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Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: Linking systems biology with vaccine development
The aim of research on infectious diseases is their prevention, and brucellosis and salmonellosis as such are classic examples of worldwide zoonoses for application of a systems biology approach for enhanced rational vaccine development. When used optimally, vaccines prevent disease manifestations, reduce transmission of disease, decrease the need for pharmaceutical intervention, and improve the health and welfare of animals, as well as indirectly protecting against zoonotic diseases of people. Advances in the last decade or so using comprehensive systems biology approaches linking genomics, proteomics, bioinformatics, and biotechnology with immunology, pathogenesis and vaccine formulation and delivery are expected to enable enhanced approaches to vaccine development. The goal of this paper is to evaluate the role of computational systems biology analysis of host:pathogen interactions (the interactome) as a tool for enhanced rational design of vaccines. Systems biology is bringing a new, more robust approach to veterinary vaccine design based upon a deeper understanding of the host pathogen interactions and its impact on the host's molecular network of the immune system. A computational systems biology method was utilized to create interactome models of the host responses to Brucella melitensis (BMEL), Mycobacterium avium paratuberculosis (MAP), Salmonella enterica Typhimurium (STM), and a Salmonella mutant (isogenic *sipA, sopABDE2) and linked to the basis for rational development of vaccines for brucellosis and salmonellosis as reviewed by Adams et al. and Ficht et al. [1,2]. A bovine ligated ileal loop biological model was established to capture the host gene expression response at multiple time points post infection. New methods based on Dynamic Bayesian Network (DBN) machine learning were employed to conduct a comparative pathogenicity analysis of 219 signaling and metabolic pathways and 1620 gene ontology (GO) categories that defined the host's biosignatures to each infectious condition. Through this DBN computational approach, the method identified significantly perturbed pathways and GO category groups of genes that define the pathogenicity signatures of the infectious agent. Our preliminary results provide deeper understanding of the overall complexity of host innate immune response as well as the identification of host gene perturbations that defines a unique host temporal biosignature response to each pathogen. The application of advanced computational methods for developing interactome models based on DBNs has proven to be instrumental in elucidating novel host responses and improved functional biological insight into the host defensive mechanisms. Evaluating the unique differences in pathway and GO perturbations across pathogen conditions allowed the identification of plausible host pathogen interaction mechanisms. Accordingly, a systems biology approach to study molecular pathway gene expression profiles of host cellular responses to microbial pathogens holds great promise as a methodology to identify, model and predict the overall dynamics of the host pathogen interactome. Thus, we propose that such an approach has immediate application to the rational design of brucellosis and salmonellosis vaccines.
In silico discovery of a new class of anolyte redoxmers for non-aqueous redox flow batteries
A novel simplicity-biased molecular structure generation method and Bayesian optimization based active learning have been used to discover a new class of heterocyclic molecules for organic non-aqueous redox flow batteries.
Accelerating quantum optics experiments with statistical learning
Quantum optics experiments, involving the measurement of low-probability photon events, are known to be extremely time-consuming. We present a methodology for accelerating such experiments using physically motivated ansatzes together with simple statistical learning techniques such as Bayesian maximum a posteriori estimation based on few-shot data. We show that it is possible to reconstruct time-dependent data using a small number of detected photons, allowing for fast estimates in under a minute and providing a one-to-two order of magnitude speed-up in data acquisition time. We test our approach using real experimental data to retrieve the second order intensity correlation function, G (2) ($τ$), as a function of time delay τ between detector counts, for thermal light as well as anti-bunched light emitted by a quantum dot driven by periodic laser pulses. The proposed methodology has a wide range of applicability and has the potential to impact the scientific discovery process across a multitude of domains.
Generating synthetic occupants for use in building performance simulation
Occupant behaviour simulation frameworks can employ synthetic populations to characterize occupancy and behavioural patterns in buildings based on observed demographic data at a certain geographical location. For buildings, very few synthetic occupant populations have been generated. This paper uses a Bayesian Networks (BN) structural learning approach to synthesize populations of occupants in a multi-family housing case study. Two additional cases of office occupants and senior housing residents are considered as a cross-case comparison. Furthermore, we draw upon the extended version of drivers-needs-actions-systems (DNAS) framework to guide the selection of variables and data imputation. Our results show that the BN approach is powerful in learning the structure of data sets. The synthetic data sets successfully match the joint distributions of the underlying combined data sets. Experiments on the multi-family housing particularly show better performance than the office and senior housing cases.
