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At least 289 records · Page 16

Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit

Abstract Summary Bayesian inference in biological modeling commonly relies on Markov chain Monte Carlo (MCMC) sampling of a multidimensional and non-Gaussian posterior distribution that is not analytically tractable. Here, we present the implementation of a practical MCMC method in the open-source software package PyBioNetFit (PyBNF), which is designed to support parameterization of mathematical models for biological systems. The new MCMC method, am, incorporates an adaptive move proposal distribution. For warm starts, sampling can be initiated at a specified location in parameter space and with a multivariate Gaussian proposal distribution defined initially by a specified covariance matrix. Multiple chains can be generated in parallel using a computer cluster. We demonstrate that am can be used to successfully solve real-world Bayesian inference problems, including forecasting of new Coronavirus Disease 2019 case detection with Bayesian quantification of forecast uncertainty. Availability and implementation PyBNF version 1.1.9, the first stable release with am, is available at PyPI and can be installed using the pip package-management system on platforms that have a working installation of Python 3. PyBNF relies on libRoadRunner and BioNetGen for simulations (e.g. numerical integration of ordinary differential equations defined in SBML or BNGL files) and Dask.Distributed for task scheduling on Linux computer clusters. The Python source code can be freely downloaded/cloned from GitHub and used and modified under terms of the BSD-3 license (https://github.com/lanl/pybnf). Online documentation covering installation/usage is available (https://pybnf.readthedocs.io/en/latest/). A tutorial video is available on YouTube (https://www.youtube.com/watch?v=2aRqpqFOiS4&t=63s). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Web-Based Software for Managing Research

aeroCOMPASS is a software system, originally designed to aid in the management of wind tunnels at Langley Research Center, that could be adapted to provide similar aid to other enterprises in which research is performed in common laboratory facilities by users who may be geographically dispersed. Included in aeroCOMPASS is Web-interface software that provides a single, convenient portal to a set of project- and test-related software tools and other application programs. The heart of aeroCOMPASS is a user-oriented document-management software subsystem that enables geographically dispersed users to easily share and manage a variety of documents. A principle of "write once, read many" is implemented throughout aeroCOMPASS to eliminate the need for multiple entry of the same information. The Web framework of aeroCOMPASS provides links to client-side application programs that are fully integrated with databases and server-side application programs. Other subsystems of aeroCOMPASS include ones for reserving hardware, tracking of requests and feedback from users, generating interactive notes, administration of a customer-satisfaction questionnaire, managing execution of tests, managing archives of metadata about tests, planning tests, and providing online help and instruction for users.

Computer software and hardware↗

Harmonized Emissions Component (HEMCO) 3.0 as a Versatile Emissions Component for Atmospheric Models: Application in the GEOS-Chem, NASA GEOS, WRF-GC, CESM2, NOAA GEFS-Aerosol, and NOAA UFS Models

Emissions are a central component of atmospheric chemistry models. The Harmonized Emissions Component (HEMCO) is a software component for computing emissions from a user-selected ensemble of emission inventories and algorithms. It allows users to re-grid, combine, overwrite, subset, and scale emissions from different inventories through a configuration file and with no change to the model source code. The configuration file also maps emissions to model species with appropriate units. HEMCO can operate in offline stand-alone mode, but more importantly it provides an online facility for models to compute emissions at runtime. HEMCO complies with the Earth System Modeling Framework (ESMF) for portability across models. We present a new version here, HEMCO 3.0, that features an improved three-layer architecture to facilitate implementation into any atmospheric model and improved capability for calculating emissions at any model resolution including multiscale and unstructured grids. The three-layer architecture of HEMCO 3.0 includes (1) the Data Input Layer that reads the configuration file and accesses the HEMCO library of emission inventories and other environmental data, (2) the HEMCO Core that computes emissions on the user-selected HEMCO grid, and (3) the Model Interface Layer that re-grids (if needed) and serves the data to the atmospheric model and also serves model data to the HEMCO Core for computing emissions dependent on model state (such as from dust or vegetation). The HEMCO Core is common to the implementation in all models, while the Data Input Layer and the Model Interface Layer are adaptable to the model environment. Default versions of the Data Input Layer and Model Interface Layer enable straightforward implementation of HEMCO in any simple model architecture, and options are available to disable features such as re-gridding that may be done by independent couplers in more complex architectures. The HEMCO library of emission inventories and algorithms is continuously enriched through user contributions so that new inventories can be immediately shared across models. HEMCO can also serve as a general data broker for models to process input data not only for emissions but for any gridded environmental datasets. We describe existing implementations of HEMCO 3.0 in (1) the GEOS-Chem “Classic” chemical transport model with shared-memory infrastructure, (2) the high-performance GEOS-Chem (GCHP) model with distributed-memory architecture, (3) the NASA GEOS Earth System Model (GEOS ESM), (4) the Weather Research and Forecasting model with GEOS-Chem (WRF-GC), (5) the Community Earth System Model Version 2 (CESM2), and (6) the NOAA Global Ensemble Forecast System – Aerosols (GEFS-Aerosols), as well as the planned implementation in the NOAA Unified Forecast System (UFS). Implementation of HEMCO in CESM2 contributes to the Multi-Scale Infrastructure for Chemistry and Aerosols (MUSICA) by providing a common emissions infrastructure to support different simulations of atmospheric chemistry across scales.

