Computational modeling of human adult neurogenesis - information theoretic analysis of biologically realistic dentate gyrus networks.
Abstract not provided.
Vineyard, Craig Michael↗
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces
Here, this paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems and then deployed for potential energy prediction for C 5 H 5 using B2PLYP-D3/6-311++G(d,p) for high-fidelity simulation data and Hartree–Fock 6-31G for low-fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Trustworthy Physics-Informed Deep Learning for Predictive Scientific Computing
This project has developed powerful trustworthy physics-informed deep learning (TPiDL) models and methods to fundamentally enhance the scale and power of computational modeling in the scientific and engineering domains. Deep learning (DL) has radically advanced the state-of-the-art in machine learning, computer vision, natural language processing, and also scientific computing. Nevertheless, progress has been driven almost entirely by empirical observations, hacks, and tricks. Under the support of this project, the graph operator learning tools and advanced trustworthy physical informed neural networks have been developed. In addition, stochastic gradient replica-exchange Markov Chain Monte Carlo (MCMC) sampling algorithms have been designed to quantify the uncertainties and speed up the training of large-scale neural networks.
97 MATHEMATICS AND COMPUTING↗
Computational Challenges for Power System Operation
As the power grid technology evolution and information technology revolution converge, power grids are witnessing a revolutionary transition, represented by emerging grid technologies and large scale deployment of new sensors and meters in networks. This transition brings opportunities, as well as computational challenges in the field of power grid analysis and operation. This paper presents some research outcomes in the areas of parallel state estimation using the preconditioned conjugated gradient method, parallel contingency analysis with a dynamic load balancing scheme and distributed system architecture. Based on this research, three types of computational challenges are identified: highly coupled applications, loosely coupled applications, and centralized and distributed applications. Recommendations for future work for power grid applications are also presented.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Jensen–Shannon divergence based novel loss functions for Bayesian neural networks
Bayesian neural networks (BNNs) are state-of-the-art machine learning methods that can naturally regularize and systematically quantify uncertainties using their stochastic parameters. Kullback–Leibler (KL) divergence-based variational inference used in BNNs suffer from unstable optimization and challenges in approximating light-tailed posteriors due to the unbounded nature of the KL divergence. To resolve these issues, we formulate a novel loss function for BNNs based on a new modification to the generalized Jensen–Shannon (JS) divergence, which is bounded. In addition, we propose a Geometric JS divergence-based loss, which is computationally efficient since it can be evaluated analytically. We found that the JS divergence-based variational inference is intractable, and hence employed a constrained optimization framework to formulate these losses. Our theoretical analysis and empirical experiments on multiple regression and classification data sets suggest that the proposed losses perform better than the KL divergence-based loss, especially when the data sets are noisy or biased. Specifically, there are approximately 5% and 8% improvements in accuracy for a noise-added CIFAR-10 dataset and a regression dataset, respectively. There is about 13% reduction in false negative predictions of a biased histopathology dataset. Additionally, we quantify and compare the uncertainty metrics for the regression and classification tasks.
97 MATHEMATICS AND COMPUTING↗
Evaluating the Observability of Network Security Monitoring Strategies With TOMATO
Not Available
42 ENGINEERING↗
Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life. Understanding the role of such enzymes is an important open question in biology. Here we develop a genome-wide method, PROPER, that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabolic genes. Enzyme promiscuity is typically studied experimentally using multicopy suppression, in which over-expression of a promiscuous ‘replacer’ gene rescues lethality caused by inactivation of a ‘target’ gene. We use PROPER to predict multicopy suppression in Escherichia coli, achieving highly significant overlap with published cases (hypergeometric p = 4.4e-13). We then validate three novel predicted target-replacer gene pairs in new multicopy suppression experiments. We next go beyond PROPER and develop a network-based approach, GEM-PROPER, that integrates PROPER with genome-scale metabolic modeling to predict promiscuous replacements via alternative metabolic pathways. GEM-PROPER predicts a new indirect replacer (thiG) for an essential enzyme (pdxB) in production of pyridoxal 5’-phosphate (the active form of Vitamin B 6 ), which we validate experimentally via multicopy suppression. Here, we perform a structural analysis of thiG to determine its potential promiscuous active site, which we validate experimentally by inactivating the pertaining residues and showing a loss of replacer activity. Thus, this study is a successful example where a computational investigation leads to a network-based identification of an indirect promiscuous replacement of a key metabolic enzyme, which would have been extremely difficult to identify directly.
