in the atomic-scale ordering of glassy versus crystalline solids leads to a daunting challenge to provide suitable metrics for describing the order within disorder, especially on length scales beyond the nearest neighbor that are characterized by rich structural complexity. Here, we address this challenge for silica, a canonical network-forming glass, by using hot versus cold compression to (i) systematically increase the structural ordering after densification and (ii) prepare two glasses with the same high-density but contrasting structures. The structure was measured by high-energy X-ray and neutron diffraction, and atomistic models were generated that reproduce the experimental results. The vibrational and thermodynamic properties of the glasses were probed by using inelastic neutron scattering and calorimetry, respectively. Traditional measures of amorphous structures show relatively subtle changes upon compacting the glass. The method of persistent homology identifies, however, distinct features in the network topology that change as the initially open structure of the glass is collapsed. The results for the same high-density glasses show that the nature of structural disorder does impact the heat capacity and boson peak in the low-frequency dynamical spectra. Densification is discussed in terms of the loss of locally favored tetrahedral structures comprising oxygen-decorated SiSi 4<:sub> tetrahedra.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Learning-based approach to plasticity in athermal sheared amorphous packings: Improving softness

The plasticity of amorphous solids undergoing shear is characterized by quasi-localized rearrangements of particles. While many models of plasticity exist, the precise relationship between the plastic dynamics and the structure of a particle’s local environment remains an open question. Previously, machine learning was used to identify a structural predictor of rearrangements called “softness.” Although softness has been shown to predict which particles will rearrange with high accuracy, the method can be difficult to implement in experiments where data are limited and the combinations of descriptors it identifies are often difficult to interpret physically. Here, we address both of these weaknesses, presenting two major improvements to the standard softness method. First, we present a natural representation of each particle’s observed mobility, allowing for the use of statistical models that are both simpler and provide greater accuracy in limited datasets. Second, we employ persistent homology as a systematic means of identifying simple, topologically informed, structural quantities that are easy to interpret and measure experimentally. We test our methods on two-dimensional athermal packings of soft spheres under quasi-static shear. We find that the same structural information that predicts small variations in the response is also predictive of where plastic events will localize. We also find that an excellent accuracy is achieved in athermal sheared packings using simply a particle’s species and the number of nearest neighbor contacts.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Topological Signatures of Adversaries in Multimodal Alignments

Topological Data Analysis for Adversarial Detection (LANL O4937) - Detects adversarial examples in vision-language models using persistent homology and two-sample testing. Combines TDA features from CLIP embeddings with statistical methods (ME, SCF, SAMMD, C2ST) for robust detection across ImageNet, CIFAR-10/100.

Bhattarai, Manish↗
DOE OSTI2023

Experimental Observations of the Topology of Convolutional Neural Network Activations

Topological data analysis (TDA) is a branch of computational mathematics, bridging algebraic topology and data science, that provides compact, noise-robust representations of complex structures. Deep neural networks (DNNs) learn millions of parameters associated with a series of transformations defined by the model architecture resulting in high-dimensional, difficult to interpret internal representations of input data. As DNNs become more ubiquitous across multiple sectors of our society, there is increasing recognition that mathematical methods are needed to aid analysts, researchers, and practitioners in understanding and interpreting how these models' internal representations relate to the final classification. In this paper we apply cutting edge techniques from TDA with the goal of gaining insight towards interpretability of convolutional neural networks used for image classification. We use two common TDA approaches to explore several methods for modeling hidden layer activations as high-dimensional point clouds, and provide experimental evidence that these point clouds capture valuable structural information about the model's process. First, we demonstrate that a distance metric based on persistent homology can be used to quantify meaningful differences between layers and discuss these distances in the broader context of existing representational similarity metrics for neural network interpretability. Second, we show that a mapper graph can provide semantic insight as to how these models organize hierarchical class knowledge at each layer. These observations demonstrate that TDA is a useful tool to help deep learning practitioners unlock the hidden structures of their models.

topological data analysis, deep learning↗
DOE OSTI2021

Evaluating State Space Discovery by Persistent Cohomology in the Spatial Representation System

Persistent cohomology is a powerful technique for discovering topological structure in data. Strategies for its use in neuroscience are still undergoing development. We comprehensively and rigorously assess its performance in simulated neural recordings of the brain's spatial representation system. Grid, head direction, and conjunctive cell populations each span low-dimensional topological structures embedded in high-dimensional neural activity space. We evaluate the ability for persistent cohomology to discover these structures for different dataset dimensions, variations in spatial tuning, and forms of noise. We quantify its ability to decode simulated animal trajectories contained within these topological structures. We also identify regimes under which mixtures of populations form product topologies that can be detected. Our results reveal how dataset parameters affect the success of topological discovery and suggest principles for applying persistent cohomology, as well as persistent homology, to experimental neural recordings.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Topological network analysis of patient similarity for precision management of acute blood pressure in spinal cord injury

