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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Informed total-error-minimizing priors: Interpretable cosmological parameter constraints despite complex nuisance effects

While Bayesian inference techniques are standard in cosmological analyses, it is common to interpret resulting parameter constraints with a frequentist intuition. This intuition can fail, for example, when marginalizing high-dimensional parameter spaces onto subsets of parameters, because of what has come to be known as projection effects or prior volume effects. We present the method of informed total-error-minimizing (ITEM) priors to address this problem. An ITEM prior is a prior distribution on a set of nuisance parameters, such as those describing astrophysical or calibration systematics, intended to enforce the validity of a frequentist interpretation of the posterior constraints derived for a set of target parameters (e.g., cosmological parameters). Our method works as follows. For a set of plausible nuisance realizations, we generate target parameter posteriors using several different candidate priors for the nuisance parameters. We reject candidate priors that do not accomplish the minimum requirements of bias (of point estimates) and coverage (of confidence regions among a set of noisy realizations of the data) for the target parameters on one or more of the plausible nuisance realizations. Of the priors that survive this cut, we select the ITEM prior as the one that minimizes the total error of the marginalized posteriors of the target parameters. As a proof of concept, we applied our method to the density split statistics measured in Dark Energy Survey Year 1 data. We demonstrate that the ITEM priors substantially reduce prior volume effects that otherwise arise and that they allow for sharpened yet robust constraints on the parameters of interest.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

A fixed mass method for the Kramers-Moyal expansion—Application to time series with outliers

Extraction of stochastic and deterministic components from empirical data—necessary for the reconstruction of the dynamics of the system—is discussed. We determine both components using the Kramers-Moyal expansion. In our earlier papers, we obtained large fluctuations in the magnitude of both terms for rare or extreme valued events in the data. Calculations for such events are burdened by an unsatisfactory quality of the statistics. In general, the method is sensitive to the binning procedure applied for the construction of histograms. Instead of the commonly used constant width of bins, we use here a constant number of counts for each bin. This approach—the fixed mass method—allows to include in the calculation events, which do not yield satisfactory statistics in the fixed bin width method. The method developed is general. To demonstrate its properties, here, we present the modified Kramers-Moyal expansion method and discuss its properties by the application of the fixed mass method to four representative heart rate variability recordings with different numbers of ectopic beats. These beats may be rare events as well as outlying, i.e., very small or very large heart cycle lengths. The properties of ectopic beats are important not only for medical diagnostic purposes but the occurrence of ectopic beats is a general example of the kind of variability that occurs in a signal with outliers. To show that the method is general, we also present results for two examples of data from very different areas of science: daily temperatures at a large European city and recordings of traffics on a highway. Using the fixed mass method, to assess the dynamics leading to the outlying events we studied the occurrence of higher order terms of the Kramers-Moyal expansion in the recordings. We found that the higher order terms of the Kramers-Moyal expansion are negligible for heart rate variability. This finding opens the possibility of the application of the Langevin equation to the whole range of empirical signals containing rare or outlying events. Note, however, that the higher order terms are non-negligible for the other data studied here and for it the Langevin equation is not applicable as a model.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Verification, Validation, and Calibration Through a Causal Lens

While typical validation and verification approaches focus on identifying the associations between data elements using statistical and machine learning methods, the novel methods in this paper focus instead on identifying causal relationships between data elements. Statistical and machine-learning-based approaches are strictly data-driven, meaning that they provide quantitative comparison measures between data sets without explicitly considering the hypotheses behind them. This can lead to the erroneous conclusion that, if two data sets are close enough, the models that generated them are similar. In addition, when experimental and simulated data differ to an extent that fails to meet the acceptance criteria, calibration techniques are used to tweak simulation model parameters to reduce the gap between the two types of data. This produces the false expectation that a simulation model will match reality. The methods presented in this paper move away from these strictly data-driven methods for validation and calibration toward more robust, model-driven methods based on causal inference. Causal inference aims to identify the possible mechanisms that might have generated data. Thus, this analysis targets the prediction of the effects when one (or more) of the identified mechanisms are altered. There are many approaches to identify, quantify, and illustrate causal relationships. For the scope of this paper, directed graphs are employed as causal models. If the directed graph lacks cycles, it is known as a directed acyclic graph. A node in such a graph represents an observed data element while a directed edge connecting two nodes represents a causal relationship between two variables. The developed causal methods are designed to extract causal models from simulation models and experimental data. Causal models capture the causal relationships between data elements (e.g., simulated and experimental data). In this context, validation and verification are performed by comparing causal models. The proposed approach does not only inform system analysts on how a simulation model matches real-world data, but also identifies elements of the simulation model that should be revised when discrepancies between simulation and experimental data are observed. Through these causal methods, analysts can identify the portion of the model equation(s) that are behind an edge connecting two variables. Hence, once the structural differences between causal models have been determined, model calibration can occur by changing only those model parameters that impact the identified causal relationships.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Assessment of software methods for estimating protein-protein relative binding affinities

