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  1. Abstract

    Data from high-energy observations are usually obtained as lists of photon events. A common analysis task for such data is to identify whether diffuse emission exists, and to estimate its surface brightness, even in the presence of point sources that may be superposed. We have developed a novel nonparametric event list segmentation algorithm to divide up the field of view into distinct emission components. We use photon location data directly, without binning them into an image. We first construct a graph from the Voronoi tessellation of the observed photon locations and then grow segments using a new adaptation of seeded region growing that we callSeeded Region Growing on Graph, after which the overall method is namedSRGonG. Starting with a set of seed locations, this results in an oversegmented data set, whichSRGonGthen coalesces using a greedy algorithm where adjacent segments are merged to minimize a model comparison statistic; we use the Bayesian Information Criterion. UsingSRGonGwe are able to identify point-like and diffuse extended sources in the data with equal facility. We validateSRGonGusing simulations, demonstrating that it is capable of discerning irregularly shaped low-surface-brightness emission structures as well as point-like sources with strengths comparable to that seen in typical X-ray data.more »We demonstrateSRGonG’s use on the Chandra data of the Antennae galaxies and show that it segments the complex structures appropriately.

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  2. Abstract

    We derive precise asymptotic results that are directly usable for confidence intervals and Wald hypothesis tests for likelihood-based generalized linear mixed model analysis. The essence of our approach is to derive the exact leading term behaviour of the Fisher information matrix when both the number of groups and number of observations within each group diverge. This leads to asymptotic normality results with simple studentizable forms. Similar analyses result in tractable leading term forms for the determination of approximate locally D-optimal designs.

  3. Abstract

    Extending computational harmonic analysis tools from the classical setting of regular lattices to the more general setting of graphs and networks is very important, and much research has been done recently. The generalized Haar–Walsh transform (GHWT) developed by Irion and Saito (2014) is a multiscale transform for signals on graphs, which is a generalization of the classical Haar and Walsh–Hadamard transforms. We propose theextendedgeneralized Haar–Walsh transform (eGHWT), which is a generalization of the adapted time–frequency tilings of Thiele and Villemoes (1996). The eGHWT examines not only the efficiency of graph-domain partitions but also that of “sequency-domain” partitionssimultaneously. Consequently, the eGHWT and its associated best-basis selection algorithm for graph signals significantly improve the performance of the previous GHWT with the similar computational cost,$$O(N \log N)$$O(NlogN), whereNis the number of nodes of an input graph. While the GHWT best-basis algorithm seeks the most suitable orthonormal basis for a given task among more than$$(1.5)^N$$(1.5)Npossible orthonormal bases in$$\mathbb {R}^N$$RN, the eGHWT best-basis algorithm can find a better one by searching through more than$$0.618\cdot (1.84)^N$$0.618·(1.84)Npossible orthonormal bases in$$\mathbb {R}^N$$RN. This article describes the details of the eGHWT best-basis algorithm and demonstrates its superiority using several examples including genuine graph signals as well as conventionalmore »digital images viewed as graph signals. Furthermore, we also show how the eGHWT can be extended to 2D signals and matrix-form data by viewing them as a tensor product of graphs generated from their columns and rows and demonstrate its effectiveness on applications such as image approximation.

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  4. Abstract

    The most dynamic electromagnetic coupling between the magnetosphere and ionosphere occurs in the polar upper atmosphere. It is critical to quantify the electromagnetic energy and momentum input associated with this coupling as its impacts on the ionosphere and thermosphere system are global and major, often leading to considerable disturbances in near‐Earth space environments. The current general circulation models of the upper atmosphere exhibit systematic biases that can be attributed to an inadequate representation of the Joule heating rate resulting from unaccounted stochastic fluctuations of electric fields associated with the magnetosphere‐ionosphere coupling. These biases exist regardless of geomagnetic activity levels. To overcome this limitation, a new multiresolution random field modeling approach is developed, and the efficacy of the approach is demonstrated using Super Dual Auroral Radar Network (SuperDARN) data carefully curated for the study during a largely quiet 4‐hour period on February 29, 2012. Regional small‐scale electrostatic fields sampled at different resolutions from a probabilistic distribution of electric field variability conditioned on actual SuperDARN LOS observations exhibit considerably more localized fine‐scale features in comparison to global large‐scale fields modeled using the SuperDARN Assimilative Mapping procedure. The overall hemispherically integrated Joule heating rate is increased by a factor of about 1.5more »due to the effect of random regional small‐scale electric fields, which is close to the lower end of arbitrarily adjusted Joule heating multiplicative factor of 1.5 and 2.5 typically used in upper atmosphere general circulation models. The study represents an important step toward a data‐driven ensemble modeling of magnetosphere‐ionosphere‐atmosphere coupling processes.

