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Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria
Drug discovery faces a crisis. The industry has used up the “obvious” space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. Here, we present proof of concept of an approach to rationally identify a “chemical vocabulary” related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
Forecasting Megaelectron-Volt Electrons Inside Earth's Outer Radiation Belt: PreMevE 2.0 Based on Supervised Machine Learning Algorithms
We present the recent progress in upgrading a predictive model for megaelectron-volt (MeV) electrons inside the Earth's outer Van Allen belt. This updated model, called PreMevE 2.0, provides improved forecasts, particularly at outer L-shells, by adding upstream solar wind speeds to the model's input parameter list that originally includes precipitating electrons observed at low Earth orbits and MeV electron fluxes in situ measured by a geosynchronous satellite. Furthermore, based on several kinds of linear and artificial neural networks algorithms, a list of models was constructed, trained, validated, and tested with 42-month MeV electron observations from Van Allen Probes. Out-of-sample test results from these models show that, with optimized model hyperparameters and input parameter combinations, the top performer from each category of models has the similar capability of making reliable 1-day (2-day) forecasts of 1-MeV electron flux distributions with performance efficiency values ~0.87 (~0.82) averaged over the L-shell range of 2.8–6.6, significantly outperforming the previous version of PreMevE particularly at L-shells > ~4.5. Interestingly, the linear regression model is often the most successful when compared to other models, which suggests the relationship between dynamics of trapped 1-MeV electrons and precipitating electrons is dominated by linear components. Results also show that PreMevE 2.0 can reasonably well predict the onsets of MeV electron events in 2-day forecasts. PreMevE 2.0 is designed to be driven by observations from longstanding space infrastructure to make high-fidelity forecasts for MeV electrons, thus can be an invaluable space weather forecasting tool for the future.
Inference of response functions with the help of machine-learning algorithms
Response functions are a key quantity to describe the near-equilibrium dynamics of strongly interacting many-body systems. Recent techniques that attempt to overcome the challenges of calculating these ab initio have employed expansions in terms of orthogonal polynomials. We employ a neural network prediction algorithm to reconstruct a response function 𝑆(𝜔) defined over a range in frequencies 𝜔. Here, we represent the calculated response function as a truncated Chebyshev series whose coefficients can be optimized to reduce the representation error. We compare the quality of response functions obtained using coefficients calculated using a neural network (NN) algorithm with those computed using the Gaussian integral transform (GIT) method. In the regime where only a small number of terms in the Chebyshev series are retained, we find that the NN scheme outperforms the GIT method.
Optimization of microwave emission from laser filamentation with a machine learning algorithm
We demonstrate that is it possible to optimize the yield of microwave radiation from plasmas generated by laser filamentation in atmosphere through manipulation of the laser wavefront. A genetic algorithm controls a deformable mirror that reconfigures the wavefront using the microwave waveform amplitude as feedback. Optimization runs performed as a function of air pressure show that the genetic algorithm can double the microwave field strength relative to when the mirror surface is flat. Here, an increase in the volume and brightness of the plasma fluorescence accompanies the increase in microwave radiation, implying an improvement in the laser beam intensity profile through the filamentation region due to the optimized wavefront.
Development of a software tool for IAEA use of the YOLOv3 machine learning algorithm
No abstract provided.
Wireless 3D Nanorod Composite Arrays based High Temperature Surface-Acoustic-Wave Sensors for Selective Gas Detection through Machine Learning Algorithms (Final Report)
This is the final scientific and technical report which summarizes the research conducted through this funded project. In this report, we first present the accomplishments of the project, major research activities and specific activities conducted, and then discuss the significant results. We also describe the opportunities for training and professional development provided to the involved students as well as the products produced. Finally, we report the impact of the research on the development of human resources and present the budgetary information.
