arXiv subjects

Wei Shi

Publications and source records attributed to Wei Shi.

153 records · Page 9Linked to original sources

arXiv2015

Geographic Partitioning Techniques for the Anonymization of Health Care Data

Hospitals and health care organizations collect large amounts of detailed health care data that is in high demand by researchers. Thus, the possessors of such data are in need of methods that allow for this data to be released without compromising the confidentiality of the individuals to whom it pertains. As the geographic aspect of this data is becoming increasingly relevant for research being conducted, it is important for an \emph{anonymization} process to pay due attention to the geographic attributes of such data. In this paper, a novel system for health care data anonymization is presented. At the core of the system is the aggregation of an initial regionalization guided by the use of a Voronoi diagram. We conduct a comparison with another geographic-based system of anonymization, GeoLeader. We show that our system is capable of producing results of a comparable quality with a much faster running time.

cs.CY↗

arXiv2015

A Novel Geographic Partitioning System for Anonymizing Health Care Data

With large volumes of detailed health care data being collected, there is a high demand for the release of this data for research purposes. Hospitals and organizations are faced with conflicting interests of releasing this data and protecting the confidentiality of the individuals to whom the data pertains. Similarly, there is a conflict in the need to release precise geographic information for certain research applications and the requirement to censor or generalize the same information for the sake of confidentiality. Ultimately the challenge is to anonymize data in order to comply with government privacy policies while reducing the loss in geographic information as much as possible. In this paper, we present a novel geographic-based system for the anonymization of health care data. This system is broken up into major components for which different approaches may be supplied. We compare such approaches in order to make recommendations on which of them to select to best match user requirements.

cs.OH↗

arXiv2015

Substrate-free layer-number identification of two-dimensional materials: A case of Mo$_{0.5}$W$_{0.5}$S$_2$ alloy

Any of two or more two-dimensional (2D) materials with similar properties can be alloyed into a new layered material, namely, 2D alloy. Individual monolayer in 2D alloys are kept together by Van der Waals interactions. The property of multilayer alloys is a function of their layer number. Here, we studied the shear (C) and layer-breathing (LB) modes of Mo$_{0.5}$W$_{0.5}$S$_2$ alloy flakes and their link to the layer number of alloy flakes. The study reveals that the disorder effect is absent in the C and LB modes of 2D alloys, and the monatomic chain model can be used to estimate the frequencies of the C and LB modes. We demonstrated how to use the C and LB mode frequency to identify the layer number of alloy flakes deposited on different substrates. This technique is independent of the substrate, stoichiometry, monolayer thickness and complex refractive index of 2D materials, offering a robust and substrate-free approach for layer-number identification of 2D materials.

cond-mat.mtrl-sci↗

arXiv2015

Phonon and Raman scattering of two-dimensional transition metal dichalcogenides from monolayer, multilayer to bulk material

Two-dimensional (2D) transition metal dichalcogenide (TMD) nanosheets exhibit remarkable electronic and optical properties. The 2D features, sizable bandgaps, and recent advances in the synthesis, characterization, and device fabrication of the representative MoS$_2$, WS$_2$, WSe$_2$, and MoSe$_2$ TMDs make TMDs very attractive in nanoelectronics and optoelectronics. Similar to graphite and graphene, the atoms within each layer in 2D TMDs are joined together by covalent bonds, while van der Waals interactions keep the layers together. This makes the physical and chemical properties of 2D TMDs layer dependent. In this review, we discuss the basic lattice vibrations of monolayer, multilayer, and bulk TMDs, including high-frequency optical phonons, interlayer shear and layer breathing phonons, the Raman selection rule, layer-number evolution of phonons, multiple phonon replica, and phonons at the edge of the Brillouin zone. The extensive capabilities of Raman spectroscopy in investigating the properties of TMDs are discussed, such as interlayer coupling, spin--orbit splitting, and external perturbations. The interlayer vibrational modes are used in rapid and substrate-free characterization of the layer number of multilayer TMDs and in probing interface coupling in TMD heterostructures. The success of Raman spectroscopy in investigating TMD nanosheets paves the way for experiments on other 2D crystals and related van der Waals heterostructures.

