Image Retrieval by Content: A Machine Learning Approach
There has been an explosive growth in the amount of image data.
machine learning pattern recognition automated dat↗
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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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Algorithmic Classification of Raman Spectra Biosignatures: Improving Life Detection Confidence
“Agnostic” biosignatures – indicators of life (or the absence of life), independent of a particular biochemistry – are increasingly considered a high standard for life detection. The Ladder of Life Detection (2018) called for investigating how combinations of independent and different potential biosignatures affect confidence. To address this gap, statistical classification of elemental abundances, isotopic fractionation, and reflectance spectroscopy (VNIR) has been implemented. Raman spectroscopy, highly desirable due to its wide availability, has the potential to improve this predictive power. This work implemented biosignature classification algorithms on Raman data alone, in preparation for combination with the other data types. Raman spectroscopy data was collected from published databases and papers as part of a manually curated dataset of “indicative” and “non-indicative of life” samples. These currently include 61 non-indicative samples (meteorites, magnetite); 3 indicative living samples (bacteria); 20 indicative non-living samples (chalk, bone); and 12 indicative mixed (with non-indicative material) samples (soil, microbial mats). Laboratory work is ongoing to characterize additional samples, particularly a greater breadth of mixed systems. Spectra were interpolated, filtered with the Savitzsky-Golay filter, and de-noised. For a preliminary examination, agnostic features were manually extracted including mean intensity, number of peaks, and mean peak width. Different peak prominences and filtering polynomials were used to refine features. Classification algorithms were implemented: k-nearest neighbors (KNN), logistic regression (LR), linear support vector machines (SVM), random forest (RF), Gaussian naïve bayes (GNB). Lastly, Monte Carlo simulations on 1,000 50%-train-test-splits were used to validate classification performance and feature significance. The preliminary feature set achieved its highest AUC of 0.52 with LR, with no strongly discriminatory features. Work to improve feature extraction, such as through deep learning with back propagation, is planned. In future work, the Raman data will be combined with the other data types, and potentially new data types such as enantiomeric excess. This project was partially supported through the NASA Ames Project EXcellence (APEX) incubator program.
Astrobiology↗
Machine Learning-Based Anomaly Detection for PMT Data Quality Monitoring in the SBN and DUNE
Maintaining high-quality detector data is essential for achieving the scientific objectives of the Short-Baseline Neutrino (SBN) Program at Fermilab. Current data quality monitoring (DQM) procedures rely primarily on threshold-based metrics and manual inspection of detector monitoring plots, making the detection of subtle or gradually developing anomalies both time-consuming and dependent on expert interpretation. This project developed and evaluated a machine-learning workflow for automatically identifying anomalous photomultiplier tube (PMT) channels in the Short-Baseline Near Detector (SBND) using optical-hit amplitude data. A Python-based analysis program was developed to process ROOT files, extract statistical features describing individual PMT amplitude distributions, and generate feature vectors for anomaly detection. These features were used to train an Isolation Forest model using data representing normal detector operation. The trained model was subsequently applied to independent detector runs to identify channels exhibiting statistically unusual behavior relative to the learned reference response. To support expert interpretation, the workflow generated complementary diagnostic products, including anomaly score distributions, normalized amplitude comparisons, decision-tree visualizations, and principal component analysis (PCA) projections. This project demonstrated the feasibility of integrating unsupervised machine learning into detector data-quality monitoring and developed a complete workflow for automated PMT performance assessment to aid expert-driven review. Beyond its technical contributions, the VFP appointment fostered a research collaboration between Aurora University and Fermilab and provided direct workforce development benefits by training the visiting faculty member in detector-scale machine-learning methods that are now being incorporated into undergraduate coursework and research. The methodology developed here provides a foundation for future applications to ProtoDUNE and other liquid argon time projection chamber (LArTPC) detectors, contributing to ongoing efforts to improve detector reliability, reduce manual monitoring requirements, and enable scalable data quality monitoring for future large-scale neutrino experiments, including the Deep Underground Neutrino Experiment (DUNE).
