Feature Selection Clustering and Prototype Placement for Turbulence Data Sets.
Abstract not provided.
Barone, Matthew F.↗
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Building Morphologies of the USA Structures Database; a Gauntlet Feature Set
Building Morphology features and training labels for 131 million buildings in the USA Structures database.
Hauser, Taylor [ORNL] (ORCID:0000000250885236)↗
A Taxonomy and Feature set for Server-Side Identification of Proxies
Malicious actors frequently use proxies and VPNs to evade detection and hide their origin. Current challenges to information security include the use of residential proxies to blend in with normal traffic and Man-in-the-Middle phishing proxies that are used to compromise accounts protected with mult-factor authentication. We advance a taxonomy and feature set for the identification of proxied traffic based on the network layer where proxying occurs. We describe how these features apply to common proxy types and how to use these features in the classification of the proxied traffic. Collection of these additional features is feasible using existing network sensors and web servers, while only adding about 30% volume to commonly deployed network sensor logs.
97 MATHEMATICS AND COMPUTING↗
Building morphologies of the USA structures database; a gauntlet feature set
In recent years there has been a proliferation of methods and data to extract building footprints from satellite imagery. However there has been very little effort to provide additional insight about these buildings beyond their spatial location and shape. Features derived from their geometries can be used to better characterize these buildings which are critical for further research and development. In this work a set of 65 unique features for every building for more than 131 million buildings covering the US has been developed. This rich feature dataset will enable researchers, policymakers and various agencies to derive additional building characteristics like height, occupancy type, and help to gain valuable and new insights of the built environment.
Environmental sciences↗
Meta2DB: Curated Shotgun Metagenomic Feature Sets and Metadata for Health State Prediction
Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13 897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on 4 January 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health.
Kok, C [Lawrence Livermore National Laboratory (LL↗
A machine learning approach for determining temperature-dependent bandgap of metal oxides utilizing Allen–Heine–Cardona theory and O’Donnell model parameterization
To evaluate the high temperature sensing properties of metal oxide and perovskite materials suitable for use in combustion environments, it is necessary to understand the temperature dependence of their bandgaps. Although such temperature-driven changes can be calculated via the Allen–Heine–Cardona (AHC) theory, which assesses electron–phonon coupling for the bandgap correction at given temperatures, this approach is computationally demanding. Another approach to predict bandgap temperature-dependence is the O’Donnell model, which uses analytical expressions with multiple fitting parameters that require bandgap information at 0 K. This work employs data-driven Gaussian process regression (GPR) to predict the parameters employed in the O’Donnell model from a set of physical features. We use a sample of 54 metal oxides for which density functional theory has been performed to calculate the bandgap at 0 K, and the AHC calculations have been carried out to determine the shift in the bandgap at non-zero temperatures. As the AHC calculations are impractical for high-throughput screening of materials, the developed GPR model attempts to alleviate this issue by predicting the O'Donnell parameters purely from physical features. To mitigate the reliability issues arising from the very small size of the dataset, we apply a Bayesian technique to improve the generalizability of the data-driven models as well as quantify the uncertainty associated with the predictions. The method captures well the overall trend of the O’Donnell parameters with respect to a reduced feature set obtained by transforming the available physical features. Quantifying the associated uncertainty helps us understand the reliability of the predictions of the O’Donnell parameters and, therefore, the bandgap as a function of temperature for any novel material.
