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Yin, Junqi

Publications and source records attributed to Yin, Junqi.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Neural network-based order parameter for phase transitions and its applications in high-entropy alloys

Phase transition is one of the most important phenomena in nature and plays a central role in materials design. All phase transitions are characterized by suitable order parameters, including the order–disorder phase transition. However, finding a representative order parameter for complex systems is non-trivial, such as for high-entropy alloys. Given the strength of dimensionality reduction of a variational autoencoder (VAE), we introduce a VAE-based order parameter. Here, we propose that the Manhattan distance in the VAE latent space can serve as a generic order parameter for order–disorder phase transitions. The physical properties of our order parameter are quantitatively interpreted and demonstrated by multiple refractory high-entropy alloys. Using this order parameter, a generally applicable alloy design concept is proposed by mimicking the natural mixing process of elements. Our physically interpretable VAE-based order parameter provides a computational technique for understanding chemical ordering in alloys, which can facilitate the development of rational alloy design strategies.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Comparative evaluation of deep learning workloads for leadership-class systems

Deep learning (DL) workloads and their performance at scale are becoming important factors to consider as we design, develop and deploy next-generation high-performance computing systems. Since DL applications rely heavily on DL frameworks and underlying compute (CPU/GPU) stacks, it is essential to gain a holistic understanding from compute kernels, models, and frameworks of popular DL stacks, and to assess their impact on science-driven, mission-critical applications. At Oak Ridge Leadership Computing Facility (OLCF), we employ a set of micro and macro DL benchmarks established through the Collaboration of Oak Ridge, Argonne, and Livermore (CORAL) to evaluate the AI readiness of our next-generation supercomputers. In this paper, we present our early observations and performance benchmark comparisons between the Nvidia V100 based Summit system with its CUDA stack and an AMD MI100 based testbed system with its ROCm stack. We take a layered perspective on DL benchmarking and point to opportunities for future optimizations in the technologies that we consider.

Yin, Junqi↗
DOE OSTI2021

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Inter-Subunit Dynamics Controls Tunnel Formation During the Oxygenation Process in Hemocyanin Hexamers

Hemocyanin from horseshoe crab in its active form is a homo-hexameric protein. It exists in open and closed conformations when transitioning between deoxygenated and oxygenated states. Here, we present a detailed dynamic atomistic investigation of the oxygenated and deoxygenated states of the hexameric hemocyanin using explicit solvent molecular dynamics simulations. We focus on the variation in solvent cavities and the formation of tunnels in the two conformational states. By employing principal component analysis and CVAE-based deep learning, we are able to differentiate between the dynamics of the deoxy- and oxygenated states of hemocyanin. Finally, our results identify the deoxygenated open conformation, which adopts a stable, closed conformation after the oxygenation process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

IMPECCABLE: Integrated Modeling Pipeline for COVID Cure by Assessing Better Leads

ABSTRACT The drug discovery process currently employed in the pharmaceutical industry typically requires about 10 years and $2-3 billion to deliver one new drug. This is both too expensive and too slow, especially in emergencies like the COVID-19 pandemic. In silico methodologies need to be improved both to select better lead compounds, so as to improve the efficiency of later stages in the drug discovery protocol, and to identify those lead compounds more quickly. No known methodological approach can deliver this combination of higher quality and speed. Here, we describe an Integrated Modeling PipEline for COVID Cure by Assessing Better LEads (IMPECCABLE) that employs multiple methodological innovations to overcome this fundamental limitation. We also describe the computational framework that we have developed to support these innovations at scale, and characterize the performance of this framework in terms of throughput, peak performance, and scientific results. We show that individual workflow components deliver 100× to 1000× improvement over traditional methods, and that the integration of methods, supported by scalable infrastructure, speeds up drug discovery by orders of magnitudes. IMPECCABLE has screened ~10 11 ligands and has been used to discover a promising drug candidate. These capabilities have been used by the US DOE National Virtual Biotechnology Laboratory and the EU Centre of Excellence in Computational Biomedicine.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Dynamic Profiling of β-Coronavirus 3CL Mpro Protease Ligand-Binding Sites

β-coronavirus (CoVs) alone has been responsible for three major global outbreaks in the 21st century. The current crisis has led to an urgent requirement to develop therapeutics. Even though a number of vaccines are available, alternative strategies targeting essential viral components are required as a backup against the emergence of lethal viral variants. One such target is the main protease (Mpro) that plays an indispensable role in viral replication. The availability of over 270 Mpro X-ray structures in complex with inhibitors provides unique insights into ligand–protein interactions. Herein, we provide a comprehensive comparison of all nonredundant ligand-binding sites available for SARS-CoV2, SARS-CoV, and MERS-CoV Mpro. Extensive adaptive sampling has been used to investigate structural conservation of ligand-binding sites using Markov state models (MSMs) and compare conformational dynamics employing convolutional variational auto-encoder-based deep learning. Our results indicate that not all ligand-binding sites are dynamically conserved despite high sequence and structural conservation across β-CoV homologs. This highlights the complexity in targeting all three Mpro enzymes with a single pan inhibitor.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Geometrical-Based Generative Adversarial Network to Enhance Digital Rock Image Quality

