Powerpropagation: A sparsity inducing weight reparameterisation

The training of sparse neural networks is becoming an increasingly important tool for reducing the computational footprint of models at training and evaluation, as well enabling the effective scaling up of models. Whereas much work over the years has been dedicated to specialised pruning techniques, little attention has been paid to the inherent effect of gradient based training on model sparsity. In this work, we introduce Powerpropagation, a new weight-parameterisation for neural networks that leads to inherently sparse models. Exploiting the behaviour of gradient descent, our method gives rise to weight updates exhibiting a “rich get richer” dynamic, leaving low-magnitude parameters largely unaffected by learning. Models trained in this manner exhibit similar performance, but have a distribution with markedly higher density at zero, allowing more parameters to be pruned safely. Powerpropagation is general, intuitive, cheap and straight-forward to implement and can readily be combined with various other techniques. To highlight its versatility, we explore it in two very different settings: Firstly, following a recent line of work, we investigate its effect on sparse training for resource-constrained settings. Here, we combine Powerpropagation with a traditional weight-pruning technique as well as recent state-of-the-art sparse-to-sparse algorithms, showing superior performance on the ImageNet benchmark. Secondly, we advocate the use of sparsity in overcoming catastrophic forgetting, where compressed representations allow accommodating a large number of tasks at fixed model capacity. In all cases our reparameterisation considerably increases the efficacy of the off-the-shelf methods

Understanding the culture of antimicrobial prescribing in agriculture: a qualitative study of UK pig veterinary surgeons

Objectives The use of antimicrobials in food-producing animals has been linked with the emergence of antimicrobial resistance in bacterial populations, with consequences for animal and public health. This study explored the underpinning drivers, motivators and reasoning behind prescribing decisions made by veterinary surgeons working in the UK pig industry. Methods A qualitative interview study was conducted with 21 veterinary surgeons purposively selected from all UK pig veterinary surgeons. Thematic analysis was used to analyse transcripts. Results Ensuring optimum pig health and welfare was described as a driver for antimicrobial use by many veterinary surgeons and was considered a professional and moral obligation. Veterinary surgeons also exhibited a strong sense of social responsibility over the need to ensure that antimicrobial use was responsible. A close relationship between management practices, health and economics was evident, with improvements in management commonly identified as being potential routes to reduce antimicrobial usage; however, these were not always considered economically viable. The relationship with clients was identified as being a source of professional stress for practitioners due to pressure from farmers requesting antimicrobial prescriptions, and concern over poor compliance of antimicrobial administration by some farmers. Conclusions The drivers behind prescribing decisions by veterinary surgeons were complex and diverse. A combination of education, improving communication between veterinary surgeons and farmers, and changes in regulations, in farm management and in consumer/retailer demands may all be needed to ensure that antimicrobial prescribing is optimal and to achieve significant reductions in use

Occurrence and diversity of Giardia duodenalis assemblages in livestock in the UK.

Giardia duodenalis is a common intestinal parasite in humans and a wide range of livestock species. It is a genetically heterogeneous parasite that has been characterized in seven distinct genetic assemblages or cryptic species, and molecular markers can be used to differentiate both animal-specific and potentially zoonotic genotypes. Little is known about G. duodenalis and the range of assemblages occurring in domestic livestock species in the UK. Here, we present data on the occurrence and molecular diversity of G. duodenalis detected in the faeces or large intestinal contents of cattle, sheep, pigs, goats and camelids from farms in the north-west of England. Both healthy and clinically diseased animals were included in the survey. The presence of Giardia spp. and assemblages was determined by sequencing of the small-subunit ribosomal RNA gene. The potential association of infection with various clinical and epidemiological parameters was studied in cattle using both univariate and multivariate analyses. Giardia spp. were detected in 127 (34.3%) of the 370 animals tested. G. duodenalis assemblage E was found to be predominant in cattle and sheep, followed by assemblage A. Mixed infections with assemblages A and E were also detected. Interestingly, some cattle, sheep and pigs were found to be infected with more unexpected assemblages (C, D, F). Pre-weaned calves were more likely to test positive than adult animals, but no association between the occurrence of overt intestinal disease and G. duodenalis infection was detected. The common occurrence of assemblage A and the finding of unusual assemblages in atypical hosts suggest that in future, a multilocus analysis should be used to confirm the actual diversity of G. duodenalis in livestock and the presence of potentially zoonotic genotypes. These data also suggest that there is a need to re-evaluate the clinical significance of G. duodenalis infection in livestock

