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At least 451 records · Page 25

All sources NASA NTRS DOE OSTI

DOE OSTI2024

Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus

Abstract High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant’s allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.

Virology↗

DOE OSTI2022

Noisy intermediate-scale quantum algorithms

A universal fault-tolerant quantum computer that can efficiently solve problems such as integer factorization and unstructured database search requires millions of qubits with low error rates and long coherence times. While the experimental advancement toward realizing such devices will potentially take decades of research, noisy intermediate-scale quantum (NISQ) computers already exist. These computers are composed of hundreds of noisy qubits, i.e., qubits that are not error corrected, and therefore perform imperfect operations within a limited coherence time. In the search for achieving quantum advantage with these devices, algorithms have been proposed for applications in various disciplines spanning physics, machine learning, quantum chemistry, and combinatorial optimization. The overarching goal of such algorithms is to leverage the limited available resources to perform classically challenging tasks. In this review, a thorough summary of NISQ computational paradigms and algorithms is provided. The key structure of these algorithms and their limitations and advantages are discussed. Finally, a comprehensive overview of various benchmarking and software tools useful for programming and testing NISQ devices is additionally provided.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1975

Space vehicle Viterbi decoder

The design and fabrication of an extremely low-power, constraint-length 7, rate 1/3 Viterbi decoder brassboard capable of operating at information rates of up to 100 kb/s is presented. The brassboard is partitioned to facilitate a later transition to an LSI version requiring even less power. The effect of soft-decision thresholds, path memory lengths, and output selection algorithms on the bit error rate is evaluated. A branch synchronization algorithm is compared with a more conventional approach. The implementation of the decoder and its test set (including all-digital noise source) are described along with the results of various system tests and evaluations. Results and recommendations are presented.

Source record↗

NASA NTRS1981

Advances in Serial MSK modems

Lumped element as well as distributed element networks are used in the Serial MSK (SMSK) modems, for 20-1000 Mbps data rate range applications, whose design and performance characteristics are described. It is noted that the use of baseband conversion filters for the modulator yields good performance in many applications, with typical matched filter designs (structurally simple to implement) causing less than 0.5 dB bit error rate performance degradation. The SMSK modem technique begins with the use of a biphased shift-keyed modulator, and then employs passive filters to obtain the MSK signal.

Ryan, C. R.↗

DOE OSTI2023

Enter Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

Identifying small molecules (e.g., metabolites) is key towards driving scientific advancement in metabolomics, and gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none characterize the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending the traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g., fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1972

A very high speed hard decision sequential decoder.

Description of a 40-megabit-per-second hard decision sequential decoder which employs the fastest commercially available digital integrated circuits - MECL III. With this decoder an internal computational rate of 70,000,000 computations per second has been achieved. The computational efficiency of the decoding algorithm has been improved by incorporating two modifications to the Fano algorithm - namely, 'double quick threshold loosening' and 'diagonal steps.' On the basis of preliminary results, an output error rate of 0.00001 can be achieved with E sub b/N sub zero less than 5.4 dB at data rates up to 40 megabits per second. The very high internal operating speed of the decoder represents a factor of five increase in speed over any previous sequential decoder.

Gilhousen, K. S.↗

DOE OSTI2019

Flat gain C + L band using optical amplifiers for 200 × 14 Gbps DWDM system

This paper has shown the analysis of 200 channels dense wavelength division multiplexing (DWDM) system with the data rate of 14 Gbps for attaining the flat gain for the channel spectrum from 1520 to 1640 nm. Analysis has also extended with the power amplification of erbium–ytterbium co-doped optical amplifier (EYBCDOWA) and Raman optical amplifier for the transmission distance of 120 km to mitigate the effect of crosstalk and bit error rate (BER). Final analysis has also recommended that this proposed system is capable to deliver the flat gain of 19.5 dB with minor variation of 0.95 dB to maintain the acceptable dense communication for long distance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1994

Testing and Performance Analysis of a 650 Mbps QPPM Modem for Free-space Laser Communications

