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A review of computational tools for design and reconstruction of metabolic pathways

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Continuous and fast calibration of the CMS experiment: design of the automated workflows and operational experience

The exploitation of the full physics potential of the LHC experiments requires fast and efficient processing of the largest possible dataset with the most refined understanding of the detector conditions. To face this challenge, the CMS collaboration has setup an infrastructure for the continuous unattended computation of the alignment and calibration constants, allowing for a refined knowledge of the most time-critical parameters already a few hours after the data have been saved to disk. This is the prompt calibration framework which, since the beginning of the LHC Run-I, enables the analysis and the High Level Trigger of the experiment to consume the most up-to-date conditions optimizing the performance of the physics objects. In the Run-II this setup has been further expanded to include even more complex calibration algorithms requiring higher statistics to reach the needed precision. This imposed the introduction of a new paradigm in the creation of the calibration datasets for unattended workflows and opened the door to a further step in performance. The paper reviews the design of these automated calibration workflows, the operational experience in the Run-II and the monitoring infrastructure developed to ensure the reliability of the service.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

THEMIS: A Parameter Estimation Framework for the Event Horizon Telescope

The Event Horizon Telescope (EHT) provides the unprecedented ability to directly resolve the structure and dynamics of black hole emission regions on scales smaller than their horizons. This has the potential to critically probe the mechanisms by which black holes accrete and launch outflows, and the structure of supermassive black hole spacetimes. However, accessing this information is a formidable analysis challenge for two reasons. First, the EHT natively produces a variety of data types that encode information about the image structure in nontrivial ways; these are subject to a variety of systematic effects associated with very long baseline interferometry and are supplemented by a wide variety of auxiliary data on the primary EHT targets from decades of other observations. Second, models of the emission regions and their interaction with the black hole are complex, highly uncertain, and computationally expensive to construct. As a result, the scientific utilization of EHT observations requires a flexible, extensible, and powerful analysis framework. We present such a framework, Themis, which defines a set of interfaces between models, data, and sampling algorithms that facilitates future development. We describe the design and currently existing components of Themis, how Themis has been validated thus far, and present additional analyses made possible by Themis that illustrate its capabilities. Importantly, we demonstrate that Themis is able to reproduce prior EHT analyses, extend these, and do so in a computationally efficient manner that can efficiently exploit modern high-performance computing facilities. Themis has already been used extensively in the scientific analysis and interpretation of the first EHT observations of M87.

79 ASTRONOMY AND ASTROPHYSICS↗

Graph theory approach to determine configurations of multidentate and high coverage adsorbates for heterogeneous catalysis

Abstract Heterogeneous catalysts constitute a crucial component of many industrial processes, and to gain an understanding of the atomic-scale features of such catalysts, ab initio density functional theory is widely employed. Recently, growing computational power has permitted the extension of such studies to complex reaction networks involving either high adsorbate coverages or multidentate adsorbates, which bind to the surface through multiple atoms. Describing all possible adsorbate configurations for such systems, however, is often not possible based on chemical intuition alone. To systematically treat such complexities, we present a generalized Python-based graph theory approach to convert atomic scale models into undirected graph representations. These representations, when combined with workflows such as evolutionary algorithms, can systematically generate high coverage adsorbate models and classify unique minimum energy multidentate adsorbate configurations for surfaces of low symmetry, including multi-elemental alloy surfaces, steps, and kinks. Two case studies are presented which demonstrate these capabilities; first, an analysis of a coverage-dependent phase diagram of absorbate NO on the Pt 3 Sn(111) terrace surface, and second, an investigation of adsorption energies, together with identifying unique minimum energy configurations, for the reaction intermediate propyne (CHCCH 3 *) adsorbed on a PdIn(021) step surface. The evolutionary algorithm approach reproduces high coverage configurations of NO on Pt 3 Sn(111) using only 15% of the number of simulations required for a brute force approach. Furthermore, the screening of potentially hundreds of multidentate adsorbates is shown to be possible without human intervention. The strategy presented is quite general and can be applied to a spectrum of complex atomic systems.