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  5. Abstract

    How to design experiments that accelerate knowledge discovery on complex biological landscapes remains a tantalizing question. We present an optimal experimental design method (coined OPEX) to identify informative omics experiments using machine learning models for both experimental space exploration and model training. OPEX-guided exploration ofEscherichia coli’s populations exposed to biocide and antibiotic combinations lead to more accurate predictive models of gene expression with 44% less data. Analysis of the proposed experiments shows that broad exploration of the experimental space followed by fine-tuning emerges as the optimal strategy. Additionally, analysis of the experimental data reveals 29 cases of cross-stress protection and 4 cases of cross-stress vulnerability. Further validation reveals the central role of chaperones, stress response proteins and transport pumps in cross-stress exposure. This work demonstrates how active learning can be used to guide omics data collection for training predictive models, making evidence-driven decisions and accelerating knowledge discovery in life sciences.

  6. Abstract The evolution of the COVID-19 pandemic is described through a time-dependent stochastic dynamic model in discrete time. The proposed multi-compartment model is expressed through a system of difference equations. Information on the social distancing measures and diagnostic testing rates are incorporated to characterize the dynamics of the various compartments of the model. In contrast with conventional epidemiological models, the proposed model involves interpretable temporally static and dynamic epidemiological rate parameters. A model fitting strategy built upon nonparametric smoothing is employed for estimating the time-varying parameters, while profiling over the time-independent parameters. Confidence bands of the parameters are obtained through a residual bootstrap procedure. A key feature of the methodology is its ability to estimate latent unobservable compartments such as the number of asymptomatic but infected individuals who are known to be the key vectors of COVID-19 spread. The nature of the disease dynamics is further quantified by relevant epidemiological markers that make use of the estimates of latent compartments. The methodology is applied to understand the true extent and dynamics of the pandemic in various states within the United States (US).
    Free, publicly-accessible full text available December 1, 2023
  7. Abstract Background Few interventions are known to reduce the incidence of respiratory failure that occurs following elective surgery (postoperative respiratory failure; PRF). We previously reported risk factors associated with PRF that occurs within the first 5 days after elective surgery (early PRF; E-PRF); however, PRF that occurs six or more days after elective surgery (late PRF; L-PRF) likely represents a different entity. We hypothesized that L-PRF would be associated with worse outcomes and different risk factors than E-PRF. Methods This was a retrospective matched case-control study of 59,073 consecutive adult patients admitted for elective non-cardiac and non-pulmonary surgical procedures at one of five University of California academic medical centers between October 2012 and September 2015. We identified patients with L-PRF, confirmed by surgeon and intensivist subject matter expert review, and matched them 1:1 to patients who did not develop PRF (No-PRF) based on hospital, age, and surgical procedure. We then analyzed risk factors and outcomes associated with L-PRF compared to E-PRF and No-PRF. Results Among 95 patients with L-PRF, 50.5% were female, 71.6% white, 27.4% Hispanic, and 53.7% Medicare recipients; the median age was 63 years (IQR 56, 70). Compared to 95 matched patients with No-PRF and 319 patients who developedmore »E-PRF, L-PRF was associated with higher morbidity and mortality, longer hospital and intensive care unit length of stay, and increased costs. Compared to No-PRF, factors associated with L-PRF included: preexisiting neurologic disease (OR 4.36, 95% CI 1.81–10.46), anesthesia duration per hour (OR 1.22, 95% CI 1.04–1.44), and maximum intraoperative peak inspiratory pressure per cm H 2 0 (OR 1.14, 95% CI 1.06–1.22). Conclusions We identified that pre-existing neurologic disease, longer duration of anesthesia, and greater maximum intraoperative peak inspiratory pressures were associated with respiratory failure that developed six or more days after elective surgery in adult patients (L-PRF). Interventions targeting these factors may be worthy of future evaluation.« less
    Free, publicly-accessible full text available December 1, 2023
  8. Abstract We present a machine learning framework to automate knowledge discovery through knowledge graph construction, inconsistency resolution, and iterative link prediction. By incorporating knowledge from 10 publicly available sources, we construct an Escherichia coli antibiotic resistance knowledge graph with 651,758 triples from 23 triple types after resolving 236 sets of inconsistencies. Iteratively applying link prediction to this graph and wet-lab validation of the generated hypotheses reveal 15 antibiotic resistant E. coli genes, with 6 of them never associated with antibiotic resistance for any microbe. Iterative link prediction leads to a performance improvement and more findings. The probability of positive findings highly correlates with experimentally validated findings ( R 2  = 0.94). We also identify 5 homologs in Salmonella enterica that are all validated to confer resistance to antibiotics. This work demonstrates how evidence-driven decisions are a step toward automating knowledge discovery with high confidence and accelerated pace, thereby substituting traditional time-consuming and expensive methods.
    Free, publicly-accessible full text available December 1, 2023
  9. We present a new method to sample conditioned trajectories of a system evolving under Langevin dynamics based on Brownian bridges. The trajectories are conditioned to end at a certain point (or in a certain region) in space. The bridge equations can be recast exactly in the form of a non-linear stochastic integro-differential equation. This equation can be very well approximated when the trajectories are closely bundled together in space, i.e., at low temperature, or for transition paths. The approximate equation can be solved iteratively using a fixed point method. We discuss how to choose the initial trajectories and show some examples of the performance of this method on some simple problems. This method allows us to generate conditioned trajectories with a high accuracy.