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The expansion and intensification of livestock production is predicted to promote the emergence of pathogens. As pathogens sometimes jump between species, this can affect the health of humans as well as livestock. Here, we investigate how livestock microbiota can act as a source of these emerging pathogens through analysis of Streptococcus suis, a ubiquitous component of the respiratory microbiota of pigs that is also a major cause of disease on pig farms and an important zoonotic pathogen. Combining molecular dating, phylogeography, and comparative genomic analyses of a large collection of isolates, we find that several pathogenic lineages of S. suis emerged in the 19th and 20th centuries, during an early period of growth in pig farming. These lineages have since spread between countries and continents, mirroring trade in live pigs. They are distinguished by the presence of three genomic islands with putative roles in metabolism and cell adhesion, and an ongoing reduction in genome size, which may reflect their recent shift to a more pathogenic ecology. Reconstructions of the evolutionary histories of these islands reveal constraints on pathogen emergence that could inform control strategies, with pathogenic lineages consistently emerging from one subpopulation of S. suis and acquiring genes through horizontal transfer from other pathogenic lineages. These results shed light on the capacity of the microbiota to rapidly evolve to exploit changes in their host population and suggest that the impact of changes in farming on the pathogenicity and zoonotic potential of S. suis is yet to be fully realized.

We consider probabilistic models for sequential observations which exhibit gradual transitions among a finite number of states. We are particularly motivated by applications such as human activity analysis where observed accelerometer time series contains segments representing distinct activities, which we call pure states, as well as periods characterized by continuous transition among these pure states. To capture this transitory behavior, the dynamical Wasserstein barycenter (DWB) model of Cheng et al. in 2021 [1] associates with each pure state a data-generating distribution and models the continuous transitions among these states as a Wasserstein barycenter of these distributions with dynamically evolving weights. Focusing on the univariate case where Wasserstein distances and barycenters can be computed in closed form, we extend [1] specifically relaxing the parameterization of the pure states as Gaussian distributions. We highlight issues related to the uniqueness in identifying the model parameters as well as uncertainties induced when estimating a dynamically evolving distribution from a limited number of samples. To ameliorate non-uniqueness, we introduce regularization that imposes temporal smoothness on the dynamics of the barycentric weights. A quantile-based approximation of the pure state distributions yields a finite dimensional estimation problem which we numerically solve using cyclic descent alternating between updates to the pure-state quantile functions and the barycentric weights. We demonstrate the utility of the proposed algorithm in segmenting both simulated and real world human activity time series.

We pursue tractable Bayesian analysis of generalized linear models (GLMs) for categorical data. Thus far, GLMs are difficult to scale to more than a few dozen categories due to non-conjugacy or strong posterior dependencies when using conjugate auxiliary variable methods. We define a new class of GLMs for categorical data called categorical-from-binary (CB) models. Each CB model has a likelihood that is bounded by the product of binary likelihoods, suggesting a natural posterior approximation. This approximation makes inference straightforward and fast; using well-known auxiliary variables for probit or logistic regression, the product of binary models admits conjugate closed-form variational inference that is embarrassingly parallel across categories and invariant to category ordering. Moreover, an independent binary model simultaneously approximates multiple CB models. Bayesian model averaging over these can improve the quality of the approximation for any given dataset. We show that our approach scales to thousands of categories, outperforming posterior estimation competitors like Automatic Differentiation Variational Inference (ADVI) and No U-Turn Sampling (NUTS) in the time required to achieve fixed prediction quality., Comment: to appear at ICML 2022

Many time series can be modeled as a sequence of segments representing high-level discrete states, such as running and walking in a human activity application. Flexible models should describe the system state and observations in stationary "pure-state" periods as well as transition periods between adjacent segments, such as a gradual slowdown between running and walking. However, most prior work assumes instantaneous transitions between pure discrete states. We propose a dynamical Wasserstein barycentric (DWB) model that estimates the system state over time as well as the data-generating distributions of pure states in an unsupervised manner. Our model assumes each pure state generates data from a multivariate normal distribution, and characterizes transitions between states via displacement-interpolation specified by the Wasserstein barycenter. The system state is represented by a barycentric weight vector which evolves over time via a random walk on the simplex. Parameter learning leverages the natural Riemannian geometry of Gaussian distributions under the Wasserstein distance, which leads to improved convergence speeds. Experiments on several human activity datasets show that our proposed DWB model accurately learns the generating distribution of pure states while improving state estimation for transition periods compared to the commonly used linear interpolation mixture models., Comment: To appear at Neurips 2021

