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At least 1,603 records · Page 89

Machine Learning Approaches for Predicting Radiation Therapy Outcomes: A Clinician's Perspective

Radiation oncology has always been deeply rooted in modeling, from the early days of isoeffect curves to the contemporary Quantitative Analysis of Normal Tissue Effects in the Clinic (QUANTEC) initiative. In recent years, medical modeling for both prognostic and therapeutic purposes has exploded thanks to increasing availability of electronic data and genomics. One promising direction that medical modeling is moving toward is adopting the same machine learning methods used by companies such as Google and Facebook to combat disease. Broadly defined, machine learning is a branch of computer science that deals with making predictions from complex data through statistical models. These methods serve to uncover patterns in data and are actively used in areas such as speech recognition, handwriting recognition, face recognition, “spam” filtering (junk email), and targeted advertising. Although multiple radiation oncology research groups have shown the value of applied machine learning (ML), clinical adoption has been slow due to the high barrier to understanding these complex models by clinicians. Here, we present a review of the use of ML to predict radiation therapy outcomes from the clinician's point of view with the hope that it lowers the “barrier to entry” for those without formal training in ML. We begin by describing 7 principles that one should consider when evaluating (or creating) an ML model in radiation oncology. We next introduce 3 popular ML methods—logistic regression (LR), support vector machine (SVM), and artificial neural network (ANN)—and critique 3 seminal papers in the context of these principles. Although current studies are in exploratory stages, the overall methodology has progressively matured, and the field is ready for larger-scale further investigation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Evaluation of Correction Methods for NASA GeneLab Transcriptomic Datasets

Conducting space biology experiments aboard the International Space Station, particularly those utilizing complex model organisms like mice, is expensive and difficult due to limited crew availability, hardware, and space. As a result, sample numbers from these studies are low, reducing the statistical power of any one experiment. Aggregating spaceflight datasets serves as a method to increase sample numbers, allowing for novel insights through bioinformatic analysis of ‘omics data from merged datasets. However, aggregating datasets can introduce unwanted variation including 1) differences in sample handling, processing, and sequencing platforms between datasets (technical variation) as well as 2) differences in experimental design between datasets such as sex or age of the model organism used. In the present study, NASA GeneLab-hosted RNAseq datasets from rodent liver tissues were used to evaluate several statistical methods to correct for this unwanted variation through two approaches, reference-based and standard. The following correction algorithms were applied with (reference-based) and/or without (standard) considering Universal Mouse RNA Reference samples: ComBat and ComBat_seq from the SVA package, median polish, empirical Bayes, and ANOVA-based algorithms from the MBatch package, and negative binomial regression normalization in the DESeq2 package. For each approach, after the correction algorithm was applied, differential gene expression (DGE) analysis of flight and ground control samples was performed with the combined data. The robustness of each tool was evaluated using BatchQC, to determine statistical differences between datasets before and after correction, Principal Component Analysis, to evaluate global gene expression in samples before and after correction, and by comparing DGE analysis of individual datasets and combined datasets before and after correction. The results showed that the reference-based approach introduced several additional (and likely artificial) DEGs when compared with the standard approach. Thus, the most robust standard correction will be implemented in the GeneLab Visualization 2.0 platform when datasets are combined.

GeneLab, RNA-seq, Batch Correction↗

ARCADIA and advanced methods licensing and implementation update

AREVA NP is implementing a consistent code and methodology suite for core design and safety analysis, based on first principles modeling with an extremely broad verification and validation data base. Thanks to the high computational power increase in the last decades methods' development and application now include capabilities that were not available in the past. An example is the 3D coupled transient core power distribution characterization, which allows more realistic modeling of plant behavior, removal of inaccuracies by high resolution and access to local information. Another one is the progressive replacement, respectively complement of old deterministic methods by order statistics. This paper provides an update of the current licensing and implementation status of the main AREVA NP new codes (ARCADIA, GALILEO, S-RELAP5) and their associated advanced methods for PWR applications. ARCADIA is the state-of-the-art neutron transport/ thermal-hydraulics (TH)/ thermal-mechanics (TM) code system for PWR applications. Development is completed, implementation started in France, the Netherlands, the U.S.A. and other countries. The extension to BWR applications is on-going. GALILEO is the state-of-the-art fuel rod performance code for PWR and BWR applications. Development is completed, implementation started in France and the U.S.A. S-RELAP5 is a thermal-hydraulic code that has been completely re-coded and modernized in terms of software architecture. S-RELAP5 has been successfully coupled with ARCADIA. It is shown that advanced codes and integrated methods for accident analysis are keys for extending the fuel cycle design space.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Bayesian optimized collection strategies for fatigue strength testing

Abstract A statistical framework is presented enabling optimal sampling and analysis of constant life fatigue data. Protocols using Bayesian maximum entropy sampling are built based on conventional staircase and stress step methods, reducing the requirement of prior knowledge for data collection. The Bayesian Staircase method shows improved parameter estimation efficiency, and the Bayesian Stress Step method shows equal accuracy to the standard method at larger step size allowing experimentalists to lessen concerns of loading history. Statistical methods for determining model suitability are shown, highlighting the influence of protocol. Experimental validation is performed, showing the applicability of the methods in laboratory testing.