60 APPLIED LIFE SCIENCES↗
Probabilistic Neural Computing with Stochastic Devices
Abstract The brain has effectively proven a powerful inspiration for the development of computing architectures in which processing is tightly integrated with memory, communication is event‐driven, and analog computation can be performed at scale. These neuromorphic systems increasingly show an ability to improve the efficiency and speed of scientific computing and artificial intelligence applications. Herein, it is proposed that the brain's ubiquitous stochasticity represents an additional source of inspiration for expanding the reach of neuromorphic computing to probabilistic applications. To date, many efforts exploring probabilistic computing have focused primarily on one scale of the microelectronics stack, such as implementing probabilistic algorithms on deterministic hardware or developing probabilistic devices and circuits with the expectation that they will be leveraged by eventual probabilistic architectures. A co‐design vision is described by which large numbers of devices, such as magnetic tunnel junctions and tunnel diodes, can be operated in a stochastic regime and incorporated into a scalable neuromorphic architecture that can impact a number of probabilistic computing applications, such as Monte Carlo simulations and Bayesian neural networks. Finally, a framework is presented to categorize increasingly advanced hardware‐based probabilistic computing technologies.
Misra, Shashank↗
Accelerating kinetic plasma simulations with machine-learning-generated initial conditions
Computational models of plasma technologies often solve for the system operating conditions by time-stepping an initial value problem to a quasi-steady solution. However, the strongly nonlinear and multi-timescale nature of plasma dynamics often necessitate millions, or even hundreds of millions, of steps to reach convergence, reducing the effectiveness of these simulations for computer-aided engineering. We consider acceleration of kinetic plasma simulations via data-driven machine-learning-generated initial conditions, which initialize the simulations close to their final quasi-steady-state, thereby reducing the number of steps to reach convergence. Three machine-learning models are developed to predict the density and ion kinetic profiles of capacitively coupled plasma discharges relevant to the microelectronics industry. The models are trained on kinetic simulations over a range of device operating frequencies and pressures. Best performance was observed when simulations were initialized with ion kinetic profiles generated by a convolutional neural network, reducing the mean number of steps to reach convergence by 17.1× when compared to initialization with a zero-dimensional global model. We also outline a workflow for continuous data-driven model improvement and simulation speedup, with the aim of generating sufficient data for full device digital twins.
Artificial neural networks↗
Resilient Plant Monitoring System: Design, Analysis, and Performance Evaluation
Resilient monitoring systems are sensor networks that degrade gracefully under malicious attacks on their sensors, causing them to project misleading information. The goal of this paper is to design, analyze, and evaluate the performance of a resilient monitoring system intended to monitor plant conditions (normal or anomalous). The architecture developed consists of four layers: data quality assessment, process variable assessment, plant condition assessment, and sensor network adaptation. Each of these layers is analyzed by either analytical or numerical tools, and the performance of the overall system is evaluated using simulations. The measure of resiliency of the resulting system is evaluated using Kullback Leibler divergence, and is shown to be sufficiently high in all scenarios considered.
97 MATHEMATICS AND COMPUTING↗
Parallel Dynamics Simulation Using a Krylov-Schwarz Linear Solution Scheme
Fast dynamics simulation of large-scale power systems is a computational challenge because of the need to solve a large set of stiff, nonlinear differential-algebraic equations at every time step. The main bottleneck in dynamic simulations is the solution of a linear system during each nonlinear iteration of Newton’s method. In this paper, we present a parallel Krylov- Schwarz linear solution scheme that uses the Krylov subspacebased iterative linear solver GMRES with an overlapping restricted additive Schwarz preconditioner. As a result, performance tests of the proposed Krylov-Schwarz scheme for several large test cases ranging from 2,000 to 20,000 buses, including a real utility network, show good scalability on different computing architectures.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Detecting Outliers in Network Transfers with Feature Extraction
Reliable file transfers are essential for successful science computations and experiments that need large complex data files to be moved across long distances. Networks use protocols such as TCP and UDP to support file transfers, and their performance degrades under packet losses and duplications, thereby adversely affecting science applications. Hence, scientists and engineers often monitor network statistics to find and repair network problems that cause such degradations.Outliers or anomalies can be detected using statistical and machine learning methods that highlight abnormal behaviors. However, without knowing what is normal, it is very difficult and subjective to determine the anomalies. In this paper, we investigate statistical and machine learning approaches to extract unknown or unsupervised features from TCP and perfSONAR data sets, with the aim to identify anomalies such as packet loss, duplication and retransmission sequencing that affect file transfer performance. Simple statistical and feature extraction methods (e.g. PCA) have shown that detecting anomalies is simpler if labeled data sets of normal behavior are available. While perfSONAR logs record losses,they do not detect duplications and reordering. We show that PCA applied to TCP statistics is able to determine abnormal behavior in the above cases. In particular, our results show that simple feature extraction techniques provide building blocks for more advanced network monitoring tools that can quickly flag anomalies using simple measurements, thereby helping to build confidence in file transfer reliability.
Rao, Nageswara S.↗
ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks
BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.