Haipeng Lin↗

Update On the Status of the FLUKA Monte Carlo Transport Code*

The FLUKA Monte Carlo transport code is a well-known simulation tool in High Energy Physics. FLUKA is a dynamic tool in the sense that it is being continually updated and improved by the authors. We review the progress achieved since the last CHEP Conference on the physics models, some technical improvements to the code and some recent applications. From the point of view of the physics, improvements have been made with the extension of PEANUT to higher energies for p, n, pi, pbar/nbar and for nbars down to the lowest energies, the addition of the online capability to evolve radioactive products and get subsequent dose rates, upgrading of the treatment of EM interactions with the elimination of the need to separately prepare preprocessed files. A new coherent photon scattering model, an updated treatment of the photo-electric effect, an improved pair production model, new photon cross sections from the LLNL Cullen database have been implemented. In the field of nucleus-- nucleus interactions the electromagnetic dissociation of heavy ions has been added along with the extension of the interaction models for some nuclide pairs to energies below 100 MeV/A using the BME approach, as well as the development of an improved QMD model for intermediate energies. Both DPMJET 2.53 and 3 remain available along with rQMD 2.4 for heavy ion interactions above 100 MeV/A. Technical improvements include the ability to use parentheses in setting up the combinatorial geometry, the introduction of pre-processor directives in the input stream. a new random number generator with full 64 bit randomness, new routines for mathematical special functions (adapted from SLATEC). Finally, work is progressing on the deployment of a user-friendly GUI input interface as well as a CAD-like geometry creation and visualization tool. On the application front, FLUKA has been used to extensively evaluate the potential space radiation effects on astronauts for future deep space missions, the activation dose for beam target areas, dose calculations for radiation therapy as well as being adapted for use in the simulation of events in the ALICE detector at the LHC.

Ferrari, A.↗

Multiple-Beam Detection of Fast Transient Radio Sources

A method has been designed for using multiple independent stations to discriminate fast transient radio sources from local anomalies, such as antenna noise or radio frequency interference (RFI). This can improve the sensitivity of incoherent detection for geographically separated stations such as the very long baseline array (VLBA), the future square kilometer array (SKA), or any other coincident observations by multiple separated receivers. The transients are short, broadband pulses of radio energy, often just a few milliseconds long, emitted by a variety of exotic astronomical phenomena. They generally represent rare, high-energy events making them of great scientific value. For RFI-robust adaptive detection of transients, using multiple stations, a family of algorithms has been developed. The technique exploits the fact that the separated stations constitute statistically independent samples of the target. This can be used to adaptively ignore RFI events for superior sensitivity. If the antenna signals are independent and identically distributed (IID), then RFI events are simply outlier data points that can be removed through robust estimation such as a trimmed or Winsorized estimator. The alternative "trimmed" estimator is considered, which excises the strongest n signals from the list of short-beamed intensities. Because local RFI is independent at each antenna, this interference is unlikely to occur at many antennas on the same step. Trimming the strongest signals provides robustness to RFI that can theoretically outperform even the detection performance of the same number of antennas at a single site. This algorithm requires sorting the signals at each time step and dispersion measure, an operation that is computationally tractable for existing array sizes. An alternative uses the various stations to form an ensemble estimate of the conditional density function (CDF) evaluated at each time step. Both methods outperform standard detection strategies on a test sequence of VLBA data, and both are efficient enough for deployment in real-time, online transient detection applications.