STAR-GALAXY CLASSIFICATION IN MULTI-BAND OPTICAL IMAGING
Ground-based optical surveys such as PanSTARRS, DES, and LSST will produce large catalogs to limiting magnitudes of r {approx}> 24. Star-galaxy separation poses a major challenge to such surveys because galaxies-even very compact galaxies-outnumber halo stars at these depths. We investigate photometric classification techniques on stars and galaxies with intrinsic FWHM <0.2 arcsec. We consider unsupervised spectral energy distribution template fitting and supervised, data-driven support vector machines (SVMs). For template fitting, we use a maximum likelihood (ML) method and a new hierarchical Bayesian (HB) method, which learns the prior distribution of template probabilities from the data. SVM requires training data to classify unknown sources; ML and HB do not. We consider (1) a best-case scenario (SVM{sub best}) where the training data are (unrealistically) a random sampling of the data in both signal-to-noise and demographics and (2) a more realistic scenario where training is done on higher signal-to-noise data (SVM{sub real}) at brighter apparent magnitudes. Testing with COSMOS ugriz data, we find that HB outperforms ML, delivering {approx}80% completeness, with purity of {approx}60%-90% for both stars and galaxies. We find that no algorithm delivers perfect performance and that studies of metal-poor main-sequence turnoff stars may be challenged by poor star-galaxy separation. Using the Receiver Operating Characteristic curve, we find a best-to-worst ranking of SVM{sub best}, HB, ML, and SVM{sub real}. We conclude, therefore, that a well-trained SVM will outperform template-fitting methods. However, a normally trained SVM performs worse. Thus, HB template fitting may prove to be the optimal classification method in future surveys.
AI-optimized detector design for the future Electron-Ion Collider: the dual-radiator RICH case
Advanced detector R&D requires performing computationally intensive and detailed simulations as part of the detector-design optimization process. Here, we propose a general approach to this process based on Bayesian optimization and machine learning that encodes detector requirements. As a case study, we focus on the design of the dual-radiator Ring Imaging Cherenkov (dRICH) detector under development as a potential component of the particle-identification system at the future Electron-Ion Collider (EIC). The EIC is a US-led frontier accelerator project for nuclear physics, which has been proposed to further explore the structure and interactions of nuclear matter at the scale of sea quarks and gluons. We show that the detector design obtained with our automated and highly parallelized framework outperforms the baseline dRICH design within the assumptions of the current model. Our technique can be applied to any detector R&D, provided that realistic simulations are available.
Nonparametric Bayesian Modeling for Automated Database Schema Matching
The problem of merging databases arises in many government and commercial applications. Schema matching, a common first step, identifies equivalent fields between databases. We introduce a schema matching framework that builds nonparametric Bayesian models for each field and compares them by computing the probability that a single model could have generated both fields. Our experiments show that our method is more accurate and faster than the existing instance-based matching algorithms in part because of the use of nonparametric Bayesian models.
Predicting fusion ignition at the National Ignition Facility with physics-informed deep learning
Here, an inertial confinement fusion experiment, carried out at the National Ignition Facility, has achieved ignition by generating fusion energy exceeding the laser energy that drove the experiment. Prior to the experiment, a generative machine learning model that combines radiation hydrodynamics simulations, deep learning, experimental data, and Bayesian statistics was used to predict, with a probability greater than 70%, that ignition was the most likely outcome for this shot.
BPP R package
The BPP package contains R code to perform Bayesian projection pursuit regression under various regression settings. Bayesian projection pursuit regression learns the functional relationship between inputs and outputs by considering a sum of functions of one dimensional projections of the inputs. This is useful as a general machine learning software.