The broadband and spectrally resolved H-band Eclipse of KELT-1b and the Role of Surface Gravity in Stratospheric Inversions in Hot Jupiters

We present a high precision H-band emission spectrum of the transiting brown dwarf KELT-1b, which we spectrophotometrically observed during a single secondary eclipse using the LUCI1 multi-object spectrograph on the Large Binocular Telescope. Using a Gaussian-process regression model, we are able to clearly measure the broadband eclipse depth as Delta-H=1418+/-94ppm. We are also able to spectrally-resolve the H-band into five separate wavechannels and measure the eclipse spectrum of KELT-1b at R~50 with an average precision of +/-135ppm. We find that the day side has an average brightness temperature of 3250+/-50K, with significant variation as a function of wavelength. Based on our observations, and previous measurements of KELT-1b's eclipse at other wavelengths, we find that KELT-1b's day side appears identical to an isolated 3200K brown dwarf, and our modeling of the atmospheric emission shows a monotonically decreasing temperature-pressure profile. This is in contrast to hot Jupiters with similar day side brightness temperatures near 3000K, all of which appear to be either isothermal or posses a stratospheric temperature inversion. We hypothesize that the lack of an inversion in KELT-1b is due to its high surface gravity, which we argue could be caused by the increased efficiency of cold-trap processes within its atmosphere

Certified community forests positively impact human wellbeing and conservation effectiveness and improve the performance of nearby national protected areas

Community forests (CFs) aim to improve human wellbeing and conservation effectiveness, though their performance remains contested. A recent innovation in protected area (PA) governance is to combine CFs with forest certification. We assess (1) the impact of certified CFs on wellbeing and conservation effectiveness; (2) gender inequality and elite capture; (3) interaction effects with neighboring national PAs. We used a novel approach that integrates field data consisting of locally identified indicators representative of multidimensional wellbeing, with remotely sensed data on conservation effectiveness and statistical matching to improve causal inference. We found that CFs positively impacted wellbeing, conservation effectiveness, and reduced gender inequality, though they did not reduce elite capture. We also detected positive interaction effects between certified CFs and neighboring national PAs. Our findings suggest that locating contrasting local and national PA governance approaches next to each other may help to maximize wellbeing and conservation benefits within complex multiuse landscapes

The role of forensic anthropology in disaster victim identification (DVI):recent developments and future prospects

Forensic anthropological knowledge has been used in disaster victim identification (DVI) for over a century, but over the past decades, there have been a number of disaster events which have seen an increasing role for the forensic anthropologist. The experiences gained from some of the latest DVI operations have provided valuable lessons that have had an effect on the role and perceived value of the forensic anthropologist as part of the team managing the DVI process. This paper provides an overview of the ways in which forensic anthropologists may contribute to DVI with emphasis on how recent experiences and developments in forensic anthropology have augmented these contributions. Consequently, this paper reviews the value of forensic anthropological expertise at the disaster scene and in the mortuary, and discusses the way in which forensic anthropologists may use imaging in DVI efforts. Tissue-sampling strategies for DNA analysis, especially in the case of disasters with a large amount of fragmented remains, are also discussed. Additionally, consideration is given to the identification of survivors; the statistical basis of identification; the challenges related to some specific disaster scenarios; and education and training. Although forensic anthropologists can play a valuable role in different phases of a DVI operation, they never practice in isolation. The DVI process requires a multidisciplinary approach and, therefore, has a close collaboration with a range of forensic specialists

Representation of Time-Varying Stimuli by a Network Exhibiting Oscillations on a Faster Time Scale

