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DOE OSTI2022

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Efficient generalized boundary detection

Fast, efficient, and robust compression-based methods for detecting boundaries in arbitrary datasets, including sequences (1D datasets), are desired. The methods, each employing three simple algorithms, approximate the information distance between two adjacent sliding windows within a dataset. One of the algorithms calculates an initial ordered list of subsequences; while a second algorithm updates the ordered list of subsequences by dropping a first entry and appending a last entry rather than calculating completely new ordered lists with each iteration. Large values in the distance metric are indicative of boundary locations. A smoothed z-score or a wavelet-based algorithm may then be used to locate peaks in the distance metric, thereby identifying boundary locations. An adaptive version of the method employs a collection of window sizes and corresponding weighting functions, making it more amenable to real datasets with unknown, complex, and changing structures.

Ting, Christina↗

NASA NTRS2012

The Re-Analysis of Ozone Profile Data from a 41-Year Series of SBUV Instruments

In this study we present the validation of ozone profiles from a number of Solar Back Scattered Ultra Violet (SBUV) and SBUV/2 instruments that were recently reprocessed using an updated (Version 8.6) algorithm. The SBUV dataset provides the longest available record of global ozone profiles, spanning a 41-year period from 1970 to 2011 (except a 5-year gap in the 1970s) and includes ozone profile records obtained from the Nimbus-4 BUV and Nimbus-7 SBUV instruments, and a series of SBUV(/2) instruments launched on NOAA operational satellites (NOAA 09, 11, 14, 16, 17, 18, 19). Although modifications in instrument design were made in the evolution from the BUV instrument to the modern SBUV(/2) model, the basic principles of the measurement technique and retrieval algorithm remain the same. The long term SBUV data record allows us to create a consistent, calibrated dataset of ozone profiles that can be used for climate studies and trend analyses. In particular, we focus on estimating the various sources of error in the SBUV profile ozone retrievals using independent observations and analysis of the algorithm itself. For the first time we include in the metadata a quantitative estimate of the smoothing error, defined as the error due to profile variability that the SBUV observing system cannot inherently measure. The magnitude of the smoothing error varies with altitude, latitude, season and solar zenith angle. Between 10 and 1 hPa the smoothing errors for the SBUV monthly zonal mean retrievals are of the order of 1 %, but start to increase above and below this layer. The largest smoothing errors, as large as 15-20%, were detected in in the troposphere. The SBUV averaging kernels, provided with the ozone profiles in version 8.6, help to eliminate the smoothing effect when comparing the SBUV profiles with high vertical resolution measurements, and make it convenient to use the SBUV ozone profiles for data assimilation and model validation purposes. The smoothing error can also be minimized by combining layers of data, and we will discuss recommendations for this approach as well. The SBUV ozone profiles have been intensively validated against satellite profile measurements obtained from the Microwave Limb Sounders (MLS) (on board the UARS and AURA satellites), Stratospheric Aerosol and Gas Experiment (SAGE) and Michelson Interferometer for Passive Atmospheric Sounding (MIPAS). Also, we compare coincident and collocated SBUV ozone retrievals with observations made by ground-based instruments, such as microwave spectrometers, lidars, Umkehr instruments and balloon-borne ozonosondes. Finally, we compare the SBUV ozone profiles with output from the NASA GSFC GEOS-CCM model. In the stratosphere between 25 and 1 hPa the mean biases and standard deviations are within 5% for monthly mean ozone profiles. Above and below this layer the vertical resolution of the SBUV algorithm decreases and the effects of vertical smoothing should be taken into account. Though the SBUV algorithm has a coarser vertical resolution in the lower stratosphere and troposphere, it is capable of precisely estimating the integrated ozone column between the surface and 25 hPa. The time series of the tropospheric - lower stratospheric ozone column derived from SBUV agrees within 5% with the corresponding values observed by an ensemble of ozone sonde stations in North Hemisphere. Drift of the ozone time series obtained from each SBUV(/2) instrument relative to ground based and satellite measurements are evaluated and some features of individual SBUV(l2) instruments are discussed. In addition to evaluating individual instruments against independent observations, we also focus on the instrument to instrument consistency in the series. Overall, Version 8.6 ozone profiles obtained from two different SBUV(l2) instruments compare within a couple of percent during overlap periods and are consistently varying in time, with some exceptions. Some of the noted discrepancies might bssociated with ozone diurnal variations, since the difference in the local time of the observations for a pair of SBUV(l2) instruments could be several hours. Other issues include the potential short-term drift in measurements as the instrument orbit drifts, and measurements are obtained at high solar zenith angles (>85 ). Based on the results of the validation, a consistent, calibrated dataset of SBUV ozone profiles has been created based on internal calibration only.

