arXiv subjects
Publications and source records attributed to Jie Peng.
This is a note on logistic regression models and logistic kernel machine models. It contains derivations to some of the expressions in a paper -- SNP Set Analysis for Detecting Disease Association Using Exon Sequence Data -- submitted to BMC proceedings by these authors.
We present results of atomistic empirical pseudopotential calculations and configuration interaction for excitons, positive and negative trions (X\pm), positive and negative quartons (X2\pm) and biexcitons. The structure investigated are laterally aligned InGaAs quantum dot molecules embedded in GaAs under a lateral electric field. The rather simple energetic of excitons becomes more complex in the case of charged quasiparticles but remains tractable. The negative trion spectrum shows four anticrossings in the presently available range of fields while the positive trion shows two. The magnitude of the anticrossings reveals many-body effects in the carrier tunneling process that should be experimentally accessible.
We study the electronic and optical properties of laterally coupled InGaAs/GaAs quantum dot molecules under lateral electric field. We find that electrons perceive the double-dot structure as a compound single object, while the holes discern two well separated dots. Through a combination of predictive atomistic modeling, detailed morphology studies, and single object micro-photoluminescence measurements, we show that this peculiar confinement results in an unusual heterogeneous behavior of electrons and holes with profound consequences on optical properties.
In this paper, we study a kernel smoothing approach for denoising a tensor field. Particularly, both simulation studies and theoretical analysis are conducted to understand the effects of the noise structure and the structure of the tensor field on the performance of different smoothers arising from using different metrics, viz., Euclidean, log-Euclidean and affine invariant metrics. We also study the Rician noise model and compare two regression estimators of diffusion tensors based on raw diffusion weighted imaging data at each voxel.
In a recent paper (Efron (2004)), Efron pointed out that an important issue in large-scale multiple hypothesis testing is that the null distribution may be unknown and need to be estimated. Consider a Gaussian mixture model, where the null distribution is known to be normal but both null parameters--the mean and the variance--are unknown. We address the problem with a method based on Fourier transformation. The Fourier approach was first studied by Jin and Cai (2007), which focuses on the scenario where any non-null effect has either the same or a larger variance than that of the null effects. In this paper, we review the main ideas in Jin and Cai (2007), and propose a generalized Fourier approach to tackle the problem under another scenario: any non-null effect has a larger mean than that of the null effects, but no constraint is imposed on the variance. This approach and that in \cite{JC} complement with each other: each approach is successful in a wide class of situations where the other fails. Also, we extend the Fourier approach to estimate the proportion of non-null effects. The proposed procedures perform well both in theory and in simulated data.
In this paper, we propose a new method remMap -- REgularized Multivariate regression for identifying MAster Predictors -- for fitting multivariate response regression models under the high-dimension-low-sample-size setting. remMap is motivated by investigating the regulatory relationships among different biological molecules based on multiple types of high dimensional genomic data. Particularly, we are interested in studying the influence of DNA copy number alterations on RNA transcript levels. For this purpose, we model the dependence of the RNA expression levels on DNA copy numbers through multivariate linear regressions and utilize proper regularizations to deal with the high dimensionality as well as to incorporate desired network structures. Criteria for selecting the tuning parameters are also discussed. The performance of the proposed method is illustrated through extensive simulation studies. Finally, remMap is applied to a breast cancer study, in which genome wide RNA transcript levels and DNA copy numbers were measured for 172 tumor samples. We identify a tran-hub region in cytoband 17q12-q21, whose amplification influences the RNA expression levels of more than 30 unlinked genes. These findings may lead to a better understanding of breast cancer pathology.
In this paper, we propose a semi-parametric model for autonomous nonlinear dynamical systems and devise an estimation procedure for model fitting. This model incorporates subject-specific effects and can be viewed as a nonlinear semi-parametric mixed effects model. We also propose a computationally efficient model selection procedure. We prove consistency of the proposed estimator under suitable regularity conditions. We show by simulation studies that the proposed estimation as well as model selection procedures can efficiently handle sparse and noisy measurements. Finally, we apply the proposed method to a plant growth data used to study growth displacement rates within meristems of maize roots under two different experimental conditions.
In this paper, we propose a computationally efficient approach -- space(Sparse PArtial Correlation Estimation)-- for selecting non-zero partial correlations under the high-dimension-low-sample-size setting. This method assumes the overall sparsity of the partial correlation matrix and employs sparse regression techniques for model fitting. We illustrate the performance of space by extensive simulation studies. It is shown that space performs well in both non-zero partial correlation selection and the identification of hub variables, and also outperforms two existing methods. We then apply space to a microarray breast cancer data set and identify a set of hub genes which may provide important insights on genetic regulatory networks. Finally, we prove that, under a set of suitable assumptions, the proposed procedure is asymptotically consistent in terms of model selection and parameter estimation.
We propose a distance between two realizations of a random process where for each realization only sparse and irregularly spaced measurements with additional measurement errors are available. Such data occur commonly in longitudinal studies and online trading data. A distance measure then makes it possible to apply distance-based analysis such as classification, clustering and multidimensional scaling for irregularly sampled longitudinal data. Once a suitable distance measure for sparsely sampled longitudinal trajectories has been found, we apply distance-based clustering methods to eBay online auction data. We identify six distinct clusters of bidding patterns. Each of these bidding patterns is found to be associated with a specific chance to obtain the auctioned item at a reasonable price.
