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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2014

Adaptable Iterative and Recursive Kalman Filter Schemes

Nonlinear filters are often very computationally expensive and usually not suitable for real-time applications. Real-time navigation algorithms are typically based on linear estimators, such as the extended Kalman filter (EKF) and, to a much lesser extent, the unscented Kalman filter. The Iterated Kalman filter (IKF) and the Recursive Update Filter (RUF) are two algorithms that reduce the consequences of the linearization assumption of the EKF by performing N updates for each new measurement, where N is the number of recursions, a tuning parameter. This paper introduces an adaptable RUF algorithm to calculate N on the go, a similar technique can be used for the IKF as well.

Zanetti, Renato↗
NASA NTRS2010

Adaptive Control of Flexible Structures Using Residual Mode Filters

Flexible structures containing a large number of modes can benefit from adaptive control techniques which are well suited to applications that have unknown modeling parameters and poorly known operating conditions. In this paper, we focus on a direct adaptive control approach that has been extended to handle adaptive rejection of persistent disturbances. We extend our adaptive control theory to accommodate troublesome modal subsystems of a plant that might inhibit the adaptive controller. In some cases the plant does not satisfy the requirements of Almost Strict Positive Realness. Instead, there maybe be a modal subsystem that inhibits this property. This section will present new results for our adaptive control theory. We will modify the adaptive controller with a Residual Mode Filter (RMF) to compensate for the troublesome modal subsystem, or the Q modes. Here we present the theory for adaptive controllers modified by RMFs, with attention to the issue of disturbances propagating through the Q modes. We apply the theoretical results to a flexible structure example to illustrate the behavior with and without the residual mode filter. We have proposed a modified adaptive controller with a residual mode filter. The RMF is used to accommodate troublesome modes in the system that might otherwise inhibit the adaptive controller, in particular the ASPR condition. This new theory accounts for leakage of the disturbance term into the Q modes. A simple three-mode example shows that the RMF can restore stability to an otherwise unstable adaptively controlled system. This is done without modifying the adaptive controller design.

Balas, Mark J.↗
NASA NTRS1999

A Robust and Scalable Software Library for Parallel Adaptive Refinement on Unstructured Meshes

The design and implementation of Pyramid, a software library for performing parallel adaptive mesh refinement (PAMR) on unstructured meshes, is described. This software library can be easily used in a variety of unstructured parallel computational applications, including parallel finite element, parallel finite volume, and parallel visualization applications using triangular or tetrahedral meshes. The library contains a suite of well-designed and efficiently implemented modules that perform operations in a typical PAMR process. Among these are mesh quality control during successive parallel adaptive refinement (typically guided by a local-error estimator), parallel load-balancing, and parallel mesh partitioning using the ParMeTiS partitioner. The Pyramid library is implemented in Fortran 90 with an interface to the Message-Passing Interface (MPI) library, supporting code efficiency, modularity, and portability. An EM waveguide filter application, adaptively refined using the Pyramid library, is illustrated.

Lou, John Z.↗
DOE OSTI2020

Target Detection via Cognitive Radars Using Change-Point Detection, Learning, and Adaptation

Many radar detection algorithms that assume a stationary environment (clutter) have been proposed and analyzed over the years. However, in practice, changes in the nonstationary environment can perturb the parameters of the clutter distribution, or even alter the clutter distribution family, which can greatly deteriorate the target detection capability. To avoid such potential performance degradation, cognitive radar systems are envisioned which are required to rapidly realize the nonstationarity, accurately learn the new characteristics of the environments, and adaptively update the detector. In this paper, aiming to develop a fully cognitive radar for target detection in nonstationary environments, we propose a unifying framework that integrates (i) change-point detection of clutter distributions by using a data-driven cumulative sum (CUSUM) algorithm and its extended version, (ii) learning/identification of clutter distribution by applying sparse theory and kernel density estimation methods, and (iii) adaptive target detection by automatically modifying the likelihood-ratio test and corresponding detection threshold. Further, with extensive numerical examples, we demonstrate the achieved improvements in detection performance due to the proposed framework in comparison to a nonadaptive case, an adaptive matched filter (AMF) method, and the clairvoyant case. Herein, we also use Wilcoxon rank-sum tests to evaluate the statistical significance of the performance improvements