X-ray microcomputed tomography (micro-CT) is a common tool for the study of porous media structures and properties. High-quality micro-CT data are required to accurately capture pore structures. Acquiring high-quality micro-CT data, however, is not always possible, owing to application limitations and experimental constraints. Therefore, we propose a geometrical-based generative adversarial network (GAN) to rapidly restore noisy micro-CT images to their clean counterparts. The training data and related ground-truth (GT) data are scanned for 7 min and 9.5 h, respectively. To evaluate the performance of the geometrical-based GAN, a 6003 voxel image that has never been used for training is reconstructed and compared with the corresponding GT image. Histogram matching and linear normalization are implemented to adjust the histogram of the reconstructed image to that of the GT image. A watershed-based segmentation method is then applied to delineate pore and solid phases. Lastly, we measure the Minkowski functionals and petrophysical properties, including absolute permeability, pore size distribution, drainage capillary pressure-saturation curve, and imbibition relative permeability, to estimate the physical accuracy of the denoised image. The results show that the proposed geometrical-based GAN can accurately restore noisy micro-CT data. By reducing the scanning time from 9.5 h to 7 min, the expenditure of collecting micro-CT can be decreased significantly. This is particularly important for applications where time-lapse images of a dynamic process are required, high-throughput imaging is necessary for real-time data analysis, or where the quantification of large sample volumes is required.

58 GEOSCIENCES↗
DOE OSTI2021

Scalable balanced training of conditional generative adversarial neural networks on image data

Here, we propose a distributed approach to train deep convolutional generative adversarial neural network (DC-CGANs) models. Our method reduces the imbalance between generator and discriminator by partitioning the training data according to data labels, and enhances scalability by performing a parallel training where multiple generators are concurrently trained, each one of them focusing on a single data label. Performance is assessed in terms of inception score, Fréchet inception distance, and image quality on MNIST, CIFAR10, CIFAR100, and ImageNet1k datasets, showing a significant improvement in comparison to state-of-the-art techniques to training DC-CGANs. Weak scaling is attained on all the four datasets using up to 1000 processes and 2000 NVIDIA V100 GPUs on the OLCF supercomputer Summit.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

A scalable algorithm for the optimization of neural network architectures

In this work, we propose a new scalable method to optimize the architecture of an artificial neural network. The proposed algorithm, called Greedy Search for Neural Network Architecture, aims to determine a neural network with minimal number of layers that is at least as performant as neural networks of the same structure identified by other hyperparameter search algorithms in terms of accuracy and computational cost. Numerical results performed on benchmark datasets show that, for these datasets, our method outperforms state-of-the-art hyperparameter optimization algorithms in terms of attainable predictive performance by the selected neural network architecture, and time-to-solution for the hyperparameter optimization to complete.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

In this work, we present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Fast and stable deep-learning predictions of material properties for solid solution alloys

We present a novel deep learning (DL) approach to produce highly accurate predictions of macroscopic physical properties of solid solution binary alloys and magnetic systems. The major idea is to make use of the correlations between different physical properties in alloy systems to improve the prediction accuracy of neural network (NN) models. We use multitasking NN models to simultaneously predict the total energy, charge density and magnetic moment. These physical properties mutually serve as constraints during the training of the multitasking NN, resulting in more reliable DL models because multiple physics properties are correctly learned by a single model. Two binary alloys, copper–gold (CuAu) and iron–platinum (FePt), were studied. Our results show that once the multitasking NN's are trained, they can estimate the material properties for a specific configuration hundreds of times faster than first-principles density functional theory calculations while retaining comparable accuracy. We used a simple measure based on the root-mean-squared errors to quantify the quality of the NN models, and found that the inclusion of charge density and magnetic moment as physical constraints leads to more stable models that exhibit improved accuracy and reduced uncertainty for the energy predictions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Toward Real-Time Analysis of Synchrotron Micro-Tomography Data: Accelerating Experimental Workflows with AI and HPC

ynchrotron light sources are routinely used to perform imaging experiments. In this paper, we review the relevant computational stages, identify bottlenecks, and highlight future opportunities to streamline data acquisition for experimental microscopy workflows. We demonstrate our preliminary exploration with an end-to-end scientific workflow on Summit based on micro-computed tomography data. Computational elements include: 1) reconstruction of volumetric image data; 2) denoising with deep neural networks; and 3) non-local means based segmentation and quantitative analysis.