A Decision Tree Based Machine Learning Algorithm for Rate Estimation
A subgraph isomorphic decision tree algorithm was developed for estimating chemical reaction rates. The algorithm essentially associates differences in rate estimation with differences in sub-structures on the reactant or reactants, and the tree splits reactions into groups with similar rates by identifying the substructural differences that affect rate estimation the most. The algorithm was trained on rates from the Reaction Mechanism Generator (RMG) database and compared with a much more traditional rate rule estimator based on the same data. Compared to the previous RMG rate rules, the prediction accuracy of the new algorithm, measured by median absolute error (MAE) factor, root mean squared error (RMSE) factor, and 2-sigma error factor, is consistently improved by a factor of two. Uncertainty estimation was also developed for the decision trees based on fitting a lognormal distribution to the leave-one-out errors at each node. Improvements in accuracy introduced by the algorithm should significantly reduce the amount of effort required to refine models and the need for additional quantum calculations and thus reduce the amount of time and cost required to create and refine biofuel models.
Towards memristor supremacy with novel machine learning algorithms
The von Neumann architecture for current computers is slowly showing signs of limitations, due to the finite bus rate between the RAM (memory) and the CPU (computing unit). In-Memory computing is an alternative to this architecture, which however is still in the early stages of development. Memristors are an analog and classical alternative, as these components can act both as a memory, or as a simple computing unit. When wired together, these can in fact be used for a variety of applications. During the course of our research, we have developed an in-depth experimental understanding of both the limitations and the real possibilities of these devices, and developed automated algorithms for their characterization; at the theoretical level, we have incorporated the experimental features to implement novel analog computing units for specific tasks. We have shown that memristors can tackle QUBO and cubic optimization problems, and exhibit tunneling phenomena.
Machine learning algorithms based on muon monitor data and simulation
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Characterization of Additively Manufactured Circular Disks Using Traditional Computed Tomography Volume Segmentation and Machine Learning Algorithms.
Abstract not provided.
Predictive Insight for MoS2 Thin Film Synthesis from Machine Learning Algorithms
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Rapid CFD Using Machine Learning Algorithms (CRADA Final Report)
This is a collaborative effort between Lawrence Livermore National Security, LLC as manager and operator of Lawrence Livermore National Laboratory (“LLNL”) and Guardian Glass, LLC ("Guardian Glass") to develop a fast-running emulator of the reactive Computational Fluid Dynamics (“CFD”) simulations needed to understand the complex reactions and flows in the glass melting, fining, and forming subprocesses. This CRADA project is sponsored under the High-Performance Computing for Manufacturing (“HPC4Mfg”) Program of the Department of Energy’s Advanced Manufacturing Office (“AMO”) within the Energy Efficiency and Renewable Energy (“EERE”) Office.
Hyperspectral Leaf Reflectance as Proxy for Photosynthetic Capacities: An Ensemble Approach Based on Multiple Machine Learning Algorithms
Not Available
Using Machine Learning Algorithm to Detect Blowing Snow and Fog in Antarctica Based on Ceilometer and Surface Meteorology Systems
Blowing snow is a common weather phenomenon in Antarctica and plays an important role in the water vapor cycle and ice sheet mass balance. Although it has a significant impact on the climate of Antarctica, people do not know much about this process. Fog events are difficult to distinguish from blowing snow events using existing detection algorithms by a ceilometer. In this study, based on ceilometer, the meteorological parameters observed by surface meteorology systems are further combined to detect blowing snow and fog using the AdaBoost algorithm. The weather phenomena recorded by human observers are ‘true’. The dataset is collected from 1 January 2016 to 31 December 2016 at the AWARE site. Among them, three-quarters of the data are used as the training set and the rest of the data as the testing set. The classification accuracy of the proposed algorithm for the testing set is about 94%. Compared with the Loeb method, the proposed algorithm can detect 89.12% of blowing snow events and 76.10% of fog events, while the Loeb method can only identify 64.29% of blowing snow events and 31.87% of fog events.
Web-Interfaced Molecular Dynamics Simulation Platform with Machine-Learning-Algorithms-Empowered Force-Fields
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