36 MATERIALS SCIENCE↗

Nonlinear Ensemble Filtering with Diffusion Models: Application to the Surface Quasigeostrophic Dynamics

The intersection between classical data assimilation methods and novel machine learning techniques has attracted significant interest in recent years. Here, we explore another promising solution in which diffusion models are used to formulate a robust nonlinear ensemble filter for sequential data assimilation. Unlike standard machine learning methods, the proposed ensemble score filter (EnSF) is completely training free and can efficiently generate a set of analysis ensemble members. Here, in this study, we apply the EnSF to a surface quasigeostrophic model and compare its performance against the popular local ensemble transform Kalman filter (LETKF), which makes Gaussian assumptions in the analysis step. Numerical tests demonstrate that EnSF maintains stable performance in the absence of localization and for a variety of experimental settings. We find that while LETKF maintains optimal performance in the case of linear observations of the entire state and a perfect model, EnSF shows improvements over LETKF when nonlinear observations are assimilated and the system is subject to unexpected model errors. A spectral decomposition of the analysis results in this nonlinear observation regime shows that the largest improvements over LETKF occur at large scales (small wavenumbers), where LETKF lacks sufficient ensemble spread. Overall, this initial application of EnSF to a geophysical model of intermediate complexity motivates further development of the algorithm for more realistic problems.

Artificial intelligence↗

An overview of the operation architectures and energy management system for multiple microgrid clusters

The emerging novel energy infrastructures, such as energy communities, smart building-based microgrids, electric vehicles enabled mobile energy storage units raise the requirements for a more interconnective and interoperable energy system. It leads to a transition from simple and isolated microgrids to relatively large-scale and complex interconnected microgrid systems named multi-microgrid clusters. In order to efficiently, optimally, and flexibly control multi-microgrid clusters, cross-disciplinary technologies such as power electronics, control theory, optimization algorithms, information and communication technologies, cyber-physical, and big-data analysis are needed. This paper introduces an overview of the relevant aspects for multi-microgrids, including the outstanding features, architectures, typical applications, existing control mechanisms, as well as the challenges.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Sample Complexity of Power System State Estimation Using Matrix Completion

In this paper, we propose an analytical framework to quantify the amount of data samples needed to obtain accurate state estimation in a power system - a problem known as sample complexity analysis in computer science. Motivated by the increasing adoption of distributed energy resources into the distribution-level grids, it becomes imperative to estimate the state of distribution grids in order to ensure stable operation. Traditional power system state estimation techniques mainly focus on the transmission network which involve solving an overdetermined system and eliminating bad data. However, distribution networks are typically underdetermined due to the large number of connection points and high cost of pervasive installation of measurement devices. In this paper, we consider the recently proposed state-estimation method for underdetermined systems that is based on matrix completion. In particular, a constrained matrix completion algorithm was proposed, wherein the standard matrix completion problem is augmented with additional equality constraints representing the physics (namely power-flow constraints). We analyze the sample complexity of this general method by proving an upper bound on the sample complexity that depends directly on the properties of these constraints that can lower number of needed samples as compared to the unconstrained problem. To demonstrate the improvement that the constraints add to state estimation, we test the method on a 141-bus distribution network case study and compare it to the traditional least squares minimization state estimation method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Alternative difference analysis scheme combining R -space EXAFS fit with global optimization XANES fit for X-ray transient absorption spectroscopy

Time-resolved X-ray absorption spectroscopy (TR-XAS), based on the laser-pump/X-ray-probe method, is powerful in capturing the change of the geometrical and electronic structure of the absorbing atom upon excitation. TR-XAS data analysis is generally performed on the laser-on minus laser-off difference spectrum. Here, a new analysis scheme is presented for the TR-XAS difference fitting in both the extended X-ray absorption fine-structure (EXAFS) and the X-ray absorption near-edge structure (XANES) regions. R -space EXAFS difference fitting could quickly provide the main quantitative structure change of the first shell. The XANES fitting part introduces a global non-derivative optimization algorithm and optimizes the local structure change in a flexible way where both the core XAS calculation package and the search method in the fitting shell are changeable. The scheme was applied to the TR-XAS difference analysis of Fe(phen) 3 spin crossover complex and yielded reliable distance change and excitation population.

