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At least 37 records · Page 2

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

Abstract Background Driven by deep learning, inter-residue contact/distance prediction has been significantly improved and substantially enhanced ab initio protein structure prediction. Currently, most of the distance prediction methods classify inter-residue distances into multiple distance intervals instead of directly predicting real-value distances. The output of the former has to be converted into real-value distances to be used in tertiary structure prediction. Results To explore the potentials of predicting real-value inter-residue distances, we develop a multi-task deep learning distance predictor (DeepDist) based on new residual convolutional network architectures to simultaneously predict real-value inter-residue distances and classify them into multiple distance intervals. Tested on 43 CASP13 hard domains, DeepDist achieves comparable performance in real-value distance prediction and multi-class distance prediction. The average mean square error (MSE) of DeepDist’s real-value distance prediction is 0.896 Å 2 when filtering out the predicted distance ≥ 16 Å, which is lower than 1.003 Å 2 of DeepDist’s multi-class distance prediction. When distance predictions are converted into contact predictions at 8 Å threshold (the standard threshold in the field), the precision of top L/5 and L/2 contact predictions of DeepDist’s multi-class distance prediction is 79.3% and 66.1%, respectively, higher than 78.6% and 64.5% of its real-value distance prediction and the best results in the CASP13 experiment. Conclusions DeepDist can predict inter-residue distances well and improve binary contact prediction over the existing state-of-the-art methods. Moreover, the predicted real-value distances can be directly used to reconstruct protein tertiary structures better than multi-class distance predictions due to the lower MSE. Finally, we demonstrate that predicting the real-value distance map and multi-class distance map at the same time performs better than predicting real-value distances alone.

59 BASIC BIOLOGICAL SCIENCES↗

A Wall-Distance Method for Turbulence Modeling

The distance from a grid point to the closest wall surface, wall distance, is a funda- mental quantity in turbulence modeling. Efficiency of wall-distance calculations has become more critical as the size of computational grids has significantly increased in recent years. This paper reports on an initial implementation of a new search-based wall-distance method that is suitable for general unstructured computational fluid dynamics (CFD) grids and tailored for requirements specific for turbulence modeling. The method represents a two-step approach to calculate the wall distance. In the first step, the wall distance is approximated for each grid point as the minimum distance from this point to a vertex of a triangular face at the wall. The point-to-vertex distance calculation is relatively inexpensive but may lead to a significant error in the wall-distance ap- proximation, especially for grid points near the wall. In the second step, for grid points located within a predefined distance ( threshold ) from the wall, the wall distance is computed as the minimum distance to wall faces. As a result, the wall distance is exact for all grid points within the threshold. This two-step approach reduces the computational cost yet achieves high and controllable accuracy in the evaluation of the wall distance. Algorithmic enhancements are presented to improve efficiency of wall-distance computations. Comprehensive assessment of the new method is reported for large-scale unstructured CFD grids generated for the Fifth AIAA CFD High-Lift Prediction Workshop. The performance of the new wall-distance method compares favorably with performance of two established methods implemented in high-performance CFD codes.

Wall Distance↗

Improving deep learning-based protein distance prediction in CASP14

Abstract Motivation Accurate prediction of residue–residue distances is important for protein structure prediction. We developed several protein distance predictors based on a deep learning distance prediction method and blindly tested them in the 14th Critical Assessment of Protein Structure Prediction (CASP14). The prediction method uses deep residual neural networks with the channel-wise attention mechanism to classify the distance between every two residues into multiple distance intervals. The input features for the deep learning method include co-evolutionary features as well as other sequence-based features derived from multiple sequence alignments (MSAs). Three alignment methods are used with multiple protein sequence/profile databases to generate MSAs for input feature generation. Based on different configurations and training strategies of the deep learning method, five MULTICOM distance predictors were created to participate in the CASP14 experiment. Results Benchmarked on 37 hard CASP14 domains, the best performing MULTICOM predictor is ranked 5th out of 30 automated CASP14 distance prediction servers in terms of precision of top L/5 long-range contact predictions [i.e. classifying distances between two residues into two categories: in contact (<8 Angstrom) and not in contact otherwise] and performs better than the best CASP13 distance prediction method. The best performing MULTICOM predictor is also ranked 6th among automated server predictors in classifying inter-residue distances into 10 distance intervals defined by CASP14 according to the precision of distance classification. The results show that the quality and depth of MSAs depend on alignment methods and sequence databases and have a significant impact on the accuracy of distance prediction. Using larger training datasets and multiple complementary features improves prediction accuracy. However, the number of effective sequences in MSAs is only a weak indicator of the quality of MSAs and the accuracy of predicted distance maps. In contrast, there is a strong correlation between the accuracy of contact/distance predictions and the average probability of the predicted contacts, which can therefore be more effectively used to estimate the confidence of distance predictions and select predicted distance maps. Availability and implementation The software package, source code and data of DeepDist2 are freely available at https://github.com/multicom-toolbox/deepdist and https://zenodo.org/record/4712084#.YIIM13VKhQM. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Improving ChemCam LIBS long-distance elemental compositions using empirical abundance trends