Kramarova, Natalya↗

NASA NTRS1991

Experiments with conjugate gradient algorithms for homotopy curve tracking

There are algorithms for finding zeros or fixed points of nonlinear systems of equations that are globally convergent for almost all starting points, i.e., with probability one. The essence of all such algorithms is the construction of an appropriate homotopy map and then tracking some smooth curve in the zero set of this homotopy map. HOMPACK is a mathematical software package implementing globally convergent homotopy algorithms with three different techniques for tracking a homotopy zero curve, and has separate routines for dense and sparse Jacobian matrices. The HOMPACK algorithms for sparse Jacobian matrices use a preconditioned conjugate gradient algorithm for the computation of the kernel of the homotopy Jacobian matrix, a required linear algebra step for homotopy curve tracking. Here, variants of the conjugate gradient algorithm are implemented in the context of homotopy curve tracking and compared with Craig's preconditioned conjugate gradient method used in HOMPACK. The test problems used include actual large scale, sparse structural mechanics problems.

Irani, Kashmira M.↗

NASA NTRS1986

A multistage time-stepping scheme for the thin-layer Navier-Stokes equations

A finite-volume scheme for numerical integration of the Euler equations was extended to allow solution of the thin-layer Navier-Stokes equations in two and three dimensions. The extended algorithm, which is based on a class of four-stage Runge-Kutta time-stepping schemes, was made numerically efficient through the following convergence acceleration technique: (1) local time stepping, (2) enthalpy damping, and (3) residual smoothing. Also, the high degree of vectorization possible with the algorithm has yielded an efficient program for vector processors. The scheme was evaluated by solving laminar and turbulent flows. Numerical results have compared well with either theoretical or other numerical solutions and/or experimental data.

Swanson, R. C., Jr.↗

NASA NTRS1992

Grid generation for 3D turbomachinery configurations

A numerical grid generation algorithm associated with the flow field about turbomachinery geometries is presented. Graphical user interface is developed with the FORMS Library to create an interactive, user-friendly working environment. This customized algorithm reduces the man-hours required to generate a grid associated with turbomachinery geometry, as compared to those required by general-purpose grid generation softwares. Bezier curves are utilized both interactively and automatically to accomplish grid line smoothness and orthogonality. Graphical user interactions are provided in the algorithm and allow the user to design and manipulate the grid lines with a mouse.

Shih, Ming-Hsin↗

NASA NTRS1992

TIGER: A graphically interactive grid system for turbomachinery applications

Numerical grid generation algorithm associated with the flow field about turbomachinery geometries is presented. Graphical user interface is developed with FORMS Library to create an interactive, user-friendly working environment. This customized algorithm reduces the man-hours required to generate a grid associated with turbomachinery geometry, as compared to the use of general-purpose grid generation softwares. Bezier curves are utilized both interactively and automatically to accomplish grid line smoothness and orthogonality. Graphical User Interactions are provided in the algorithm, allowing the user to design and manipulate the grid lines with a mouse.

