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At least 199 records · Page 11

Neural architecture search via similarity adaptive guidance

Evolutionary neural network architecture search (ENAS) has attracted the attention of many experts due to its global optimization capabilities to automatically search for convolutional neural network architectures based on the target task. The current search space for ENAS is not to design a fully structured network, but to search for smaller cell architectures to reduce search costs. However, blind search strategies do not effectively utilize the potential experience of the population. In order to utilize the potential experience learned by the current population to guide the evolutionary search of the population, we propose a similarity guided neural network architecture search algorithm based on cell architecture, which utilizes the similarity between pairwise architectures in the population as empirical knowledge learned by the population. Our proposed algorithm provides a novel method for calculating architecture similarity, which calculates architecture similarity separately from the cell and macro-structure. Then we decouple the connections and operations in the cell and calculate connection and operation similarity separately. In addition, we propose adaptive similarity selection and binary tournament selection strategies to enhance the algorithm’s global and local search capabilities and effectively explore the search space. Finally, we design an improved single-point crossover operator to enhance the local search ability of the evolutionary operator. The experimental results show that SAGNAS is a competitive algorithm that achieves 97.44% and 81.60% in CIFAR10 and CIFAR100 with only 1.9 GPU-days spent.

97 MATHEMATICS AND COMPUTING↗

Numerical parameter optimizations of the Ignition and Growth model for a HMX plastic bonded explosive

We present here a novel method for optimizing parameters of the Ignition and Growth (I&G) reactive flow model for high explosives. The I&G model predicts the shock initiation response of explosives subjected to dynamic loading. However, calibrating the model is a time-consuming process because it has several parameters, typically requires multiple data sets, and there are no direct correlations between parameters and data. In this study, we couple a scalable optimization algorithm to simulations of shock initiation experiments in the multi-physics code ALE3D. We develop four I&G model parameter sets for the HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazocane)-based explosive LX-07 [90 wt. % HMX, 10 wt. % Viton A] based on minimizing the difference between calculations and measurements at the embedded pressure gauges in 1D gun shock experiments. Our study shows that a cost function based on both shock time of arrival and pressure pulse shape demonstrates the best agreement with experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualization System for Evolutionary Neural Networks for Deep Learning

Deep learning is actively used in a wide range of fields for scientific discovery. To effectively apply deep learning to a particular problem, it is important to select an appropriate network architecture and other hyper-parameters (at each layer). Evolving architectures and hyper-parameters using a genetic algorithm is one current approach to search the huge space of all possible configurations to find those more optimal for the problem. However, examining an evolutionary process and tuning the genetic algorithm are challenging, pushing most users to treat the process as a black box. To address this challenge, we propose a visualization system for evolutionary neural networks for deep learning. The key feature of our visualization system is to provide a visual analytics environment for evaluating a genetic algorithm in order to improve the underlying operations to reduce time to find good solutions. Our system is able to not only visualize how a genetic algorithm traverses its search space but also allows users to examine evolving networks in-depth to get insights to improve performance through interactive visualization components.

Chae, Junghoon↗

AST: An Automated Sequence-Sampling Method for Improving the Taxonomic Diversity of Gene Phylogenetic Trees

A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.

59 BASIC BIOLOGICAL SCIENCES↗

BEYOND MIXING-LENGTH THEORY: A STEP TOWARD 321D

We examine the physical basis for algorithms to replace mixing-length theory (MLT) in stellar evolutionary computations. Our 321D procedure is based on numerical solutions of the Navier–Stokes equations. These implicit large eddy simulations (ILES) are three-dimensional (3D), time-dependent, and turbulent, including the Kolmogorov cascade. We use the Reynolds-averaged Navier–Stokes (RANS) formulation to make concise the 3D simulation data, and use the 3D simulations to give closure for the RANS equations. We further analyze this data set with a simple analytical model, which is non-local and time-dependent, and which contains both MLT and the Lorenz convective roll as particular subsets of solutions. A characteristic length (the damping length) again emerges in the simulations; it is determined by an observed balance between (1) the large-scale driving, and (2) small-scale damping. The nature of mixing and convective boundaries is analyzed, including dynamic, thermal and compositional effects, and compared to a simple model. We find that (1) braking regions (boundary layers in which mixing occurs) automatically appear beyond the edges of convection as defined by the Schwarzschild criterion, (2) dynamic (non-local) terms imply a non-zero turbulent kinetic energy flux (unlike MLT), (3) the effects of composition gradients on flow can be comparable to thermal effects, and (4) convective boundaries in neutrino-cooled stages differ in nature from those in photon-cooled stages (different Péclet numbers). The algorithms are based upon ILES solutions to the Navier–Stokes equations, so that, unlike MLT, they do not require any calibration to astronomical systems in order to predict stellar properties. Implications for solar abundances, helioseismology, asteroseismology, nucleosynthesis yields, supernova progenitors and core collapse are indicated.