Comparative network analysis↗
The Effect of the Prior and the Experimental Design on the Inference of the Precision Matrix in Gaussian Chain Graph Models
Here, we investigate whether (and how) experimental design could aid in the estimation of the precision matrix in a Gaussian chain graph model, especially the interplay between the design, the effect of the experiment and prior knowledge about the effect. Estimation of the precision matrix is a fundamental task to infer biological graphical structures like microbial networks. We compare the marginal posterior precision of the precision matrix under four priors: flat, conjugate Normal-Wishart, Normal-MGIG and a general independent. Under the flat and conjugate priors, the Laplace-approximated posterior precision is not a function of the design matrix rendering useless any efforts to find an optimal experimental design to infer the precision matrix. In contrast, the Normal-MGIG and general independent priors do allow for the search of optimal experimental designs, yet there is a sharp upper bound on the information that can be extracted from a given experiment. We confirm our theoretical findings via a simulation study comparing (i) the KL divergence between prior and posterior and (ii) the Stein’s loss difference of MAPs between random and no experiment. Our findings provide practical advice for domain scientists conducting experiments to better infer the precision matrix as a representation of a biological network.
54 ENVIRONMENTAL SCIENCES↗
Learning likelihood ratios with neural network classifiers
The likelihood ratio is a crucial quantity for statistical inference in science that enables hypothesis testing, construction of confidence intervals, reweighting of distributions, and more. Many modern scientific applications, however, make use of data- or simulation-driven models for which computing the likelihood ratio can be very difficult or even impossible. By applying the so-called “likelihood ratio trick,” approximations of the likelihood ratio may be computed using clever parametrizations of neural network-based classifiers. A number of different neural network setups can be defined to satisfy this procedure, each with varying performance in approximating the likelihood ratio when using finite training data. We present a series of empirical studies detailing the performance of several common loss functionals and parametrizations of the classifier output in approximating the likelihood ratio of two univariate and multivariate Gaussian distributions as well as simulated high-energy particle physics datasets.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Propagating uncertainties in large-scale hemodynamics models via network uncertainty quantification and reduced-order modeling
Numerical simulations of the cardiovascular system are affected by uncertainties arising from a substantial lack of data related to the boundary conditions and the physical parameters of the mathematical models. Quantifying the impact of this uncertainty on the numerical results along the circulatory network is challenged by the complexity of both the morphology of the domain and the local dynamics. Here, we propose to integrate (i) the Transverse Enriched Pipe Element Methods (TEPEM) as a reduced-order model for effectively computing the 3D local hemodynamics; and (ii) a combination of uncertainty quantification via Polynomial Chaos Expansion and classical relaxation methods – called network uncertainty quantification (NetUQ) – for effectively propagating random variables that encode uncertainties throughout the networks. The findings demonstrate the computational effectiveness of computing the propagation of uncertainties in networks with nontrivial topology, including portions of the cerebral and the coronary systems.
97 MATHEMATICS AND COMPUTING↗
Resilient information and inference networks under mixed-trust sensing
With ubiquitous digitization, sensing, and computational intelligence deployed in increasingly more and broader domains, including critical infrastructure, potentially misleading and destabilizing effects of multimodal anomalies and adversarial behavior are growing in importance. Here, we develop randomized and reinforcement learning-based strategies for strategically recruiting and utilizing deployed (and, thus, vulnerable and potentially faulty and/or compromised) nodes from information and inference networks, while defending against adversaries that attempt to misguide assessments of inferred variables. Recognizing that, besides communication and other costs, sampling from any observable node can either provide true data or dangerously expose our inference to misinformation (without being easily distinguishable what actually happens), the proposed strategies proceed by progressively recruiting nodes and cautiously scaling their information contribution based on assumed, or, in our reinforcement learning approach, intelligently weighed trustworthiness, with the learning approach also considering network-wide, threat-inclusive risk/value tradeoffs. While avoiding the hardware, communication, analytical and computational burden of explicit redundancy, the proposed defensive schemes enable on-the-fly assessments of underlying processes, and system-wide situational awareness with demonstrable resilience against adversarial activities.
97 - MATHEMATICS AND COMPUTING↗
Deep Neural Networks are Adaptive to Function Regularity and Data Distribution in Approximation and Estimation
Deep learning has exhibited remarkable results across diverse areas. To understand its success, substantial research has been directed towards its theoretical foundations. Nev- ertheless, the majority of these studies examine how well deep neural networks can model functions with uniform regularities. In this paper, we explore a different angle: how deep neural networks can adapt to varying degrees of smoothness in functions and nonuni- form data distributions across different locations and scales. More precisely, we focus on a broad class of functions defined by nonlinear tree-based approximation methods. This class encompasses a range of function types, such as functions with uniform regularities and discontinuous functions. We develop nonparametric approximation and estimation theories for this class using deep ReLU networks. Our results show that deep neural networks are adaptive to the nonuniform smoothness of functions and nonuniform data distributions at different locations and scales. We apply our results to several function classes, and derive the corresponding approximation and generalization errors. The validity of our results is demonstrated through numerical experiments.
97 MATHEMATICS AND COMPUTING↗