Thompson, David R.↗

Machine learning predicts new anti-CRISPR proteins

The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only protein sequence information. Using a training set of known anti-CRISPRs, we built a model based on XGBoost ranking. We then applied AcRanker to predict candidate anti-CRISPRs from predicted prophage regions within self-targeting bacterial genomes and discovered two previously unknown anti-CRISPRs: AcrllA20 (ML1) and AcrIIA21 (ML8). We show that AcrIIA20 strongly inhibits Streptococcus iniae Cas9 (SinCas9) and weakly inhibits Streptococcus pyogenes Cas9 (SpyCas9). We also show that AcrIIA21 inhibits SpyCas9, Streptococcus aureus Cas9 (SauCas9) and SinCas9 with low potency. The addition of AcRanker to the anti-CRISPR discovery toolkit allows researchers to directly rank potential anti-CRISPR candidate genes for increased speed in testing and validation of new anti-CRISPRs. A web server implementation for AcRanker is available online at http://acranker.pythonanywhere.com/.

59 BASIC BIOLOGICAL SCIENCES↗

Flight Tests of a Remaining Flying Time Prediction System for Small Electric Aircraft in the Presence of Faults

This paper addresses the problem of building trust in the online prediction of a battery powered aircraft's remaining flying time. A series of flight tests is described that make use of a small electric powered unmanned aerial vehicle (eUAV) to verify the performance of the remaining flying time prediction algorithm. The estimate of remaining flying time is used to activate an alarm when the predicted remaining time is two minutes. This notifies the pilot to transition to the landing phase of the flight. A second alarm is activated when the battery charge falls below a specified limit threshold. This threshold is the point at which the battery energy reserve would no longer safely support two repeated aborted landing attempts. During the test series, the motor system is operated with the same predefined timed airspeed profile for each test. To test the robustness of the prediction, half of the tests were performed with, and half were performed without, a simulated powertrain fault. The pilot remotely engages a resistor bank at a specified time during the test flight to simulate a partial powertrain fault. The flying time prediction system is agnostic of the pilot's activation of the fault and must adapt to the vehicle's state. The time at which the limit threshold on battery charge is reached is then used to measure the accuracy of the remaining flying time predictions. Accuracy requirements for the alarms are considered and the results discussed.

Hogge, Edward F.↗

Optimal Bayesian supervised domain adaptation for RNA sequencing data

Abstract Motivation When learning to subtype complex disease based on next-generation sequencing data, the amount of available data is often limited. Recent works have tried to leverage data from other domains to design better predictors in the target domain of interest with varying degrees of success. But they are either limited to the cases requiring the outcome label correspondence across domains or cannot leverage the label information at all. Moreover, the existing methods cannot usually benefit from other information available a priori such as gene interaction networks. Results In this article, we develop a generative optimal Bayesian supervised domain adaptation (OBSDA) model that can integrate RNA sequencing (RNA-Seq) data from different domains along with their labels for improving prediction accuracy in the target domain. Our model can be applied in cases where different domains share the same labels or have different ones. OBSDA is based on a hierarchical Bayesian negative binomial model with parameter factorization, for which the optimal predictor can be derived by marginalization of likelihood over the posterior of the parameters. We first provide an efficient Gibbs sampler for parameter inference in OBSDA. Then, we leverage the gene-gene network prior information and construct an informed and flexible variational family to infer the posterior distributions of model parameters. Comprehensive experiments on real-world RNA-Seq data demonstrate the superior performance of OBSDA, in terms of accuracy in identifying cancer subtypes by utilizing data from different domains. Moreover, we show that by taking advantage of the prior network information we can further improve the performance. Availability and implementation The source code for implementations of OBSDA and SI-OBSDA are available at the following link. https://github.com/SHBLK/BSDA. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗

Remaining Flying Time Prediction Implementing Battery Prognostics Framework for Electric UAV's