A growing number of computational tools have been developed to accurately and rapidly predict the impact of amino acid mutations on protein-protein relative binding affinities. Such tools have many applications, for example, designing new drugs and studying evolutionary mechanisms. In the search for accuracy, many of these methods employ expensive yet rigorous molecular dynamics simulations. By contrast, non-rigorous methods use less exhaustive statistical mechanics, allowing for more efficient calculations. However, it is unclear if such methods retain enough accuracy to replace rigorous methods in binding affinity calculations. This trade-off between accuracy and computational expense makes it difficult to determine the best method for a particular system or study. Here, eight non-rigorous computational methods were assessed using eight antibody-antigen and eight non-antibody-antigen complexes for their ability to accurately predict relative binding affinities (ΔΔG) for 654 single mutations. In addition to assessing accuracy, we analyzed the CPU cost and performance for each method using a variety of physico-chemical structural features. This allowed us to posit scenarios in which each method may be best utilized. Most methods performed worse when applied to antibody-antigen complexes compared to non-antibody-antigen complexes. Rosetta-based JayZ and EasyE methods classified mutations as destabilizing (ΔΔG < -0.5 kcal/mol) with high (83–98%) accuracy and a relatively low computational cost for non-antibody-antigen complexes. Some of the most accurate results for antibody-antigen systems came from combining molecular dynamics with FoldX with a correlation coefficient (r) of 0.46, but this was also the most computationally expensive method. Overall, our results suggest these methods can be used to quickly and accurately predict stabilizing versus destabilizing mutations but are less accurate at predicting actual binding affinities. This study highlights the need for continued development of reliable, accessible, and reproducible methods for predicting binding affinities in antibody-antigen proteins and provides a recipe for using current methods.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Evaluating Space Object Conjunction Probabilities Using Characteristic Function Inversion

This report discusses an approach to computing the probability of a conjunction between two space objects in the short-term encounter scenario. A conjunction is defined here as an event where the miss distance between the objects is less than some specified value. The scenario assumptions are that the motion of the objects is linear, their positions are Gaussian distributed, and their velocities are known and constant. Under these assumptions, the squared-miss distance is shown to have the generalized chi-square distribution. An established statistical technique called characteristic function inversion is employed to evaluate the distribution and obtain conjunction probabilities. The method is closely related to a recent approach based on moment generating function inversion, and a qualitative comparison of the approaches is provided. Last, the method is tested on several benchmark test cases where it agrees with numerical integration on the cases with conjunction probabilities above 10 –12 . However, the exact probability in these cases is usually not needed and this probability can be bounded above using an independent Gaussian approximation. Overall, the report shows how to compute conjunction probabilities using a standard statistical method, though numerical integration seems to perform equally well.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

An algebraic method for constructing stable and consistent autoregressive filters

In this paper, we introduce an algebraic method to construct stable and consistent univariate autoregressive (AR) models of low order for filtering and predicting nonlinear turbulent signals with memory depth. By stable, we refer to the classical stability condition for the AR model. By consistent, we refer to the classical consistency constraints of Adams–Bashforth methods of order-two. One attractive feature of this algebraic method is that the model parameters can be obtained without directly knowing any training data set as opposed to many standard, regression-based parameterization methods. It takes only long-time average statistics as inputs. The proposed method provides a discretization time step interval which guarantees the existence of stable and consistent AR model and simultaneously produces the parameters for the AR models. In our numerical examples with two chaotic time series with different characteristics of decaying time scales, we find that the proposed AR models produce significantly more accurate short-term predictive skill and comparable filtering skill relative to the linear regression-based AR models. These encouraging results are robust across wide ranges of discretization times, observation times, and observation noise variances. Finally, we also find that the proposed model produces an improved short-time prediction relative to the linear regression-based AR-models in forecasting a data set that characterizes the variability of the Madden–Julian Oscillation, a dominant tropical atmospheric wave pattern.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Systematic and statistical uncertainties of the hilbert-transform based high-precision FID frequency extraction method

