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Results for “support vector machines (SVMs)”

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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16 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2018

Sparse Coding for N-Gram Feature Extraction and Training for File Fragment Classification

File fragment classification is an important step in the task of file carving in digital forensics. In file carving, files must be reconstructed based on their content as a result of their fragmented storage on disk or in memory. Existing methods for classification of file fragments typically use hand-engineered features such as byte histograms or entropy measures. In this paper, we propose an approach using sparse coding that enables automated feature extraction. Sparse coding, or sparse dictionary learning, is an unsupervised learning algorithm, and is capable of extracting features based simply on how well those features can be used to reconstruct the original data. With respect to file fragments, we learn sparse dictionaries for n-grams, continuous sequences of bytes, of different sizes. These dictionaries may then be used to estimate n-gram frequencies for a given file fragment, but for significantly larger n-gram sizes than are typically found in existing methods which suffer from combinatorial explosion. To demonstrate the capability of our sparse coding approach, we used the resulting features to train standard classifiers such as support vector machines (SVMs) over multiple file types. Experimentally, we achieved significantly better classification results with respect to existing methods, especially when the features were used in supplement to existing hand-engineered features.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Machine Learning–Based Condition Monitoring of a Circulating Water System of a Canadian Nuclear Plant

With the need to maintain long-term reliable energy using nuclear power plants, there is an underlying demand to ensure that the maintenance of plant components and systems is also done in an efficient and cost-effective manner. One way to achieve this is by moving from time-based maintenance to condition-based maintenance. The research presented in this paper focuses on applying statistical and machine-learning-based methods to capture anomalies within data for fault detection to further develop into condition monitoring. This paper focuses on system data for a circulating water system (CWS) of a pressurized heavy-water reactor for detecting anomalies. The different methodologies used for detecting and capturing anomalies in the CWS data are matrix profile, density-based spatial clustering of applications with noise (DBSCAN), and support vector machines (SVMs). Matrix profile and DBSCAN are used to distinguish between normal data and anomalous data. This paper presents a hybrid method using DBSCAN and SVM when a portion of the data is used for DBSCAN to generate clusters. This portion of data is then used to train the SVM along with the clusters generated by DBSCAN as output. SVM is then tested on unseen data as a predictive tool, which can work in real time to categorize data points as either normal or anomalous. This paper presents results that show the high accuracies of DBSCAN and SVM in capturing anomalies within the data for a CWS for fault detection. Thus, the maintenance plan would be focused on component condition rather than a time-based schedule by switching to an automated system to identify and predict faults within a CWS.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2025

Parallel sorting algorithm classification: is manual instrumentation necessary?

Understanding parallel algorithms is crucial for accelerating scientific simulations on complex, distributed memory, high-performance computers. Modern algorithm classification approaches learn semantics directly from source code to differentiate between algorithms, however, accessing source code is not always possible. We can learn about parallel algorithms from observing their performance, as programs running the same algorithms and using the same hardware should exhibit similar performance characteristics. We present an approach to learn algorithm classes from parallel performance data directly in order to classify algorithms without access to the source code. We extend previous work to enable classifying parallel sorting algorithms using automatic instrumentation instead of requiring manual region annotations in the source code. In this work, we design and demonstrate a study for classification of parallel sorting algorithms using parallel performance data collected from automatic instrumentation, and evaluate the performance of our new methodology on classification. We leverage Caliper to collect the performance data, Thicket for our exploratory data analysis (EDA), and PyTorch and Scikit-learn to evaluate the effectiveness of random forests, support vector machines (SVMs), decision trees, neural networks, and logistic regressions on parallel performance data. Additionally, we study noise in parallel performance data, whether the removal of noise and pre-processing of the data is necessary to accurately classify parallel sorting algorithms, and determine the effectiveness of features created from performance data. In conclusion, we demonstrate classification accuracy for these five different models of up to 97.7% across four different parallel algorithm classes.

