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Rao V.,Duke University | Teh Y.W.,South Parks Road
Journal of Machine Learning Research | Year: 2013

Markov jump processes (or continuous-time Markov chains) are a simple and important class of continuous-time dynamical systems. In this paper, we tackle the problem of simulating from the posterior distribution over paths in these models, given partial and noisy observations. Our approach is an auxiliary variable Gibbs sampler, and is based on the idea of uniformization. This sets up a Markov chain over paths by alternately sampling a finite set of virtual jump times given the current path, and then sampling a new path given the set of extant and virtual jump times. The first step involves simulating a piecewise-constant inhomogeneous Poisson process, while for the second, we use a standard hidden Markov model forward filtering-backward sampling algorithm. Our method is exact and does not involve approximations like time-discretization. We demonstrate how our sampler extends naturally toMJP-based models likeMarkov-modulated Poisson processes and continuous-time Bayesian networks, and show significant computational benefits over state-ofthe- art MCMC samplers for these models. © 2013 Vinayak Rao and Yee Whye Teh. Source


Kirby K.J.,South Parks Road
Hacquetia | Year: 2015

Wood-pastures are important for their open-ground biodiversity and for the old trees they contain. However, younger trees to replace the current generation of old trees are often scarce, a potential threat to the future of the habitat mosaic and of species dependent on the trees. A simple model was used to illustrate how many younger trees might be expected under different assumptions of desired final density of old trees and rates of loss as trees age for an oak-dominated wood-pasture. From these the overall canopy cover of the landscape was estimated under an active pollarding regime and where the trees grow to full crown size. Canopy cover was often five times as great under full crown as under a pollarding regime; much of the canopy cover was in the younger (often missing) cohorts. The openness of current wood-pastures is in part a consequence of the absence of a sustainable tree population structure. Some protected sites may be too small to allow space for the missing generation of trees and at the same time retain current levels of openness. Analogies between current wood-pasture structures and 'natural wood-pastures' of the pre-Neolithic era must take account of the missing generations of trees. © by Keith J. Kirby 2015. Source


Pearce E.,South Parks Road
Proceedings. Biological sciences / The Royal Society | Year: 2013

Previous research has identified morphological differences between the brains of Neanderthals and anatomically modern humans (AMHs). However, studies using endocasts or the cranium itself are limited to investigating external surface features and the overall size and shape of the brain. A complementary approach uses comparative primate data to estimate the size of internal brain areas. Previous attempts to do this have generally assumed that identical total brain volumes imply identical internal organization. Here, we argue that, in the case of Neanderthals and AMHs, differences in the size of the body and visual system imply differences in organization between the same-sized brains of these two taxa. We show that Neanderthals had significantly larger visual systems than contemporary AMHs (indexed by orbital volume) and that when this, along with their greater body mass, is taken into account, Neanderthals have significantly smaller adjusted endocranial capacities than contemporary AMHs. We discuss possible implications of differing brain organization in terms of social cognition, and consider these in the context of differing abilities to cope with fluctuating resources and cultural maintenance. Source


New Zealand straddles the obliquely convergent boundary between the Pacific and Australian plates, with subduction of Pacific plate along the Hikurangi margin. Finite plate reconstructions predict ~. 800. km of relative plate motion since ~. 43. Ma, with 80-90° clockwise rotation of the Hikurangi margin since ~. 20. Ma, at an average rate of 4-4.5°/Myr, and the short-term deformation (<10. kyr) shows that rotation is still active. Paleomagnetic measurements in Cretaceous and Cenozoic sedimentary and volcanic rocks record rotation about vertical axes of crustal blocks along the Hikurangi margin, conforming closely with that indicated by the plate reconstructions. Since ~. 20. Ma, this was accommodated relative to the Australian plate by along strike gradients of extension and shortening, together with dextral shear on arcuate strike-slip faults. The ends of the rotating part of the Hikurangi margin define hinges. In the south, this is accommodated by dextral shear in the Marlborough Fault Zone, and crustal blocks, 1-50. km across, have rotated 50-130°clockwise, creating the eastern part of the New Zealand Orocline. In the north, the hinge is an onshore arcuate zone of dextral shear, 10-50. km wide, with normal faulting. The Paleogene rotational history is poorly constrained, but the few paleomagnetic observations are consistent with distributed shear of basement terranes in a zone of dextral simple shear, < 200 km wide, running up the western part of the New Zealand, and linking with subduction farther north, creating the western half of the New Zealand Orocline. The overall pattern of rotation shows that the continental lithosphere in the Australian Plate is weak, so that deformation is controlled mainly by boundary forces along the plate interface, and passively follows the change in trend of the subduction zone through time. © 2011 Elsevier B.V. Source


Pearce E.,South Parks Road | Pearce E.,University of Oxford | Stringer C.,Natural History Museum in London | Dunbar R.I.M.,South Parks Road
Proceedings of the Royal Society B: Biological Sciences | Year: 2013

Previous research has identified morphological differences between the brains of Neanderthals and anatomically modern humans (AMHs). However, studies using endocasts or the cranium itself are limited to investigating external surface features and the overall size and shape of the brain. A complementary approach uses comparative primate data to estimate the size of internal brain areas. Previous attempts to do this have generally assumed that identical total brain volumes imply identical internal organization. Here, we argue that, in the case of Neanderthals and AMHs, differences in the size of the body and visual system imply differences in organization between the same-sized brains of these two taxa. We show that Neanderthals had significantly larger visual systems than contemporary AMHs (indexed by orbital volume) and that when this, along with their greater body mass, is taken into account, Neanderthals have significantly smaller adjusted endocranial capacities than contemporary AMHs. We discuss possible implications of differing brain organization in terms of social cognition, and consider these in the context of differing abilities to cope with fluctuating resources and cultural maintenance. © 2013 The Author(s) Published by the Royal Society. All rights reserved. Source

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