Pulsed nuclear magnetic resonance (NMR) is widely used in high-precision magnetic field measurements. The absolute value of the magnetic field is determined from the precession frequency of nuclear magnetic moments. The Hilbert transform is widely used to extract the phase function from the observed free induction decay (FID) signal and then its frequency. In this paper, a detailed implementation of a Hilbert-transform based FID frequency extraction method is described. How artifacts and noise level in the FID signal affect the extracted phase function are derived analytically. A method of mitigating the artifacts in the extracted phase function of an FID is discussed. Correlations between noises of the phase function samples are studied for different noise spectra. We discovered that the error covariance matrix for the extracted phase function is nearly singular and improper for constructing the $\chi^2$ used in the fitting routine. A down-sampling method for fixing the singular covariance matrix has been developed, so that the minimum $\chi^2$-fit yields properly the statistical uncertainty of the extracted frequency. Other practical methods of obtaining the statistical uncertainty are also discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2018

Measuring greenhouse gas emissions from international air travel of a country’s residents methodological development and application for Sweden

Highlights: • A new method for estimating a country's GHG emissions from international air travel. • A reliable method based on total statistics of departures and on surveys for distance to final destination. • Total emissions for Swedish residents' air travel increased by 61% between 1990 and 2014 • In 2014 Swedish residents air travel emissions was on par with emissions from Swedish car traffic - Abstract: Global civil aviation accounts for 4–5% of total greenhouse gas emissions and these emissions are increasing. In the absence of sufficiently effective global climate instruments, national instruments might be considered as a complement, in which case some way of allocating emissions from international air travel between countries is needed. The purpose of this paper is to develop an accounting method that reflects one country's greenhouse gas emissions from international air travel, and to apply this methodology to Sweden. The new methodology consists of three parts: the number of international air trips made by the country's residents; the average distance of these trips; and the greenhouse gas emissions per passenger km. For Sweden, data for 1990 to 2014 show an increase in the number of trips by Sweden's population of 3.6% per year, resulting in, on average, one international journey (round trip 5800 km) per capita in 2014. The average distance to the final destination has increased only marginally due to simultaneous growth in both long and short trips. However, global average greenhouse gas emissions per passenger km have decreased by 1.9% per year between 1990 and 2014. Because the increase in the number of their trips has outweighed the decrease in emissions per km, the total emissions from Swedish residents' international air travel have increased by 61% between 1990 and 2014. The total emissions from Swedish residents' air travel, including both CO{sub 2} and non-CO{sub 2}-effects, were 11 Mt CO{sub 2} equivalents in 2014, which is the same level as the emissions from Swedish car traffic. This type of reliable data is important when designing policies and for getting public support for new policies.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Survey of Image Denoising Methods for Medical Image Classification

Medical imaging devices, such as X-ray machines, inherently produce images that suffer from visual noise. Our objectives were to (i.) determine the effect of image denoising on a medical image classification task, and (ii.) determine if there exists a correlation between image denoising performance and medical image classification performance. We performed the medical image classification task on chest X-rays using the DenseNet-121 convolutional neural network (CNN) and used the peak signal-to-noise ratio (PSNR) and structural similarity (SSIM) metrics as the image denoising performance measures. We first found that different denoising methods can make a statistically significant difference in classification performance for select labels. We also found that denoising methods affect fine-tuned models more than randomly-initialized models and that fine-tuned models have significantly higher and more uniform performance than randomly-initialized models. Lastly, we found that there is no significant correlation between PSNR and SSIM values and classification performance for our task.

Michael, Peter↗
DOE OSTI2017

Measuring the Properties of Dark Energy with Photometrically Classified Pan-STARRS Supernovae. I. Systematic Uncertainty from Core-collapse Supernova Contamination