Algorithm Classification↗
DOE OSTI2019

Predicting Reaction Products and Automating Reactive Trajectory Characterization in Molecular Simulations with Support Vector Machines

A machine learning-based methodology for the prediction of chemical reaction products, along with automated elucidation of mechanistic details via phase space analysis of reactive trajectories, is introduced using low-dimensional heuristic models and then applied to ab initio computer simulations of the photodissociation of acetaldehyde, an important chemical system in atmospheric chemistry. Our method is centered around training Support Vector Machines (SVMs) to identify optimal separatrices that delineate the regions of phase space that lead to different chemical reaction products. In contrast to the more common “black box” type machine learning methodologies for analyzing chemical simulation data, this SVM-based methodology allows for mechanistic insight to be gleaned from further analysis of the positioning of the phase space points used to train the SVM with respect to the separatrices. For example, a pair of phase space points that are in close proximity to each other but on opposite sides of a separatrix may be situated on opposite sides of a transition state, while phase space points occurring early in a simulation that are distant from a separatrix are likely to belong to trajectories that are highly biased toward the product state associated with the basin of attraction to which they belong. In addition to inferring mechanistic details about multiple-pathway chemical reactions, our method can also be used to increase reactive trajectory sampling efficiency in molecular simulations via rejection sampling, with trajectories leading to undesired product states being identified and terminated early in the simulation rather than being carried to completion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Multiscale Based Characterization and Classification of Urban Land-Use

Machine learning and deep learning provide a means for generating urban land-use maps with relatively little human effort compared to manually digitizing images. This is especially important for supporting global and regional initiatives focused on sustainability, planning, health, pro-poor policy, infrastructure, and population distribution estimates. Many of these initiatives work in areas where geospatial data is scarce, such as the global south, and often use land-use maps to help achieve their goals. In this study, we develop a typology for automated labeling of urban land-use data that captures the variation in structural patterns within cities. A comparison of classification accuracy between convolutional neural networks (CNNs) and support vector machines (SVMs) coupled with handcrafted features is conducted. Through experimental validation on two highly dense cities in Africa, we report on new insights and the potential benefits offered by both multiscale handcrafted features and multiscale-CNNs even with limited training data.

Arndt, Jacob↗
DOE OSTI2015

Predicting adenocarcinoma recurrence using computational texture models of nodule components in lung CT

Purpose: To investigate the importance of presurgical computed tomography (CT) intensity and texture information from ground-glass opacities (GGO) and solid nodule components for the prediction of adenocarcinoma recurrence. Methods: For this study, 101 patients with surgically resected stage I adenocarcinoma were selected. During the follow-up period, 17 patients had disease recurrence with six associated cancer-related deaths. GGO and solid tumor components were delineated on presurgical CT scans by a radiologist. Computational texture models of GGO and solid regions were built using linear combinations of steerable Riesz wavelets learned with linear support vector machines (SVMs). Unlike other traditional texture attributes, the proposed texture models are designed to encode local image scales and directions that are specific to GGO and solid tissue. The responses of the locally steered models were used as texture attributes and compared to the responses of unaligned Riesz wavelets. The texture attributes were combined with CT intensities to predict tumor recurrence and patient hazard according to disease-free survival (DFS) time. Two families of predictive models were compared: LASSO and SVMs, and their survival counterparts: Cox-LASSO and survival SVMs. Results: The best-performing predictive model of patient hazard was associated with a concordance index (C-index) of 0.81 ± 0.02 and was based on the combination of the steered models and CT intensities with survival SVMs. The same feature group and the LASSO model yielded the highest area under the receiver operating characteristic curve (AUC) of 0.8 ± 0.01 for predicting tumor recurrence, although no statistically significant difference was found when compared to using intensity features solely. For all models, the performance was found to be significantly higher when image attributes were based on the solid components solely versus using the entire tumors (p < 3.08 × 10{sup −5}). Conclusions: This study constitutes a novel perspective on how to interpret imaging information from CT examinations by suggesting that most of the information related to adenocarcinoma aggressiveness is related to the intensity and morphological properties of solid components of the tumor. The prediction of adenocarcinoma relapse was found to have low specificity but very high sensitivity. Our results could be useful in clinical practice to identify patients for which no recurrence is expected with a very high confidence using a presurgical CT scan only. It also provided an accurate estimation of the risk of recurrence after a given duration t from surgical resection (i.e., C-index = 0.81 ± 0.02)