42 ENGINEERING↗
NASA NTRS1998

Application of Least Mean Square Algorithms to Spacecraft Vibration Compensation

This paper describes the application of the Least Mean Square (LMS) algorithm in tandem with the Filtered-X Least Mean Square algorithm for controlling a science instrument's line-of-sight pointing. Pointing error is caused by a periodic disturbance and spacecraft vibration. A least mean square algorithm is used on-orbit to produce the transfer function between the instrument's servo-mechanism and error sensor. The result is a set of adaptive transversal filter weights tuned to the transfer function. The Filtered-X LMS algorithm, which is an extension of the LMS, tunes a set of transversal filter weights to the transfer function between the disturbance source and the servo-mechanism's actuation signal. The servo-mechanism's resulting actuation counters the disturbance response and thus maintains accurate science instrumental pointing. A simulation model of the Upper Atmosphere Research Satellite is used to demonstrate the algorithms.

Woodard , Stanley E.↗
NASA NTRS1987

Speckle noise reduction of 1-look SAR imagery

Speckle noise is inherent to synthetic aperture radar (SAR) imagery. Since the degradation of the image due to this noise results in uncertainties in the interpretation of the scene and in a loss of apparent resolution, it is desirable to filter the image to reduce this noise. In this paper, an adaptive algorithm based on the calculation of the local statistics around a pixel is applied to 1-look SAR imagery. The filter adapts to the nonstationarity of the image statistics since the size of the blocks is very small compared to that of the image. The performance of the filter is measured in terms of the equivalent number of looks (ENL) of the filtered image and the resulting resolution degradation. The results are compared to those obtained from different techniques applied to similar data. The local adaptive filter (LAF) significantly increases the ENL of the final image. The associated loss of resolution is also lower than that for other commonly used speckle reduction techniques.

Nathan, Krishna S.↗
NASA NTRS1986

Design of adaptive control systems by means of self-adjusting transversal filters

The design of closed-loop adaptive control systems based on nonparametric identification was addressed. Implementation is by self-adjusting Least Mean Square (LMS) transversal filters. The design concept is Model Reference Adaptive Control (MRAC). Major issues are to preserve the linearity of the error equations of each LMS filter, and to prevent estimation bias that is due to process or measurement noise, thus providing necessary conditions for the convergence and stability of the control system. The controlled element is assumed to be asymptotically stable and minimum phase. Because of the nonparametric Finite Impulse Response (FIR) estimates provided by the LMS filters, a-priori information on the plant model is needed only in broad terms. Following a survey of control system configurations and filter design considerations, system implementation is shown here in Single Input Single Output (SISO) format which is readily extendable to multivariable forms. In extensive computer simulation studies the controlled element is represented by a second-order system with widely varying damping, natural frequency, and relative degree.

Merhav, S. J.↗
NASA NTRS1983

Adaptive control of a flexible beam using least square lattice filters

This paper presents an indirect adaptive control scheme for the control of flexible structures using recursive least square lattice filters. The identification scheme uses lattice filters which provide an on-line estimate of the number of modes, mode shapes and modal amplitudes. These modes are coupled and a transformation to decouple them in order to obtain the natural modes is presented. The decoupled modal amplitude time series are then used in an equation error identification scheme to identify the model parameters in an autoregressive moving average (ARMA) form. The control is based on modal pole placement scheme with the objective of vibration suppression. The control gains are calculated based on the identified ARMA parameters. Before using the identified parameters for control, detailed testing and validation procedures are carried out on the identified parameters. The full adaptive control scheme is demonstrated using the simulation for the 12 foot free-free beam apparatus at NASA Langley Research Center.

Sundararajan, N.↗
NASA NTRS1973

RFI analysis applied to the TDRSS system

The effect of radio frequency interference (RFI) on the proposed Tracking and Data Relay Satellite System (TDRSS) was assessed. The method of assessing RFI was to create a discrete emitter listing containing all the required parameters of transmitters in the applicable VHF and UHF frequency bands. The transmitter and spacecraft receiver characteristics were used to calculate the RFI contribution due to each emitter. The individual contributions were summed to obtain the total impact in the operational bandwidth. Using an as yet incomplete emitter base, it is concluded that the 136- to 137-MHz band should be used by TDRSS rather than the whole 136- to 138-MHz band because of the higher interference levels in the 137- to 138 MHz band. Even when restricting the link to 136 to 137 MHz, the existing link design is marginal, and it is recommended that interference reduction units, such as the adaptive digital filter, be incorporated in the TDRSS ground station.

