Birth/birth-death processes and their computable transition probabilities with biological applications

Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation. In this paper, we introduce the birth(death)/birth-death process, a tractable bivariate extension of the birth-death process. We develop an efficient and robust algorithm to calculate the transition probabilities of birth(death)/birth-death processes using a continued fraction representation of their Laplace transforms. Next, we identify several exemplary models arising in molecular epidemiology, macro-parasite evolution, and infectious disease modeling that fall within this class, and demonstrate advantages of our proposed method over existing approaches to inference in these models. Notably, the ubiquitous stochastic susceptible-infectious-removed (SIR) model falls within this class, and we emphasize that computable transition probabilities newly enable direct inference of parameters in the SIR model. We also propose a very fast method for approximating the transition probabilities under the SIR model via a novel branching process simplification, and compare it to the continued fraction representation method with application to the 17th century plague in Eyam. Although the two methods produce similar maximum a posteriori estimates, the branching process approximation fails to capture the correlation structure in the joint posterior distribution

A Formalization of The Natural Gradient Method for General Similarity Measures

In optimization, the natural gradient method is well-known for likelihood maximization. The method uses the Kullback-Leibler divergence, corresponding infinitesimally to the Fisher-Rao metric, which is pulled back to the parameter space of a family of probability distributions. This way, gradients with respect to the parameters respect the Fisher-Rao geometry of the space of distributions, which might differ vastly from the standard Euclidean geometry of the parameter space, often leading to faster convergence. However, when minimizing an arbitrary similarity measure between distributions, it is generally unclear which metric to use. We provide a general framework that, given a similarity measure, derives a metric for the natural gradient. We then discuss connections between the natural gradient method and multiple other optimization techniques in the literature. Finally, we provide computations of the formal natural gradient to show overlap with well-known cases and to compute natural gradients in novel frameworks

Spin Injection into a Luttinger Liquid

We study the effect of spin injection into a Luttinger liquid. The spin-injection-detection setup of Johnson and Silsbee is considered; here spins injected into the Luttinger liquid induce, across an interface with a ferromagnetic metal, either a spin-dependent current ($I_s$) or a spin-dependent boundary voltage ($V_s$). We find that the spin-charge separation nature of the Luttinger liquid affects $I_s$ and $V_s$ in a very different fashion. In particular, in the Ohmic regime, $V_s$ depends on the spin transport properties of the Luttinger liquid in essentially the same way as it would in the case of a Fermi liquid. The implications of our results for the spin-injection-detection experiments in the high $T_c$ cuprates are discussed.Comment: 4 pages, REVTEX, 2 figures. Minor changes and corrections to typos. To appear in Phys. Rev. Let

Andreev Reflection and Spin Injection into s−s- and d−d-wave Superconductors

We study the effect of spin injection into $s-$ and $d-$wave superconductors, with an emphasis on the interplay between boundary and bulk spin transport properties. The quantities of interest include the amount of non-equilibrium magnetization ($m$), as well as the induced spin-dependent current ($I_s$) and boundary voltage ($V_s$). In general, the Andreev reflection makes each of the three quantities depend on a different combination of the boundary and bulk contributions. The situation simplifies either for half-metallic ferromagnets or in the strong barrier limit, where both $V_s$ and $m$ depend solely on the bulk spin transport/relaxation properties. The implications of our results for the on-going spin injection experiments in high $T_c$ cuprates are discussed.Comment: 4 pages, REVTEX, 1 figure included; typos correcte

Correlation Induced Insulator to Metal Transitions

We study a spinless two-band model at half-filling in the limit of infinite dimensions. The ground state of this model in the non-interacting limit is a band-insulator. We identify transitions to a metal and to a charge-Mott insulator, using a combination of analytical, Quantum Monte Carlo, and zero temperature recursion methods. The metallic phase is a non-Fermi liquid state with algebraic local correlation functions with universal exponents over a range of parameters.Comment: 12 pages, REVTE

Kosterlitz-Thouless Transition and Short Range Spatial Correlations in an Extended Hubbard Model

We study the competition between intersite and local correlations in a spinless two-band extended Hubbard model by taking an alternative limit of infinite dimensions. We find that the intersite density fluctuations suppress the charge Kondo energy scale and lead to a Fermi liquid to non-Fermi liquid transition for repulsive on-site density-density interactions. In the absence of intersite interactions, this transition reduces to the known Kosterlitz-Thouless transition. We show that a new line of non-Fermi liquid fixed points replace those of the zero intersite interaction problem.Comment: 11 pages, 2 figure

Mixed-valent regime of the two-channel Anderson impurity as a model for UBe_13

We investigate the mixed-valent regime of a two-configuration Anderson impurity model for uranium ions, with separate quadrupolar and magnetic doublets. With a new Monte Carlo approach and the non-crossing approximation we find: (i) A non-Fermi-liquid fixed point with two-channel Kondo model critical behavior; (ii) Distinct energy scales for screening the low-lying and excited doublets; (iii) A semi-quantitative explanation of magnetic-susceptibility data for U$_{1-x}$Th$_x$Be$_{13}$ assuming 60-70% quadrupolar doublet ground-state weight, supporting the quadrupolar-Kondo interpretation.Comment: 4 Pages, 3 eps figures; submitted to Phys. Rev. Let

Fixed-point elimination in the intuitionistic propositional calculus

It is a consequence of existing literature that least and greatest fixed-points of monotone polynomials on Heyting algebras-that is, the algebraic models of the Intuitionistic Propositional Calculus-always exist, even when these algebras are not complete as lattices. The reason is that these extremal fixed-points are definable by formulas of the IPC. Consequently, the $\mu$-calculus based on intuitionistic logic is trivial, every $\mu$-formula being equivalent to a fixed-point free formula. We give in this paper an axiomatization of least and greatest fixed-points of formulas, and an algorithm to compute a fixed-point free formula equivalent to a given $\mu$-formula. The axiomatization of the greatest fixed-point is simple. The axiomatization of the least fixed-point is more complex, in particular every monotone formula converges to its least fixed-point by Kleene's iteration in a finite number of steps, but there is no uniform upper bound on the number of iterations. We extract, out of the algorithm, upper bounds for such n, depending on the size of the formula. For some formulas, we show that these upper bounds are polynomial and optimal

Screening Breakdown on the Route toward the Metal-Insulator Transition in Modulation Doped Si/SiGe Quantum Wells

Exploiting the spin resonance of two-dimensional (2D) electrons in SiGe/Si quantum wells we determine the carrier-density-dependence of the magnetic susceptibility. Assuming weak interaction we evaluate the density of states at the Fermi level D(E_F), and the screening wave vector, q_TF. Both are constant at higher carrier densities n, as for an ideal 2D carrier gas. For n < 3e11 cm-2, they decrease and extrapolate to zero at n = 7e10 cm-2. Calculating the mobility from q_TF yields good agreement with experimental values justifying the approach. The decrease in D(E_F) is explained by potential fluctuations which lead to tail states that make screening less efficient and - in a positive feedback - cause an increase of the potential fluctuations. Even in our high mobility samples the fluctuations exceed the electron-electron interaction leading to the formation of puddles of mobile carriers with at least 1 micrometer diameter.Comment: 4 pages, 3 figure