The ChemCam instrument on the Curiosity rover provides chemical compositions of Martian rocks and soils using remote laser-induced breakdown spectroscopy (LIBS). The elemental calibration is stable as a function of distance for Ti, Fe, Mg, and Ca. The calibration shows small, systematically increasing abundance trends as a function of distance for Al, Na, K, and to some extent, Si. The distance effect is known to be due to a dependence with distance on the relative strengths of atomic transition lines. Emission lines representing transitions from relatively low energy levels remain intense at longer distances while emission lines representing transitions from higher energy levels decrease in intensity more rapidly as a function of distance. The multivariate algorithms used to determine elemental compositions rely on a large number of emission lines in many cases, so rather than trying to correct all emission lines, a study was made of the predicted compositions as a function of distance, in order to determine an empirical correction. Abundance trends can be well approximated by a linear trend with distance within the ranges of abundances and distances observed up to ~6 m. Data from 11 distinct geological members and data groups of the Murray formation in Gale crater, Mars, were used to form the model, selecting the members and data groups yielding the best statistics. The model was tested using data from several targets observed from two different distances, and using data from the Kimberley formation, the composition of which is significantly different from the Murray formation, showing that the model works on other compositions beyond those used to build the model. For long-distance observations up to ~6 m, corrections can be made back to an equivalent composition at the median distance of ChemCam observations (2.6 m). Finally, the model has been validated up to 6.2 m, although ChemCam is able to observe bedrock targets to >7 m, and iron meteorites to distances of >9 m.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Lightning Strike Distance Distribution Beyond a Preexisting Lightning Area

The 45th Weather Squadron (45 WS) asked the Applied Meteorology Unit (AMU) to review the 30-year-old, lightning stand-off distances of 5 nautical miles (nmi) for applicability to today's operations. This was based on the realization that previous lightning strike distance studies did not match how 45 WS issues lightning warnings (Roeder, 2008). The previous lightning distance studies were from the point of origin of the lightning or the average starting location that would tend to be in the core of the thunderstorm. However, the 45 WS issues lightning warnings based on the edge of a preexisting lightning area. Before beginning the AMU project, it took several years to develop a method to calculate a distance distribution beyond a preexisting area (Roeder, 2015). The AMU pulled Lightning Detection and Ranging (LDAR) sensor data from 1/1/2013 to 12/31/2013. This dataset consisted of 37 million individual source data points from the LDAR sensors. Only sources within 50 km north, south, east or west of the LDAR grid center were included in the dataset. This limited the use of LDAR data to that with the greatest accuracy of source detection and increased data processing. Points were grouped into flashes based on spatial and temporal criteria. Based on the sensitivity analysis the AMU performed on the flash clustering algorithm, a time value of 0.3 seconds was found to model flashes adequately. Distance parameters were tested from 1,500 to 7,500 meters (m) in 500 m increments. Distance parameters of both 3,000 m and 4,000 m produced results in the plotting tool that were most representative of the physical behavior of lightning. Thus statistics were gathered for the most representative of these spatial and temporal criteria on the flash size and the polygon expansion distance in order to find the correct data distributions. The best fit curves for the LDAR polygon expansion frequency vs. distances for both the 3 kilometer (km) and 4 km distance threshold values were exponential decay functions and had R2 values of > 0.998, indicating good model fits. The equations of the best fit curves were then used to calculate a desired safety radius of 4 nmi for either 3 km or 4 km distance threshold criteria. The AMU analysis concludes the safe reduction of the 5 nmi lightning warning circles to 4 nmi should improve the operational impact by 36% if based on distance from the center of the property area being protected. If based on the edge of the property being protected, then the reduction is 4.5 nmi to 4 nmi and the operational impact is decreased by 21%. For the 6 nmi lightning warning circles, the recommended 4 nmi stand-off distance will result in a safe reduction of operational impact of 31% if based on the center of the area being protected, or 16% if based on the edge of the property.