36 MATERIALS SCIENCE↗
High-Temperature Gas Sensor Materials with Properties Predicted via First-Principles Calculations with Machine Learning Modeling and Experimental Corroboration
Understanding the temperature dependence of functional properties of sensing materials is vital for their applications in combustion environments. The electron-phonon coupling that derives the electronic structure change with temperatures is a key property of interest as it affects other sensing responses. Herein, we first assess the temperature dependence of band gap renormalization in sensing materials by employing Allen-Heine-Cardona (AHC) theory with density functional theory (DFT) simulations corroborated with experimental observation. As the AHC calculations are impractical for high-throughput screening of materials, we employ data-driven Gaussian process regression to predict the parameters employed in the O’Donnell empirical model from a set of physical features. To mitigate the reliability issues arising from the small size of the dataset, we apply a Bayesian technique to improve the generalizability of the data-driven models as well as to quantify the uncertainty associated with theoretical predictions. These models capture well the overall trend of the O’Donnell parameters with respect to a reduced feature set obtained by transforming the available physical features. Quantifying the associated uncertainty helps us understand the reliability of the predictions and, therefore, the variation of bandgap as a function of temperature for other novel materials. The predicted candidates from machine learning models are further validated by experiments and DFT calculations.
bandgap renormalization↗
WinnowML: Stable feature selection for maximizing prediction accuracy of time-based system modeling
Online deep learning (ODL) has become an important methodology for modeling time-based performance of computer systems. An open problem is the intelligent selection of features from raw workload traces of computer systems. The best methods are overly sensitive to noisy data, causing frequent feature changes and re-training. Using all available features inflates training time and introduces model artifacts if some features should have been dropped. We present WinnowML, a method for automatically determining the most relevant feature subset for a predictive time-series model. WinnowML combines existing feature ranking algorithms and a history of each feature's ranking to iteratively rank a feature set to lower prediction error and maximize long term relevance. From this ranked feature set, the most relevant and stable subset is selected to train a model. Experimentally, we show how WinnowML can lower a model's mean absolute relative error up to 42% on average compared to the closest performing approach. Additionally, we lower the fluctuation in feature ranking and selection up to 65%. We also demonstrate how to combine WinnowML and a model search tool to provide improvements in performance of up to 14.5% when compared to using all the feature available.
Bel, Oceane MS↗
Independent malware detection architecture
A system and method (referred to as the system) detect malware by training a rule-based model, a functional based model, and a deep learning-based model from a memory snapshot of a malware free operating state of a monitored device. The system extracts a feature set from a second memory snapshot captured from an operating state of the monitored device and processes the feature set by the rule-based model, the functional-based model, and the deep learning-based model. The system identifies identifying instances of malware on the monitored device without processing data identifying an operating system of the monitored device, data associated with a prior identification of the malware, data identifying a source of the malware, data identifying a location of the malware on the monitored device, or any operating system specific data contained within the monitored device.
Smith, Jared M.↗
A reproducible study design for the MIMIC-IV in-hospital mortality task
Open, tabular electronic health record (EHR) datasets such as MIMIC-III and MIMIC-IV have become critical resources for developing machine learning (ML) models addressing clinical prediction tasks, including hospital readmission, length of stay, and in-hospital mortality (IHM). While MIMIC-III has benefited from well-established preprocessing pipelines and standardized feature sets, MIMIC-IV remains comparatively challenging to work with because there are no standardized benchmarks to support reproducibility and comparability across studies. To address this limitation, we present a rigorously curated MIMIC-IV custom feature set optimized for IHM prediction, constructed through a reproducible preprocessing pipeline and feature selection strategy.
97 MATHEMATICS AND COMPUTING↗
A Full-Stack Exploration of Language-Based Parallelism in Fortran 2023
This poster explores native parallel features in Fortran 2023 through the lens of supporting applications with libraries, compilers, and parallel runtimes. The language revision informally named Fortran 2008 introduced parallelism in the form of Single Program Multiple Data (SPMD) execution with two broad feature sets: (1) loop-level parallelism via do concurrent and (2) a Partitioned Global Address Space (PGAS) comprised of distributed “coarray” data structures. Fortran’s native parallelism has demonstrated high performance [1] and reduced the burden of inserting what sometimes amounts to more directives than code. Several compilers support both feature sets, typically by translating do concurrent into serial do loops annotated by parallel directives and by translating SPMD/PGAS features into direct calls to a communication library. Our research focuses primarily on two questions: (1) can the compiler’s parallel runtime library be developed in the language being compiled (Fortran) and (2) can we define an interface to the runtime that liberates compilers from being hardwired to one runtime and vice versa. We are answering these questions by developing the Parallel Runtime Interface for Fortran (PRIF) [2] and the Co-Array Fortran Framework of Efficient Interfaces to Network Environments (Caffeine) [3]. Caffeine is initially targeting adoption by LLVM Flang, a new open-source Fortran compiler developed by a broad community in industry, academia, and government labs. We are also exploring the use of these features in Inference-Engine, a deep learning library designed to facilitate neural network training and inference for high-performance computing applications written in modern Fortran.