36 MATERIALS SCIENCE↗

The optimization of high resolution topographic data for 1D hydrodynamic models

The main focus of our research presented in this paper is to optimize and use high resolution topographical data (HRTD) for hydrological modelling. Optimization of HRTD is done by generating adaptive mesh by measuring distance of coarse mesh and the surface of the dataset and adapting the mesh from the perspective of keeping the geometry as close to initial resolution as possible. Technique described in this paper enables computation of very accurate 1-D hydrodynamic models. In the paper, we use HEC-RAS software as a solver. For comparison, we have chosen the amount of generated cells/grid elements (in whole discretization domain and selected cross sections) with respect to preservation of the accuracy of the computational domain. Generation of the mesh for hydrodynamic modelling is strongly reliant on domain size and domain resolution. Topographical dataset used in this paper was created using LiDAR method and it captures 5.9km long section of a catchment of the river Olše. We studied crucial changes in topography for generated mesh. Assessment was done by commonly used statistical and visualization methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

A Qualitative Strategy for Fusion of Physics into Empirical Models for Process Anomaly Detection

To facilitate the automated online monitoring of power plants, a systematic and qualitative strategy for anomaly detection is presented. This strategy is essential to provide credible reasoning on why and when an empirical versus hybrid (i.e., physics-supported) approach should be used and to determine the ideal mix of these two approaches for a defined anomaly detection scope. Empirical methods are usually based on pattern, statistical, and causal inference. Hybrid methods include the use of physics models to train and test data methods, reduce data dimensionality, reduce data-model complexity, augment data, and reduce empirical uncertainty; hybrid methods also include the use of data to tune physics models. The presented strategy is driven by key decision points related to data relevance, simple modeling feasibility, data inference, physics-modeling value, data dimensionality, physics knowledge, method of validation, performance, data availability, and suitability for training and testing, cause-effect, entropy inference, and model fitting. The strategy is demonstrated through a pilot use case for the application of anomaly detection to capture a valve packing leak at the high-pressure coolant injection system of a nuclear power plant.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

An Analysis Methodology for the Gamma-ray Large Area Space Telescope

The Large Area Telescope (LAT) instrument on the Gamma Ray Large Area Space Telescope (GLAST) has been designed to detect high-energy gamma rays and determine their direction of incidence and energy. We propose a reconstruction algorithm based on recent advances in statistical methodology. This method, alternative to the standard event analysis inherited from high energy collider physics experiments, incorporates more accurately the physical processes occurring in the detector, and makes full use of the statistical information available. It could thus provide a better estimate of the direction and energy of the primary photon.

Morris, Robin D.↗

Prediction of slant path rain attenuation statistics at various locations

The paper describes a method for predicting slant path attenuation statistics at arbitrary locations for variable frequencies and path elevation angles. The method involves the use of median reflectivity factor-height profiles measured with radar as well as the use of long-term point rain rate data and assumed or measured drop size distributions. The attenuation coefficient due to cloud liquid water in the presence of rain is also considered. Absolute probability fade distributions are compared for eight cases: Maryland (15 GHz), Texas (30 GHz), Slough, England (19 and 37 GHz), Fayetteville, North Carolina (13 and 18 GHz), and Cambridge, Massachusetts (13 and 18 GHz).

Goldhirsh, J.↗

Statistical mechanics of 'negative temperature' states

Consideration of the dynamics of a two-dimensional guiding center plasma, recently shown by Taylor and McNamara (1971) to be identical to the dynamics of the discrete vortex model of Onsager (1949). A semirigorous application of the methods of equilibrium statistical mechanics to the guiding center plasma (or equivalently, the line vortex system) is presented. An adaptation of the apparatus of the theory of probability is attempted, in the form given by Khinchin (1949) to obtain ensemble-average predictions for the states of the guiding center plasma. Interest focuses primarily on the regime in which the interaction energy is high enough to be above the Onsager 'negative temperature' threshold.

