Efficient Learning of the Parameters of Non-Linear Models using Differentiable Resampling in Particle Filters

It has been widely documented that the sampling and resampling steps in particle filters cannot be differentiated. The {\itshape reparameterisation trick} was introduced to allow the sampling step to be reformulated into a differentiable function. We extend the {\itshape reparameterisation trick} to include the stochastic input to resampling therefore limiting the discontinuities in the gradient calculation after this step. Knowing the gradients of the prior and likelihood allows us to run particle Markov Chain Monte Carlo (p-MCMC) and use the No-U-Turn Sampler (NUTS) as the proposal when estimating parameters. We compare the Metropolis-adjusted Langevin algorithm (MALA), Hamiltonian Monte Carlo with different number of steps and NUTS. We consider two state-space models and show that NUTS improves the mixing of the Markov chain and can produce more accurate results in less computational time.Comment: 35 pages, 10 figure

Consensus on circulatory shock and hemodynamic monitoring. Task force of the European Society of Intensive Care Medicine.

OBJECTIVE: Circulatory shock is a life-threatening syndrome resulting in multiorgan failure and a high mortality rate. The aim of this consensus is to provide support to the bedside clinician regarding the diagnosis, management and monitoring of shock. METHODS: The European Society of Intensive Care Medicine invited 12 experts to form a Task Force to update a previous consensus (Antonelli et al.: Intensive Care Med 33:575-590, 2007). The same five questions addressed in the earlier consensus were used as the outline for the literature search and review, with the aim of the Task Force to produce statements based on the available literature and evidence. These questions were: (1) What are the epidemiologic and pathophysiologic features of shock in the intensive care unit ? (2) Should we monitor preload and fluid responsiveness in shock ? (3) How and when should we monitor stroke volume or cardiac output in shock ? (4) What markers of the regional and microcirculation can be monitored, and how can cellular function be assessed in shock ? (5) What is the evidence for using hemodynamic monitoring to direct therapy in shock ? Four types of statements were used: definition, recommendation, best practice and statement of fact. RESULTS: Forty-four statements were made. The main new statements include: (1) statements on individualizing blood pressure targets; (2) statements on the assessment and prediction of fluid responsiveness; (3) statements on the use of echocardiography and hemodynamic monitoring. CONCLUSIONS: This consensus provides 44 statements that can be used at the bedside to diagnose, treat and monitor patients with shock

Glacier-wide seasonal and annual geodetic mass balances from Pléiades stereo images: application to the Glacier d'Argentière, French Alps

International audienceAbstract The increased availability of high-resolution and high-quality digital elevation models (DEMs) allows for the investigation of small-scale glaciological changes and improved precision in geodetic mass-balance estimates. However, high precision and careful methodological choices are required to retrieve glacier-wide mass changes at annual to seasonal time scales. Here, we used a 7-year time series of 12 DEMs of the Glacier d'Argentière, in the French Alps, derived from the Pléiades optical satellites to assess the ability of sub-metre stereoscopic satellite images to retrieve annual-to-seasonal mass balances. We found good agreement between the five annual and the four winter mass-balance values estimated using a geodetic method and those of in situ glaciological measurements: mean values via the geodetic method are −0.66 m w.e. and 1.47 m w.e. for annual and winter balances, respectively; mean absolute discrepancies are 0.25 m w.e. (annual) and 0.36 m w.e. (winter). Our study identified three main limitations of this methodology: (i) the intrinsic DEM precision; (ii) the lack of control over the satellite acquisition dates; and (iii) the density assumption. The consistency between the methods demonstrates the potential of short time-scale glacier mass-balance monitoring using very high-resolution satellite images

Plant mutations: slaying beautiful hypotheses by surprising evidence

The Weismann theory (1) states that hereditary traits are transmitted exclusively from the germline. The theory is valid in most animals (2) where germline cells are set aside early in development (1). In plants, germline segregation is generally assumed to occur late in development (3-5), which leads to several predictions on the fate of somatic mutations occurring in plant tissues: mutations have generally low frequency in plant tissues (6); mutations at high frequency have a higher chance of intergenerational transmission; branching topology of the tree dictates mutation distribution (7); and, exposure to UV radiation increases mutagenesis (8). We produced a unique plant dataset of 60 high-coverage whole-genome sequences of two tropical tree species and identified 18,274 de novo somatic mutations, almost all at low frequency in tissues. We demonstrate that: 1) low-frequency mutations are transmitted to the next generation; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought

Low-frequency somatic mutations are heritable in tropical trees Dicorynia guianensis and Sextonia rubra

Significance The origin and fate of new mutations have received less attention in plants than in animals. Similarly to animals, plant mutations are expected to accumulate with growth and time and under exposure to ultraviolet light. However, contrary to animals, plant reproductive organs form late in an individual's development, allowing the transmission to the progeny of mutations accumulated along growth. Here, we resequenced DNA from different branches differentially exposed to sunlight of two tropical tree species. We showed that new mutations are generally rare in plant tissues and do not mimic branching patterns but can nevertheless be transmitted to the progeny. Our findings provide a perspective on heritable plant mutation and its pivotal role as the engine of evolution

Plant mutations: slaying beautiful hypotheses by surprising evidence

International audienceMutation is the source of all genetic diversity, on which selection can act allowing adaptation. Early differentiation between soma and the germline in animal development protects the germline, and thus the offspring, from the accumulation of somatic mutations. In plants, somatic mutations are expected to occur and accumulate along the branches and the differentiation between soma and germline is debated. There are several predictions on the fate of somatic mutations occurring in plant tissues: exposure to UV radiation increases mutagenesis; mutations have generally low frequency in plant tissues; branching topology of the tree dictates mutation distribution; and mutations at high frequency have a higher chance of being transmitted to the next generation. We produced a unique plant dataset of 60 highcoverage whole-genome sequences of two tropical tree species (Dicorynia guianensis and Sextonia rubra) and identified 18,274 de novo somatic mutations on branches exposed to high and low light, almost all at low frequency in tissues. We demonstrate that: 1) mutation rates and mutation spectra are not demonstrably affected by differences in UV exposure; 2) mutation phylogenies deviate from the branching topology of the tree; and 3) low-frequency mutations are transmitted to the next generation. Altogether, our results suggest far more complex links between plant growth, ageing, UV exposure, and mutation rates than commonly thought. Specially, the transmissibility of low frequency mutations, which are the most abundant, indicates a non-negligible role of low frequency somatic mutations as heritable mutations fuelling plant evolution