79 ASTRONOMY AND ASTROPHYSICS↗

Machine learning strategy for accelerated design of polymer dielectrics

The ability to efficiently design new and advanced dielectric polymers is hampered by the lack of sufficient, reliable data on wide polymer chemical spaces, and the difficulty of generating such data given time and computational/experimental constraints. Here, we address the issue of accelerating polymer dielectrics design by extracting learning models from data generated by accurate state-of-the-art first principles computations for polymers occupying an important part of the chemical subspace. The polymers are ‘fingerprinted’ as simple, easily attainable numerical representations, which are mapped to the properties of interest using a machine learning algorithm to develop an on-demand property prediction model. Further, a genetic algorithm is utilised to optimise polymer constituent blocks in an evolutionary manner, thus directly leading to the design of polymers with given target properties. Furthermore, while this philosophy of learning to make instant predictions and design is demonstrated here for the example of polymer dielectrics, it is equally applicable to other classes of materials as well.

36 MATERIALS SCIENCE↗

A PETSc Parallel-in-Time Solver based on MGRIT algorithm

We address the development of a modular implementation of the MGRIT (MultiGrid-In-Time) algorithm to solve linear and nonlinear systems that arise from the discretization of evolutionary models with a parallel-in-time approach in the context of the PETSc (the Portable, Extensible Toolkit for Scientific computing) library. Our aim is to give the opportunity of predicting the performance gain achievable when using the MGRIT approach instead of the Time Stepping integrator (TS). To this end, we analyze the performance parameters of the algorithm that provide a-priori the best number of processing elements and grid levels to use to address the scaling of MGRIT, regarded as a parallel iterative algorithm proceeding along the time dimension.

Mele, Valeria↗

Evolutionary NAS in Light of Model Stability for Accurate Continual Learning

Continual learning, the capability to learn new knowledge from streaming data without forgetting the previous knowledge, is a critical requirement for dynamic learning systems, especially for emerging edge devices such as self-driving cars and drones. However, continual learning is still facing the catastrophic forgetting problem. Previous work illustrate that model performance on continual learning is not only related to the learning algorithms but also strongly dependent on the inherited model, i.e., the model where continual learning starts. The better stability of the inherited model, the less catastrophic forgetting and thus, the inherited model should be elaborately selected. Inspired by this finding, we develop an evolutionary neural architecture search (ENAS) algorithm that emphasizes the Stability of the inherited model, namely ENAS-S. ENAS-S aims to find optimal architectures for accurate continual learning on edge devices. On CIFAR-10 and CIFAR-100, we present that ENAS-S achieves competitive architectures with lower catastrophic forgetting and smaller model size when learning from a data stream, as compared with handcrafted DNNs.

Du, Xiaocong↗

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗

Drive-pressure optimization in ramp-wave compression experiments through differential evolution

Ramp-wave dynamic-compression experiments are used to examine quasi-isentropic loading paths in materials. The gradual and continuous increase in pressure created by ramp waves make these types of experiments ideal for studying nonequilibrium material behavior, such as solidification kinetics. In ramp-wave compression experiments, the input drive pressure to the experimental setup may be exerted through one of a number of different mechanisms (e.g., magnetic fields, gas-gun-driven impactors, or high-energy lasers) and is generally required for simulating such experiments. Yet, regardless of the specific mechanism, this drive pressure cannot be measured directly (measurements are generally taken at a location near the back of the experimental setup through a transparent window), leading to an inverse problem where one must determine the drive pressure at the front of the experimental setup (i.e., the input) that corresponds to the particle velocity (the output) measured near the back of the experimental setup. Furthermore, we solve this inverse problem using a heuristic optimization algorithm, known as differential evolution, coupled with a multiphysics, hydrodynamics code that simulates the compression of the experimental setup. By running many rounds of forward simulations of the experimental setup, our optimization process iteratively searches for a drive pressure that is optimized to closely reproduce the experimentally measured particle velocity near the back of the experimental setup. While our optimization methodology requires a significant number of hydrodynamics simulations to be conducted, many of these can be performed in parallel, which greatly reduces the time cost of our methodology. One novel aspect of our method for determining the drive pressure is that it does not require physical modeling of the drive mechanism and can thus be broadly applied to many types of ramp-compression experiments, regardless of the drive mechanism.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Application of Hybrid Genetic Algorithm Routine in Optimizing Food and Bioengineering Processes

Optimization is a crucial step in the analysis of experimental results. Deterministic methods only converge on local optimums and require exponentially more time as dimensionality increases. Stochastic algorithms are capable of efficiently searching the domain space, however convergence is not guaranteed. This article demonstrates the novelty of hybrid genetic algorithm which combines both stochastic and deterministic routine for improved optimization results. A new hybrid genetic algorithm developed is applied to the Ackley benchmark function as well as case studies in foods, biofuels, and biotechnology processes. For each case study the hybrid genetic algorithm found a better optimum candidate than reported by the sources. In the case of food processing the hybrid genetic predicted 5% higher anthocyanin yield. Optimization of bio-oil production using HGA resulted in a 4.73 % higher yield. In enzyme production process HGA predicted 2.18 IU/gds of higher xylanase yield. In conclusion, hybridization of genetic algorithm with a deterministic algorithm resulted in maximum optimum compared to the statistical methods.