Montgomery, D.↗

Pattern recognition of satellite cloud imagery for improved weather prediction

The major accomplishment was the successful development of a method for extracting time derivative information from geostationary meteorological satellite imagery. This research is a proof-of-concept study which demonstrates the feasibility of using pattern recognition techniques and a statistical cloud classification method to estimate time rate of change of large-scale meteorological fields from remote sensing data. The cloud classification methodology is based on typical shape function analysis of parameter sets characterizing the cloud fields. The three specific technical objectives, all of which were successfully achieved, are as follows: develop and test a cloud classification technique based on pattern recognition methods, suitable for the analysis of visible and infrared geostationary satellite VISSR imagery; develop and test a methodology for intercomparing successive images using the cloud classification technique, so as to obtain estimates of the time rate of change of meteorological fields; and implement this technique in a testbed system incorporating an interactive graphics terminal to determine the feasibility of extracting time derivative information suitable for comparison with numerical weather prediction products.

Gautier, Catherine↗

Statistical searches for microlensing events in large, non-uniformly sampled time-domain surveys: A test using palomar transient factory data

Many photometric time-domain surveys are driven by specific goals, such as searches for supernovae or transiting exoplanets, which set the cadence with which fields are re-imaged. In the case of the Palomar Transient Factory (PTF), several sub-surveys are conducted in parallel, leading to non-uniform sampling over its ∼20,000 deg{sup 2} footprint. While the median 7.26 deg{sup 2} PTF field has been imaged ∼40 times in the R band, ∼2300 deg{sup 2} have been observed >100 times. We use PTF data to study the trade off between searching for microlensing events in a survey whose footprint is much larger than that of typical microlensing searches, but with far-from-optimal time sampling. To examine the probability that microlensing events can be recovered in these data, we test statistics used on uniformly sampled data to identify variables and transients. We find that the von Neumann ratio performs best for identifying simulated microlensing events in our data. We develop a selection method using this statistic and apply it to data from fields with >10 R-band observations, 1.1 × 10{sup 9} light curves, uncovering three candidate microlensing events. We lack simultaneous, multi-color photometry to confirm these as microlensing events. However, their number is consistent with predictions for the event rate in the PTF footprint over the survey's three years of operations, as estimated from near-field microlensing models. This work can help constrain all-sky event rate predictions and tests microlensing signal recovery in large data sets, which will be useful to future time-domain surveys, such as that planned with the Large Synoptic Survey Telescope.

79 ASTRONOMY AND ASTROPHYSICS↗

Neutron and Gamma Correlations using CGM in MCNP 6.2.0

The general-purpose Monte Carlo radiation-transport code MCNP6{sup TM} came from the integration of MCNP5{sup TM} and MCNPX{sup TM}. The most recent release of MCNP, version 6.2.0, is scheduled for release in early 2017, which includes a variety of bug fixes and new features to the code. MCNP traditionally models nuclear reactions using Monte Carlo sampling techniques on measured and modeled cross-sectional data contained within ACE (A Compact Evaluated Nuclear Data File) libraries. In addition to reaction cross-sections, ACE libraries contain information relating to the production of secondary particles, such as secondary neutrons and photons. For example, an incident neutron on a nucleus can produce a nuclear reaction in the form (n, M{sub n}n'), where n is the incident neutron and M{sub n} is the number of secondary neutrons n' produced. Using this notation, different reactions can be described based on their neutron multiplicity, such as neutron capture (M{sub n} = 0), elastic and inelastic scattering (M{sub n} = 1), and reactions with multiple secondary neutrons (M{sub n} > 1). Accounting for secondary γ-rays emitted from the residual nuclei, this reaction can further be generalized as n, Mnn'M to describe a reaction producing M{sub n} neutrons and M -rays. These values M{sub n} and M are referred to as the neutron and multiplicities, respectively. ACE libraries contain the cross-sectional data for each reaction, and their corresponding statistically averaged multiplicities for neutrons and photons, M-bar{sub n} and M-bar{sub γ}. However, there are several limitations to reaction sampling using ACE libraries. First, the data contained within ACE libraries is limited by the accuracy of the model and/or experiment, which out of necessity can greatly simplify the true physics behind a reaction. For example, the value M{sub γ} in a (n, M{sub n}n'M{sub γ}γ) reaction is determined by the statistically averaged multiplicity M-bar{sub γ} instead of a distribution. Consequently, MCNP, unable to produce a continuous distribution, will utilizes a binary sampling around M-bar{sub γ}. While this sampling method provides a statistically average M{sub γ} over a large simulation, it is an inaccurate representation of an individual reaction and its corresponding secondary particles. Secondary neutrons are affected in a similar manner, such that different kinds of secondary neutrons can be sampled from the same interaction (eg., an inelastic neutron with an [n, 2n] neutron). Lastly, the random sampling technique for secondary particles remains completely independent of the sampled reaction, eliminating the ability to correlate secondary particles for a given reaction. To supplement these data libraries, additional codes and models describing certain nuclear reactions are employed. These codes can fill in the information missing from ACE, provide a better model to the true physics distribution, and can provide true correlated secondary particles, which has many useful applications in research and industry.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Time series modeling of human operator dynamics in manual control tasks

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency responses of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that has not been previously modeled to demonstrate the strengths of the method.