Flash clustering algorithm↗

The Problem of Hipparcos Distances to Open Clusters: Constraints from Multicolor a Main-Sequence Fitting - Report 1

Parallax data from the Hipparcos mission allow the direct distance to open clusters to be compared with the distance inferred from main-sequence (MS) fitting. There are surprising differences between the two distance measurements. indicating either the need for changes in the cluster compositions or reddening, underlying problems with the technique of MS fitting, or systematic errors in the Hipparcos parallaxes at the 1 mas level. We examine the different possibilities, focusing on MS fitting in both metallicity-sensitive B-V and metallicity-insensitive V-I for five well-studied systems (the Hyades, Pleiades, alpha Per, Praesepe, and Coma Ber). The Hipparcos distances to the Hyades and alpha Per are within 1 sigma of the MS-fitting distance in B-V and V-I, while the Hipparcos distances to Coma Ber and the Pleiades are in disagreement with the MS-fitting distance at more than the 3 sigma level. There are two Hipparcos measurements of the distance to Praesepe; one is in good agreement with the MS-fitting distance and the other disagrees at the 2 sigma level. The distance estimates from the different colors are in conflict with one another for Coma but in agreement for the Pleiades. Changes in the relative cluster metal abundances, age related effects, helium, and reddening are shown to be unlikely to explain the puzzling behavior of the Pleiades. We present evidence for spatially dependent systematic errors at the 1 mas level in the parallaxes of Pleiades stars. The implications of this result are discussed.

Pinsonneault, Marc H.↗

A Short-Range Distance Sensor with Exceptional Linearity

A sensor has been demonstrated that can measure distance over a total range of about 300 microns to an accuracy of about 0.1 nm (resolution of about 0.01 nm). This represents an exceptionally large dynamic range of operation - over 1,000,000. The sensor is optical in nature, and requires the attachment of a mirror to the object whose distance is being measured. This work resulted from actively developing a white light interferometric system to be used to measure the depths of defects in the Space Shuttle Orbiter windows. The concept was then applied to measuring distance. The concept later expanded to include spectrometer calibration. In summary, broadband (i.e., white) light is launched into a Michelson interferometer, one mirror of which is fixed and one of which is attached to the object whose distance is to be measured. The light emerging from the interferometer has traveled one of two distances: either the distance to the fixed mirror and back, or the distance to the moving mirror and back. These two light beams mix and produce an interference pattern where some wavelengths interfere constructively and some destructively. Sending this light into a spectrometer allows this interference pattern to be analyzed, yielding the net distance difference between the two paths. The unique feature of this distance sensor is its ability to measure accurately distance over a dynamic range of more than one million, the ratio of its range (about 300 microns) to its accuracy (about 0.1 nanometer). Such a large linear operating range is rare and arises here because both amplitude and phase-matching algorithms contribute to the performance. The sensor is limited by the need to attach a mirror of some kind to the object being tracked, and by the fairly small total range, but the exceptional dynamic range should make it of interest.

