Partial AUC Estimation and Regression

Accurate disease diagnosis is critical for health care. New diagnostic and screening tests must be evaluated for their abilities to discriminate disease from non-diseased states. The partial area under the ROC curve (partial AUC) is a measure of diagnostic test accuracy. We present an interpretation of the partial AUC that gives rise to a new non-parametric estimator. This estimator is more robust than existing estimators, which make parametric assumptions. We show that the robustness is gained with only a moderate loss in efficiency. We describe a regression modelling framework for making inference about covariate effects on the partial AUC. Such models can help refine an understanding of test accuracy. Model parameters can be estimated using binary regression methods. We use the regression framework to compare two Prostate-Specific Antigen biomarkers and to evaluate the dependence of biomarker accuracy on the time prior to clinical diagnosis of prostate cancer

Semi-parametric Regression for the Area Under the Receiver Operating Characteristic Curve

Medical advances continue to provide new and potentially better means for detecting disease. Such is true in cancer, for example, where biomarkers are sought for early detection and where improvements in imaging methods may pick up the initial functional and molecular changes associated with cancer development. In other binary classification tasks, computational algorithms such as Neural Networks, Support Vector Machines and Evolutionary Algorithms have been applied to areas as diverse as credit scoring, object recognition, and peptide-binding prediction. Before a classifier becomes an accepted technology, it must undergo rigorous evaluation to determine its ability to discriminate between states. Characterization of factors influencing classier performance is an important step in this process. Analysis of covariates may reveal sub-populations in which classifier performance is greatest or identify features of the classifier that improve accuracy. We develop regression methods for the non-parametric area under the ROC curve, a well-accepted summary measure of classifier accuracy. The estimating function generalizes standard approaches, and, interestingly, is related to the two-sample Mann-Whitney U-statistic. Implementation is straightforward as it is an adaptation of binary regression methods. Asymptotic theory is non-standard because the regressor variables are cross-correlated. Nevertheless, simulation studies show the method produces estimates with small bias and reasonable coverage probability. Application of the method to evaluate the covariate effects on a new device for diagnosing hearing impairment reveals that the device performs better in the more severely impaired subjects and that certain test parameters, which are adjustable by the device operator, are key to test performance

Gapless finite-TT theory of collective modes of a trapped gas

We present predictions for the frequencies of collective modes of trapped Bose-condensed $^{87}$Rb atoms at finite temperature. Our treatment includes a self-consistent treatment of the mean-field from finite-$T$ excitations and the anomolous average. This is the first gapless calculation of this type for a trapped Bose-Einstein condensed gas. The corrections quantitatively account for the downward shift in the $m=2$ excitation frequencies observed in recent experiments as the critical temperature is approached.Comment: 4 pages Latex and 2 postscript figure

PUPHS2D 2.0 User\u27s Manual

The Purdue University Program for Heterostructure Simulation in Two Dimensions (PUPHS2D) solves Poisson\u27s equation and the electron and hole continuity equations within a two-dimensional heterostructure device. The program will compute the electrostatic potential, electron and hole densities, recombination rate, and other quantities of interest as a function of applied bias. Like its predecessor, version 2.0 allows extensive analysis of solar cells, including computation of the current-voltage characteristics of two-terminal devices, solar cell parameters, quantum efficiency, and current versus solar intensity. Extensions to version 2.Q include transient analysis and bipolar transistor capability. The heterojunction bipolar transistor routines allow computation of dc currents as a function of applied bias, as well as quasi-static evaluation of the high-frequency behavior. A simplified energy balance equation has been added in the interest of more accurately computing high-field characteristics, and should be viewed as a preliminary step toward this goal. PUPHS2D stands as an accurate model for computing low-field device characteristics and recombinative losses. While PUPHS2D was written for the ternary AlxGai1-xAs, all material specific parameters are contained within a single subroutine (BANDX), except for absorption coefficient and carrier mobilities which are computed in subroutines ALGABS and SETMOB, respectively. Material-specific parameters used for the energy balance equation are found in subroutines INITMU and INITAU. The program may be readily modified to analyze other semiconductors. For a more thorough discussion of the theoretical basis and numerical implementation of PUPHS2D, the user is directed to the references. Materials parameters are described in reference [I]. Various phases of the development of PUPHS2D have been supported by the Semiconductor Research Corporation, Sandia National Laboratories/ the Eastman Kodak Company, and by Research Triangle Institute

FISH1D 2.1 User’s Manual

FISH1D is a computer program that solves the one-dimensional Poisson equation for electrostatic Fields In Semiconductor Heterostructures. The program will print or plot the electrostatic potential, electric field, electron and hole densities, dopant density, ionized dopant density, and other quantities of interest versus position at an applied bias voltage (assuming zero current). A capacitance or sheet carrier concentration versus voltage analysis may also be performed. While FISH1D was originally written for the ternary AlxGa1_xAs, it has been modified to simulate CdxHg1_xTe, ZnSe, GexSi1_x, and Si as well, and the program can be readily modified to analyze other semiconductors through the addition of new material subroutines or using the most recent option, the MATDEF card. This card enables the user to enter new material definitions by layers in the input deck without having to recompile, an advantage of FISH1D 2.1 over FISH1D 2.0. The primary purpose of this document is explain how to use FISH1D; for a more thorough discussion of the numerical implementation of FISH1D, the user is directed to the references. A theoretical basis for FISH1D is provided in Appendix I of this manual. The development of FISH1D was supported by the Semiconductor Research Corporation, the National Science Foundation Materials Research Laboratory, and by the Eastman Kodak Company

Coherent control of stimulated Raman scattering using chirped laser pulses

A novel method for the control of stimulated Raman scattering and hot electron production in short-pulse laser-plasma interactions is proposed. It relies on the use of a linear frequency chirp in nonbandwidth limited pulses. Theoretical calculations show that a 12% bandwidth will eliminate Raman forward scattering for a plasma density that is 1% of the critical density. The predicted changes to the growth rate are confirmed in two-dimensional particle-in-cell simulations. Relevance to areas of current research is also discussed. © 2001 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/70620/2/PHPAEN-8-8-3531-1.pd

Damped Bogoliubov excitations of a condensate interacting with a static thermal cloud

We calculate the damping of condensate collective excitations at finite temperatures arising from the lack of equilibrium between the condensate and thermal atoms. We neglect the non-condensate dynamics by fixing the thermal cloud in static equilibrium. We derive a set of generalized Bogoliubov equations for finite temperatures that contain an explicit damping term due to collisional exchange of atoms between the two components. We have numerically solved these Bogoliubov equations to obtain the temperature dependence of the damping of the condensate modes in a harmonic trap. We compare these results with our recent work based on the Thomas-Fermi approximation.Comment: 9 pages, 3 figures included. Submitted to PR