In this paper the problem of building trust in the online safety prediction of an fixed wing small electric unmanned aerial vehicles (e-UAV) for remaining flying time is addressed. A series of flight tests are described to verify the performance of the remaining flying time prediction algorithm. The estimate of remaining flying time is used to activate an alarm when the predicted remaining time falls below a threshold of two minutes. This updates the pilot to transition to the landing sequence of the flight profile. A second alarm is activated when the battery state of charge (SOC) falls below a specified safety limit threshold. This SOC threshold is the point at which the battery energy reserve would no longer safely support enough aborted landing attempts. During the test flights, the motor system is operated with the same predefined timed airspeed profile for each test. To test the robustness of the developed prediction algorithm, partial tests were performed with and remaining were performed without a simulated power train fault. To simulate a partial power train fault in the e-UAV the pilot engages a resistor bank at a specified time during the test flight. The flying time prediction system is agnostic of the pilot's activation of the fault and must adapt to the vehicle's state. The time at which the limit threshold on battery SOC is reached, it is then used to measure the accuracy of the remaining flying time predictions. This is demonstrated through comparing results from two battery models being developed. Accuracy requirements for the alarms are considered and the results discussed.

Kulkarni, Chetan↗

Integration of pH Control into Chi.Bio Reactors and Demonstration with Small-Scale Enzymatic Poly(ethylene terephthalate) Hydrolysis

Small-scale bioreactors that are affordable and accessible would be of major benefit to the research community. In previous work, an open-source, automated bioreactor system was designed to operate up to the 30 mL scale with online optical monitoring, stirring, and temperature control, and this system, dubbed Chi.Bio, is now commercially available at a cost that is typically 1–2 orders of magnitude less than commercial bioreactors. In this work, we further expand the capabilities of the Chi.Bio system by enabling continuous pH monitoring and control through hardware and software modifications. For hardware modifications, we sourced low-cost, commercial pH circuits and made straightforward modifications to the Chi.Bio head plate to enable continuous pH monitoring. For software integration, we introduced closed-loop feedback control of the pH measured inside the Chi.Bio reactors and integrated a pH-control module into the existing Chi.Bio user interface. We demonstrated the utility of pH control through the small-scale depolymerization of the synthetic polyester, poly(ethylene terephthalate) (PET), using a benchmark cutinase enzyme, and compared this to 250 mL bioreactor hydrolysis reactions. The results in terms of PET conversion and rate, measured both by base addition and product release profiles, are statistically equivalent, with the Chi.Bio system allowing for a 20-fold reduction of purified enzyme required relative to the 250 mL bioreactor setup. Through inexpensive modifications, the ability to conduct pH control in Chi.Bio reactors widens the potential slate of biochemical reactions and biological cultivations for study in this system, and may also be adapted for use in other bioreactor platforms.