Here we introduce a new reconstruction technique for two-dimensional Bragg Scattering Tomography (BST), based on the Radon transform models of [arXiv preprint, arXiv:2004.10961 (2020)]. Our method uses a combination of ideas from multibang control and microlocal analysis to construct an objective function which can regularize the BST artifacts; specifically the boundary artifacts due to sharp cutoff in sinogram space (as observed in [arXiv preprint, arXiv:2007.00208 (2020)]), and artifacts arising from approximations made in constructing the model used for inversion. We then test our algorithm in a variety of Monte Carlo (MC) simulated examples of practical interest in airport baggage screening and threat detection. The data used in our studies is generated with a novel Monte-Carlo code presented here. The model, which is available from the authors upon request, captures both the Bragg scatter effects described by BST as well as beam attenuation and Compton scatter., Comment: 26 pages, 17 figures

We present a new inner-outer iterative algorithm for edge enhancement in imaging problems. At each outer iteration, we formulate a Tikhonov-regularized problem where the penalization is expressed in the 2-norm and involves a regularization operator designed to improve edge resolution as the outer iterations progress, through an adaptive process. An efficient hybrid regularization method is used to project the Tikhonov-regularized problem onto approximation subspaces of increasing dimensions (inner iterations), while conveniently choosing the regularization parameter (by applying well-known techniques, such as the discrepancy principle or the ${\mathcal L}$-curve criterion, to the projected problem). This procedure results in an automated algorithm for edge recovery that does not involve regularization parameter tuning by the user, nor repeated calls to sophisticated optimization algorithms, and is therefore particularly attractive from a computational point of view. A key to the success of the new algorithm is the design of the regularization operator through the use of an adaptive diagonal weighting matrix that effectively enforces smoothness only where needed. We demonstrate the value of our approach on applications in X-ray CT image reconstruction and in image deblurring, and show that it can be computationally much more attractive than other well-known strategies for edge preservation, while providing solutions of greater or equal quality.

Two common problems in time series analysis are the decomposition of the data stream into disjoint segments that are each in some sense "homogeneous" - a problem known as Change Point Detection (CPD) - and the grouping of similar nonadjacent segments, a problem that we call Time Series Segment Clustering (TSSC). Building upon recent theoretical advances characterizing the limiting distribution-free behavior of the Wasserstein two-sample test (Ramdas et al. 2015), we propose a novel algorithm for unsupervised, distribution-free CPD which is amenable to both offline and online settings. We also introduce a method to mitigate false positives in CPD and address TSSC by using the Wasserstein distance between the detected segments to build an affinity matrix to which we apply spectral clustering. Results on both synthetic and real data sets show the benefits of the approach.

Solar-powered electrochemical production of hydrogen through water electrolysis is an active and important research endeavor. However, technologies and roadmaps for implementation of this process do not exist. In this perspective paper, we describe potential pathways for solar-hydrogen technologies into the marketplace in the form of photoelectrochemical or photovoltaic-driven electrolysis devices and systems. We detail technical approaches for device and system architectures, economic drivers, societal perceptions, political impacts, technological challenges, and research opportunities. Implementation scenarios are broken down into short-term and long-term markets, and a specific technology roadmap is defined. In the short term, the only plausible economical option will be photovoltaic-driven electrolysis systems for niche applications. In the long term, electrochemical solar-hydrogen technologies could be deployed more broadly in energy markets but will require advances in the technology, significant cost reductions, and/ or policy changes. Ultimately, a transition to a society that significantly relies on solar-hydrogen technologies will benefit from continued creativity and influence from the scientific community.

Solar-powered electrochemical production of hydrogen through water electrolysis is an active and important research endeavor. However, technologies and roadmaps for implementation of this process do not exist. In this perspective paper, we describe potential pathways for solar-hydrogen technologies into the marketplace in the form of photoelectrochemical or photovoltaic-driven electrolysis devices and systems. We detail technical approaches for device and system architectures, economic drivers, societal perceptions, political impacts, technological challenges, and research opportunities. Implementation scenarios are broken down into short-term and long-term markets, and a specific technology roadmap is defined. In the short term, the only plausible economical option will be photovoltaic-driven electrolysis systems for niche applications. In the long term, electrochemical solar-hydrogen technologies could be deployed more broadly in energy markets but will require advances in the technology, significant cost reductions, and/or policy changes. Ultimately, a transition to a society that significantly relies on solar-hydrogen technologies will benefit from continued creativity and influence from the scientific community.