The Pan-STARRS (PS1) Medium Deep Survey discovered over 5000 likely supernovae (SNe) but obtained spectral classifications for just 10% of its SN candidates. We measured spectroscopic host galaxy redshifts for 3147 of these likely SNe and estimate that ∼1000 are Type Ia SNe (SNe Ia) with light-curve quality sufficient for a cosmological analysis. We use these data with simulations to determine the impact of core-collapse SN (CC SN) contamination on measurements of the dark energy equation of state parameter, w. Using the method of Bayesian Estimation Applied to Multiple Species (BEAMS), distances to SNe Ia and the contaminating CC SN distribution are simultaneously determined. We test light-curve-based SN classification priors for BEAMS as well as a new classification method that relies upon host galaxy spectra and the association of SN type with host type. By testing several SN classification methods and CC SN parameterizations on large SN simulations, we estimate that CC SN contamination gives a systematic error on w (σ{sub w}{sup CC}) of 0.014, 29% of the statistical uncertainty. Our best method gives σ{sub w}{sup CC}=0.004, just 8% of the statistical uncertainty, but could be affected by incomplete knowledge of the CC SN distribution. This method determines the SALT2 color and shape coefficients, α and β, with ∼3% bias. However, we find that some variants require α and β to be fixed to known values for BEAMS to yield accurate measurements of w. Finally, the inferred abundance of bright CC SNe in our sample is greater than expected based on measured CC SN rates and luminosity functions.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Highly accelerated life testing (HALT): A review from a statistical perspective

Despite its use in one form or another for at least four decades, HALT and related techniques [e.g., highly accelerated-stress screening (HASS) and stress audits (HASA)] are not well understood within the statistical community and remain controversial. This largely reflects a conflict in motivation between engineers, testing under harsh conditions to discover and eliminate failure modes, and statisticians, taking a more cautious approach to develop quantitative estimates of parameters such as mean time between failures (MTBF). Here, this review article will clarify HALT concepts and methods and explain where it fits within the universe of methods that involve the application of accelerating factors to compress the time required to evaluate or enhance product reliability. A major distinction is between methods such as HALT, a high-stress test-analyze-fix-test iterative process directed at improving reliability by discovering and fixing weak points in a design, and quantitative accelerated life testing (QALT), whose goal is the estimation of product life for a fixed design. We discuss methods such as physics of failure that offer some hope of bridging the gap between the qualitative nature of HALT, and purely quantitative statistical methods. We present a variety of engineering applications of HALT including metal fatigue, piping and pressure vessels, structural damage, radiation damage, and rotating machinery. We also discuss potential synergies between HALT and QALT, such as rapid identification, through HALT, of failure modes requiring quantitative analysis. For further study, extensive references to the applicable literature are provided as well as an appendix that describes related methods.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Measuring representative volume elements from high-resolution grain-scale strain fields

Most crystalline materials present a highly heterogeneous response at the microscale, which can be affected by both internal factors (such as microstructural parameters) and external factors (such as loading). Relating microscale inhomogeneities to the macroscale response of a material requires the use of homogenisation techniques, usually based on the concept of a representative volume element (RVE)—the smallest volume of material that represents the global average response. Here, in this work, we present a new and robust experimental method of measuring the size of a strain-based RVE from high-resolution grain-scale strain fields obtained using digital image correlation (DIC). The proposed method is based on the statistical (stereological) nature of the RVE, which has been widely adopted in numerical studies, and involves dividing a strain field into randomly selected regions of varying sizes and statistically analysing the distributions of average strains within them. To validate the new method, we generate a large number of synthetic strain fields from a fractional Gaussian noise algorithm. The proposed stereological method is shown to be capable of producing reliable RVE measurements from a very large range of possible microscale strain fields while at the same time being robust in that it can produce RVE measurement results even in cases where other existing methods may be unable to do so. The proposed method has a low field-of-view requirement, only needing a field-of-view about 1.2 times as large as the RVE to produce reliable measurements. In addition, the stereological method offers significant flexibility since its statistical nature allows for control over how strict the RVE measurement should be in each case.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Upper Subcritical Limit Calculations with Correlated Integral Experiments

The American National Standards Institute (ANSI) and American Nuclear Society (ANS) standard for Validation of Neutron Transport Methods for Nuclear Criticality Safety Calculations defines the Upper Subcritical Limit (USL) as “a limit on the calculated k effective value established to ensure that conditions calculated to be subcritical will actually be subcritical.” Often, USL calculations are based on statistical techniques that infer information about a nuclear system of interest (application) from a set of known/well characterized similar systems (experiments). In determining a USL, it is common to statistically determine a calculation bias and bias uncertainty. Bias is “the systematic difference between calculated results and experimental data.” The bias uncertainty is “the uncertainty that accounts for the combined effects of uncertainties in the benchmarks, the calculational models of the benchmarks, and the calculational methods.” Both the bias and the bias uncertainty are often inferred through statistical methods applied to the selected set of experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Validating Nuclear Data Uncertainties Obtained from a Statistical Analysis of Experimental Data with the “Physical Uncertainty Bounds” Method