The testing and performance of a prototype modem developed at NASA Lewis Research Center for high-speed free-space direct detection optical communications is described. The testing was performed under laboratory conditions using computer control with specially developed test equipment that simulates free-space link conditions. The modem employs quaternary pulse position modulation (QPPM) at 325 Megabits per second (Mbps) on two optical channels, which are multiplexed to transmit a single 650 Mbps data stream. The measured results indicate that the receiver's automatic gain control (AGC), phased-locked-loop slot clock recovery, digital symbol clock recovery, matched filtering, and maximum likelihood data recovery circuits were found to have only 1.5 dB combined implementation loss during bit-error-rate (BER) performance measurements. Pseudo random bit sequences and real-time high quality video sources were used to supply 650 Mbps and 325 Mbps data streams to the modem. Additional testing revealed that Doppler frequency shifting can be easily tracked by the receiver, that simulated pointing errors are readily compensated for by the AGC circuits, and that channel timing skew affects the BER performance in an expected manner. Overall, the needed technologies for a high-speed laser communications modem were demonstrated.

Mortensen, Dale J.↗

NASA NTRS1995

Transfer function bounds on the performance of turbo codes

In this article we apply transfer function bounding techniques to obtain upper bounds on the bit-error rate for maximum likelihood decoding of turbo codes constructed with random permutations. These techniques are applied to two turbo codes with constraint length 3 and later extended to other codes. The performance predicted by these bounds is compared with simulation results. The bounds are useful in estimating the 'error floor' that is difficult to measure by simulation, and they provide insight on how to lower this floor. More refined bounds are needed for accurate performance measures at lower signal-to-noise ratios.

Divsalar, D.↗

DOE OSTI2018

Role of intensity fluctuations in quantum cryptography with coherent states

A new type of attack in quantum cryptography with coherent states is considered. This attack calls for only a possibility of changing (within some limits) the intensity of the states reaching a receiver. The critical quantum bit error rate (QBER) of the B92 protocol with a strong reference state is calculated for different limitations on intensity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1992

ATDRSS 300 MB/S modem program

The 300 Mbps modem was developed for direct application to the next generation high data rate Time Division Multiple Access (TDMA) communication system. This modem utilizes continuous phase modulation combined with a restricted range Reed-Solomon Codec to achieve a bandwidth efficiency of 3 bits/sec/hz. The constant envelope amplitude signal allows one to operate the power amplifier in its saturation mode without significant spectral regrowth or bit error rate degradation.

Ryan, Carl R.↗

NASA NTRS1989

Quantization effects in Viterbi decoding rate 1/n convolutional codes

A Viterbi decoder's performance loss due to quantizing data from the additive white Gaussian noise (AWGN) channel is studied. An optimal quantization scheme and branch metric calculation method are presented. The uniformly quantized channel capacity C(sub u)(q) is used to determine the smallest number of quantization bits q that does not cause a significant loss. The quantizer stepsize which maximizes C(sub u)(q) almost minimizes the decoder bit error rate (BER). However, a slightly larger stepsize is better, like the value that minimizes the Bhattacharyya bound. The range and renormalization of state metrics is analyzed, in particular for K = 15 decoders such as the Big Viterbi Decoder (BVD) for the Galileo mission. These results are required to design reduced hardware complexity Viterbi decoders with a negligible quantization loss.

Onyszchuk, I. M.↗

DOE OSTI2023

INVESTIGATION OF HUMAN RELIABILITY ANALYSIS METHODS FOR ANALYZING PRE-INITIATORS

As a type of human actions defined in human reliability analysis (HRA), pre-initiator refers to the human actions that may lead to the unavailability of systems, typically committed during maintenance, test, or calibration. This paper investigates representative HRA methods used for analyzing pre-initiators. The HRA methods are Technique for Human Error Rate Prediction (THERP), Korean Standard HRA (K-HRA) and Standard Plant Risk HRA (SPAR-H). In this paper, characteristics of each HRA method are compared for qualitative and quantification aspects. Two pre-initiators, i.e., a calibration task and a valve restoration task, are analyzed using the HRA methods to compare human error probabilities. Then, insights from the analysis and additional research requirements are discussed in this paper.