Colón Santana, Juan A. [Unlisted, US, IL]↗
An Advanced Open-Source Platform for Air Quality Analysis, Visualization, and Prediction
Ambient air pollution is the largest environmental health risk factor, leading to several million premature deaths globally per year. The challenge of combating poor air quality is exacerbated by growing urban populations, changing emissions, and a warming climate. While there have been many advances monitoring and modeling of atmospheric composition, reflected in the dramatic increase in archived Earth Observations, there is no single measurement or method that alone can provide an accurate depiction of the entire atmosphere. The rapidly growing collections of observational and modeling data require us to be smarter about what data to include, and how such data is used. In recent years, NASA has invested significantly in advancing the concepts for Analytics Collaborative Framework (ACF) [5] and New Observing Strategies (NOS) [4] to tackle our software infrastructure need for harmonized data management and dynamic acquisition of diverse measurements for on-demand, interactive, multivariate analysis, and access [3]. It is not enough to have a big data, standalone analytics solution; it is critical that we start integrating data from remote sensing, modeling, and in-situ networks in a harmonized manner that enables timely and data-driven decision-making for air quality management. This work presents the design and development of an Air Quality Analytics Collaborative Framework (AQ ACF), as part of NASA’s Advanced Information Systems Technology (AIST) effort, to establish a data, machine-learning, and numerically driven platform for air quality analysis, visualization, and prediction.
Liu, Qian↗
Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning
River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.
54 ENVIRONMENTAL SCIENCES↗
S AP F LOWER : an automated tool for sap flow data preprocessing, gap-filling, and analysis using deep learning
Sap flow, a critical process in plant water use and ecosystem water cycles, is often measured using thermal dissipation probes (TDP) due to their ease of installation and continuous data collection. However, sap flow data frequently include noise, outliers, and gaps, creating challenges for analysis and requiring substantial manual processing. We developed S AP F LOWER , a tool that automates data preprocessing, model training, gap-filling, sapwood area scaling and modeling, and water use analysis. It integrates autocleaning, machine learning and deep learning models (e.g. random forest, Gaussian process regression, long short-term memory (LSTM), bidirectional LSTM (BiLSTM)), and efficient workflows to process sap flow data. S AP F LOWER can remove over 90% of noisy data while preserving legitimate variations and achieve high accuracy in gap-filling based on user-determined parameters. Random forest, LSTM, and BiLSTM models reduced root mean square error to 10% or less for long-term gaps. Model training and prediction can be performed efficiently within seconds. S AP F LOWER significantly enhances the efficiency and accessibility of TDP data analysis by automating complex tasks, enabling researchers without programming expertise to employ advanced techniques. Future improvements will focus on species-specific corrections for TDP and support for additional measurement methods. S AP F LOWER is openly available on GitHub (https://github.com/JiaxinWang123/SapFlower) and Zenodo (doi: 10.5281/zenodo.13665919).
ecosystem water balance↗
Taxi-Out Time Prediction for Departures at Charlotte Airport Using Machine Learning Techniques
Predicting the taxi-out times of departures accurately is important for improving airport efficiency and takeoff time predictability. In this paper, we attempt to apply machine learning techniques to actual traffic data at Charlotte Douglas International Airport for taxi-out time prediction. To find the key factors affecting aircraft taxi times, surface surveillance data is first analyzed. From this data analysis, several variables, including terminal concourse, spot, runway, departure fix and weight class, are selected for taxi time prediction. Then, various machine learning methods such as linear regression, support vector machines, k-nearest neighbors, random forest, and neural networks model are applied to actual flight data. Different traffic flow and weather conditions at Charlotte airport are also taken into account for more accurate prediction. The taxi-out time prediction results show that linear regression and random forest techniques can provide the most accurate prediction in terms of root-mean-square errors. We also discuss the operational complexity and uncertainties that make it difficult to predict the taxi times accurately.
Safe and efficient surface operations↗
Explainable Machine Learning for Functional Data
Black-box machine learning models are recognized as useful tools for prediction applications, but the algorithmic complexity of some models causes interpretation challenges. Explainability methods have been proposed to provide insight into these models, but there is little research focused on supervised modeling with functional data inputs. We argue that, especially in applications of high consequence, it is important to explicitly model the functional dependence in a black-box analysis to not obscure or misrepresent patterns in explanations. As such, we propose the V ariable importance E xplainable E lastic S hape A nalysis (VEESA) pipeline for training supervised machine learning models with functional inputs. The pipeline is an analysis process that includes the data preprocessing, modeling, and post-hoc explanations. The preprocessing is done using elastic functional principal components analysis, which accounts for vertical and horizontal variability in functional data and, ultimately, allows for explanations in the original data space that identify the important functional variability without bias due to correlated variables. Here, we demonstrate the pipeline on two high-consequence applications: explosives classification for national security and inkjet printer identification in forensic science. The applications exhibit the VEESA pipeline’s ability to provide an understanding of the characteristics of the functional data useful for prediction. Code for implementing the pipeline is available in the veesa R package (and supplemental python code).
Elastic Shape Analysis↗
Multivariate statistical analysis software technologies for astrophysical research involving large data bases
We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complete database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful, and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications, and has produced real, published results.