In this paper we demonstrate the utility of fusing energy-resolved observations of Compton scattered photons with traditional attenuation data for the joint recovery of mass density and photoelectric absorption in the context of limited view tomographic imaging applications. We begin with the development of a physical and associated numerical model for the Compton scatter process. Using this model, we propose a variational approach recovering these two material properties. In addition to the typical data-fidelity terms, the optimization functional includes regularization for both the mass density and photoelectric coefficients. We consider a novel edge-preserving method in the case of mass density. To aid in the recovery of the photoelectric information, we draw on our recent method in \cite{r15} and employ a non-local regularization scheme that builds on the fact that mass density is more stably imaged. Simulation results demonstrate clear advantages associated with the use of both scattered photon data and energy resolved information in mapping the two material properties of interest. Specifically, comparing images obtained using only conventional attenuation data with those where we employ only Compton scatter photons and images formed from the combination of the two, shows that taking advantage of both types of data for reconstruction provides far more accurate results.

Multi-task/Multi-output learning seeks to exploit correlation among tasks to enhance performance over learning or solving each task independently. In this paper, we investigate this problem in the context of Gaussian Processes (GPs) and propose a new model which learns a mixture of latent processes by decomposing the covariance matrix into a sum of structured hidden components each of which is controlled by a latent GP over input features and a "weight" over tasks. From this sum structure, we propose a parallelizable parameter learning algorithm with a predetermined initialization for the "weights". We also notice that an ensemble parameter learning approach using mini-batches of training data not only reduces the computation complexity of learning but also improves the regression performance. We evaluate our model on two datasets, the smaller Swiss Jura dataset and another relatively larger ATMS dataset from NOAA. Substantial improvements are observed compared with established alternatives., Comment: main body: 9 pages, supplemental material: 7 pages. This version corrected a few typos in previous version

Despite their importance for humans, there is little consensus on the function of antibiotics in nature for the bacteria that produce them. Classical explanations suggest that bacteria use antibiotics as weapons to kill or inhibit competitors, whereas a recent alternative hypothesis states that antibiotics are signals that coordinate cooperative social interactions between coexisting bacteria. Here we distinguish these hypotheses in the prolific antibiotic-producing genus Streptomyces and provide strong evidence that antibiotics are weapons whose expression is significantly influenced by social and competitive interactions between competing strains. We show that cells induce facultative responses to cues produced by competitors by (i) increasing their own antibiotic production, thereby decreasing costs associated with constitutive synthesis of these expensive products, and (ii) by suppressing antibiotic production in competitors, thereby reducing direct threats to themselves. These results thus show that although antibiotic production is profoundly social, it is emphatically not cooperative. Using computer simulations, we next show that these facultative strategies can facilitate the maintenance of biodiversity in a community context by converting lethal interactions between neighboring colonies to neutral interactions where neither strain excludes the other. Thus, just as bacteriocins can lead to increased diversity via rock–paper–scissors dynamics, so too can antibiotics via elicitation and suppression. Our results reveal that social interactions are crucial for understanding antibiosis and bacterial community dynamics, and highlight the potential of interbacterial interactions for novel drug discovery by eliciting pathways that mediate interference competition.

Despite their importance for humans, there is little consensus on the function of antibiotics in nature for the bacteria that produce them. Classical explanations suggest that bacteria use antibiotics as weapons to kill or inhibit competitors, whereas a recent alternative hypothesis states that antibiotics are signals that coordinate cooperative social interactions between coexisting bacteria. Here we distinguish these hypotheses in the prolific antibiotic-producing genus Streptomyces and provide strong evidence that antibiotics are weapons whose expression is significantly influenced by social and competitive interactions between competing strains. We show that cells induce facultative responses to cues produced by competitors by (i) increasing their own antibiotic production, thereby decreasing costs associated with constitutive synthesis of these expensive products, and (ii) by suppressing antibiotic production in competitors, thereby reducing direct threats to themselves. These results thus show that although antibiotic production is profoundly social, it is emphatically not cooperative. Using computer simulations, we next show that these facultative strategies can facilitate the maintenance of biodiversity in a community context by converting lethal interactions between neighboring colonies to neutral interactions where neither strain excludes the other. Thus, just as bacteriocins can lead to increased diversity via rock–paper–scissors dynamics, so too can antibiotics via elicitation and suppression. Our results reveal that social interactions are crucial for understanding antibiosis and bacterial community dynamics, and highlight the potential of interbacterial interactions for novel drug discovery by eliciting pathways that mediate interference competition.