Mcclure, James↗
DOE OSTI2020

Smoky Mountain Data Challenge 2020: An Open Call to Solve Data Problems in the Areas of Neutron Science, Material Science, Urban Modeling and Dynamics, Geophysics, and Biomedical Informatics

The 2020 Smoky Mountains Computational Sciences and Engineering Conference enlists research scientists from across Oak Ridge National Laboratory (ORNL) to be data sponsors and help create data analytics challenges for eminent data sets at the laboratory. This work describes the significance of each of the seven data sets and their as- sociated challenge questions. The challenge questions for each data set were required to cover multiple difficulty levels. An international call for participation was sent to students, and researchers asking them to form teams of up to four people to apply novel data analytics techniques to these data sets.

Parete-Koon, Suzanne↗
DOE OSTI2020

Data optimization for large batch distributed training of deep neural networks

Distributed training in deep learning (DL) is common practice as data and models grow. The current practice for distributed training of deep neural networks faces the challenges of communication bottlenecks when operating at scale, and model accuracy deterioration with an increase in global batch size. Present solutions focus on improving message exchange efficiency as well as implementing techniques to tweak batch sizes and models in the training process. The loss of training accuracy typically happens because the loss function gets trapped in a local minima. We observe that the loss landscape minimization is shaped by both the model and training data and propose a data optimization approach that utilizes machine learning to implicitly smooth out the loss landscape resulting in fewer local minima. Our approach filters out data points which are less important to feature learning, enabling us to speed up the training of models on larger batch sizes to improved accuracy.

Gahlot, Shubhankar↗
DOE OSTI2020

Performance Evaluation of Python Based Data Analytics Frameworks in Summit: Early Experiences

The explosion in the volumes of data generated from ever-larger simulation campaigns and experiments or observations necessitates competent tools for data wrangling and analysis). While the Oak Ridge Leadership Computing Facility (OLCF) provides a variety of tools to perform data wrangling and data analysis tasks, Python based tools often lack scalability, or the ability to fully exploit the computational capability of OLCF’s Summit supercomputer. NVIDIA RAPIDS and Dask offer a promising solution to accelerate and distribute data analytics workloads from personal computers to heterogeneous supercomputing systems. We discuss early performance evaluation results of RAPIDS and Dask on Summit to understand their capabilities, scalability, and limitations. Our evaluation includes a subset of RAPIDS libraries, i.e., cuDF, cuML, and cuGraph, and Chainer’s CuPy, and their multi-GPU variants when available.We also draw on the observed trends from the performance evaluation results to discuss best practices for maximizing performance.

Hernandez Arreguin, Benjamin↗
DOE OSTI2020

Monte Carlo simulation of order-disorder transition in refractory high entropy alloys: A data-driven approach

High entropy alloys (HEAs) are a series of novel materials that demonstrate many exceptional mechanical properties. To understand the origin of these attractive properties, it is important to investigate the thermodynamics and elucidate the evolution of various chemical phases. In this work, we introduce a machine learning approach to construct the effective Hamiltonian and study the thermodynamics of HEAs through canonical Monte Carlo simulation. The main characteristic of our method is to use pairwise interactions between atoms as the machine learning features and systematically improve the representativeness of the dataset using active learning from the Monte Carlo samples. We find this method produces highly robust and accurate effective Hamiltonians that give less than 0.1 mRy test error for all the three refractory HEAs: MoNbTaW, MoNbTaVW, and MoNbTaTiW. Using replica exchange to speed up the MC simulation, we calculated the specific heats and short-range order parameters in a wide range of temperatures. For all the studied materials, we find there are two major order-disorder transitions occurring respectively at T 1 and T 2 , where T 1 is near room temperature but T 2 is much higher. Further, we demonstrate that the transition at T 1 is caused by W and Nb while the one at T 2 is caused by the other elements. By comparing with experiments, the results demonstrate that the order-disorder transitions have a profound impact on the strength and ductility of HEAs.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Machine-learning informed prediction of high-entropy solid solution formation: Beyond the Hume-Rothery rules

The empirical rules for the prediction of solid solution formation proposed so far in the literature usually have very compromised predictability. Some rules with seemingly good predictability were, however, tested using small data sets. Based on an unprecedented large dataset containing 1252 multicomponent alloys, machine-learning methods showed that the formation of solid solutions can be very accurately predicted (93%). The machine-learning results help identify the most important features, such as molar volume, bulk modulus, and melting temperature. As such a new thermodynamics-based rule was developed to predict solid–solution alloys. The new rule is nonetheless slightly less accurate (73%) but has roots in the physical nature of the problem. The new rule is employed to predict solid solutions existing in the three blocks, each of which consists of 9 elements. The predictions encompass face-centered cubic (FCC), body-centered cubic (BCC), and hexagonal closest packed (HCP) structures in a high throughput manner. The validity of the prediction is further confirmed by CALculations of PHAse Diagram (CALPHAD) calculations with high consistency (94%). Since the new thermodynamics-based rule employs only elemental properties, applicability in screening for solid solution high-entropy alloys is straightforward and efficient.

36 MATERIALS SCIENCE↗