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MRI texture features as biomarkers to predict MGMT methylation status in glioblastomas

Purpose: Imaging biomarker research focuses on discovering relationships between radiological features and histological findings. In glioblastoma patients, methylation of the O{sup 6}-methylguanine methyltransferase (MGMT) gene promoter is positively correlated with an increased effectiveness of current standard of care. In this paper, the authors investigate texture features as potential imaging biomarkers for capturing the MGMT methylation status of glioblastoma multiforme (GBM) tumors when combined with supervised classification schemes. Methods: A retrospective study of 155 GBM patients with known MGMT methylation status was conducted. Co-occurrence and run length texture features were calculated, and both support vector machines (SVMs) and random forest classifiers were used to predict MGMT methylation status. Results: The best classification system (an SVM-based classifier) had a maximum area under the receiver-operating characteristic (ROC) curve of 0.85 (95% CI: 0.78–0.91) using four texture features (correlation, energy, entropy, and local intensity) originating from the T2-weighted images, yielding at the optimal threshold of the ROC curve, a sensitivity of 0.803 and a specificity of 0.813. Conclusions: Results show that supervised machine learning of MRI texture features can predict MGMT methylation status in preoperative GBM tumors, thus providing a new noninvasive imaging biomarker.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Annular Core Research Reactor (ACRR) Pulse Curve Characterization

Reactor pulse characterization at the Annular Core Research Reactor (ACRR) at Sandia Technical Area V (TA-V) is commonly done through photo conductive detection (PCD) and calorimeter detectors. Each of these offer a mode of analyzing a digital signal with different advantages/methods for determination of integrated dose or temporal based metrology. This report outlines a method and code that takes the millions of data points from such detectors and delivers a characteristic pulse trendline through two main methods: digital signal filtration and machine learning, in particular, Support Vector Machines (SVMs). Each method's endpoint is to deliver a characteristic curve for the many bucket environments of ACRR while considering other points of interest including delayed gamma removal for prompt dose metrics. This work draws and adds on previous work detailing the delayed gamma fraction contributions from CINDER simulations of the ACRR. Results from this project show a method to determine characteristic curves in a way that has previously been limited by data set size.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2022

Support Vector Machines for Estimating Decision Boundaries with Numerical Simulations

Many engineering design problems can be formulated as decisions between two possible options. This is the case, for example, when a quantity of interest must be maintained below or above some threshold. The threshold thereby determines which input parameters lead to which option, and creates a boundary between the two options known as the decision boundary. This report details a machine learning approach for estimating decision boundaries, based on support vector machines (SVMs), that is amenable to large scale computational simulations. Because it is computationally expensive to evaluate each training sample, the approach iteratively estimates the decision boundary in a manner that requires relatively few training samples to glean useful estimates. The approach is then demonstrated on three example problems from structural mechanics and heat transport.

25 ENERGY STORAGE↗
DOE OSTI2022

Support Vector Machines for Classification of Direct Energy Deposition Standoff Distance for Improved Process Control

A critical factor in the implementation of direct energy deposition is the ability to maintain the standoff distance between the nozzle and the build surface, as this influences powder capture efficiency and overall part quality. Due to process-related variations, layer height may vary, causing unintended variation in standoff distance and poor build quality. While prior work has utilized contact probing to qualify standoff distance during processing, in situ methods for qualification of standoff distance are of major interest. The present work seeks to understand efficacy of image-based methods for classifying standoff distance variation in real-time using support vector machines (SVMs). It was hypothesized that the size of the melt pool and the amount of spatter will have significant correlations with deviations in the standoff distance; thus, SVMs were used on a dataset that is comprised of morphological features of melt pool size and image entropy. The SVM model was used to classify melt pool images into categories according to standoff distance variation from nominal. K-folds cross validation was used to find the optimal hyperparameters for the SVM model. To understand the impact of the selected features on the classification performance and inference speed, multiple models were trained with differing numbers of included features. Results for classification score, inference time, and image preprocessing/feature extraction from these data are reported. The present results show that the SVM model was able to predict the standoff distance classification with an accuracy of 97 percent and a speed of 0.122 s per image, making it a viable solution for real-time control of standoff distance.