Zhan, Fei↗

Scalable Pattern Matching in Metadata Graphs via Constraint Checking

Pattern matching is a fundamental tool for answering complex graph queries. Unfortunately, existing solutions have limited capabilities: They do not scale to process large graphs and/or support only a restricted set of search templates or usage scenarios. Moreover, the algorithms at the core of the existing techniques are not suitable for today’s graph processing infrastructures relying on horizontal scalability and shared-nothing clusters, as most of these algorithms are inherently sequential and difficult to parallelize. In this article we present an algorithmic pipeline that bases pattern matching on constraint checking. The key intuition is that each vertex and edge participating in a match has to meet a set of constraints implicitly specified by the search template. These constraints can be verified independently and typically are less expensive to compute than searching the full template. The pipeline we propose generates these constraints and iterates over them to eliminate all the vertices and edges that do not participate in any match, thus reducing the background graph to a subgraph that is the union of all template matches—the complete set of all vertices and edges that participate in at least one match. Additional analysis can be performed on this annotated, reduced graph, such as full match enumeration, match counting, or computing vertex/edge centrality. Furthermore, a vertex-centric formulation for constraint checking algorithms exists, and this makes it possible to harness existing high-performance, vertex-centric graph processing frameworks. This technique (i) enables highly scalable pattern matching in metadata (labeled) graphs; (ii) supports arbitrary patterns with 100% precision; (iii) enables tradeoffs between precision and time-to-solution, while always selects all vertices and edges that participate in matches, thus offering 100% recall; and (iv) supports a set of popular data analytics scenarios. We implement our approach on top of HavoqGT, an open-source asynchronous graph processing framework, and demonstrate its advantages through strong and weak scaling experiments on massive scale real-world (up to 257 billion edges) and synthetic (up to 4.4 trillion edges) labeled graphs, respectively, and at scales (1,024 nodes / 36,864 cores), orders of magnitude larger than used in the past for similar problems. This article serves two purposes: First, it synthesises the knowledge accumulated during a long-term project. Second, it presents new system features, usage scenarios, optimizations, and comparisons with related work that strengthen the confidence that pattern matching based on iterative pruning via constraint checking is an effective and scalable approach in practice. The new contributions include the following: (i) We demonstrate the ability of the constraint checking approach to efficiently support two additional search scenarios that often emerge in practice, interactive incremental search and exploratory search. (ii) We empirically compare our solution with two additional state-of-the-art systems, Arabsque and TriAD. (iii) We show the ability of our solution to accommodate a more diverse range of datasets with varying properties, e.g., scale, skewness, label distribution, and match frequency. (iv) We introduce or extend a number of system features (e.g., work aggregation, load balancing, and the ability to cap the generated traffic) and design optimizations and demonstrate their advantages with respect to improving performance and scalability. (v) We present bottleneck analysis and insights into artifacts that influence performance. (vi) We present a theoretical complexity argument that motivates the performance gains we observe.

97 MATHEMATICS AND COMPUTING↗

Sample Complexity of Power System State Estimation using Matrix Completion: Preprint

In this paper, we propose an analytical framework to quantify the amount of data samples needed to obtain accurate state estimation in a power system-a problem known as \emph{sample complexity} analysis in computer science. Motivated by the increasing adoption of distributed energy resources into the distribution-level grids, it becomes imperative to estimate the state of distribution grids in order to ensure stable operation. Traditional power system state estimation techniques mainly focus on the transmission network which involve solving an overdetermined system and eliminating bad data. However, distribution networks are typically \emph{underdetermined} due to the large number of connection points and high cost of pervasive installation of measurement devices. In this paper, we consider the recently proposed state-estimation method for underdetermined systems that is based on \emph{matrix completion}. In particular, a \emph{constrained} matrix completion algorithm was proposed, wherein the standard matrix completion problem is augmented with additional equality constraints representing the physics (namely power-flow constraints). We analyze the sample complexity of this general method by proving an upper bound on the sample complexity that depends directly on the properties of these constraints that can lower number of needed samples as compared to the unconstrained problem. To demonstrate the improvement that the constraints add to state estimation, we test the method on a 141-bus distribution network case study and compare it to the traditional least squares minimization state estimation method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Algorithmic Improvements to MCNP5 for High-Resolution Fusion Neutronics Analyses