Rasmussen, Katherine↗
Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits
Abstract Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops and forests. Biosurveillance, a critical component of threat mitigation, requires risk prediction based on fungal lifestyles and traits. Recent studies have revealed distinct genomic patterns associated with specific groups of plant pathogenic fungi. We sought to establish whether these phytopathogenic genomic patterns hold across diverse taxonomic and ecological groups from the Ascomycota and Basidiomycota, and furthermore, if those patterns can be used in a predictive capacity for biosurveillance. Using a supervised machine learning approach that integrates phylogenetic and genomic data, we analyzed 387 fungal genomes to test a proof-of-concept for the use of genomic signatures in predicting fungal phytopathogenic lifestyles and traits during biosurveillance activities. Our machine learning feature sets were derived from genome annotation data of carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, and transcription factors. We found that machine learning could successfully predict fungal lifestyles and traits across taxonomic groups, with the best predictive performance coming from feature sets comprising CAZyme, peptidase, and SMC data. While phylogeny was an important component in most predictions, the inclusion of genomic data improved prediction performance for every lifestyle and trait tested. Plant pathogenicity was one of the best-predicted traits, showing the promise of predictive genomics for biosurveillance applications. Furthermore, our machine learning approach revealed expansions in the number of genes from specific CAZyme and peptidase families in the genomes of plant pathogens compared to non-phytopathogenic genomes (saprotrophs, endo- and ectomycorrhizal fungi). Such genomic feature profiles give insight into the evolution of fungal phytopathogenicity and could be useful to predict the risks of unknown fungi in future biosurveillance activities.
59 BASIC BIOLOGICAL SCIENCES↗
Automated Estimation of the DARHT Radiographic Spot Size from Spatially Modulated Images
We wrote a software routine to find local extrema and calculate the contrast in the image for each feature set. The input is a KTO image in the standard DARHT orientation, pre-processed by flat-fielding, dark frame subtraction and de-warping. Table 1 shows contrast results for five contemporaneous DARHT images of the KTO. For some very dense feature sets, contrast measurements are not possible due to a lack of local extrema, and in this case no contrast value is given in the table. Highlighted in bold are the contrast values for each image that bound the threshold C = 0.01. The contrast is varying rapidly enough with spatial frequency that we can interpolate between these values to find an estimate of the spatial frequency at the threshold value.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Machine Learning Framework for Conotoxin Class and Molecular Target Prediction
Conotoxins are small and highly potent neurotoxic peptides derived from the venom of marine cone snails which have captured the interest of the scientific community due to their pharmacological potential. These toxins display significant sequence and structure diversity, which results in a wide range of specificities for several different ion channels and receptors. Despite the recognized importance of these compounds, our ability to determine their binding targets and toxicities remains a significant challenge. Predicting the target receptors of conotoxins, based solely on their amino acid sequence, remains a challenge due to the intricate relationships between structure, function, target specificity, and the significant conformational heterogeneity observed in conotoxins with the same primary sequence. We have previously demonstrated that the inclusion of post-translational modifications, collisional cross sections values, and other structural features, when added to the standard primary sequence features, improves the prediction accuracy of conotoxins against non-toxic and other toxic peptides across varied datasets and several different commonly used machine learning classifiers. Here, we present the effects of these features on conotoxin class and molecular target predictions, in particular, predicting conotoxins that bind to nicotinic acetylcholine receptors (nAChRs). We also demonstrate the use of the Synthetic Minority Oversampling Technique (SMOTE)-Tomek in balancing the datasets while simultaneously making the different classes more distinct by reducing the number of ambiguous samples which nearly overlap between the classes. In predicting the alpha, mu, and omega conotoxin classes, the SMOTE-Tomek PCA PLR model, using the combination of the SS and P feature sets establishes the best performance with an overall accuracy (OA) of 95.95%, with an average accuracy (AA) of 93.04%, and an f1 score of 0.959. Using this model, we obtained sensitivities of 98.98%, 89.66%, and 90.48% when predicting alpha, mu, and omega conotoxin classes, respectively. Similarly, in predicting conotoxins that bind to nAChRs, the SMOTE-Tomek PCA SVM model, which used the collisional cross sections (CCSs) and the P feature sets, demonstrated the highest performance with 91.3% OA, 91.32% AA, and an f1 score of 0.9131. The sensitivity when predicting conotoxins that bind to nAChRs is 91.46% with a 91.18% sensitivity when predicting conotoxins that do not bind to nAChRs.
