Model predictive control simulations with block-hierarchical differential–algebraic process models
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97 MATHEMATICS AND COMPUTING↗
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Structural conserved moiety splitting of a stoichiometric matrix
Characterising biochemical reaction network structure in mathematical terms enables the inference of functional biochemical consequences from network structure with existing mathematical techniques and spurs the development of new mathematics that exploits the peculiarities of biochemical network structure. The structure of a biochemical network may be specified by reaction stoichiometry, that is, the relative quantities of each molecule produced and consumed in each reaction of the network. A biochemical network may also be specified at a higher level of resolution in terms of the internal structure of each molecule and how molecular structures are transformed by each reaction in a network. The stoichiometry for a set of reactions can be compiled into a stoichiometric matrix N ϵ Z mxn where each row corresponds to a molecule and each column corresponds to a reaction. We demonstrate that a stoichiometric matrix may be split into the sum of m - rank(N) moiety transition matrices, each of which corresponds to a subnetwork accessible to a structurally identifiable conserved moiety. The existence of this moiety matrix splitting is a property that distinguishes a stoichiometric matrix from an arbitrary rectangular matrix.
59 BASIC BIOLOGICAL SCIENCES↗
A virtual host model of Mycobacterium tuberculosis infection identifies early immune events as predictive of infection outcomes
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59 BASIC BIOLOGICAL SCIENCES↗
Toward multiscale simulations of tailored microstructure formation in metal additive manufacturing
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36 MATERIALS SCIENCE↗
Physics guided neural networks for modelling of non-linear dynamics
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97 MATHEMATICS AND COMPUTING↗
Evaluating adaptive and predictive power management strategies for optimizing visualization performance on supercomputers
Power is becoming an increasingly scarce resource on the next generation of supercomputers, and should be used wisely to improve overall performance. One strategy for improving power usage is hardware overprovisioning, i.e., systems with more nodes than can be run at full power simultaneously without exceeding the system-wide power limit. With this study, we compare two strategies for allocating power throughout an overprovisioned system – adaptation and prediction – in the context of visualization workloads. While adaptation has been suitable for workloads with more regular execution behaviors, it may not be as suitable on visualization workloads, since they can have variable execution behaviors. This study considers a total of 104 experiments, which vary the rendering workload, power budget, allocation strategy, and node concurrency, including tests processing data sets up to 1 billion cells and using up to 18,432 cores across 512 nodes. Overall, we find that prediction is a superior strategy for this use case, improving performance up to 27% compared to an adaptive strategy.
97 MATHEMATICS AND COMPUTING↗
Design-time performance modeling of compositional parallel programs
Performance models are powerful instruments for understanding the performance of parallel systems and uncovering their bottlenecks. Already during system design, performance models can help ponder alternative development options. However, creating a performance model – whether theoretically or empirically – for an entire application that does not exist yet is challenging. In this paper, we propose to generate performance models of full programs from performance models of their components using formal composition operators derived from parallel design patterns. As long as the design of the overall system follows such a pattern, its performance model can be predicted with reasonable accuracy without an actual implementation. In conclusion, we demonstrate our approach with design patterns of varying complexity, including pipeline, task pool, and eventually MapReduce, which is representative of a broad class of data-analytics applications.
97 MATHEMATICS AND COMPUTING↗
Towards real-time forecasting of natural gas production by harnessing graph theory for stochastic discrete fracture networks
In this work, we compare hydrocarbon production curves obtained from a graph-based reduced-order model with the high-fidelity Discrete Fracture Network (DFN) predictions for a fracture network created using data from a real shale site. We observe that the bounds for the high fidelity DFN model lie within the bounds for the reduced order model, implying that the reduced-order model provides a conservative estimate. Moreover, we found that except for first-passage times and late arriving mass, the production curves from the reduced-order model predict transport accurately. However, it is to be noted that the results are inspite of trading a three-dimensional geometry for a reduced system in the form of a graph, one that is 500–1000 times faster in terms of computational efficiency (for this particular application). In addition, we also compare the production curves for large drawdown and small drawdown using our graph approach. The reduced-order model is successful in showing that the long term productivity is higher in case of small drawdown although the initial productivity is higher for large drawdown. Thus, this reduced-order model offers great potential in uncertainty quantification for production, as well as in providing operators with information to make real-time decisions for optimal production.