09 BIOMASS FUELS↗

The HectoMAP Cluster Survey: Spectroscopically Identified Clusters and their Brightest Cluster Galaxies (BCGs)

We apply a friends-of-friends (FoF) algorithm to identify galaxy clusters and we use the catalog to explore the evolutionary synergy between brightest cluster galaxies (BCGs) and their host clusters. We base the cluster catalog on the dense HectoMAP redshift survey (2000 redshifts deg -2 ). The HectoMAP FoF catalog includes 346 clusters with 10 or more spectroscopic members within the range 0.05 < z < 0.55 and with a median z = 0.29. We list these clusters and their members. We also include central velocity dispersions (σ*, BCG ) for the FoF cluster BCGs, a distinctive feature of the HectoMAP FoF catalog. HectoMAP clusters with higher galaxy number density (80 systems) are all genuine clusters with a strong concentration and a prominent BCG in Subaru/Hyper Suprime-Cam images. The phase-space diagrams show the expected elongation along the line of sight. Lower-density systems include some low reliability systems. We establish a connection between BCGs and their host clusters by demonstrating that σ*, BCG /σ cl decreases as a function of cluster velocity dispersion (σ cl ), in contrast, numerical simulations predict a constant σ*, BCG /σ cl . Sets of clusters at two different redshifts show that BCG evolution in massive systems is slow over the redshift range z < 0.4. The data strongly suggest that minor mergers may play an important role in BCG evolution in clusters with σ cl ≳ 300 km s -1 . For lower mass systems (σ cl < 300 km s -1 ), major mergers may play a significant role. The coordinated evolution of BCGs and their host clusters provides an interesting test of simulations in high-density regions of the universe.

79 ASTRONOMY AND ASTROPHYSICS↗

A genetic meta-algorithm-assisted inversion approach: hydrogeological study for the determination of volumetric rock properties and matrix and fluid parameters in unsaturated formations

An evolutionary inversion approach is suggested for the interpretation of nuclear and resistivity logs measured by direct-push tools in shallow unsaturated sediments. The efficiency of formation evaluation is improved by estimating simultaneously (1) the petrophysical properties that vary rapidly along a drill hole with depth and (2) the zone parameters that can be treated as constant, in one inversion procedure. In the workflow, the fractional volumes of water, air, matrix and clay are estimated in adjacent depths by linearized inversion, whereas the clay and matrix properties are updated using a float-encoded genetic meta-algorithm. The proposed inversion method provides an objective estimate of the zone parameters that appear in the tool response equations applied to solve the forward problem, which can significantly increase the reliability of the petrophysical model as opposed to setting these parameters arbitrarily. The global optimization meta-algorithm not only assures the best fit between the measured and calculated data but also gives a reliable solution, practically independent of the initial model, as laboratory data are unnecessary in the inversion procedure. The feasibility test uses engineering geophysical sounding logs observed in an unsaturated loessy-sandy formation in Hungary. The multi-borehole extension of the inversion technique is developed to determine the petrophysical properties and their estimation errors along a profile of drill holes. The genetic meta-algorithmic inversion method is recommended for hydrogeophysical logging applications of various kinds to automatically extract the volumetric ratios of rock and fluid constituents as well as the most important zone parameters in a reliable inversion procedure.

58 GEOSCIENCES↗

Natural evolutionary strategies for variational quantum computation

Abstract Natural evolutionary strategies (NES) are a family of gradient-free black-box optimization algorithms. This study illustrates their use for the optimization of randomly initialized parameterized quantum circuits (PQCs) in the region of vanishing gradients. We show that using the NES gradient estimator the exponential decrease in variance can be alleviated. We implement two specific approaches, the exponential and separable NES, for parameter optimization of PQCs and compare them against standard gradient descent. We apply them to two different problems of ground state energy estimation using variational quantum eigensolver and state preparation with circuits of varying depth and length. We also introduce batch optimization for circuits with larger depth to extend the use of ES to a larger number of parameters. We achieve accuracy comparable to state-of-the-art optimization techniques in all the above cases with a lower number of circuit evaluations. Our empirical results indicate that one can use NES as a hybrid tool in tandem with other gradient-based methods for optimization of deep quantum circuits in regions with vanishing gradients.