Concerns within the nuclear data community led to substantial increases of Neutron Data Standards (NDS) uncertainties from its previous to the current version. For example, those associated with the NDS reference cross section 239 Pu(n,f) increased from 0.6–1.6% to 1.3–1.7% from 0.1–20 MeV. These cross sections, among others, were adopted, e.g., by ENDF/B-VII.1 (previous NDS) and ENDF/B-VIII.0 (current NDS). There has been a strong desire to be able to validate these increases based on objective criteria given their impact on our understanding of various application uncertainties. Here, the “Physical Uncertainty Bounds” method (PUBs) by Vaughan et al. is applied to validate evaluated uncertainties obtained by a statistical analysis of experimental data. We investigate with PUBs whether ENDF/B-VII.1 or ENDF/B-VIII.0 239 Pu(n,f) cross-section uncertainties are more realistic given the information content used for the actual evaluation. It is shown that the associated conservative (1.5–1.8%) and minimal realistic (1.1–1.3%) uncertainty bounds obtained by PUBs enclose ENDF/B-VIII.0 uncertainties and indicate that ENDF/B-VII.1 uncertainties are underestimated.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Hawai‘i Play Fairway (Final Report)

Most of Hawai'i's geothermal resources are blind—their manifestations, such as hot springs and steam vents, do not appear on the ground surface because the heated water flows far below. With the exception of $K\bar{i}lauea East Rift Zone$, in most areas of Hawai'i, high lateral permeability in the first kilometer below ground surface prevents surface thermal features from developing. As a methodology for discovering these blind resources, Play Fairway Analysis (PFA) involves finding potential locations of blind hydrothermal systems and describing potential geothermal sources in rift-zone settings. Using the PFA to find Hawai'i's geothermal resources, the University of Hawai'i (UH) conducted the Hawai‘i Play Fairway Project, Hawai'i's first statewide geothermal resource assessment since 1985. Sponsored by the U.S. Department of Energy, the Hawai'i Play Fairway Project provided an updated resource assessment, a roadmap for additional exploration activities, and the identification of areas for further exploration. Benefitting from UH's core competency in earth sciences and experienced geothermal researchers, the project comprised three phases. During the first phase, the team identified, compiled, and ranked existing geologic, groundwater, and geophysical datasets relevant to subsurface heat, fluid and permeability. Using a Bayesian statistical approach, the team developed a statistical methodology to integrate these data into a resource probability map. The team evaluated the confidence in the probability value and considered development viability of areas with geothermal resources. With these analyses, the team identified 10 locations in the Hawaiian Islands for exploration activities. For the second phase, the team collected new groundwater data in 10 locations across the state and new geophysical data on $L\bar{a}na‘i, Maui$, and central Hawai'i Island and modeled topographically induced stress to better characterize subsurface permeability. Analyzing the subsurface stresses, the team evaluated the potential for fracture-induced permeability. The team inverted the MT and gravity data to produce 3D models of resistivity and density, respectively, on $L\bar{a}na‘i$, across $Haleakal\bar{a}'s$ SW rift (Maui), and surrounding Mauna Kea (Hawai‘i Island). The team developed and applied a new method for incorporating depth information about resistivity, density, and potential for fracture-induced permeability into the statistical method for computing resource probability in these three focus areas. The team incorporated the new groundwater results with the new geophysical results and the calculations of potential for fracture-induced permeability to produce updated maps of resource probability and confidence. Through combining data from the first and second phases, the team determined locations for further exploration during the third phase. For MT and gravity surveys, the team recommended $Kaua'i's$ $L\bar{i}hu'e$ $Basin$, the east rift of $Maui's$ $Haleakal\bar{a}$ volcano, and the southwest rift of Hawai'i Island's Mauna Loa volcano. The MT and gravity surveys aimed to enable improved confidence in the resource potential in these locations. For drilling deep groundwater well(s), the team recommended Southeast Mauna Kea and $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$. During the third phase, further exploration involved drilling a groundwater well in $L\bar{a}na's$ $P\bar{a}l\bar{a}wai$ $Basin$ and performing more geophysical surveys. We deepened an existing water well proximal to our target area on $L\bar{a}na'i$ due to funding constraints that precluded us from spudding a new well that would exceed 1km depth. Drilling was preceded by a number of substantial elements including: writing an Environmental Assessment and the subsequent legal process, performance of deviation logging, lowering a camera down the well, coordinating site preparation with $P\bar{u}lama$ $L\bar{a}na'i$, shipping the UH-owned rig interisland, procuring supplies, and leading 3 community meetings on $L\bar{a}na'i$. Drilling occurred 24/7 the entire month of June 2019 over which time $L\bar{a}na'i$ $Well$ 10 was deepened from 427 m to 1057 m, with continuous core collected. We measured a roughly linear temperature gradient averaging 42°C/km and a maximum bottom hole temperature of 66°C. This gradient is more than twice the background for Hawai'i and within a range of gradients measured in this depth range for some exploration wells within KERZ. We consider these results encouraging for $L\bar{a}na'i's$ resource potential and recommend following with a slim hole within $L\bar{a}na'i's$ caldera (our target zone) to ~ 2 km. Further, the positive implications such results have for the island of O‘ahu are substantial - the shield stage of O'ahu's volcanoes ended 1-2 My earlier. However, O'ahu uses more electricity than the rest of the islands combined, and the utility recently called for 500-700MW of firm, dispatchable renewable electricity on O'ahu by 2033. In Phase 3, we also collected limited new encouraging groundwater data, and updated our thoughts on the probabilities of fluid and permeability at resource depths (Pr F = 1; Pr P = mostly unconstrained). Ultimately, we advocate for using our final probability of heat, and confidence in this probability, to drive the next phase of exploration. We contend further development of geothermal in Hawai‘i will enable the state to achieve its 100% renewable policy objective and Hawai'i to transition off of fossil fuels through geothermal discovery and development. The project not only produced a large amount of data and expanded the existing knowledge of Hawai'i's geothermal resources, but also produced publications, theses, presentations, core photos, datasets, media reports, television interviews, community events, and a blog. Students and new professionals benefitted from the project's hands-on research experiences and educational opportunities and earned awards and recognition.