59 BASIC BIOLOGICAL SCIENCES↗
Development of a Deep Learning Model for Predicting the Drag Coefficients of Spherical and Non-Spherical Particles,
There is yet to be a well-established drag model for non-spherical particles required in a particle-laden flow that could cover a wide range of sphericities. This talk will explore the development of a general drag model for non-spherical particles by applying deep learning using available experimental data available in the literature. The integration of several raw experimental measurements from different sources and research directions allows the training of robust Artificial Intelligence and Machine Learning (ML) models. Neural networks are an ML approach inspired by the inner biological workings of the brain. This work aims to develop a Deep Neural Network (DNN) that predicts drag coefficient values with the ability to adapt appropriately to unseen data. Given the limited number of data points available and the variance found within the data collected from various sources, challenges may arise when looking to train the model. Our study tests and implements various model regularization techniques and assesses different loss and activation functions for the proposed DNN. The proposed model considers a broader range of features other than sphericity and Reynold number. These features include density ratio, solid volume fraction, lengthwise and crosswise sphericity, and more. Furthermore, we present the features that play a significant role in predicting different drag coefficients through feature importance. Within the investigated parameter ranges in this study, the following conclusions can be achieved and summarized below: • An improved drag coefficient model can be developed by considering more features such as, aspect ratio, lengthwise sphericity, crosswise sphericity, and density ratio. • DNN model can predict better results compared to traditional methods using MAE metric. • The proposed model addresses data challenges such as limited data and extreme data points through expanded feature-set and regularization. • Three major features that mostly affect the drag coefficient were identified from a feature importance analysis.
Presa-Reyes, Maria↗
Machine Learning Model Geotiffs - Applications of Machine Learning Techniques to Geothermal Play Fairway Analysis in the Great Basin Region, Nevada
This submission contains geotiffs, supporting shapefiles and readmes for the inputs and output models of algorithms explored in the Nevada Geothermal Machine Learning project, meant to accompany the final report. Layers include: Artificial Neural Network (ANN), Extreme Learning Machine (ELM), Bayesian Neural Network (BNN), Principal Component Analysis (PCA/PCAk), Non-negative Matrix Factorization (NMF/NMFk), input rasters of feature sets, and positive/negative training sites. See readme .txt files and final report for additional metadata. A submission linking the full codebase for generating machine learning output models is available under "related resources" on this page.
15 GEOTHERMAL ENERGY↗
ML Pipeline (Machine Learning Pipeline) [SWR-22-35]
The Machine Learning Pipeline (ML Pipeline) allows the user to fit a model to predict a dependent variable, y, based on a feature set, X. ML Pipeline gives the ability to automatically generate features with its Feature Engineering function, automatically select the most important features with its Feature Selection function, fit the model with its Fit function, and evaluate the model with its Evaluate function. ML Pipeline's functionality can not only help the user predict values for the desired variable it also gives the user a better understanding of which features are important and how effective the model is. ML Pipeline accomplishes all this, while remaining simple to use and interpret.
Schiek, Andrew↗