Djorgovski, S. George↗
Multivariate Statistical Analysis Software Technologies for Astrophysical Research Involving Large Data Bases
We developed a package to process and analyze the data from the digital version of the Second Palomar Sky Survey. This system, called SKICAT, incorporates the latest in machine learning and expert systems software technology, in order to classify the detected objects objectively and uniformly, and facilitate handling of the enormous data sets from digital sky surveys and other sources. The system provides a powerful, integrated environment for the manipulation and scientific investigation of catalogs from virtually any source. It serves three principal functions: image catalog construction, catalog management, and catalog analysis. Through use of the GID3* Decision Tree artificial induction software, SKICAT automates the process of classifying objects within CCD and digitized plate images. To exploit these catalogs, the system also provides tools to merge them into a large, complex database which may be easily queried and modified when new data or better methods of calibrating or classifying become available. The most innovative feature of SKICAT is the facility it provides to experiment with and apply the latest in machine learning technology to the tasks of catalog construction and analysis. SKICAT provides a unique environment for implementing these tools for any number of future scientific purposes. Initial scientific verification and performance tests have been made using galaxy counts and measurements of galaxy clustering from small subsets of the survey data, and a search for very high redshift quasars. All of the tests were successful and produced new and interesting scientific results. Attachments to this report give detailed accounts of the technical aspects of the SKICAT system, and of some of the scientific results achieved to date. We also developed a user-friendly package for multivariate statistical analysis of small and moderate-size data sets, called STATPROG. The package was tested extensively on a number of real scientific applications and has produced real, published results.
Djorgovski, S. G.↗
A Science Gateway for the Repeatable Analysis of Machine Learning Predicted Gravity Anomalies
In recent years, deep learning has become an increasingly popular alternative for modeling in geoscience applications due to its scalability and efficiency. However, the interpretability, compute, data volume, and hyperparameter tuning requirements of deep learning models make development and monitoring difficult. Furthermore, model explainability and communicating results obtained by these models to users or domain experts is a challenge, as domain experts in geoscience also need to have a deep understanding of how those models function in order to support their scientific works. Here, we describe a science gateway and machine learning pipeline for predicting gravity anomalies from geophysical data. The gateway, built on open-source technologies, provides a holistic view of the pipeline through interactive visualizations aimed at enabling efficient exploratory data analysis. The repeatability, reproducibility, and monitoring capabilities of this overall system allow us to iterate and analyze at scale. Using this pipeline and gateway, we can repeatedly produce accurate high-resolution gravity anomaly datasets. By describing the underlying technologies, implementation, and results, here we provide a foundation for the broader adoption of science gateways into cross-cutting geoscience and machine learning research projects as a means to improve the scientific discovery and collaboration in the geophysics and computational sciences community.
58 GEOSCIENCES↗
Machine learning analysis of high-repetition-rate two-dimensional Thomson scattering spectra from laser-produced plasmas
With the emergence of high-repetition-rate two-dimensional Thomson scattering (TS) measurements, improving spectral data analysis is a key area of interest. Here, we present a new way to derive the electron temperature and density of laser-driven blast waves in plasmas from their TS spectra with machine learning (ML). This analysis occurs in both the non-collective (α < 1) and collective (α > 1) scattering regimes with the goal of autonomously and more accurately determining T c and n e both where spectral data has been collected and to give the ability to predict these attributes in regions where data has not been collected. We introduce three ML models, one trained only on experimental data, one only on synthetic data, and one using transfer learning, and compare their speed and accuracy with the conventional TS inversion algorithms in the open source PlasmaPy python package.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Predicting Dynamic-to-Static Correction Factor from Petrophysical Data and Chemostratigraphy using Unsupervised Machine Learning
Estimating static mechanical properties of stratigraphic layers is critical for optimizing subsurface engineering applications. To estimate dynamic-to-static correction factor F ds (static-to-dynamic Young’s modulus ratio) across the Caney shale interval in Oklahoma, USA, we integrated triaxial test measurements and petrophysical data, including well logs and X-ray fluorescence (XRF) using unsupervised machine learning (ML). We used a novel workflow that includes principal component analysis (PCA) to reduce data set dimensionality of well logs and XRF data sets—both separately and combined—creating three scenarios, and later applied inverse distance weighting (IDW) to derive F ds profiles for these scenarios. Furthermore, we applied K-means clustering on each scenario to predict depositional facies, and built a stiffness zonation profile through chemostratigraphic analysis of the terrigenous elements to validate the predicted F ds . The predicted F ds profile from each scenario using the PCA-IDW method was compared with the constant F ds approach from our previous study by calculating the root mean square error (RMSE). The combined data sets scenario yielded the lowest RMSE value of 0.113, while the RMSE values for the well logs and XRF scenarios were 0.131 and 0.129, respectively. In addition, the predicted F ds from the XRF scenario well-matched the stiffness zonation from the chemostratigraphic analysis that was built using the optimized K-means clustering of nine clusters for that scenario. These methods and findings offer a valuable tool for refining lithological classification and improving the F ds profile, potentially enhancing drilling and stimulation strategies for subsurface energy engineering applications.