Jenny, J. A.↗
NASA NTRS1975

High resolution frequency analysis techniques with application to the redshift experiment

High resolution frequency analysis methods, with application to the gravitational probe redshift experiment, are discussed. For this experiment a resolution of .00001 Hz is required to measure a slowly varying, low frequency signal of approximately 1 Hz. Major building blocks include fast Fourier transform, discrete Fourier transform, Lagrange interpolation, golden section search, and adaptive matched filter technique. Accuracy, resolution, and computer effort of these methods are investigated, including test runs on an IBM 360/65 computer.

Decher, R.↗
NASA NTRS1984

Active Control Technology Experience with the Space Shuttle in the Landing Regime

The shuttle program took on the challenge of providing a manual landing capability for an operational vehicle returning from orbit. Some complex challenges were encountered in developing the longitudinal flying qualities required to land the orbiter manually in an operational environmental. Approach and landing test flights indicated a tendency for pilot-induced oscillation near landing. Changes in the operational procedures reduced the difficulty of the landing task, and an adaptive stick filter was incorporated to reduce the severity of any pilot-induced oscillatory motions. Fixed-base, moving-base, and in-flight simulations were used for the evaluations, and in general, flight simulation was the only reliable means of assessing the low-speed longitudinal flying qualities problems. Overall, the orbiter control system and operational procedures have produced a good capability for routinely performing precise landings in a large, unpowered vehicle with a low lift-to-drag ratio.

Powers, B. G.↗
NASA NTRS1985

Low-speed longitudinal orbiter qualities

The shuttle program took on the challenge of providing a manual landing capability for an operational vehicle returning from orbit. Some complex challenges were encountered in developing the longitudinal flying qualities required to land the orbiter manually in an operational environment. Approach and landing test flights indicated a tendency for pilot-induced oscillation near landing. Changes in the operational procedures reduced the difficulty of the landing task, and an adaptive stick filter was incorporated to reduce the severity of any pilot-induced oscillatory motions. Fixed-base, movingbase, and in-flight simulations were used for the evaluations, and in general, flight simulation was the only reliable means of assessing the low-speed longitudinal flying qualities problems. Overall, the orbiter control system and operational procedures have produced a good capability to routinely perform precise landings with a large, unpowered vehicle with a low lift-to-drag ratio.

Powers, B. G.↗
NASA NTRS1985

Active control technology experience with the Space Shuttle in the landing regime

The shuttle program took on the challenge of providing a manual landing capability for an operational vehicle returning from orbit. Some complex challenges were encountered in developing the longitudinal flying qualities required to land the orbiter manually in an operational environment. Approach and landing test flights indicated a tendency for pilot-induced oscillation near landing. Changes in the operational procedures reduced the difficulty of the landing task, and an adaptive stick filter was incorporated to reduce the severity of any pilot-induced oscillatory motions. Fixed-base, moving-base, and in-flight simulations were used for the evaluations, and in general, flight simulation has been the only reliable means of assessing the low-speed longitudinal flying qualities problems. Overall, the orbiter control system and operational procedures have produced a good capability for routinely performing precise landings in a large, unpowered vehicle with a low lift-to-drag ratio.

Powers, B. G.↗
NASA NTRS1987

Frequency domain laser velocimeter signal processor: A new signal processing scheme

A new scheme for processing signals from laser velocimeter systems is described. The technique utilizes the capabilities of advanced digital electronics to yield a smart instrument that is able to configure itself, based on the characteristics of the input signals, for optimum measurement accuracy. The signal processor is composed of a high-speed 2-bit transient recorder for signal capture and a combination of adaptive digital filters with energy and/or zero crossing detection signal processing. The system is designed to accept signals with frequencies up to 100 MHz with standard deviations up to 20 percent of the average signal frequency. Results from comparative simulation studies indicate measurement accuracies 2.5 times better than with a high-speed burst counter, from signals with as few as 150 photons per burst.

Meyers, James F.↗
NASA NTRS1986

Space Shuttle longitudinal landing flying qualities

The Space Shuttle program took on the challenge of providing a manual landing capability for an operational vehicle returning from orbit. Some complex challenges were encountered in developing the longitudinal flying qualities required to land the Orbiter manually in an operational environment. Approach and landing test flights indicated a tendency of pilot-induced oscillation near landing. Changes in the operational procedures reduced the difficulty of the landing task, and an adaptive stick filter was incorporated to reduce the severity of any pilot-induced oscillatory motions. Fixed-base, moving-base, and in-flight simulations were used for the evaluations. Overall, the Orbiter control system and operational procedures produced a good capability to perform routinely precise landings with a large, unpowered vehicle that has a low lift-to-drag ratio.

Powers, B. G.↗