In this paper, we consider the problem of estimating the covariance kernel and its eigenvalues and eigenfunctions from sparse, irregularly observed, noise corrupted and (possibly) correlated functional data. We present a method based on pre-smoothing of individual sample curves through an appropriate kernel. We show that the naive empirical covariance of the pre-smoothed sample curves gives highly biased estimator of the covariance kernel along its diagonal. We attend to this problem by estimating the diagonal and off-diagonal parts of the covariance kernel separately. We then present a practical and efficient method for choosing the bandwidth for the kernel by using an approximation to the leave-one-curve-out cross validation score. We prove that under standard regularity conditions on the covariance kernel and assuming i.i.d. samples, the risk of our estimator, under $L^2$ loss, achieves the optimal nonparametric rate when the number of measurements per curve is bounded. We also show that even when the sample curves are correlated in such a way that the noiseless data has a separable covariance structure, the proposed method is still consistent and we quantify the role of this correlation in the risk of the estimator.
In this paper we consider two closely related problems : estimation of eigenvalues and eigenfunctions of the covariance kernel of functional data based on (possibly) irregular measurements, and the problem of estimating the eigenvalues and eigenvectors of the covariance matrix for high-dimensional Gaussian vectors. In Peng and Paul (2007), a restricted maximum likelihood (REML) approach has been developed to deal with the first problem. In this paper, we establish consistency and derive rate of convergence of the REML estimator for the functional data case, under appropriate smoothness conditions. Moreover, we prove that when the number of measurements per sample curve is bounded, under squared-error loss, the rate of convergence of the REML estimators of eigenfunctions is near-optimal. In the case of Gaussian vectors, asymptotic consistency and an efficient score representation of the estimators are obtained under the assumption that the effective dimension grows at a rate slower than the sample size. These results are derived through an explicit utilization of the intrinsic geometry of the parameter space, which is non-Euclidean. Moreover, the results derived in this paper suggest an asymptotic equivalence between the inference on functional data with dense measurements and that of the high dimensional Gaussian vectors.
We calculated the image potentials of single-walled carbon nanotubes of various structures in the condition of field emission with a quantum chemistry method. The image potential of the single-walled carbon nanotubes can be well fitted with the image potential of an ideal metal sphere in a size comparable to an atom. The image potential is not sensitive to both the applied field and the structure of the tube. When the image potential is included, the emission current would be one order larger.
The simulation of field electron emission from arrays of micrometer-long open-ended (5, 5) carbon nanotubes is performed in the framework of quantum theory of many electrons. It is found that the applied external field is strongly screened when the spacing distance is shorter than the length of the carbon nanotubes. The optimal spacing distance is two to three times of the nanotube length, slightly depending on the applied external fields. The electric screening can be described by a factor that is a exponential function of the ratio of the spacing distance to the length of the carbon nanotubes. For a given length, the field enhancement factor decreases sharply as the screening factor larger than 0.05. The simulation implies that the thickness of the array should be larger than a value but it does not help the emission much by increasing the thickness a great deal.
In this paper, we consider the problem of estimating the eigenvalues and eigenfunctions of the covariance kernel (i.e., the functional principal components) from sparse and irregularly observed longitudinal data. We approach this problem through a maximum likelihood method assuming that the covariance kernel is smooth and finite dimensional. We exploit the smoothness of the eigenfunctions to reduce dimensionality by restricting them to a lower dimensional space of smooth functions. The estimation scheme is developed based on a Newton-Raphson procedure using the fact that the basis coefficients representing the eigenfunctions lie on a Stiefel manifold. We also address the selection of the right number of basis functions, as well as that of the dimension of the covariance kernel by a second order approximation to the leave-one-curve-out cross-validation score that is computationally very efficient. The effectiveness of our procedure is demonstrated by simulation studies and an application to a CD4 counts data set. In the simulation studies, our method performs well on both estimation and model selection. It also outperforms two existing approaches: one based on a local polynomial smoothing of the empirical covariances, and another using an EM algorithm.
The field electron emission from the single-walled carbon nanotubes with their open ends terminated by -BH, -NH, and -O has been simulated. The apex-vacuum barrier and the emission current have been calculated. It has been found that -BH and -NH suppress the apex-vacuum barrier significantly and lead to higher emission current in contrast to the -O terminated structure in the same applied field. The calculated binding energy implies that the carbon nanotubes terminated with -BH and -NH are more stable than those saturated by oxygen atoms or by hydrogen atoms.
A 1 $μ$m long, field emitting, (5,5) single-walled, carbon nanotube (SWCNT) closed with a fullerene cap, and a similar open nanotube with hydrogen-atom termination, have been simulated using the MNDO (Modified Neglect of Diatomic Overlap) quantum-mechanical method. Both contain about 80 000 atoms. It is found that field penetration and band-bending, and various forms of chemically and electrically induced apex dipole, play roles. Field penetration may help to explain electroluminescence associated with field emitting carbon nanotubes. Charge-density oscillations, induced by the hydrogen adsorption, are also found. Many of the effects can be related to known effects that occur with metallic or semiconductor field emitters; this helps both to explain the effects and to unify our knowledge about field electron emitters. However, it is currently unclear how best to treat correlation-and-exchange effects when defining the CNT emission barrier. A new form of definition for the field enhancement factor (FEF) is used. Predicted FEF values for these SWCNTs are significantly less than values predicted by simple classical formulae. The FEF for the closed SWCNT decreases with applied field; the FEF for the H-terminated open SWCNT is less than the FEF for the closed SWCNT, but increases with applied field. Physical explanations for this behavior are proposed. Curved Fowler-Nordheim plots are predicted. Overall, the predicted field emission performance of the H-terminated open SWCNT is slightly better than that of the closed SWCNT, essentially because a C-H dipole is formed that reduces the height of the tunnelling barrier. In general, the physics of a charged SWCNT seems more complex than hitherto realised.