15 GEOTHERMAL ENERGY↗
DOE OSTI2020

Enhanced Co-Expression Extrapolation (COXEN) Gene Selection Method for Building Anti-Cancer Drug Response Prediction Models

The co-expression extrapolation (COXEN) method has been successfully used in multiple studies to select genes for predicting the response of tumor cells to a specific drug treatment. Here, we enhance the COXEN method to select genes that are predictive of the efficacies of multiple drugs for building general drug response prediction models that are not specific to a particular drug. The enhanced COXEN method first ranks the genes according to their prediction power for each individual drug and then takes a union of top predictive genes of all the drugs, among which the algorithm further selects genes whose co-expression patterns are well preserved between cancer cases for building prediction models. We apply the proposed method on benchmark in vitro drug screening datasets and compare the performance of prediction models built based on the genes selected by the enhanced COXEN method to that of models built on genes selected by the original COXEN method and randomly picked genes. Models built with the enhanced COXEN method always present a statistically significantly improved prediction performance (adjusted p-value ≤ 0.05). Our results demonstrate the enhanced COXEN method can dramatically increase the power of gene expression data for predicting drug response.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MODELING THE Ly α FOREST IN COLLISIONLESS SIMULATIONS

Cosmological hydrodynamic simulations can accurately predict the properties of the intergalactic medium (IGM), but only under the condition of retaining the high spatial resolution necessary to resolve density fluctuations in the IGM. This resolution constraint prohibits simulating large volumes, such as those probed by BOSS and future surveys, like DESI and 4MOST. To overcome this limitation, we present “Iteratively Matched Statistics” (IMS), a novel method to accurately model the Ly α forest with collisionless N -body simulations, where the relevant density fluctuations are unresolved. We use a small-box, high-resolution hydrodynamic simulation to obtain the probability distribution function (PDF) and the power spectrum of the real-space Ly α forest flux. These two statistics are iteratively mapped onto a pseudo-flux field of an N -body simulation, which we construct from the matter density. We demonstrate that our method can reproduce the PDF, line of sight and 3D power spectra of the Ly α forest with good accuracy (7%, 4%, and 7% respectively). We quantify the performance of the commonly used Gaussian smoothing technique and show that it has significantly lower accuracy (20%–80%), especially for N -body simulations with achievable mean inter-particle separations in large-volume simulations. In addition, we show that IMS produces reasonable and smooth spectra, making it a powerful tool for modeling the IGM in large cosmological volumes and for producing realistic “mock” skies for Ly α forest surveys.

79 ASTRONOMY AND ASTROPHYSICS↗