Simmons, Steven↗

SpecDis: Value Added Distance Catalog for 4 Million Stars from DESI Year-1 Data

We present the SpecDis value-added stellar distance catalog accompanying DESI Data Release 1. SpecDis trains a feed-forward neural network (NN) with Gaia parallaxes and gets the distance estimates. To build up an unbiased training sample, we do not apply selections on parallax error or signal-to-noise (S/N) of the stellar spectra, and instead, we incorporate parallax error into the loss function. Moreover, we employ principal component analysis to reduce the noise and dimensionality of stellar spectra. Validated by independent external samples of member stars with precise distances from globular clusters, dwarf galaxies, stellar streams, combined with blue horizontal branch stars, we demonstrate that our distance measurements show no significant bias up to 100 kpc, and are much more precise than Gaia parallax beyond 7 kpc. The median distance uncertainties are 23%, 19%, 11%, and 7% for S/N < 20, 20 ≤ S/N < 60, 60 ≤ S/N < 100, and S/N ≥ 100. Selecting stars with ${\mathrm{log}}\,g\lt 3.8$ and distance uncertainties smaller than 25%, we have more than 74,000 giant candidates within 50 kpc of the Galactic center and 1500 candidates beyond this distance. Additionally, we develop a Gaussian mixture model to identify unresolvable equal-mass binaries by modeling the discrepancy between the NN-predicted and the geometric absolute magnitudes from Gaia parallaxes and identify 120,000 equal-mass binary candidates. Our final catalog provides distances and distance uncertainties for >4 million stars, offering a valuable resource for Galactic astronomy.

astronomy data analysis↗

Revisiting the refined Distance Conjecture

The Distance Conjecture of Ooguri and Vafa holds that any infinite-distance limit in the moduli space of a quantum gravity theory must be accompanied by a tower of exponentially light particles, which places tight constraints on the low-energy effective field theories in these limits. One attempt to extend these constraints to the interior of moduli space is the refined Distance Conjecture, which holds that the towers of light particles predicted by the Distance Conjecture must appear any time a modulus makes a super-Planckian excursion in moduli space. In this note, however, we point out that a tower which satisfies the Distance Conjecture in an infinite-distance limit of moduli space may be parametrically heavier than the Planck scale for an arbitrarily long geodesic distance. This means that the refined Distance Conjecture, in its most naive form, does not place meaningful constraints on low-energy effective field theory. This motivates alternative refinements of the Distance Conjecture, which place an absolute upper bound on the tower mass scale in the interior of moduli space. We explore two possibilities, providing evidence for them and briefly discussing their implications.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Support Vector Machines for Classification of Direct Energy Deposition Standoff Distance for Improved Process Control

A critical factor in the implementation of direct energy deposition is the ability to maintain the standoff distance between the nozzle and the build surface, as this influences powder capture efficiency and overall part quality. Due to process-related variations, layer height may vary, causing unintended variation in standoff distance and poor build quality. While prior work has utilized contact probing to qualify standoff distance during processing, in situ methods for qualification of standoff distance are of major interest. The present work seeks to understand efficacy of image-based methods for classifying standoff distance variation in real-time using support vector machines (SVMs). It was hypothesized that the size of the melt pool and the amount of spatter will have significant correlations with deviations in the standoff distance; thus, SVMs were used on a dataset that is comprised of morphological features of melt pool size and image entropy. The SVM model was used to classify melt pool images into categories according to standoff distance variation from nominal. K-folds cross validation was used to find the optimal hyperparameters for the SVM model. To understand the impact of the selected features on the classification performance and inference speed, multiple models were trained with differing numbers of included features. Results for classification score, inference time, and image preprocessing/feature extraction from these data are reported. The present results show that the SVM model was able to predict the standoff distance classification with an accuracy of 97 percent and a speed of 0.122 s per image, making it a viable solution for real-time control of standoff distance.

Klesmith, Zoe↗

Empirical Estimation of Shortest Route Length along U.S. Interstate Highways Based on Great Circle Distance

In this study, 98 regression models were specified for easily estimating shortest distances based on great circle distances along the U.S. interstate highways nationwide and for each of the continental 48 states. This allows transportation professionals to quickly generate distance, or even distance matrix, without expending significant efforts on complicated shortest path calculations. For simple usage by all professionals, all models are present in the simple linear regression form. Only one explanatory variable, the great circle distance, is considered to calculate the route distance. For each geographic scope (i.e., the national or one of the states), two different models were considered, with and without the intercept. Based on the adjusted R-squared, it was observed that models without intercepts generally have better fitness. Additionally, all these models generally have good fitness with the linear regression relationship between the great circle distance and route distance. At the state level, significant variations in the slope coefficients between the state-level models were also observed. Furthermore, a preliminary analysis of the effect of highway density on this variation was conducted.

33 ADVANCED PROPULSION SYSTEMS↗