Anand, Abhinav (ORCID:0000000280812310)↗

Reconstructing magnetic deflections from sets of proton images using differential evolution

Proton imaging is a powerful technique for imaging electromagnetic fields within an experimental volume, in which spatial variations in proton fluence are a result of deflections to proton trajectories due to interaction with the fields. When deflections are large, proton trajectories can overlap, and this nonlinearity creates regions of greatly increased proton fluence on the image, known as caustics. The formation of caustics has been a persistent barrier to reconstructing the underlying fields from proton images. We have developed a new method for reconstructing the path-integrated magnetic fields, which begins to address the problem posed by caustics. Our method uses multiple proton images of the same object, each image at a different energy, to fill in the information gaps and provide some uniqueness when reconstructing caustic features. We use a differential evolution algorithm to iteratively estimate the underlying deflection function, which accurately reproduces the observed proton fluence at multiple proton energies simultaneously. We test this reconstruction method using synthetic proton images generated for three different, cylindrically symmetric field geometries at various field amplitudes and levels of proton statistics and present reconstruction results from a set of experimental images. Here, the method we propose requires no assumption of deflection linearity and can reliably solve for fields underlying linear, nonlinear, and caustic proton image features for the selected geometries and is shown to be fairly robust to noise in the input proton intensity.

47 OTHER INSTRUMENTATION↗

Multi-Objective Hyperparameter Optimization for Spiking Neural Network Neuroevolution

Neuroevolution has had significant success over recent years, but there has been relatively little work applying neuroevolution approaches to spiking neural networks (SNNs). SNNs are a type of neural network that includes temporal processing component, are not easily trained using other methods, and can be deployed into energy-efficient neuromorphic hardware. In this work, we investigate two evolutionary approaches for training SNNs. We explore the impact of the hyperparameters of the evolutionary approaches, including tournament size, population size, and representation type, on the performance of the algorithms. We present a multi-objective Bayesian-based hyperparameter optimization approach to tune the hyperparameters to produce the most accurate and smallest SNNs. We show that the hyperparameters can significantly affect the performance of these algorithms. We also perform sensitivity analysis and demonstrate that every hyperparameter value has the potential to perform well, assuming other hyperparameter values are set correctly.

Parsa, Maryam↗

An Adaptive Unified Differential Evolution Algorithm for Global Optimization

In this paper, we propose a new adaptive unified differential evolution algorithm for single-objective global optimization. Instead of the multiple mutation strate- gies proposed in conventional differential evolution algorithms, this algorithm employs a single equation unifying multiple strategies into one expression. It has the virtue of mathematical simplicity and also provides users the flexibility for broader exploration of the space of mutation operators. By making all control parameters in the proposed algorithm self-adaptively evolve during the process of optimization, it frees the application users from the burden of choosing appro- priate control parameters and also improves the performance of the algorithm. In numerical tests using thirteen basic unimodal and multimodal functions, the proposed adaptive unified algorithm shows promising performance in compari- son to several conventional differential evolution algorithms.

43 PARTICLE ACCELERATORS↗

Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants

Premise: The genomes of polyploid plants archive the evolutionary events leading to their present forms. However, plant polyploid genomes present numerous hurdles to the genome comparison algorithms for classification of polyploid types and exploring genome dynamics. Methods: Here, the problem of intra- and inter-genome comparison for examining polyploid genomes is reframed as a metagenomic problem, enabling the use of the rapid and scalable MinHashing approach. To determine how types of polyploidy are described by this metagenomic approach, plant genomes were examined from across the polyploid spectrum for both k-mer composition and frequency with a range of k-mer sizes. In this approach, no subgenome-specific k-mers are identified; rather, whole-chromosome k-mer subspaces were utilized. Results: Given chromosome-scale genome assemblies with sufficient subgenome-specific repetitive element content, literature-verified subgenomic and genomic evolutionary relationships were revealed, including distinguishing auto- from allopolyploidy and putative progenitor genome assignment. The sequences responsible were the rapidly evolving landscape of transposable elements. An investigation into the MinHashing parameters revealed that the downsampled k-mer space (genomic signatures) produced excellent approximations of sequence similarity. Furthermore, the clustering approach used for comparison of the genomic signatures is scrutinized to ensure applicability of the metagenomics-based method. Discussion: The easily implementable and highly computationally efficient MinHashing-based sequence comparison strategy enables comparative subgenomics and genomics for large and complex polyploid plant genomes. Such comparisons provide evidence for polyploidy-type subgenomic assignments. In cases where subgenome-specific repeat signal may not be adequate given a chromosomes' global k-mer profile, alternative methods that are more specific but more computationally complex outperform this approach.

59 BASIC BIOLOGICAL SCIENCES↗