03 NATURAL GAS↗
Time-series learning of latent-space dynamics for reduced-order model closure
In this work, we study the performance of long short-term memory networks (LSTMs) and neural ordinary differential equations (NODEs) in learning latent-space representations of dynamical equations for an advection-dominated problem given by the viscous Burgers equation. Our formulation is devised in a nonintrusive manner with an equation-free evolution of dynamics in a reduced space with the latter being obtained through a proper orthogonal decomposition. In addition, we leverage the sequential nature of learning for both LSTMs and NODEs to demonstrate their capability for closure in systems that are not completely resolved in the reduced space. We assess our hypothesis for two advection-dominated problems given by the viscous Burgers equation. We observe that both LSTMs and NODEs are able to reproduce the effects of the absent scales for our test cases more effectively than does intrusive dynamics evolution through a Galerkin projection. This result empirically suggests that time-series learning techniques implicitly leverage a memory kernel for coarse-grained system closure as is suggested through the Mori–Zwanzig formalism.
97 MATHEMATICS AND COMPUTING↗
Exasim: Generating discontinuous Galerkin codes for numerical solutions of partial differential equations on graphics processors
Not Available
97 MATHEMATICS AND COMPUTING↗
Version [OpenIPSL 2.0.0] - [iTesla Power Systems Library (iPSL): A Modelica library for phasor time-domain simulations]
This paper describes Open-Instance Power System Library (OpenIPSL) version 2.0.0 and its most recent enhancements. This new version brings upgrades that include more robust models that are better documented, and example systems that illustrate certain functionalities to users. Repository and library documentations have been enhanced and expanded, and the library is now released under a new license. Changes are meant to foster user and developer communities, while providing more attractive frameworks for collaborative work to be carried out with the library.
97 MATHEMATICS AND COMPUTING↗
Designing accurate emulators for scientific processes using calibration-driven deep models
Abstract Predictive models that accurately emulate complex scientific processes can achieve speed-ups over numerical simulators or experiments and at the same time provide surrogates for improving the subsequent analysis. Consequently, there is a recent surge in utilizing modern machine learning methods to build data-driven emulators. In this work, we study an often overlooked, yet important, problem of choosing loss functions while designing such emulators. Popular choices such as the mean squared error or the mean absolute error are based on a symmetric noise assumption and can be unsuitable for heterogeneous data or asymmetric noise distributions. We propose Learn-by-Calibrating, a novel deep learning approach based on interval calibration for designing emulators that can effectively recover the inherent noise structure without any explicit priors. Using a large suite of use-cases, we demonstrate the efficacy of our approach in providing high-quality emulators, when compared to widely-adopted loss function choices, even in small-data regimes.
97 MATHEMATICS AND COMPUTING↗
Cost function dependent barren plateaus in shallow parametrized quantum circuits
Variational quantum algorithms (VQAs) optimize the parameters θ of a parametrized quantum circuit V(θ) to minimize a cost function C. While VQAs may enable practical applications of noisy quantum computers, they are nevertheless heuristic methods with unproven scaling. Here, we rigorously prove two results, assuming V(θ) is an alternating layered ansatz composed of blocks forming local 2-designs. Our first result states that defining C in terms of global observables leads to exponentially vanishing gradients (i.e., barren plateaus) even when V(θ) is shallow. Hence, several VQAs in the literature must revise their proposed costs. On the other hand, our second result states that defining C with local observables leads to at worst a polynomially vanishing gradient, so long as the depth of V(θ) is Ο(logn). Our results establish a connection between locality and trainability. We illustrate these ideas with large-scale simulations, up to 100 qubits, of a quantum autoencoder implementation.
97 MATHEMATICS AND COMPUTING↗
Controlling the pandemic during the SARS-CoV-2 vaccination rollout
There is a consensus that mass vaccination against SARS-CoV-2 will ultimately end the COVID-19 pandemic. However, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. We investigate relaxation scenarios using an age-structured transmission model that has been fitted to age-specific seroprevalence data, hospital admissions, and projected vaccination coverage for Portugal. Our analyses suggest that the pressing need to restart socioeconomic activities could lead to new pandemic waves, and that substantial control efforts prove necessary throughout 2021. Using knowledge on control measures introduced in 2020, we anticipate that relaxing measures completely or to the extent as in autumn 2020 could launch a wave starting in April 2021. Additional waves could be prevented altogether if measures are relaxed as in summer 2020 or in a step-wise manner throughout 2021. We discuss at which point the control of COVID-19 would be achieved for each scenario.