09 BIOMASS FUELS↗

Electromagnetic Pain Relief/Blocking: Feasibility Assessment

Context/Background: Astronauts use pharmaceuticals during spaceflight to manage acute and chronic pain, but use of analgesics will have drawbacks for exploration-class missions because the shelf life of these medications is limited, resupply will be curtailed, astronauts may develop tolerance and/or addiction to these medications, and side effects can include impairment of cognitive abilities. Electromagnetic devices have been developed that treat pain terrestrially by affecting neuromodulation–dubbed “electroceuticals”, these devices have varied mechanisms of action that either stimulate or suppress neural activity in the central nervous system or peripheral nerves. Objective/Purpose: The available literature was reviewed and FDA-approved pain treatments (both pharmacological and non-pharmacological), as well as those currently under development, were assessed for their suitability for use in exploration class spaceflight missions. Data Sources: Due to the COVID-19 pandemic and the resulting closure of libraries, data sources were restricted to those available digitally. Online database searches included PubMed, U.S. Patent and Trademark Office, federal grant award databases (National Aeronautics and Space Administration (NASA), Department of Defense (DoD), National Institutes of Health (NIH)), and general internet searches. More than 1,600 records were reviewed in this effort. Study Selection/Eligibility Criteria: Targeted searches included different aspects of pain management. Priority was given to review studies, to cover as much of the available literature as possible in this limited effort. Study Appraisal and Synthesis Methods/Data Extraction and Data Synthesis: The titles of the studies and the awards that were obtained by searching online databases were reviewed and further information was sought for the relevant titles. Abstracts or award summaries were generally available online; for journal abstracts, full text articles were either available online or were requested via interlibrary loan. Results: An overwhelming majority of the literature focuses on the treatment of chronic rather than acute pain because it is assumed that acute pain only rarely fails to resolve and instead transitions into chronic pain when the central nervous system becomes hypersensitized. The available electromagnetic devices marketed for pain treatment have varying levels of invasiveness, use different mechanisms of action, and have demonstrated varying efficacy when evaluated scientifically. A truly noninvasive, highly efficient device is desired for use during spaceflight. One portable, self-contained, FDA-approved device was identified that, from preliminarily assessment, best met these criteria; the device noninvasively applies pulsed shortwave therapy (PSWT) to modify pain signals from peripheral nerves, however, the device has limited battery life and the effects are relatively non-selective in type of neural signal modified. Limitations: This current effort, although extensive, did not identify a comprehensive list of all alternatives for pain treatment. Once the pandemic limitations are lifted, a longer, more thorough effort may find additional options. Conclusions/Implications: The ideal electromagnetic pain treatment device for use on exploration-class spaceflight missions does not yet exist, but it may be available soon. It is not feasible for NASA to develop medical devices due to the schedule constraints for pending exploration-class missions, but adapting a promising device that is already FDA-approved might be an option. Monitoring research that is ongoing at other federal agencies is recommended, and further review of the candidate PSWT device identified in this current effort may be warranted.

Carol Mullenax↗

Electromagnetic Pain Relief/Blocking: Feasibility Assessment

CONTEXT/BACKGROUND Astronauts use pharmaceuticals during spaceflight to manage acute and chronic pain, but use of analgesics will have drawbacks for exploration-class missions because the shelf life of these medications is limited, resupply will be curtailed, astronauts may develop tolerance and/or addiction to these medications, and side effects can include impairment of cognitive abilities. Electromagnetic devices have been developed that treat pain terrestrially by affecting neuromodulation–dubbed “electroceuticals”, these devices have varied mechanisms of action that either stimulate or suppress neural activity in the central nervous system or peripheral nerves. OBJECTIVE/PURPOSE The available literature was reviewed and FDA-approved pain treatments (both pharmacological and non-pharmacological), as well as those currently under development, were assessed for their suitability for use in exploration class spaceflight missions. DATA SOURCES Due to the COVID-19 pandemic and the resulting closure of libraries, data sources were restricted to those available digitally. Online database searches included PubMed, U.S. Patent and Trademark Office, federal grant award databases (National Aeronautics and Space Administration (NASA), Department of Defense (DoD), National Institutes of Health (NIH)), and general internet searches. More than 1,600 records were reviewed in this effort. STUDY SELECTION/ELIGIBILITY CRITERIA Targeted searches included different aspects of pain management. Priority was given to review studies, to cover as much of the available literature as possible in this limited effort. STUDY APPRAISAL AND SYNTHESIS METHODS/DATA EXTRACTION AND DATA SYNTHESIS The titles of the studies and the awards that were obtained by searching online databases were reviewed and further information was sought for the relevant titles. Abstracts or award summaries were generally available online; for journal abstracts, full text articles were either available online or were requested via interlibrary loan. RESULTS An overwhelming majority of the literature focuses on the treatment of chronic rather than acute pain because it is assumed that acute pain only rarely fails to resolve and instead transitions into chronic pain when the central nervous system becomes hypersensitized. The available electromagnetic devices marketed for pain treatment have varying levels of invasiveness, use different mechanisms of action, and have demonstrated varying efficacy when evaluated scientifically. A truly noninvasive, highly efficient device is desired for use during spaceflight. One portable, self-contained, FDA-approved device was identified that, from preliminarily assessment, best met these criteria; the device noninvasively applies pulsed shortwave therapy (PSWT) to modify pain signals from peripheral nerves, however, the device has limited battery life and the effects are relatively non-selective in type of neural signal modified. LIMITATIONS This current effort, although extensive, did not identify a comprehensive list of all alternatives for pain treatment. Once the pandemic limitations are lifted, a longer, more thorough effort may find additional options. CONCLUSIONS/IMPLICATIONS The ideal electromagnetic pain treatment device for use on exploration-class spaceflight missions does not yet exist, but it may be available soon. It is not feasible for NASA to develop medical devices due to the schedule constraints for pending exploration-class missions, but adapting a promising device that is already FDA-approved might be an option. Monitoring research that is ongoing at other federal agencies is recommended, and further review of the candidate PSWT device identified in this current effort may be warranted.