cond-mat.mtrl-sci↗

arXiv2014

EXTRA: An Exact First-Order Algorithm for Decentralized Consensus Optimization

Recently, there have been growing interests in solving consensus optimization problems in a multi-agent network. In this paper, we develop a decentralized algorithm for the consensus optimization problem $$\min\limits_{x\in\mathbb{R}^p}~\bar{f}(x)=\frac{1}{n}\sum\limits_{i=1}^n f_i(x),$$ which is defined over a connected network of $n$ agents, where each function $f_i$ is held privately by agent $i$ and encodes the agent's data and objective. All the agents shall collaboratively find the minimizer while each agent can only communicate with its neighbors. Such a computation scheme avoids a data fusion center or long-distance communication and offers better load balance to the network. This paper proposes a novel decentralized EXact firsT-ordeR Algorithm (abbreviated as EXTRA) to solve the consensus optimization problem. "exact" means that it can converge to the exact solution. EXTRA can use a fixed large step size, {which is independent of the network size}, and has synchronized iterations. The local variable of every agent $i$ converges uniformly and consensually to an exact minimizer of $\bar{f}$. In contrast, the well-known decentralized gradient descent (DGD) method must use diminishing step sizes in order to converge to an exact minimizer. EXTRA and DGD have the same choice of mixing matrices and similar per-iteration complexity. EXTRA, however, uses the gradients of last two iterates, unlike DGD which uses just that of last iterate. EXTRA has the best known convergence rates among the existing first-order decentralized algorithms. Specifically, if $f_i$'s are convex and have Lipschitz continuous gradients, EXTRA has an ergodic convergence rate $O(\frac{1}{k})$ in terms of the first-order optimality residual. If $\bar{f}$ is also restricted strongly convex, EXTRA converges to an optimal solution at a linear rate $O(C^{-k})$ for some constant $C>1$.

math.OC↗

arXiv2014

On the Linear Convergence of the ADMM in Decentralized Consensus Optimization

In decentralized consensus optimization, a connected network of agents collaboratively minimize the sum of their local objective functions over a common decision variable, where their information exchange is restricted between the neighbors. To this end, one can first obtain a problem reformulation and then apply the alternating direction method of multipliers (ADMM). The method applies iterative computation at the individual agents and information exchange between the neighbors. This approach has been observed to converge quickly and deemed powerful. This paper establishes its linear convergence rate for decentralized consensus optimization problem with strongly convex local objective functions. The theoretical convergence rate is explicitly given in terms of the network topology, the properties of local objective functions, and the algorithm parameter. This result is not only a performance guarantee but also a guideline toward accelerating the ADMM convergence.

math.OC↗

arXiv2014

Assessing Technical Performance in Differential Gene Expression Experiments with External Spike-in RNA Control Ratio Mixtures

There is a critical need for standard approaches to assess, report, and compare the technical performance of genome-scale differential gene expression experiments. We assess technical performance with a proposed "standard" dashboard of metrics derived from analysis of external spike-in RNA control ratio mixtures. These control ratio mixtures with defined abundance ratios enable assessment of diagnostic performance of differentially expressed transcript lists, limit of detection of ratio (LODR) estimates, and expression ratio variability and measurement bias. The performance metrics suite is applicable to analysis of a typical experiment, and here we also apply these metrics to evaluate technical performance among laboratories. An interlaboratory study using identical samples shared amongst 12 laboratories with three different measurement processes demonstrated generally consistent diagnostic power across 11 laboratories. Ratio measurement variability and bias were also comparable amongst laboratories for the same measurement process. Different biases were observed for measurement processes using different mRNA enrichment protocols.

q-bio.GN↗

arXiv2013

featureCounts: An efficient general-purpose program for assigning sequence reads to genomic features

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.

q-bio.GN↗

arXiv2011

Design and modeling of a transistor vertical-cavity surface-emitting laser

A multiple quantum well (MQW) transistor vertical-cavity surface-emitting laser (T-VCSEL) is designed and numerically modeled. The important physical models and parameters are discussed and validated by modeling a conventional VCSEL and comparing the results with the experiment. The quantum capture/escape process is simulated using the quantum-trap model and shows a significant effect on the electrical output of the T-VCSEL. The parameters extracted from the numerical simulation are imported into the analytic modeling to predict the frequency response and simulate the large-signal modulation up to 40 Gbps.

physics.optics↗