Shih, Ming-Hsin↗

DOE OSTI2023

Real-time estimation of the electron temperature profile in DIII-D by leveraging neural-network surrogate models

Control of both the magnitude and the shape of tokamak profiles will be necessary to achieve stable, high-performance plasmas. In order to reject disturbances in real time, feedback-control algorithms rely on accurate real-time knowledge of the plasma state. When diagnostics alone are insufficient, either because they are limited in number or their measurements are too noisy, observers can be used to combine diagnostic data with a response model to provide a better estimation of different plasma properties. An observer has been developed to estimate the electron temperature profile in real time using both diagnostic data from the Thomson scattering system and a model based on the electron heat transport equation describing the evolution of the electron temperature profile. Here, neural network surrogate models are leveraged to help improve the overall model prediction while staying within computation time constraints for real-time use. The observer algorithm is shown in offline tests to produce smooth profiles that are consistent with both the diagnostic data and the electron heat transport equation. When implemented into the real-time plasma control system, this observer will provide valuable information on the electron temperature profile to many potential feedback-control applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2025

Toroid Signal Processing Container with Redis Integration

This report presents the research, design, and implementation of a Toroid Signal Processing Container with Redis Integration, conducted during my internship assignment. The project focused on developing a modular signal processing sys- tem capable of performing baseline correction, droop compensation, and real- time data communication for beam diagnostic signals. Using Redis as a message broker and configuration manager, the system ensures modularity, scalability, and efficient inter-process communication. Signal correction algorithms, such as Asymmetric Least Squares (ALS) baseline smoothing and a numerical droop correction approach, were implemented and tested using Linac beam data. The results confirm that this system improves signal fidelity and supports real-time analysis requirements, offering valuable contributions to the field of beam instrumentation and data acquisition systems.

Bowers, Elliot [Cabrillo Coll.]↗

NASA NTRS1985

Algebraic grid generation using tensor product B-splines

Finite difference methods are more successful if the accompanying grid has lines which are smooth and nearly orthogonal. The development of an algorithm which produces such a grid when given the boundary description. Topological considerations in structuring the grid generation mapping are discussed. The concept of the degree of a mapping and how it can be used to determine what requirements are necessary if a mapping is to produce a suitable grid is examined. The grid generation algorithm uses a mapping composed of bicubic B-splines. Boundary coefficients are chosen so that the splines produce Schoenberg's variation diminishing spline approximation to the boundary. Interior coefficients are initially chosen to give a variation diminishing approximation to the transfinite bilinear interpolant of the function mapping the boundary of the unit square onto the boundary grid. The practicality of optimizing the grid by minimizing a functional involving the Jacobian of the grid generation mapping at each interior grid point and the dot product of vectors tangent to the grid lines is investigated. Grids generated by using the algorithm are presented.

Saunders, B. V.↗

NASA NTRS1987

Multigrid solution of inviscid transonic flow through rotating blade passages

A fast Euler solver for three dimensional inviscid transonic flow in rotating domains is described. The time dependent Euler equations are discretized spatially with finite volumes, and are advanced temporally with a multiple stage time stepping scheme. A dramatic increase in the rate of convergence for steady solutions is achieved with a multigrid algorithm that employs the multistage scheme as its smoothing procedure. The effectiveness of the multistage scheme as a multigrid driver is enhanced by the utilization of analytically determined combinations of the governing parameters.

Smith, Wayne A.↗

NASA NTRS1990

Adaptive box filters for removal of random noise from digital images

Adaptive box-filtering algorithms to remove random bit errors and to smooth noisy data have been developed. For both procedures, the standard deviation of those pixels within a local box surrounding each pixel is used. A series of two or three filters with decreasing box sizes can be run to clean up extremely noisy images and to remove bit errors near sharp edges. The second filter, for noise smoothing, is similar to the 'sigma filter' of Lee (1983). The technique effectively reduces speckle in radar images without eliminating fine details.