Biezad, D. J.↗

Time Series Modeling of Human Operator Dynamics in Manual Control Tasks

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency response of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that was previously modeled to demonstrate the strengths of the method.

Biezad, D. J.↗

Validation Testing and Statistical Analysis of the Rotary Tumbler Fabric Abrasion Method

The Artemis space suit glove environmental protection garment (EPG) will be the first line of protection used to shield the crewmember’s hands from the environments encountered during extravehicular activity (EVA). As the Artemis missions will include more extreme environments than those experienced on the International Space Station, development, verification, and validation of gloves requires the development of new test methods. A previous paper focused on the development of a test procedure to characterize lunar EVA glove fabrics using ASTM standardized test methods and the design and validation of a new standardized test procedure for comparing abrasion resistance between fabrics using a dust and rock filled rotary tumbler. Preliminary results of testing were presented in that paper. This paper reports on the validation testing and statistical analysis of the newly developed tumbler abrasion test method.

Robert J Jones↗

A continuous symmetry breaking measure for finite clusters using Jensen-Shannon divergence

A quantitative measure of symmetry breaking is introduced that allows the quantification of which symmetries are most strongly broken due to the introduction of some kind of defect in a perfect structure. The method uses a statistical approach based on the Jensen-Shannon divergence. The measure is calculated by comparing the transformed atomic density function with its original. Software code is presented that carries the calculations out numerically using Monte Carlo methods. The behavior of this symmetry breaking measure is tested for various cases including finite size crystallites (where the surfaces break the crystallographic symmetry), atomic displacements from high symmetry positions, and collective motions of atoms due to rotations of rigid octahedra. Finally, the approach provides a powerful tool for assessing local symmetry breaking and offers new insights that can help researchers understand how different structural distortions affect different symmetry operations.

atomic & molecular structure↗

Level density of the sd-nuclei—Statistical shell-model predictions

Accurate knowledge of the nuclear level density is important both from a theoretical viewpoint as a powerful instrument for studying nuclear structure and for numerous applications. For example, astrophysical reactions responsible for the nucleosynthesis in the universe can be understood only if we know the nuclear level density. We use the configuration-interaction nuclear shell model to predict nuclear level density for all nuclei in the sd-shell, both total and for individual spins (only with positive parity). To avoid the diagonalization in large model spaces we use the moments method based on statistical properties of nuclear many-body systems. In the cases where the diagonalization is possible, the results of the moments method practically coincide with those from the shell-model calculations. Using the computed level densities, we fit the parameters of the Constant Temperature phenomenological model, which can be used by practitioners in their studies of nuclear reactions at excitation energies appropriate for the sd-shell nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SU-E-T-56: A Novel Approach to Computing Expected Value and Variance of Point Dose From Non-Gated Radiotherapy Delivery

Purpose: Randomness in patient internal organ motion phase at the beginning of non-gated radiotherapy delivery may introduce uncertainty to dose received by the patient. Concerns of this dose deviation from the planned one has motivated many researchers to study this phenomenon although unified theoretical framework for computing it is still missing. This study was conducted to develop such framework for analyzing the effect. Methods: Two reasonable assumptions were made: a) patient internal organ motion is stationary and periodic; b) no special arrangement is made to start a non -gated radiotherapy delivery at any specific phase of patient internal organ motion. A statistical ensemble was formed consisting of patient’s non-gated radiotherapy deliveries at all equally possible initial organ motion phases. To characterize the patient received dose, statistical ensemble average method is employed to derive formulae for two variables: expected value and variance of dose received by a patient internal point from a non-gated radiotherapy delivery. Fourier Series was utilized to facilitate our analysis. Results: According to our formulae, the two variables can be computed from non-gated radiotherapy generated dose rate time sequences at the point’s corresponding locations on fixed phase 3D CT images sampled evenly in time over one patient internal organ motion period. The expected value of point dose is simply the average of the doses to the point’s corresponding locations on the fixed phase CT images. The variance can be determined by time integration in terms of Fourier Series coefficients of the dose rate time sequences on the same fixed phase 3D CT images. Conclusion: Given a non-gated radiotherapy delivery plan and patient’s 4D CT study, our novel approach can predict the expected value and variance of patient radiation dose. We expect it to play a significant role in determining both quality and robustness of patient non-gated radiotherapy plan.

60 APPLIED LIFE SCIENCES↗