Sensory processing is associated with gamma frequency oscillations (30–80 Hz) in sensory cortices. This raises the question whether gamma oscillations can be directly involved in the representation of time-varying stimuli, including stimuli whose time scale is longer than a gamma cycle. We are interested in the ability of the system to reliably distinguish different stimuli while being robust to stimulus variations such as uniform time-warp. We address this issue with a dynamical model of spiking neurons and study the response to an asymmetric sawtooth input current over a range of shape parameters. These parameters describe how fast the input current rises and falls in time. Our network consists of inhibitory and excitatory populations that are sufficient for generating oscillations in the gamma range. The oscillations period is about one-third of the stimulus duration. Embedded in this network is a subpopulation of excitatory cells that respond to the sawtooth stimulus and a subpopulation of cells that respond to an onset cue. The intrinsic gamma oscillations generate a temporally sparse code for the external stimuli. In this code, an excitatory cell may fire a single spike during a gamma cycle, depending on its tuning properties and on the temporal structure of the specific input; the identity of the stimulus is coded by the list of excitatory cells that fire during each cycle. We quantify the properties of this representation in a series of simulations and show that the sparseness of the code makes it robust to uniform warping of the time scale. We find that resetting of the oscillation phase at stimulus onset is important for a reliable representation of the stimulus and that there is a tradeoff between the resolution of the neural representation of the stimulus and robustness to time-warp. Author Summary Sensory processing of time-varying stimuli, such as speech, is associated with high-frequency oscillatory cortical activity, the functional significance of which is still unknown. One possibility is that the oscillations are part of a stimulus-encoding mechanism. Here, we investigate a computational model of such a mechanism, a spiking neuronal network whose intrinsic oscillations interact with external input (waveforms simulating short speech segments in a single acoustic frequency band) to encode stimuli that extend over a time interval longer than the oscillation's period. The network implements a temporally sparse encoding, whose robustness to time warping and neuronal noise we quantify. To our knowledge, this study is the first to demonstrate that a biophysically plausible model of oscillations occurring in the processing of auditory input may generate a representation of signals that span multiple oscillation cycles.National Science Foundation (DMS-0211505); Burroughs Wellcome Fund; U.S. Air Force Office of Scientific Researc

The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state

We introduce and analyze a minimal model of epigenetic silencing in budding yeast, built upon known biomolecular interactions in the system. Doing so, we identify the epigenetic marks essential for the bistability of epigenetic states. The model explicitly incorporates two key chromatin marks, namely H4K16 acetylation and H3K79 methylation, and explores whether the presence of multiple marks lead to a qualitatively different systems behavior. We find that having both modifications is important for the robustness of epigenetic silencing. Besides the silenced and transcriptionally active fate of chromatin, our model leads to a novel state with bivalent (i.e., both active and silencing) marks under certain perturbations (knock-out mutations, inhibition or enhancement of enzymatic activity). The bivalent state appears under several perturbations and is shown to result in patchy silencing. We also show that the titration effect, owing to a limited supply of silencing proteins, can result in counter-intuitive responses. The design principles of the silencing system is systematically investigated and disparate experimental observations are assessed within a single theoretical framework. Specifically, we discuss the behavior of Sir protein recruitment, spreading and stability of silenced regions in commonly-studied mutants (e.g., sas2, dot1) illuminating the controversial role of Dot1 in the systems biology of yeast silencing.Comment: Supplementary Material, 14 page

Accurate masses and radii of normal stars: modern results and applications

This paper presents and discusses a critical compilation of accurate, fundamental determinations of stellar masses and radii. We have identified 95 detached binary systems containing 190 stars (94 eclipsing systems, and alpha Centauri) that satisfy our criterion that the mass and radius of both stars be known to 3% or better. To these we add interstellar reddening, effective temperature, metal abundance, rotational velocity and apsidal motion determinations when available, and we compute a number of other physical parameters, notably luminosity and distance. We discuss the use of this information for testing models of stellar evolution. The amount and quality of the data also allow us to analyse the tidal evolution of the systems in considerable depth, testing prescriptions of rotational synchronisation and orbital circularisation in greater detail than possible before. The new data also enable us to derive empirical calibrations of M and R for single (post-) main-sequence stars above 0.6 M(Sun). Simple, polynomial functions of T(eff), log g and [Fe/H] yield M and R with errors of 6% and 3%, respectively. Excellent agreement is found with independent determinations for host stars of transiting extrasolar planets, and good agreement with determinations of M and R from stellar models as constrained by trigonometric parallaxes and spectroscopic values of T(eff) and [Fe/H]. Finally, we list a set of 23 interferometric binaries with masses known to better than 3%, but without fundamental radius determinations (except alpha Aur). We discuss the prospects for improving these and other stellar parameters in the near future.Comment: 56 pages including figures and tables. To appear in The Astronomy and Astrophysics Review. Ascii versions of the tables will appear in the online version of the articl