Eliason, Eric M.↗

NASA NTRS1991

Surface reconstruction from scattered data through pruning of unstructured grids

This paper describes an algorithm for reconstructing a surface from a randomly digitized object. Scan data (treated as a cloud of points) is first tesselated out to its convex hull using Delaunay triangulation. The line-of-sight between each surface point and the scanning device is traversed, and any tetrahedra which are pierced by it are removed. The remaining tetrahedra form an approximate solid model of the scanned object. Due to the inherently limited resolution of any scan, this algorithm requires two additional procedures to produce a smooth, polyhedral surface: one process removes long, narrow tetrahedra which span indentations in the surface between digitized points; the other smooths sharp edges. The results for a moderately resolved sample body and a highly resolved aircraft are displayed.

Maksymiuk, C. M.↗

NASA NTRS1992

Data reduction using cubic rational B-splines

A geometric method is proposed for fitting rational cubic B-spline curves to data that represent smooth curves including intersection or silhouette lines. The algorithm is based on the convex hull and the variation diminishing properties of Bezier/B-spline curves. The algorithm has the following structure: it tries to fit one Bezier segment to the entire data set and if it is impossible it subdivides the data set and reconsiders the subset. After accepting the subset the algorithm tries to find the longest run of points within a tolerance and then approximates this set with a Bezier cubic segment. The algorithm uses this procedure repeatedly to the rest of the data points until all points are fitted. It is concluded that the algorithm delivers fitting curves which approximate the data with high accuracy even in cases with large tolerances.

Chou, Jin J.↗

NASA NTRS1993

The implementation of a lossless data compression module in an advanced orbiting system: Analysis and development

Data compression has been proposed for several flight missions as a means of either reducing on board mass data storage, increasing science data return through a bandwidth constrained channel, reducing TDRSS access time, or easing ground archival mass storage requirement. Several issues arise with the implementation of this technology. These include the requirement of a clean channel, onboard smoothing buffer, onboard processing hardware and on the algorithm itself, the adaptability to scene changes and maybe even versatility to the various mission types. This paper gives an overview of an ongoing effort being performed at Goddard Space Flight Center for implementing a lossless data compression scheme for space flight. We will provide analysis results on several data systems issues, the performance of the selected lossless compression scheme, the status of the hardware processor and current development plan.

Yeh, Pen-Shu↗

NASA NTRS1993

Stochastic Parameters in Lunar Laser Ranging

This oral presentation describes the techniques, algorithms, and results of incorporatng a Kalman-smoothing technique into the square-root information filter when estimating deterministic and stochastic parameters relating to Earth, the Moon, and the lunar and planetary ephemerides.

lunar laser ranging ephemerides stochastic paramet↗

NASA NTRS2019

Towards Resilient Autonomous Navigation of Drones

Robots and particularly drones are especially useful in exploring extreme environments that pose hazards to humans. To ensure safe operations in these situations, usually perceptually degraded and without good GNSS, it is critical to have a reliable and robust state estimation solution. The main body of literature in robot state estimation focuses on developing complex algorithms favoring accuracy. Typically, these approaches rely on a strong underlying assumption: the main estimation engine will not fail during operation. In contrast, we propose an architecture that pursues robustness in state estimation by considering redundancy and heterogeneity in both sensing and estimation algorithms. The architecture is designed to expect and detect failures and adapt the behavior of the system to ensure safety. To this end, we present HeRO (Heterogeneous Redundant Odometry): a stack of estimation algorithms running in parallel supervised by a resiliency logic. This logic carries out three main functions: a) perform confidence tests both in data quality and algorithm health; b) re-initialize those algorithms that might be malfunctioning; c) generate a smooth state estimate by multiplexing the inputs based on their quality. The state and quality estimates are used by the guidance and control modules to adapt the mobility behaviors of the system. The validation and utility of the approach are shown with real experiments on a ying robot for the use case of autonomous exploration of subterranean environments, with particular results from the STIX event of the DARPA Subterranean Challenge.

Agha-mohammadi, Ali-akbar↗

DOE OSTI2025

Toroid Signal Processing Container with Redis Integration

Bowers, Elliot [Cabrillo Coll.; Fermilab]↗