Recent years have seen growing interest in exploiting dual- and multi-energy measurements in computed tomography (CT) in order to characterize material properties as well as object shape. Material characterization is performed by decomposing the scene into constitutive basis functions, such as Compton scatter and photoelectric absorption functions. While well motivated physically, the joint recovery of the spatial distribution of photoelectric and Compton properties is severely complicated by the fact that the data are several orders of magnitude more sensitive to Compton scatter coefficients than to photoelectric absorption, so small errors in Compton estimates can create large artifacts in the photoelectric estimate. To address these issues, we propose a model-based iterative approach which uses patch-based regularization terms to stabilize inversion of photoelectric coefficients, and solve the resulting problem though use of computationally attractive Alternating Direction Method of Multipliers (ADMM) solution techniques. Using simulations and experimental data acquired on a commercial scanner, we demonstrate that the proposed processing can lead to more stable material property estimates which should aid materials characterization in future dual- and multi-energy CT systems.

The overarching goal of this research is to develop and demonstrate a comprehensive approach for field characterization of DNAPL source zones which quantifies the key features that control plume response. Here the intent is to integrate targeted (local-scale) in situ tests with transect-based observations of downstream contaminant flux or concentration and information on subsurface geologic variability. To address its primary goal, the research encompasses the following specific objectives: (1) identification of the most information rich metrics for linking NAPL architecture to plume response; (2) development and refinement of in situ test methods and modeling tools that can be used to quantify identified metrics in targeted regions of the source zone; (3) integration of these metrics and tools with current machine learning characterization methods for an overall source zone assessment protocol; and (4) development of simplified models for prediction of plume response. The research approach integrates batch, column and aquifer cell experiments with mathematical modeling and data processing tools to identify and quantify features of the DNAPL architecture controlling down gradient plume response.

We present a novel approach for the inverse problem in electrical impedance tomography based on regularized quadratic regression. Our contribution introduces a new formulation for the forward model in the form of a nonlinear integral transform, which maps changes in the electrical properties of a domain to their respective variations in boundary data. Using perturbation theory the transform is approximated to yield a high-order misfit function which is then used to derive a regularized inverse problem. In particular, we consider the nonlinear problem to second-order accuracy; hence our approximation method improves upon the local linearization of the forward mapping. The inverse problem is approached using Newton's iterative algorithm, and results from simulated experiments are presented. With a moderate increase in computational complexity, the method yields superior results compared to those of regularized linear regression and can be implemented to address the nonlinear inverse problem., Research Promotion Foundation (Cyprus), Massachusetts Institute of Technology. Laboratory for Energy and the Environment (Cyprus Institute Program for Energy, Environment and Water Resources (CEEW))

The development of energy selective, photon counting X-ray detectors allows for a wide range of new possibilities in the area of computed tomographic image formation. Under the assumption of perfect energy resolution, here we propose a tensor-based iterative algorithm that simultaneously reconstructs the X-ray attenuation distribution for each energy. We use a multi-linear image model rather than a more standard "stacked vector" representation in order to develop novel tensor-based regularizers. Specifically, we model the multi-spectral unknown as a 3-way tensor where the first two dimensions are space and the third dimension is energy. This approach allows for the design of tensor nuclear norm regularizers, which like its two dimensional counterpart, is a convex function of the multi-spectral unknown. The solution to the resulting convex optimization problem is obtained using an alternating direction method of multipliers (ADMM) approach. Simulation results shows that the generalized tensor nuclear norm can be used as a stand alone regularization technique for the energy selective (spectral) computed tomography (CT) problem and when combined with total variation regularization it enhances the regularization capabilities especially at low energy images where the effects of noise are most prominent.

This paper presents several strategies for spectral de-noising of hyperspectral images and hypercube reconstruction from a limited number of tomographic measurements. In particular we show that the non-noisy spectral data, when stacked across the spectral dimension, exhibits low-rank. On the other hand, under the same representation, the spectral noise exhibits a banded structure. Motivated by this we show that the de-noised spectral data and the unknown spectral noise and the respective bands can be simultaneously estimated through the use of a low-rank and simultaneous sparse minimization operation without prior knowledge of the noisy bands. This result is novel for for hyperspectral imaging applications. In addition, we show that imaging for the Computed Tomography Imaging Systems (CTIS) can be improved under limited angle tomography by using low-rank penalization. For both of these cases we exploit the recent results in the theory of low-rank matrix completion using nuclear norm minimization.