Neutronics analyses of the ITER experimental fusion reactor rely on increasingly complex geometry models and estimates of energy-dependent neutron flux and radiation dose-rate distributions generated at ever higher resolutions. There are significant practical challenges with applying the Monte Carlo N-Particle (MCNP) continuous-energy transport code to high-resolution analyses. For models consisting of more than 100 000 surfaces and cells, geometry initialization can take several hours, thus slowing down model integration and transport analysis efforts. In multithreaded simulations, the amount of memory consumed by superimposed mesh tally data increases in proportion to the number of threads. This behavior limits either the tally resolution or the number of processor cores that can be utilized in the simulation. This paper describes algorithmic improvements that were implemented in a modified version of MCNP5 to overcome these limitations. These improvements are referred to as the Oak Ridge National Laboratory Transformative Neutronics (ORNL-TN) upgrade. Here, a comparison of the performance and memory usage of both MCNP5 and ORNL-TN on several relevant fusion neutronics models is presented. In these tests and in actual high-resolution neutronics analyses, ORNL-TN reduces geometry processing times from hours to a few seconds and increases in-memory mesh tally capacity from the order of 10 8 to 10 10 space-energy bins.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Data reduction through optimized scalar quantization for more compact neural networks

Raw data generation for several existing and planned large physics experiments now exceeds TB/s rates, generating untenable data sets in very little time. Those data often demonstrate high dimensionality while containing limited information. Meanwhile, Machine Learning algorithms are now becoming an essential part of data processing and data analysis. Those algorithms can be used offline for post processing and post data analysis, or they can be used online for real time processing providing ultra low latency experiment monitoring. Both use cases would benefit from data throughput reduction while preserving relevant information: one by reducing the offline storage requirements by several orders of magnitude and the other by allowing ultra fast online inferencing with low complexity Machine Learning models. Moreover, reducing the data source throughput also reduces material cost, power and data management requirements. In this work we demonstrate optimized nonuniform scalar quantization for data source reduction. This data reduction allows lower dimensional representations while preserving the relevant information of the data, thus enabling high accuracy Tiny Machine Learning classifier models for online fast inferences. We demonstrate this approach with an initial proof of concept targeting the CookieBox, an array of electron spectrometers used for angular streaking, that was developed for LCLS-II as an online beam diagnostic tool. We used the Lloyd-Max algorithm with the CookieBox dataset to design an optimized nonuniform scalar quantizer. Optimized quantization lets us reduce input data volume by 69% with no significant impact on inference accuracy. When we tolerate a 2% loss on inference accuracy, we achieved 81% of input data reduction. Finally, the change from a 7-bit to a 3-bit input data quantization reduces our neural network size by 38%.

97 MATHEMATICS AND COMPUTING↗

Multilevel techniques for compression and reduction of scientific data—the univariate case

We present a multilevel technique for the compression and reduction of univariate data and give an optimal complexity algorithm for its implementation. A hierarchical scheme offers the flexibility to produce multiple levels of partial decompression of the data so that each user can work with a reduced representation that requires minimal storage whilst achieving the required level of tolerance. The algorithm is applied to the case of turbulence modelling in which the datasets are traditionally not only extremely large but inherently non-smooth and, as such, rather resistant to compression. Here, we decompress the data for a range of relative errors, carry out the usual analysis procedures for turbulent data, and compare the results of the analysis on the reduced datasets to the results that would be obtained on the full dataset. The results obtained demonstrate the promise of multilevel compression techniques for the reduction of data arising from large scale simulations of complex phenomena such as turbulence modelling.

97 MATHEMATICS AND COMPUTING↗

Concurrent implicit spectral deferred correction scheme for low-Mach number combustion with detailed chemistry

We present a parallel multi-implicit time integration scheme for the advection-diffusion-reaction systems arising from the equations governing low-Mach number combustion with complex chemistry. Here, our strategy employs parallelisation across the method to accelerate the serial Multi-Implicit Spectral Deferred Correction (MISDC) scheme used to couple the advection, diffusion, and reaction processes. In our approach, the diffusion solves and the reaction solves are performed concurrently by different processors. Our analysis shows that the proposed parallel scheme is stable for stiff problems and that the sweeps converge to the fixed-point solution at a faster rate than with serial MISDC. We present numerical examples to demonstrate that the new algorithm is high-order accurate in time, and achieves a parallel speedup compared to serial MISDC.