Klesmith, Zoe↗
DOE OSTI2023

Analysis of an optical imaging system prototype for autonomously monitoring zooplankton in an aquaculture facility

Traditional approaches to biomonitoring in aquatic systems, such as sample collection, sorting, and identification, require significant time and effort, thereby limiting the spatiotemporal resolution of sample collection. Additionally, collection and preservation of samples for subsequent taxonomic identification and enumeration leads to mortality of organisms. Recent advances in technologies that utilize optical imaging and machine learning have provided new opportunities to expedite biomonitoring and lead to significant cost savings. These technologies can be advantageous to scientists or managers that conduct routine biomonitoring to inform operations, as in the case of aquaculture facilities. The Small Aquatic Organism optical imaging system (SAO) is a high-throughput optical imaging and classification prototype system that relies on computer vision and machine learning (Support Vector Machines, or SVMs) to autonomously identify and enumerate aquatic organisms. The SAO provides a more sustainable method of collecting large volumes of data and has the benefit of being used in situ. In this study, we tested the performance of the SAO in providing comparable results to manual zooplankton community monitoring in ten ponds at an aquaculture facility. We performed a side-by-side study comparing the sampling methods of plankton tow nets, where major zooplankton taxonomic classes were manually identified and enumerated, to sampling with the SAO. Vouchered samples were used to develop a training library for the SAO, where classes consisted of water boatman and zooplankton groups: cladocerans, copepod adults, copepod nauplii, and rotifers. SAO imagery was manually classified and compared with predicted results for validation. Accuracy for the SVM classifier of the SAO was 37.4 %. Convolutional Neural Networks (CNN) and Random Forest classifiers were also applied to SAO imagery and image features for comparison. The best CNN model and our Random Forest model had accuracies of 80.4 % and 46.6 % respectively. Challenges faced included the small size of copepod nauplii and rotifers and the limited resolution of the imaging camera, although there are tradeoffs between imaging resolution and the sample processing rate. Furthermore, our comparison shows that advancement in both optical imaging and ML are needed in order for the SAO prototype to yield comparable results to manual community monitoring in an aquaculture facility.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Predicting novel substrates for enzymes with minimal experimental effort with active learning

Enzymatic substrate promiscuity is more ubiquitous than previously thought, with significant consequences for understanding metabolism and its application to biocatalysis. This realization has given rise to the need for efficient characterization of enzyme promiscuity. Enzyme promiscuity is currently characterized with a limited number of human-selected compounds that may not be representative of the enzyme's versatility. While testing large numbers of compounds may be impractical, computational approaches can exploit existing data to determine the most informative substrates to test next, thereby more thoroughly exploring an enzyme's versatility. Here, to demonstrate this, we used existing studies and tested compounds for four different enzymes, developed support vector machine (SVM) models using these datasets, and selected additional compounds for experiments using an active learning approach. SVMs trained on a chemically diverse set of compounds were discovered to achieve maximum accuracies of similar to 80% using similar to 33% fewer compounds than datasets based on all compounds tested in existing studies. Active learning-selected compounds for testing resolved apparent conflicts in the existing training data, while adding diversity to the dataset. Finally, the application of these algorithms to wide arrays of metabolic enzymes would result in a library of SVMs that can predict high-probability promiscuous enzymatic reactions and could prove a valuable resource for the design of novel metabolic pathways.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

