A Repelling-Attracting Metropolis Algorithm for Multimodality

Although the Metropolis algorithm is simple to implement, it often has difficulties exploring multimodal distributions. We propose the repelling-attracting Metropolis (RAM) algorithm that maintains the simple-to-implement nature of the Metropolis algorithm, but is more likely to jump between modes. The RAM algorithm is a Metropolis-Hastings algorithm with a proposal that consists of a downhill move in density that aims to make local modes repelling, followed by an uphill move in density that aims to make local modes attracting. The downhill move is achieved via a reciprocal Metropolis ratio so that the algorithm prefers downward movement. The uphill move does the opposite using the standard Metropolis ratio which prefers upward movement. This down-up movement in density increases the probability of a proposed move to a different mode. Because the acceptance probability of the proposal involves a ratio of intractable integrals, we introduce an auxiliary variable which creates a term in the acceptance probability that cancels with the intractable ratio. Using several examples, we demonstrate the potential for the RAM algorithm to explore a multimodal distribution more efficiently than a Metropolis algorithm and with less tuning than is commonly required by tempering-based methods

Lower Bounds for Oblivious Near-Neighbor Search

We prove an $\Omega(d \lg n/ (\lg\lg n)^2)$ lower bound on the dynamic cell-probe complexity of statistically $\mathit{oblivious}$ approximate-near-neighbor search ($\mathsf{ANN}$) over the $d$-dimensional Hamming cube. For the natural setting of $d = \Theta(\log n)$, our result implies an $\tilde{\Omega}(\lg^2 n)$ lower bound, which is a quadratic improvement over the highest (non-oblivious) cell-probe lower bound for $\mathsf{ANN}$. This is the first super-logarithmic $\mathit{unconditional}$ lower bound for $\mathsf{ANN}$ against general (non black-box) data structures. We also show that any oblivious $\mathit{static}$ data structure for decomposable search problems (like $\mathsf{ANN}$) can be obliviously dynamized with $O(\log n)$ overhead in update and query time, strengthening a classic result of Bentley and Saxe (Algorithmica, 1980).Comment: 28 page

Complexity, parallel computation and statistical physics

The intuition that a long history is required for the emergence of complexity in natural systems is formalized using the notion of depth. The depth of a system is defined in terms of the number of parallel computational steps needed to simulate it. Depth provides an objective, irreducible measure of history applicable to systems of the kind studied in statistical physics. It is argued that physical complexity cannot occur in the absence of substantial depth and that depth is a useful proxy for physical complexity. The ideas are illustrated for a variety of systems in statistical physics.Comment: 21 pages, 7 figure

Ecological host fitting of Trypanosoma cruzi TcI in Bolivia: mosaic population structure, hybridization and a role for humans in Andean parasite dispersal.

An improved understanding of how a parasite species exploits its genetic repertoire to colonize novel hosts and environmental niches is crucial to establish the epidemiological risk associated with emergent pathogenic genotypes. Trypanosoma cruzi, a genetically heterogeneous, multi-host zoonosis, provides an ideal system to examine the sylvatic diversification of parasitic protozoa. In Bolivia, T. cruzi I, the oldest and most widespread genetic lineage, is pervasive across a range of ecological clines. High-resolution nuclear (26 loci) and mitochondrial (10 loci) genotyping of 199 contemporaneous sylvatic TcI clones was undertaken to provide insights into the biogeographical basis of T. cruzi evolution. Three distinct sylvatic parasite transmission cycles were identified: one highland population among terrestrial rodent and triatomine species, composed of genetically homogenous strains (Ar = 2.95; PA/L = 0.61; DAS = 0.151), and two highly diverse, parasite assemblages circulating among predominantly arboreal mammals and vectors in the lowlands (Ar = 3.40 and 3.93; PA/L = 1.12 and 0.60; DAS = 0.425 and 0.311, respectively). Very limited gene flow between neighbouring terrestrial highland and arboreal lowland areas (distance ~220 km; FST = 0.42 and 0.35) but strong connectivity between ecologically similar but geographically disparate terrestrial highland ecotopes (distance >465 km; FST = 0.016-0.084) strongly supports ecological host fitting as the predominant mechanism of parasite diversification. Dissimilar heterozygosity estimates (excess in highlands, deficit in lowlands) and mitochondrial introgression among lowland strains may indicate fundamental differences in mating strategies between populations. Finally, accelerated parasite dissemination between densely populated, highland areas, compared to uninhabited lowland foci, likely reflects passive, long-range anthroponotic dispersal. The impact of humans on the risk of epizootic Chagas disease transmission in Bolivia is discussed