clastic rock↗
Exploring Continuous Seismic Data at an Industry Facility Using Unsupervised Machine Learning
Seismic data recorded at industrial sites contain valuable information on anthropogenic activities. With advances in machine learning and computing power, new opportunities have emerged to explore the seismic wavefield in these complex environments. We applied two unsupervised machine learning algorithms to analyze continuous seismic data collected from an industrial facility in Texas, United States. The Uniform Manifold Approximation and Projection for Dimension Reduction algorithm was used to reduce the dimensionality of the data and generate 2D embeddings. Then, the Hierarchical Density-Based Spatial Clustering of Applications with Noise method was employed to automatically group these embeddings into distinct signal clusters. Our analysis of over 1400 hr (around 59 days) of continuous seismic data revealed five and seven signal clusters at two separate stations. At both stations, we identified clusters associated with background noise and vehicle traffic, with the latter’s temporal patterns aligning closely with the facility’s work schedule. Furthermore, the algorithms detected signal clusters from unknown sources and underline the ability of unsupervised machine learning for uncovering previously unrecognized patterns. Our analysis demonstrates the effectiveness of unsupervised approaches in examining continuous seismic data without requiring prior knowledge or pre-existing labels.
58 GEOSCIENCES↗
Machine learning BPS spectra and the gap conjecture
We explore statistical properties of Bogomol’nyi-Prasad-Sommerfield q-series for strongly coupled supersymmetric theories that correspond to a particular family of three-manifolds. We discover that gaps between exponents in the -series are statistically more significant at the beginning of the -series compared to gaps that appear in higher powers of. Our observations are obtained by calculating saliencies of -series features used as input data for principal component analysis, which is a standard example of an explainable machine learning technique that allows for a direct calculation and a better analysis of feature saliencies.
97 MATHEMATICS AND COMPUTING↗
Current and future directions in network biology
Network biology is an interdisciplinary field bridging computational and biological sciences that has proved pivotal in advancing the understanding of cellular functions and diseases across biological systems and scales. Although the field has been around for two decades, it remains nascent. It has witnessed rapid evolution, accompanied by emerging challenges. These stem from various factors, notably the growing complexity and volume of data together with the increased diversity of data types describing different tiers of biological organization. We discuss prevailing research directions in network biology, focusing on molecular/cellular networks but also on other biological network types such as biomedical knowledge graphs, patient similarity networks, brain networks, and social/contact networks relevant to disease spread. In more detail, we highlight areas of inference and comparison of biological networks, multimodal data integration and heterogeneous networks, higher-order network analysis, machine learning on networks, and network-based personalized medicine. Following the overview of recent breakthroughs across these five areas, we offer a perspective on future directions of network biology. Additionally, we discuss scientific communities, educational initiatives, and the importance of fostering diversity within the field. This article establishes a roadmap for an immediate and long-term vision for network biology.
59 BASIC BIOLOGICAL SCIENCES↗
On the Need to Align Intent and Implementation in Uncertainty Quantification for Machine Learning
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).
Trivedi, Shubhendu [MIT] (ORCID:0000000312374301)↗
Research Data Alliance: Understanding Big Data Analytics Applications in Earth Science
The Research Data Alliance (RDA) enables data to be shared across barriers through focused working groups and interest groups, formed of experts from around the world - from academia, industry and government. Its Big Data Analytics (BDA) interest groups seeks to develop community based recommendations on feasible data analytics approaches to address scientific community needs of utilizing large quantities of data. BDA seeks to analyze different scientific domain applications (e.g. earth science use cases) and their potential use of various big data analytics techniques. These techniques reach from hardware deployment models up to various different algorithms (e.g. machine learning algorithms such as support vector machines for classification). A systematic classification of feasible combinations of analysis algorithms, analytical tools, data and resource characteristics and scientific queries will be covered in these recommendations. This contribution will outline initial parts of such a classification and recommendations in the specific context of the field of Earth Sciences. Given lessons learned and experiences are based on a survey of use cases and also providing insights in a few use cases in detail.
Riedel, Morris↗