A Comparative Review of Dimension Reduction Methods in Approximate Bayesian Computation

Approximate Bayesian computation (ABC) methods make use of comparisons between simulated and observed summary statistics to overcome the problem of computationally intractable likelihood functions. As the practical implementation of ABC requires computations based on vectors of summary statistics, rather than full data sets, a central question is how to derive low-dimensional summary statistics from the observed data with minimal loss of information. In this article we provide a comprehensive review and comparison of the performance of the principal methods of dimension reduction proposed in the ABC literature. The methods are split into three nonmutually exclusive classes consisting of best subset selection methods, projection techniques and regularization. In addition, we introduce two new methods of dimension reduction. The first is a best subset selection method based on Akaike and Bayesian information criteria, and the second uses ridge regression as a regularization procedure. We illustrate the performance of these dimension reduction techniques through the analysis of three challenging models and data sets.Comment: Published in at http://dx.doi.org/10.1214/12-STS406 the Statistical Science (http://www.imstat.org/sts/) by the Institute of Mathematical Statistics (http://www.imstat.org

End states, ladder compounds, and domain wall fermions

A magnetic field applied to a cross linked ladder compound can generate isolated electronic states bound to the ends of the chain. After exploring the interference phenomena responsible, I discuss a connection to the domain wall approach to chiral fermions in lattice gauge theory. The robust nature of the states under small variations of the bond strengths is tied to chiral symmetry and the multiplicative renormalization of fermion masses.Comment: 10 pages, 4 figures; final version for Phys. Rev. Let

Polarization and angular distribution of the radiation emitted in laser-assisted recombination

The effect of an intense external linear polarized radiation field on the angular distributions and polarization states of the photons emitted during the radiative recombination is investigated. It is predicted, on symmetry grounds, and corroborated by numerical calculations of approximate recombination rates, that emission of elliptically polarized photons occurs when the momentum of the electron beam is not aligned to the direction of the oscillating field. Moreover, strong modifications to the angular distributions of the emitted photons are induced by the external radiation field.Comment: 5 pages, 3 figure

HIV with contact-tracing: a case study in Approximate Bayesian Computation

Missing data is a recurrent issue in epidemiology where the infection process may be partially observed. Approximate Bayesian Computation, an alternative to data imputation methods such as Markov Chain Monte Carlo integration, is proposed for making inference in epidemiological models. It is a likelihood-free method that relies exclusively on numerical simulations. ABC consists in computing a distance between simulated and observed summary statistics and weighting the simulations according to this distance. We propose an original extension of ABC to path-valued summary statistics, corresponding to the cumulated number of detections as a function of time. For a standard compartmental model with Suceptible, Infectious and Recovered individuals (SIR), we show that the posterior distributions obtained with ABC and MCMC are similar. In a refined SIR model well-suited to the HIV contact-tracing data in Cuba, we perform a comparison between ABC with full and binned detection times. For the Cuban data, we evaluate the efficiency of the detection system and predict the evolution of the HIV-AIDS disease. In particular, the percentage of undetected infectious individuals is found to be of the order of 40%

Scaling in Complex Systems: Analytical Theory of Charged Pores

In this paper we find an analytical solution of the equilibrium ion distribution for a toroidal model of a ionic channel, using the Perfect Screening Theorem (PST). The ions are charged hard spheres, and are treated using a variational Mean Spherical Approximation (VMSA) . Understanding ion channels is still a very open problem, because of the many exquisite tuning details of real life channels. It is clear that the electric field plays a major role in the channel behaviour, and for that reason there has been a lot of work on simple models that are able to provide workable theories. Recently a number of interesting papers have appeared that discuss models in which the effect of the geometry, excluded volume and non-linear behaviour is considered. We present here a 3D model of ionic channels which consists of a charged, deformable torus with a circular or elliptical cross section, which can be flat or vertical (close to a cylinder). Extensive comparisons to MC simulations were performed. The new solution opens new possibilities, such as studying flexible pores, and water phase transformations inside the pores using an approach similar to that used on flat crystal surfaces

Quantum dynamics of the avian compass

The ability of migratory birds to orient relative to the Earth's magnetic field is believed to involve a coherent superposition of two spin states of a radical electron pair. However, the mechanism by which this coherence can be maintained in the face of strong interactions with the cellular environment has remained unclear. This Letter addresses the problem of decoherence between two electron spins due to hyperfine interaction with a bath of spin 1/2 nuclei. Dynamics of the radical pair density matrix are derived and shown to yield a simple mechanism for sensing magnetic field orientation. Rates of dephasing and decoherence are calculated ab initio and found to yield millisecond coherence times, consistent with behavioral experiments

A corresponding states approach to Small-Angle-Scattering for polydisperse ionic colloidal fluids

Approximate scattering functions for polydisperse ionic colloidal fluids are obtained by a corresponding states approach. This assumes that all pair correlation functions $g_{\alpha \beta}(r)$ of a polydisperse fluid are conformal to those of an appropriate monodisperse binary fluid (reference system) and can be generated from them by scaling transformations. The correspondence law extends to ionic fluids a {\it scaling approximation} (SA) successfully proposed for nonionic colloids in a recent paper. For the primitive model of charged hard spheres in a continuum solvent, the partial structure factors of the monodisperse binary reference system are evaluated by solving the Orstein-Zernike (OZ) integral equations coupled with an approximate closure. The SA is first tested within the mean spherical approximation (MSA) closure, which allows analytical solutions. The results are found in good overall agreement with exact MSA predictions up to relevant polidispersity. The SA is shown to be an improvement over the ``decoupling approximation'' extended to the ionic case. The simplicity of the SA scheme allows its application also when the OZ equations can be solved only numerically. An example is then given by using the hypernetted chain (HNC) closure. Shortcomings of the SA approach, its possible use in the analysis of experimental scattering data and other related points are also briefly addressed.Comment: 29 pages, 7 postscript figures (included), Latex 3.0, uses aps.sty, to appear in Phys. Rev. E (1999

Flavor-Symmetry Restoration and Symanzik Improvement for Staggered Quarks

We resolve contradictions in the literature concerning the origins and size of unphysical flavor-changing strong interactions generated by the staggered-quark discretization of QCD. We show that the leading contributions are tree-level in \order(a^2) and that they can be removed by adding three correction terms to the link operator in the standard action. These corrections are part of the systematic Symanzik improvement of the staggered-quark action. We present a new improved action for staggered quarks that is accurate up to errors of \order(a^4,a^2\alpha_s) --- more accurate than most, if not all, other discretizations of light-quark dynamics.Comment: 7 page