60 APPLIED LIFE SCIENCES↗
Quantum algorithmic measurement
There has been recent promising experimental and theoretical evidence that quantum computational tools might enhance the precision and efficiency of physical experiments. However, a systematic treatment and comprehensive framework are missing. Here we initiate the systematic study of experimental quantum physics from the perspective of computational complexity. To this end, we define the framework of quantum algorithmic measurements (QUALMs), a hybrid of black box quantum algorithms and interactive protocols. We use the QUALM framework to study two important experimental problems in quantum many-body physics: determining whether a system’s Hamiltonian is time-independent or time-dependent, and determining the symmetry class of the dynamics of the system. We study abstractions of these problems and show for both cases that if the experimentalist can use her experimental samples coherently (in both space and time), a provable exponential speedup is achieved compared to the standard situation in which each experimental sample is accessed separately. Our work suggests that quantum computers can provide a new type of exponential advantage: exponential savings in resources in quantum experiments.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Automated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility
Mechanistic understanding of large molecule conversion and the discovery of suitable heterogeneous catalysts have been lagging due to the combinatorial inventory of intermediates and the inability of humans to enumerate all structures. Here, we introduce an automated framework to predict stable configurations on transition metal surfaces and demonstrate its validity for adsorbates with up to 6 carbon and oxygen atoms on 11 metals, enabling the exploration of ~10 8 potential configurations. It combines a graph enumeration platform, force field, multi-fidelity DFT calculations, and first-principles trained machine learning. Clusters in the data reveal groups of catalysts stabilizing different structures and expose selective catalysts for showcase transformations, such as the ethylene epoxidation on Ag and Cu and the lack of C-C scission chemistry on Au. Deviations from the commonly assumed atom valency rule of small adsorbates are also manifested. This library can be leveraged to identify catalysts for converting large molecules computationally.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Metaplastic and energy-efficient biocompatible graphene artificial synaptic transistors for enhanced accuracy neuromorphic computing
CMOS-based computing systems that employ the von Neumann architecture are relatively limited when it comes to parallel data storage and processing. In contrast, the human brain is a living computational signal processing unit that operates with extreme parallelism and energy efficiency. Although numerous neuromorphic electronic devices have emerged in the last decade, most of them are rigid or contain materials that are toxic to biological systems. In this work, we report on biocompatible bilayer graphene-based artificial synaptic transistors (BLAST) capable of mimicking synaptic behavior. The BLAST devices leverage a dry ion-selective membrane, enabling long-term potentiation, with ~50 aJ/µm 2 switching energy efficiency, at least an order of magnitude lower than previous reports on two-dimensional material-based artificial synapses. The devices show unique metaplasticity, a useful feature for generalizable deep neural networks, and we demonstrate that metaplastic BLASTs outperform ideal linear synapses in classic image classification tasks. With switching energy well below the 1 fJ energy estimated per biological synapse, the proposed devices are powerful candidates for bio-interfaced online learning, bridging the gap between artificial and biological neural networks.
97 MATHEMATICS AND COMPUTING↗
Generalization in quantum machine learning from few training data
Modern quantum machine learning (QML) methods involve variationally optimizing a parameterized quantum circuit on a training data set, and subsequently making predictions on a testing data set (i.e., generalizing). In this work, we provide a comprehensive study of generalization performance in QML after training on a limited number N of training data points. We show that the generalization error of a quantum machine learning model with T trainable gates scales at worst as $\sqrt{T/N}$. When only K$\ll$T gates have undergone substantial change in the optimization process, we prove that the generalization error improves to $\sqrt{K/N}$. Our results imply that the compiling of unitaries into a polynomial number of native gates, a crucial application for the quantum computing industry that typically uses exponential-size training data, can be sped up significantly. We also show that classification of quantum states across a phase transition with a quantum convolutional neural network requires only a very small training data set. Other potential applications include learning quantum error correcting codes or quantum dynamical simulation. Our work injects new hope into the field of QML, as good generalization is guaranteed from few training data.
97 MATHEMATICS AND COMPUTING↗