Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

The use of fossil evidence to calibrate divergence time estimation has a long history. More recently Bayesian MCMC has become the dominant method of divergence time estimation and fossil evidence has been re-interpreted as the specification of prior distributions on the divergence times of calibration nodes. These so-called "soft calibrations" have become widely used but the statistical properties of calibrated tree priors in a Bayesian setting has not been carefully investigated. Here we clarify that calibration densities, such as those defined in BEAST 1.5, do not represent the marginal prior distribution of the calibration node. We illustrate this with a number of analytical results on small trees. We also describe an alternative construction for a calibrated Yule prior on trees that allows direct specification of the marginal prior distribution of the calibrated divergence time, with or without the restriction of monophyly. This method requires the computation of the Yule prior conditional on the height of the divergence being calibrated. Unfortunately, a practical solution for multiple calibrations remains elusive. Our results suggest that direct estimation of the prior induced by specifying multiple calibration densities should be a prerequisite of any divergence time dating analysis

Correlations in a BEC collision: First-principles quantum dynamics with 150 000 atoms

The quantum dynamics of colliding Bose-Einstein condensates with 150 000 atoms are simulated directly from the Hamiltonian using the stochastic positive-P method. Two-body correlations between the scattered atoms and their velocity distribution are found for experimentally accessible parameters. Hanbury Brown-Twiss or thermal-like correlations are seen for copropagating atoms, while number correlations for counterpropagating atoms are even stronger than thermal correlations at short times. The coherent phase grains grow in size as the collision progresses with the onset of growth coinciding with the beginning of stimulated scattering. The method is versatile and usable for a range of cold atom systems.Comment: 4 pages, 4 figures. v2: Rewording and style changes, minor except for rewrite of background on the positive-P representation. Original research unchange

Stochastic gauges in quantum dynamics for many-body simulations

Quantum dynamics simulations can be improved using novel quasiprobability distributions based on non-orthogonal hermitian kernel operators. This introduces arbitrary functions (gauges) into the stochastic equations, which can be used to tailor them for improved calculations. A possible application to full quantum dynamic simulations of BEC's is presented.Comment: 4 pages, 2 figure

Accelerating Reinforcement Learning by Composing Solutions of Automatically Identified Subtasks

This paper discusses a system that accelerates reinforcement learning by using transfer from related tasks. Without such transfer, even if two tasks are very similar at some abstract level, an extensive re-learning effort is required. The system achieves much of its power by transferring parts of previously learned solutions rather than a single complete solution. The system exploits strong features in the multi-dimensional function produced by reinforcement learning in solving a particular task. These features are stable and easy to recognize early in the learning process. They generate a partitioning of the state space and thus the function. The partition is represented as a graph. This is used to index and compose functions stored in a case base to form a close approximation to the solution of the new task. Experiments demonstrate that function composition often produces more than an order of magnitude increase in learning rate compared to a basic reinforcement learning algorithm

GPS and property surveying

In 2010 the Global Positioning System (GPS) developed by the United States military was the best known Global Navigation Satellite System (GNSS). Others included Russia’s GLONASS, China’s COMPASS and Europe’s GALILEO systems. Although military satellite navigation systems can be traced back to the 1960s, their civilian uses emerged in the 1980s, initially limited to navigation positioning, not property surveying. Property surveying methods have varied both between and within nations. However, GPS surveying with some supporting legislation, had, by the early years of the 21st century, sufficiently developed to meet the needs of the property sector. This chapter looks at this development, and its implications with respect to cadastral surveying

An Exploration into the Ethics of Cloning Endangered Species

Researchers are cloning endangered species, expanding the debate on human cloning to include both the value of evolution and the question of whether ethical issues affecting endangered species should be defined in terms of human medical benefit. In this paper, the author explores these questions and others with evolutionary biologist Kathryn Rodriguez-Clark, philosopher Holmes Rolston, III, and toxicologist Don Sparling. Whether or not we are ready to formulate ethics on the subject, if we do not enter into a serious dialogue now, then we allow the question of whether to clone any species—including our own— to be decided for us

Motion sickness and migraine: optokinetic stimulation increases scalp tenderness, pain sensitivity in the fingers and photophobia

The aim of this study was to determine whether scalp tenderness and photophobia, two well-recognized symptoms of migraine, develop during the motion sickness induced by optokinetic stimulation. To investigate whether motion sickness has a general influence on pain perception, pain was also assessed in the fingertips. After optokinetic stimulation, nausea increased more and headache persisted longer in 21 migraine sufferers than in 15 non-headache controls. Scalp tenderness increased during optokinetic stimulation in nauseated subjects, and pain in the fingertips increased more and photophobia persisted longer in migraine sufferers than controls. These findings suggest that the disturbance responsible for nausea also sensitizes trigeminal nociceptive neurones or releases inhibitory controls on their discharge. A low nausea threshold and a propensity for sensitization to develop rapidly in nociceptive pathways may increase susceptibility to migraine