Background: Predicting neurological recovery after spinal cord injury (SCI) is challenging. Using topological data analysis, we have previously shown that mean arterial pressure (MAP) during SCI surgery predicts long-term functional recovery in rodent models, motivating the present multicenter study in patients. Methods: Intra-operative monitoring records and neurological outcome data were extracted (n = 118 patients). We built a similarity network of patients from a low-dimensional space embedded using a non-linear algorithm, Isomap, and ensured topological extraction using persistent homology metrics. Confirmatory analysis was conducted through regression methods. Results: Network analysis suggested that time outside of an optimum MAP range (hypotension or hypertension) during surgery was associated with lower likelihood of neurological recovery at hospital discharge. Logistic and LASSO (least absolute shrinkage and selection operator) regression confirmed these findings, revealing an optimal MAP range of 76–[104-117] mmHg associated with neurological recovery. Conclusions: We show that deviation from this optimal MAP range during SCI surgery predicts lower probability of neurological recovery and suggest new targets for therapeutic intervention. Funding: NIH/NINDS: R01NS088475 (ARF); R01NS122888 (ARF); UH3NS106899 (ARF); Department of Veterans Affairs: 1I01RX002245 (ARF), I01RX002787 (ARF); Wings for Life Foundation (ATE, ARF); Craig H. Neilsen Foundation (ARF); and DOD: SC150198 (MSB); SC190233 (MSB); DOE: DE-AC02-05CH11231 (DM).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A Fast Algorithm for Computing Zigzag Representatives

Zigzag filtrations of simplicial complexes generalize the usual filtrations by allowing simplex deletions in addition to simplex insertions. The barcodes computed from zigzag filtrations encode the evolution of homological features. Although one can locate a particular feature at any index in the filtration using existing algorithms, the resulting representatives may not be compatible with the zigzag: a representative cycle at one index may not map into a representative cycle at its neighbor. For this, one needs to compute compatible representative cycles along each bar in the barcode. It is known that the barcode for a zigzag filtration with m insertions and deletions can be computed $O(m^ω)$ in time, where $ω < 2.373$ is the matrix multiplication exponent. However, it is not known how to compute the compatible representatives so efficiently. For a non-zigzag filtration, the classical matrix-based algorithm provides representatives in $O(m^3)$ time, which can be improved to $O(m^ω)$. However, no known algorithm for zigzag filtrations computes the representatives with the $O(m^3)$ time bound. We present an $O(m^3 n)$ time algorithm for this problem, where $n ≤ m$ is the size of the largest complex in the filtration.

Persistent homology↗
DOE OSTI2022

Local Versus Global Distances for Zigzag and Multi-Parameter Persistence Modules

In this paper, we establish explicit and broadly applicable relationships between persistence-based distances computed locally and globally. In particular, we show that the bottleneck distance and the Wasserstein distance between two zigzag persistence modules restricted to an interval is always bounded above by the distance between the unrestricted versions. While this result is not surprising, it could have potential practical implications. We give two related applications for metric graph distances, as well as an extension for the matching distance between multi-parameter persistence modules.

persistent homology, metric graph, inequality↗
DOE OSTI2024

Tracking the topology of neural manifolds across populations

Neural manifolds summarize the intrinsic structure of the information encoded by a population of neurons. Advances in experimental techniques have made simultaneous recordings from multiple brain regions increasingly commonplace, raising the possibility of studying how these manifolds relate across populations. However, when the manifolds are nonlinear and possibly code for multiple unknown variables, it is challenging to extract robust and falsifiable information about their relationships. We introduce a framework, called the method of analogous cycles, for matching topological features of neural manifolds using only observed dissimilarity matrices within and between neural populations. We demonstrate via analysis of simulations and in vivo experimental data that this method can be used to correctly identify multiple shared circular coordinate systems across both stimuli and inferred neural manifolds. Conversely, the method rejects matching features that are not intrinsic to one of the systems. Further, as this method is deterministic and does not rely on dimensionality reduction or optimization methods, it is amenable to direct mathematical investigation and interpretation in terms of the underlying neural activity. We thus propose the method of analogous cycles as a suitable foundation for a theory of cross-population analysis via neural manifolds.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Cadmus v1.0

This software package is for distributed computation of persistent (co)homology. It is primarily intended for Topological Data Analysis (TDA) audience and scientists who use TDA methods and apply them to datasets that are too big to handle on a single machine. There are very few codes available for this; Cadmus outperforms DIPHA, if the user is interested in cohomology. The accompanying paper explaining the algorithm was accepted to ALENEX 26.

Nigmetov, Arnur [Lawrence Berkeley National Labora↗
DOE OSTI2024

Microbial species and intraspecies units exist and are maintained by ecological cohesiveness coupled to high homologous recombination

Abstract Recent genomic analyses have revealed that microbial communities are predominantly composed of persistent, sequence-discrete species and intraspecies units (genomovars), but the mechanisms that create and maintain these units remain unclear. By analyzing closely-related isolate genomes from the same or related samples and identifying recent recombination events using a novel bioinformatics methodology, we show that high ecological cohesiveness coupled to frequent-enough and unbiased (i.e., not selection-driven) horizontal gene flow, mediated by homologous recombination, often underlie these diversity patterns. Ecological cohesiveness was inferred based on greater similarity in temporal abundance patterns of genomes of the same vs. different units, and recombination was shown to affect all sizable segments of the genome (i.e., be genome-wide) and have two times or greater impact on sequence evolution than point mutations. These results were observed in bothSalinibacter ruber, an environmental halophilic organism, andEscherichia coli, the model gut-associated organism and an opportunistic pathogen, indicating that they may be more broadly applicable to the microbial world. Therefore, our results represent a departure compared to previous models of microbial speciation that invoke either ecology or recombination, but not necessarily their synergistic effect, and answer an important question for microbiology: what a species and a subspecies are.

Science & Technology - Other Topics↗