C A Mullenax↗

Speaker-targeted Synthetic Speech Detection

Text-to-speech technologies are evolving quickly towards realistic-sounding human-like voices. As this technology improves, so does the opportunity for malpractice in speaker identification (SID) via spoofing, the process of impersonating a voice biometric via synthesis. More data typically equates to a more realistic voice model, which poses an issue for well-known subjects, such as politicians and celebrities, who have vast amounts of multimedia available online. Detection of synthetic speech has relied on signal processing techniques that focus on the generation of new acoustic features and train deep learning models to detect when an audio file has been manipulated through the characterization of unnatural changes or artifacts. However, these techniques do not use any information from the speaker they are evaluating. This paper proposes to incorporate information from the speaker-of-interest (SoI) into the models to avoid specific spoofing attacks for certain vulnerable people. The wealth of data for well-known people can also be used to train a speaker-specific spoofing detector with a higher level of accuracy than a speaker-independent model. The paper proposes a new xResNet-PLDA system and compares it to three different baseline systems: a state-of-the-art speaker identification system, an xResNet system trained to discriminate between bona fide and fake speech, and a speaker identification system in which the PLDA and calibration models were trained with bona fide and fake speech. We evaluated the systems in two different scenarios — a cross-validation scenario and a hold-out scenario — with three different databases. We show how the proposed system outperforms dramatically the baseline systems in each scenario and for each database. Finally, we show how using a small amount of the SoI’s speech to adapt global calibration parameters improves the performance of the system, especially in unseen conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Adaptive Discovery and Mixed-Variable Optimization of Next Generation Synthesizable Microelectronic Materials

Design of new microelectronic materials is characterized by several challenges such as high-dimensionality of the atomic structure-composition variable space, formidable cost of directly using high-fidelity simulations for design optimization, dispersity in literature-reported similar materials and synthesis methods, complex physical mechanisms, and mixed qualitative and quantitative design variables that lead to a disjointed design space. Even though machine learning (ML) techniques have been employed to expedite materials innovation, existing methods treat ML and design optimization as two separate processes, failing to resolve the fundamental challenges associated with high dimensionality and mixed-variable complexity. We have developed a ML enhanced mixed-variable material design optimization framework to efficiently extract useful information from existing data in literature and physics-based simulations to guide the autonomous search for optimal materials. Our proposed framework is composed of four computational modules: (1) a natural language processing (NLP) based virtual screening module, (2) classification based concept exploration module, (3) a density functional theory (DFT)-based high-fidelity evaluation model, and (4) a novel latent-variable Gaussian process (LVGP) ML model for mixed-variable problems with uncertainty quantification, which seamlessly integrates with Bayesian Optimization (BO) and achieves superb efficiency through embedded physics-based dimension reduction. Our approach is demonstrated and validated using the testbed of functional materials exhibiting metal-insulation transitions (MITs), with the targeted reversible resistivity changes (∼10^5) near room temperature. At the end of the 30-month project, we have developed a series of new ML techniques using NLP, conditional variational autoencoders, active learning, latent-variable Gaussian processes, integrated with Bayesian optimization. Our project has resulted in new predicted MITs compounds and improved understanding of MITs microscopic mechanisms, which in turn will revolutionize microelectronics science to provide energy-saving solutions. Our research has improved both creativity and efficiency in transforming rare-event discoveries of new functional materials to persistent innovations. In addition to open-sourcing the online MIT database and the classification model, the LVGP open source code has been downloaded more than 15,000 times within two years. More than 40 MIT compounds have been identified and many have been pursued experimentally via collaborators. The research results are published in close to 20 collaborative papers in high-impact journals, such as Chem. Mater., Appl. Phys. Rev., Sci. Rep., among others of design space.