Quantifying Uncertainties of Microscopic Nuclear Theories
The goal of this project was to produce modernized nuclear data libraries of light ion fusion reactions and actinide fission product yields. Such libraries are essential input in both stockpile science but also fundamental science (nucleosynthesis, superheavy nuclei). When such libraries are used to model complex processes involving exotic, very short-lived nuclei that have not been measured experimentally, the underlying nuclear data come from theoretical models, the predictive power of which needs to be quantified, together with its uncertainties. By teaming up nuclear theorists and statisticians, we built comprehensive theoretical frameworks based on the most fundamental theories of fusion and fission that we coupled for the first time with a Bayesian framework with machine learning techniques for uncertainty quantification. Our results include: (1) statistical emulators for neutron-alpha scattering, and the fission product mass yields of neutron-induced fission of 239 Pu, which will enable developers to generate random realizations of the corresponding data for uncertainty quantification (UQ) in applications; (2) the first complete and most accurate ab initio prediction of the S-factor for proton capture on 7 Be, which – combined with UQ – may become the recommended value at solar energies in the next review of solar fusion cross sections; (3) statistical emulators for fission mass yields in the neutron-induced fission of 239 Pu; (4) the first quantification of how uncertainties in nuclear forces impact fission properties that are relevant in nucleosynthesis simulations to explain how heavy elements are formed in the Cosmos.
Bayesian Methods in Inertial Confinement Fusion Research: Embracing uncertainty and Learning More from our Data .
Abstract not provided.
Simulation Based Inference with Domain Adaptation for Strong Gravitational Lensing
Simulation based inference leverages machine learning to carry out Bayesian inference for systems with intractable likelihoods. However, transitioning a network trained on simulated data to real data runs the risk of encountering domain shift, leading to performance losses. We attempt to implement domain adaptation into the sbi neural posterior estimation framework using the Maximum Mean Discrepancy as an additional network loss. We test two network architectures and use masked autoregressive flow for density estimation. We test the network on a set of 400,000 simulated strong gravitational lensing images generated using deeplenstronomy. The source domain is defined as low noise whereas the target domain has a noise profile sampled from experimentally derived DES survey conditions. We find that, while DA does lead to performance improvements, they are marginal at ~6% less inference error. We also find a similar marginal improvement in uncertainty calibration at around 8%.
Potential Use of a Bayesian Network for Discriminating Flash Type from Future GOES-R Geostationary Lightning Mapper (GLM) data
Continuous monitoring of the ratio of cloud flashes to ground flashes may provide a better understanding of thunderstorm dynamics, intensification, and evolution, and it may be useful in severe weather warning. The National Lighting Detection Network TM (NLDN) senses ground flashes with exceptional detection efficiency and accuracy over most of the continental United States. A proposed Geostationary Lightning Mapper (GLM) aboard the Geostationary Operational Environmental Satellite (GOES-R) will look at the western hemisphere, and among the lightning data products to be made available will be the fundamental optical flash parameters for both cloud and ground flashes: radiance, area, duration, number of optical groups, and number of optical events. Previous studies have demonstrated that the optical flash parameter statistics of ground and cloud lightning, which are observable from space, are significantly different. This study investigates a Bayesian network methodology for discriminating lightning flash type (ground or cloud) using the lightning optical data and ancillary GOES-R data. A Directed Acyclic Graph (DAG) is set up with lightning as a "root" and data observed by GLM as the "leaves." This allows for a direct calculation of the joint probability distribution function for the lighting type and radiance, area, etc. Initially, the conditional probabilities that will be required can be estimated from the Lightning Imaging Sensor (LIS) and the Optical Transient Detector (OTD) together with NLDN data. Directly manipulating the joint distribution will yield the conditional probability that a lightning flash is a ground flash given the evidence, which consists of the observed lightning optical data [and possibly cloud data retrieved from the GOES-R Advanced Baseline Imager (ABI) in a more mature Bayesian network configuration]. Later, actual GLM and NLDN data can be used to refine the estimates of the conditional probabilities used in the model; i.e., the Bayesian network is a learning network. Methods for efficient calculation of the conditional probabilities (e.g., an algorithm using junction trees), finding data conflicts, goodness of fit, and dealing with missing data will also be addressed.