JGI-Trichoderma v1.0

There is a series of Python and bash scripts to parse genomics datasets used to evaluate the coevolution of gene families and the feature importance of gene families using an SVM classifier. - Cover analysis: takes a list of single-copy genes in a set of genomes, aligns and builds the gene trees to determine if two gene families have a signature of covariation with one another. It parses the files to run phykit cover script described here: https://jlsteenwyk.com/PhyKIT/usage/index.html - SVM-classifier: This Python script is an SVM-based genomic classifier designed for biological data analysis. It combines machine learning with feature selection to identify important genomic markers and classify biological samples. Core Functionality: The script uses Support Vector Machines from scikit-learn to classify genomic data, incorporating SelectKBest for automated feature selection and leave-one-out cross-validation for performance assessment. It operates in multiple modes: feature ranking, optimal combination discovery, and sample prediction. Primary Applications: Genomic sample classification and biomarker discovery Feature importance analysis in high-dimensional biological datasets Prediction of sample categories based on genomic profiles Research applications requiring robust classification of biological data Key Advantages: High-dimensional handling: SVMs excel with genomic data's typical high feature-to-sample ratios Integrated feature selection: Reduces noise and computational overhead while identifying key markers Probability estimation: Provides confidence scores essential for biological interpretation Validation robustness: Leave-one-out cross-validation ensures reliable performance metrics Operational flexibility: Multiple analysis modes support different research phases from exploration to prediction

Stecca Steindorff, Andrei [Lawrence Berkeley Natio↗
DOE OSTI2019

Discriminating Tailing Piles using VNIR Imagery and SVMs

This report describes a brief investigation into the use of multispectral satellite imagery and a machine learning technique to discriminate between the soils in two tailing piles in the U1a Complex at the Nevada National Security Site. The south pile dates from the late 1960s and the north pile dates from the early 2000s and is where recent tailings have been dumped. Our approach is to use commercially available satellite imagery of the U1a tailing piles and a Support Vector Machine (SVM) to discriminate between the soils in these piles. Experiments were performed using multispectral pixels selected from around the U1a Complex to train the support vector machine. Pixels in the scene were then classified by the SVM. Classification performance was assessed qualitatively through study of the classification imagery output by the SVM. These qualitative assessments provide the conclusions drawn by the investigation: 1. A SVM can be used to discriminate between different types of materials in satellite imagery. 2. The VNIR imagery used in this investigation does not provide the features needed by the SVM to discriminate between the two tailing piles at the U1a Complex-the soils look too similar in these spectral bands to discriminate. The remainder of the report details the experiments performed to reach these conclusions and the limitations and caveats associated with the conclusions.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2014

Support Vector Machine-Based Prediction of Local Tumor Control After Stereotactic Body Radiation Therapy for Early-Stage Non-Small Cell Lung Cancer

Background: Several prognostic factors for local tumor control probability (TCP) after stereotactic body radiation therapy (SBRT) for early stage non-small cell lung cancer (NSCLC) have been described, but no attempts have been undertaken to explore whether a nonlinear combination of potential factors might synergistically improve the prediction of local control. Methods and Materials: We investigated a support vector machine (SVM) for predicting TCP in a cohort of 399 patients treated at 13 German and Austrian institutions. Among 7 potential input features for the SVM we selected those most important on the basis of forward feature selection, thereby evaluating classifier performance by using 10-fold cross-validation and computing the area under the ROC curve (AUC). The final SVM classifier was built by repeating the feature selection 10 times with different splitting of the data for cross-validation and finally choosing only those features that were selected at least 5 out of 10 times. It was compared with a multivariate logistic model that was built by forward feature selection. Results: Local failure occurred in 12% of patients. Biologically effective dose (BED) at the isocenter (BED{sub ISO}) was the strongest predictor of TCP in the logistic model and also the most frequently selected input feature for the SVM. A bivariate logistic function of BED{sub ISO} and the pulmonary function indicator forced expiratory volume in 1 second (FEV1) yielded the best description of the data but resulted in a significantly smaller AUC than the final SVM classifier with the input features BED{sub ISO}, age, baseline Karnofsky index, and FEV1 (0.696 ± 0.040 vs 0.789 ± 0.001, P<.03). The final SVM resulted in sensitivity and specificity of 67.0% ± 0.5% and 78.7% ± 0.3%, respectively. Conclusions: These results confirm that machine learning techniques like SVMs can be successfully applied to predict treatment outcome after SBRT. Improvements over traditional TCP modeling are expected through a nonlinear combination of multiple features, eventually helping in the task of personalized treatment planning.

62 RADIOLOGY AND NUCLEAR MEDICINE↗