36 MATERIALS SCIENCE↗

Pressure-Driven Fiber-Optic Sensor for Online Corrosion Monitoring

For many industrial applications, corrosion is a life-limiting phenomenon and therefore requires careful consideration and rigorous experimental testing before structural materials can be reliably deployed, particularly in harsh chemical environments. The traditional approach to measuring corrosion requires exposing many samples to the intended environment and then extracting them individually at discrete intervals for postexposure characterization. This approach does not provide a high degree of temporal resolution, nor does it provide any real-time information regarding dynamic changes in corrosion rates. Additionally, developing an online corrosion monitor capable of surviving harsh chemical environments could provide valuable information regarding the structural health of components and changing process conditions that could accelerate corrosion. To this end, a corrosion sensor was developed based on a pressure-driven Fabry-Pérot cavity (FPC). This sensor uses a pressure control system to internally pressurize the FPC formed between the sensor’s housing and a metal-embedded singlemode optical fiber. Simultaneous measurement of the change in FPC length using low-coherence interferometry and the applied pressure enables the calculation of the relative changes in the sensor’s diaphragm thickness due to corrosion on its outer surface. Measurements were made in situ while actively corroding the sensor and were validated against surveillance specimens that were corroded simultaneously. The uncertainties in the measured corrosion were analyzed using error propagation of the uncertainties in the measured pressures and displacements and were found to be <1% of the initial diaphragm thickness.

42 ENGINEERING↗

Robust and Simple ADMM Penalty Parameter Selection

We present a new method for online selection of the penalty parameter for the alternating direction method of multipliers (ADMM) algorithm. ADMM is a widely used method for solving a range of optimization problems, including those that arise in signal and image processing. In its standard form, ADMM includes a scalar hyperparameter, known as the penalty parameter, which usually has to be tuned to achieve satisfactory empirical convergence. In this work, we develop a framework for analyzing the ADMM algorithm applied to a quadratic problem as an affine fixed point iteration. Using this framework, we develop a new method for automatically tuning the penalty parameter by detecting when it has become too large or small. We analyze this and several other methods with respect to their theoretical properties, i.e., robustness to problem transformations, and empirical performance on several optimization problems. Our proposed algorithm is based on a theoretical framework with clear, explicit assumptions and approximations, is theoretically covariant/invariant to problem transformations, is simple to implement, and exhibits competitive empirical performance.

42 ENGINEERING↗

Intelliquench: An Adaptive Machine Learning System for Detection of Superconducting Magnet Quenches

In superconducting magnets, the irreversible transition of a portion of the conductor to resistive state is called a “quench.” Having large stored energy, magnets can be damaged by quenches due to localized heating, high voltage, or large force transients. Unfortunately, current quench protection systems can only detect a quench after it happens, and mitigating risks in Low Temperature Superconducting (LTS) accelerator magnets often requires fast response (down to ms). Additionally, protection of High Temperature Superconducting (HTS) magnets is still suffering from prohibitively slow quench detection. In this study, we lay the groundwork for a quench prediction system using an auto-encoder fully-connected deep neural network. After dynamically trained with data features extracted from acoustic sensors around the magnet, the system detects anomalous events seconds before the quench in most of our data. While the exact nature of the events is under investigation, we show that the system can “forecast” a quench before it happens under magnet training conditions through a randomized experiment. This opens up the way of integrated data processing, potentially leading to faster and better diagnostics and detection of magnet quenches

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

A bi-level advanced control framework for large-scale control of buildings with system-level impact

Increased electricity consumption combined with new forms of generation is testing the reliability of our grid infrastructure. This work describes a method to improve the reliability of the grid through large-scale advanced building control. This paper develops a bi-level distributed control framework to shift the load of 153 buildings to achieve a system-level objective of tracking a power reference signal. This bi-level control is based on the previously-developed ANPV-MPC, a predictive controller that uses a Bayesian neural network to generate an accurate control model and adapt to changing conditions over time. By shifting the building electricity demand to better match the available power, the grid system supplying the buildings is more reliable as evidenced by the analysis of node voltages across an IEEE 13-bus distribution system. The proposed bi-level control framework tracks the system-level power reference with enough accuracy to regulate node voltages across the IEEE 13-bus distribution system within ANSI limits of ±5%. Additionally, the adaptive nature of ANPV-MPC allows each building across the system to adapt to changing conditions, further amplifying the system-level reliability.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