Optimal Estimation Framework for Ocean Color Atmospheric Correction and Pixel-level Uncertainty Quantification
Ocean color remote sensing requires compensation for atmospheric scattering and absorption (aerosol, Rayleigh, and trace gases), referred to as atmospheric correction (AC). AC allows inference of parameters such as spectrally resolved remote sensing reflectance ( R rs )(λ) ; sr 1 ) at the ocean surface from the top-of-atmosphere reflectance. Often, the uncertainty of this process is not fully explored. Bayesian inference techniques provide a simultaneous AC and uncertainty assessment via a full posterior distribution of the relevant variables, given the prior distribution of those variables and the radiative transfer (RT) likelihood function. Given uncertainties in the algorithm inputs, the Bayesian framework enables better constraints on the AC process by using the complete spectral information compared to traditional approaches that use only a subset of bands for AC. This paper investigates a Bayesian inference research method (Optimal Estimation, OE) for ocean color AC by simultaneously retrieving atmospheric and ocean properties using all visible and near-infrared spectral bands. The OE algorithm analytically approximates the posterior distribution of parameters based on normality assumptions and provides a potentially viable operational algorithm with a reduced computational expense. We developed a Neural Network (NN) RT forward model look-up-table-based emulator to increase algorithm efficiency further and thus speed up the likelihood computations. We then applied the OE algorithm to synthetic data and observations from the MODerate resolution Imaging Spectroradiometer (MODIS) on NASA’s Aqua spacecraft. We compared the R rs )(λ) retrieval and its uncertainty estimates from the OE method with in-situ validation data from the SeaWiFS Bio-optical Archive and Storage System (SeaBASS) and Aerosol Robotic Network Ocean Color (AERONET-OC) datasets. The OE algorithm improved R rs )(λ) estimates relative to the NASA standard operational algorithm by improving all statistical metrics at 443, 555, and 667 nm. Unphysical negative R rs )(λ) , which often appear in complex water conditions, was reduced by a factor of 3. The OE-derived pixel-level R rs )(λ) uncertainty estimates were also assessed relative to in-situ data and were shown to have skill.
Simulation based inference with domain adaptation for strong gravitational lensing
Simulation based inference leverages machine learning to carry out Bayesian inference in systems with intractable likelihoods. However, transitioning a network trained on simulated data to real data runs the risk of encountering domain shift, leading to performance losses. We attempt to implement domain adaptation into the sbi neural posterior estimation framework using the Maximum Mean Discrepancy as an additional network loss, using masked autoregressive fow (MAF) as our density estimator. We test the network on a set of 400,000 simulated strong gravitational lensing images generated using deeplenstronomy. The source domain is defined as low noise whereas the target domain has a noise profile sampled from experimentally derived DES survey conditions. We find that SBI appears robust against small changes in the data with similar performance on source and target. Moreover, while DA does lead to performance improvements, they are marginal at 6% less inference error.
Determining Multi-Component Phase Diagrams with Desired Characteristics Using Active Learning
Herein, we demonstrate how to predict and experimentally validate phase diagrams for multi-component systems from a high-dimensional virtual space of all possible phase diagrams involving several elements based on small existing experimental data. The experimental data for bulk phases for known systems represents a sampling from this space, and screening the space allows multi-component phase diagrams with given design criteria to be built. This approach uses machine learning methods to predict phase diagrams and Bayesian experimental design to minimize experiments for refinement and validation, all within an active learning loop. The approach is proven by predicting and synthesizing the ferroelectric ceramic system (1-ω)(Ba 0.61 Ca 0.28 Sr 0.11 TiO 3 )-ω(BaTi 0.888 Zr 0.0616 Sn 0.0028 Hf 0.0476 O 3 ) with a relatively high transition temperature and triple point, as well as the NiTi-based pseudo-binary phase diagram (1-ω)(Ti 0.309 Ni 0.485 Hf 0.20 Zr 0.006 )-ω(Ti 0.309 Ni 0.485 Hf 0.07 Zr 0.068 Nb 0.068 ) designed for high transition temperature (ω ≤ 1). Each phase diagram is validated and optimized through only three new experiments. The complexity of these compounds is beyond the reach of today’s computational methods.
Bayesian averaging for ground state masses of atomic nuclei in a Machine Learning approach
We present global predictions of the ground state mass of atomic nuclei based on a novel Machine Learning algorithm. We combine precision nuclear experimental measurements together with theoretical predictions of unmeasured nuclei. This hybrid data set is used to train a probabilistic neural network. In addition to training on this data, a physics-based loss function is employed to help refine the solutions. The resultant Bayesian averaged predictions have excellent performance compared to the testing set and come with well-quantified uncertainties which are critical for contemporary scientific applications. We assess extrapolations of the model’s predictions and estimate the growth of uncertainties in the region far from measurements.