Adaptive data acquisition multiplexing system and method

A reconfigurable telemetry multiplexer is described which includes a monitor-terminal and a plurality of remote terminals. The remote terminals each include signal conditioning for a plurality of sensors for measuring parameters which are converted by an analog to digital converter. CPU's in the remote terminals store instructions for prompting system configuration and reconfiguration commands. The measurements, instructions, and the terminal's present configuration and status data are transmitted to the monitor-terminal and displayed. In response to menu-driven prompts generated and displayed at the monitor-terminal, data generation request commands, status and health commands, and the like are input at the monitor-terminal and transmitted to the remote terminals. The CPU in each remote terminal receives the various commands, stores them in electrically alterable memory, and reacts in accordance with the commands to reconfigure a plurality of aspects of the system. The CPU in each terminal also generates parameter measurements, status and health signals, and transmits these signals of the respective terminals to the monitor-terminal for low data rate operator viewing and to higher rate external transmission/monitor equipment. Reconfiguration may be in real time during the general period of parameter measurement acquisition, and may include alteration of the gain, automatic gain rescaling, bias, and or sampling rates associated with one or more of the parameter measurements made by the remote terminals

The Omega Counter, a Frequency Counter Based on the Linear Regression

This article introduces the {\Omega} counter, a frequency counter -- or a frequency-to-digital converter, in a different jargon -- based on the Linear Regression (LR) algorithm on time stamps. We discuss the noise of the electronics. We derive the statistical properties of the {\Omega} counter on rigorous mathematical basis, including the weighted measure and the frequency response. We describe an implementation based on a SoC, under test in our laboratory, and we compare the {\Omega} counter to the traditional {\Pi} and {\Lambda} counters. The LR exhibits optimum rejection of white phase noise, superior to that of the {\Pi} and {\Lambda} counters. White noise is the major practical problem of wideband digital electronics, both in the instrument internal circuits and in the fast processes which we may want to measure. The {\Omega} counter finds a natural application in the measurement of the Parabolic Variance, described in the companion article arXiv:1506.00687 [physics.data-an].Comment: 8 pages, 6 figure, 2 table

Mangetic phase transition for three-dimensional Heisenberg weak random anisotropy model: Monte Carlo study

Magnetic phase transition (MPT) to magnetic quasi-long-range order (QLRO) phase in a three-dimensional Heisenberg weak (D/J=4) random anisotropy (RA) model is investigated by Monte Carlo simulation. The isotropic and cubic distributions of RA axes are considered for simple-cubic-lattice systems. Finite-size scaling analysis shows that the critical couplings for the former and latter are K_c= 0.70435(2) and K_c=0.70998(4), respectively. While the critical exponent 1/\nu =1.40824(0) is the same for both cases. A second-order MPT to the QLRO phase is therefore evidenced to be possible in favor with the existence of the QLRO predicted by recent functional renormalization group theories.Comment: 9 pages, 3 figures. to be appeared in Journal of Applied Physics Volume 105 Issue 7 on April 1, 200

The Computational Complexity of Generating Random Fractals

In this paper we examine a number of models that generate random fractals. The models are studied using the tools of computational complexity theory from the perspective of parallel computation. Diffusion limited aggregation and several widely used algorithms for equilibrating the Ising model are shown to be highly sequential; it is unlikely they can be simulated efficiently in parallel. This is in contrast to Mandelbrot percolation that can be simulated in constant parallel time. Our research helps shed light on the intrinsic complexity of these models relative to each other and to different growth processes that have been recently studied using complexity theory. In addition, the results may serve as a guide to simulation physics.Comment: 28 pages, LATEX, 8 Postscript figures available from [email protected]