Random frog: An efficient reversible jump Markov Chain Monte Carlo-like approach for variable selection with applications to gene selection and disease classification

The identification of disease-relevant genes represents a challenge in microarray-based disease diagnosis where the sample size is often limited. Among established methods, reversible jump Markov Chain Monte Carlo (RJMCMC) methods have proven to be quite promising for variable selection. However, the design and application of an RJMCMC algorithm requires, for example, special criteria for prior distributions. Also, the simulation from joint posterior distributions of models is computationally extensive, and may even be mathematically intractable. These disadvantages may limit the applications of RJMCMC algorithms. Therefore, the development of algorithms that possess the advantages of RJMCMC methods and are also efficient and easy to follow for selecting disease-associated genes is required. Here we report a RJMCMC-like method, called random frog that possesses the advantages of RJMCMC methods and is much easier to implement. Using the colon and the estrogen gene expression datasets, we show that random frog is effective in identifying discriminating genes. The top 2 ranked genes for colon and estrogen are Z50753, U00968, and Y10871_at, Z22536_at, respectively. (The source codes with GNU General Public License Version 2.0 are freely available to non-commercial users at: http://code.google.com/p/randomfrog/.)     

A perturbed martingale approach to global optimization

A new global stochastic search, guided mainly through derivative-free directional information computable from the sample statistical moments of the design variables within a Monte Carlo setup, is proposed. The search is aided by imparting to the directional update term additional layers of random perturbations referred to as ‘coalescence’ and ‘scrambling’. A selection step, constituting yet another avenue for random perturbation, completes the global search. The direction-driven nature of the search is manifest in the local extremization and coalescence components, which are posed as martingale problems that yield gain-like update terms upon discretization. As anticipated and numerically demonstrated, to a limited extent, against the problem of parameter recovery given the chaotic response histories of a couple of nonlinear oscillators, the proposed method appears to offer a more rational, more accurate and faster alternative to most available evolutionary schemes, prominently the particle swarm optimization.     

Rejoinder on “Statistical reasoning with set-valued information: Ontic vs. epistemic views”

This note replies to comments made on our contribution to the Low Quality Data debate.     

Self-Reinforced High-Density Polyethylene Prepared by Low Frequency Vibration-Assisted Injection Molding. II: Microstructure Investigation

Scanning electron microscopy (SEM), differential scanning calorimetry (DSC), and wide angle X-ray diffraction (WAXD) were employed to study the microstructure of self-reinforced high-density polyethylene (HDPE) prepared by conventional injection molding (CIM) and a low frequency vibration-assisted injection molding (VAIM). SEM micrographs following permanganic etching showed the self-reinforcement of HDPE is mainly due to the existence of shish-kebab morphology within the core region for VAIM-processed HDPE samples. Pronounced molecular alignment was identified by the WAXD data. An approximate 9% increase in the crystallinity was confirmed by DSC. Both preferred molecular orientation and increased crystallinity serve to yield stronger VAIM-processed injection moldings.     

Combinatorial and approximative analyses in a spatially random division process

For a spatial characteristic, there exist commonly fat-tail frequency distributions of fragment-size and -mass of glass, areas enclosed by city roads, and pore size/volume in random packings. In order to give a new analytical approach for the distributions, we consider a simple model which constructs a fractal-like hierarchical network based on random divisions of rectangles. The stochastic process makes a Markov chain and corresponds to directional random walks with splitting into four particles. We derive a combinatorial analytical form and its continuous approximation for the distribution of rectangle areas, and numerically show a good fitting with the actual distribution in the averaging behavior of the divisions.     

Operational issues and network effects in vaccine markets

One of the most important concerns for managing public health is the prevention of infectious diseases. Although vaccines provide the most effective means for preventing infectious diseases, there are two main reasons why it is often difficult to reach a socially optimal level of vaccine coverage: (i) the emergence of operational issues (such as yield uncertainty) on the supply side, and (ii) the existence of negative network effects on the consumption side. In particular, uncertainties about production yield and vaccine imperfections often make manufacturing some vaccines a risky process and may lead the manufacturer to produce below the socially optimal level. At the same time, negative network effects provide incentives to potential consumers to free ride off the immunity of the vaccinated population. In this research, we consider how a central policy-maker can induce a socially optimal vaccine coverage through the use of incentives to both consumers and the vaccine manufacturer. We consider a monopoly market for an imperfect vaccine; we show that a fixed two-part subsidy is unable to coordinate the market, but derive a two-part menu of subsidies that leads to a socially efficient level of coverage.     

Collective risk models with dependence

In actuarial science, collective risk models, in which the aggregate claim amount of a portfolio is defined in terms of random sums, play a crucial role. In these models, it is common to assume that the number of claims and their amounts are independent, even if this might not always be the case. We consider collective risk models with different dependence structures. Due to the importance of such risk models in an actuarial setting, we first investigate a collective risk model with dependence involving the family of multivariate mixed Erlang distributions. Other models based on mixtures involving bivariate and multivariate copulas in a more general setting are then presented. These different structures allow to link the number of claims to each claim amount, and to quantify the aggregate claim loss. Then, we use Archimedean and hierarchical Archimedean copulas in collective risk models, to model the dependence between the claim number random variable and the claim amount random variables involved in the random sum. Such dependence structures allow us to derive a computational methodology for the assessment of the aggregate claim amount. While being very flexible, this methodology is easy to implement, and can easily fit more complicated hierarchical structures.     

Orbits in a stochastic Goodwin–Lotka–Volterra model

This paper examines the cycling behavior of a deterministic and a stochastic version of the economic interpretation of the Lotka–Volterra model, the Goodwin model. We provide a characterization of orbits in the deterministic highly non-linear model. We then study a stochastic version, with Brownian noise introduced via a heterogeneous productivity factor. Existence conditions for a solution to the system are provided. We prove that the system produces cycles around a unique equilibrium point in finite time for general volatility levels, using stochastic Lyapunov techniques for recurrent domains. Numerical insights are provided.