Dual energy computerized tomography has gained great interest because of its ability to characterize the chemical composition of a material rather than simply providing relative attenuation images as in conventional tomography. The purpose of this paper is to introduce a novel polychromatic dual energy processing algorithm with an emphasis on detection and characterization of piecewise constant objects embedded in an unknown, cluttered background. Physical properties of the objects, specifically the Compton scattering and photoelectric absorption coefficients, are assumed to be known with some level of uncertainty. Our approach is based on a level-set representation of the characteristic function of the object and encompasses a number of regularization techniques for addressing both the prior information we have concerning the physical properties of the object as well as fundamental, physics-based limitations associated with our ability to jointly recover the Compton scattering and photoelectric absorption properties of the scene. In the absence of an object with appropriate physical properties, our approach returns a null characteristic function and thus can be viewed as simultaneously solving the detection and characterization problems. Unlike the vast majority of methods which define the level set function non-parametrically, i.e., as a dense set of pixel values), we define our level set parametrically via radial basis functions (RBF's) and employ a Gauss-Newton type algorithm for cost minimization. Numerical results show that the algorithm successfully detects objects of interest, finds their shape and location, and gives a adequate reconstruction of the background.

The problem studied in this paper is ultrasound image reconstruction from frequency-domain measurements of the scattered field from an object with contrast in attenuation and sound speed. The case where the object has uniform but unknown contrast in these properties relative to the background is considered. Background clutter is taken into account in a physically realistic manner by considering an exact scattering model for randomly located small scatterers that vary in sound speed. The resulting statistical characteristics of the interference is incorporated into the imaging solution, which includes applying a total-variation minimization based approach where the relative effect of perturbation in sound speed to attenuation is included as a parameter. Convex optimization methods provide the basis for the reconstruction algorithm. Numerical data for inversion examples are generated by solving the discretized Lippman-Schwinger equation for the object and speckle-forming scatterers in the background. A statistical model based on the Born approximation is used for reconstruction of the object profile. Results are presented for a two dimensional problem in terms of classification performance and compared to minimum-l2-norm reconstruction. Classification using the proposed method is shown to be robust down to a signal-to-clutter ratio of less than 1 dB., Comment: 25 pages, 10 figures

The 29 papers in this special issue were originally presented at the 2008 International Geoscience and Remote Sensing Symposium (IGARSS'08), held from July 6 to 11 in Boston, MA., IEEE Geoscience and Remote Sensing Society

Photometry of astrophysical sources, galaxies and stars, in crowded field images, if an old problem, is still a challenging goal, as new space survey missions are launched, releasing new data with increased sensibility, resolution and field of view. The GALEX mission, observes in two UV bands and produces deep sky images of millions of galaxies or stars mixed together. These UV observations are of lower resolution than same field observed in visible bands, and with a very faint signal, at the level of the photon noise for a substantial fraction of objects. Our purpose is to use the better known optical counterparts as prior information in a Bayesian approach to deduce the UV flux. Photometry of extended sources has been addressed several times using various techniques: background determination via sigma clipping, adaptative-aperture, point-spread-function photometry, isophotal photometry, to lists some. The Bayesian approach of using optical priors for solving the UV photometry has already been applied by our team in a previous work. Here we describe the improvement of using the extended shape inferred by deblending the high resolution optical images and not only the position of the optical sources. The resulting photometric accuracy has been tested with simulation of crowded UV fields added on top of real UV images. Finally, this helps to converge to smaller and flat residual and increase the faint source detection threshold. It thus gives the opportunity to work on 2nd order effects, like improving the knowledge of the background or point-spread function by iterating on them.

The theory of compressive sensing (CS) enables the reconstruction of a sparse or compressible image or signal from a small set of linear, non-adaptive (even random) projections. However, in many applications, including object and target recognition, we are ultimately interested in making a decision about an image rather than computing a reconstruction. We propose here a framework for compressive classification that operates directly on the compressive measurements without first reconstructing the image. We dub the resulting dimensionally reduced matched filter the smashed filter. The first part of the theory maps traditional maximum likelihood hypothesis testing into the compressive domain; we find that the number of measurements required for a given classification performance level does not depend on the sparsity or compressibility of the images but only on the noise level. The second part of the theory applies the generalized maximum likelihood method to deal with unknown transformations such as the translation, scale, or viewing angle of a target object. We exploit the fact the set of transformed images forms a low-dimensional, nonlinear manifold in the high-dimensional image space. We find that the number of measurements required for a given classification performance level grows linearly in the dimensionality of the manifold but only logarithmically in the number of pixels/samples and image classes. Using both simulations and measurements from a new single-pixel compressive camera, we demonstrate the effectiveness of the smashed filter for target classification using very few measurements.

The problem of detecting and classify buried objects situ electromagnetic induction (EMI) sensing technologies has received considerable attention in recent years in a range of application areas including unexploded ordinance (UXO) and landmine remediation. In the last decade or so, considerable advances have been made in the area of EMI instrumentation yielding sensors capable of providing data both in the time and frequency domains which convey far more information concerning the structure of buried objects than is the case with older metal detectors.