97 MATHEMATICS AND COMPUTING↗

Materials Fingerprinting Classification

Significant progress in many classes of materials could be made with the availability of experimentally-derived large datasets composed of atomic identities and three-dimensional coordinates. Methods for visualizing the local atomic structure, such as atom probe tomography (APT), which routinely generate datasets comprised of millions of atoms, are an important step in realizing this goal. However, state-of-the-art APT instruments generate noisy and sparse datasets that provide information about elemental type, but obscure atomic structures, thus limiting their subsequent value for materials discovery. The application of a materials fingerprinting process, a machine learning algorithm coupled with topological data analysis, provides an avenue by which here-to-fore unprecedented structural information can be extracted from an APT dataset. As a proof of concept, the material fingerprint is applied to high-entropy alloy APT datasets containing body-centered cubic (BCC) and face-centered cubic (FCC) crystal structures. A local atomic configuration centered on an arbitrary atom is assigned a topological descriptor, with which it can be characterized as a BCC or FCC lattice with near perfect accuracy, despite the inherent noise in the dataset. Finally, this successful identification of a fingerprint is a crucial first step in the development of algorithms which can extract more nuanced information, such as chemical ordering, from existing datasets of complex materials.

36 MATERIALS SCIENCE↗

Optimization of stepwise clustering algorithm in backward trajectory analysis

In recent years, the backward trajectory model has been widely used in the research of meteorological and atmospheric environmental quality. This paper presents a comprehensive study on a stepwise clustering analysis algorithm in the clustering process of backward trajectory model and an application of the clustering analysis of single-particle backward trajectory in 2016 in Changchun City. This study starts with an analysis of the original stepwise clustering algorithm and its application to a clustering process of 8784 backward trajectories during 48 h in Changchun City as a benchmark test case. Then, two improvements are made in the algorithm: First, in the process of finding the optimal classification, the algorithm complexity is improved from original O(n 3 ) to O(log(n)*n 2 ) through algorithm improvement. The algorithm performance is enhanced by log(n) times. Next, in the process of re-establishing the classification, the algorithm complexity is improved from the original O(m*n 2 ) to O(m*log(n)*n), that is another algorithm performance improvement by a factor of log(n). Therefore, the accumulative execution efficiency improvement through the algorithm optimization is 2*log(n) times, which has been further verified in the practical application in Changchun City.

97 MATHEMATICS AND COMPUTING↗

Compressed Sensing with Sparse Corruptions: Fault-Tolerant Sparse Collocation Approximations

The recovery of approximately sparse or compressible coefficients in a polynomial chaos expansion is a common goal in many modern parametric uncertainty quantification (UQ) problems. However, relatively little effort in UQ has been directed toward theoretical and computational strategies for addressing the sparse corruptions problem, where a small number of measurements are highly corrupted. Such a situation has become pertinent today since modern computational frameworks are sufficiently complex with many interdependent components that may introduce hardware and software failures, some of which can be difficult to detect and result in a highly polluted simulation result. In this paper we present a novel compressive sampling--based theoretical analysis for a regularized $\ell^1$ minimization algorithm that aims to recover sparse expansion coefficients in the presence of measurement corruptions. Our recovery results are uniform (the theoretical guarantees hold for all compressible signals and compressible corruptions vectors) and prescribe algorithmic regularization parameters in terms of a user-defined a priori estimate on the ratio of measurements that are believed to be corrupted. We also propose an iteratively reweighted optimization algorithm that automatically refines the value of the regularization parameter and empirically produces superior results. Lastly, our numerical results test our framework on several medium to high dimensional examples of solutions to parameterized differential equations and demonstrate the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗

Compressed sensing with sparse corruptions: Fault-tolerant sparse collocation approximations

The recovery of approximately sparse or compressible coefficients in a polynomial chaos expansion is a common goal in many modern parametric uncertainty quantification (UQ) problems. However, relatively little effort in UQ has been directed toward theoretical and computational strategies for addressing the sparse corruptions problem, where a small number of measurements are highly corrupted. Such a situation has become pertinent today since modern computational frameworks are sufficiently complex with many interdependent components that may introduce hardware and software failures, some of which can be difficult to detect and result in a highly polluted simulation result. In this paper we present a novel compressive sampling-based theoretical analysis for a regularized t1 minimization algorithm that aims to recover sparse expansion coefficients in the presence of measurement corruptions. Our recovery results are uniform (the theoretical guarantees hold for all compressible signals and compressible corruptions vectors), and prescribe algorithmic regularization parameters in terms of a user-defined a priori estimate on the ratio of measurements that are believed to be corrupted. We also propose an iteratively reweighted optimization algorithm that automatically refines the value of the regularization parameter, and empirically produces superior results. Our numerical results test our framework on several medium-to-high dimensional examples of solutions to parameterized differential equations, and demonstrate the effectiveness of our approach.

97 MATHEMATICS AND COMPUTING↗