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

INVESTIGATION OF HUMAN RELIABILITY ANALYSIS METHODS FOR ANALYZING PRE-INITIATORS

99 GENERAL AND MISCELLANEOUS↗

DOE OSTI2023

High-fidelity parallel entangling gates on a neutral-atom quantum computer

The ability to perform entangling quantum operations with low error rates in a scalable fashion is a central element of useful quantum information processing. Neutral-atom arrays have recently emerged as a promising quantum computing platform, featuring coherent control over hundreds of qubits and any-to-any gate connectivity in a flexible, dynamically reconfigurable architecture. The main outstanding challenge has been to reduce errors in entangling operations mediated through Rydberg interactions. Here we report the realization of two-qubit entangling gates with 99.5% fidelity on up to 60 atoms in parallel, surpassing the surface-code threshold for error correction. Our method uses fast, single-pulse gates based on optimal control, atomic dark states to reduce scattering and improvements to Rydberg excitation and atom cooling. We benchmark fidelity using several methods based on repeated gate applications, characterize the physical error sources and outline future improvements. Finally, we generalize our method to design entangling gates involving a higher number of qubits, which we demonstrate by realizing low-error three-qubit gates. By enabling high-fidelity operation in a scalable, highly connected system, these advances lay the groundwork for large-scale implementation of quantum algorithms, error-corrected circuits and digital simulations.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2018

Coping with silent and fail-stop errors at scale by combining replication and checkpointing

This paper provides a model and an analytical study of replication as a technique to cope with silent errors, as well as a mixture of both silent and fail-stop errors on large-scale platforms. Compared with fail-stop errors that are immediately detected when they occur, silent errors require a detection mechanism. To detect silent errors, many application-specific techniques are available, either based on algorithms (e.g., ABFT), invariant preservation or data analytics, but replication remains the most transparent and least intrusive technique. We explore the right level (duplication, triplication or more) of replication for two frameworks: (i) when the platform is subject to only silent errors, and (ii) when the platform is subject to both silent and fail-stop errors. A higher level of replication is more expensive in terms of resource usage but enables to tolerate more errors and to even correct some errors, hence there is a trade-off to be found. Replication is combined with checkpointing and comes with two flavors: process replication and group replication. Process replication applies to message-passing applications with communicating processes. Each process is replicated, and the platform is composed of process pairs, or triplets. Group replication applies to black-box applications, whose parallel execution is replicated several times. The platform is partitioned into two halves (or three thirds). In both scenarios, results are compared before each checkpoint, which is taken only when both results (duplication) or two out of three results (triplication) coincide. Otherwise, one or more silent errors have been detected, and the application rolls back to the last checkpoint, as well as when fail-stop errors have struck. We provide a detailed analytical study for all of these scenarios, with formulas to decide, for each scenario, the optimal parameters as a function of the error rate, checkpoint cost, and platform size. We also report a set of extensive simulation results that nicely corroborates the analytical model.

Checkpointing↗

NASA NTRS1991

Design of a communications system for multiple telemetry data channels operating simultaneously with a coherent turn-around ranging channel

This paper presents a simple technique to design a phase-modulated residual carrier communications link for optimum performance. The emphasis is on two data channels which are operated simultaneously with a ranging signal. The data channels employ PCM/PM and PCM/PSK/PM modulation schemes for high and low data rate channels, respectively. The technique proposed here selects the optimum (1) subcarrier frequency to minimize the interference between the two data channels, and (2) modulation indices for optimum balance of power between the two telemetry data channels and the coherent turn around ranging channel. The selected set of optimum modulation indices will allow for the specified bit error rate (BER) degradations in the two data channels. Although this technique is proposed to optimize the performance degradation for two data channels, generalizations can be made for more than two data channels.

Nguyen, Tien M.↗

NASA NTRS1996

CW Interference Effects on High Data Rate Transmission Through the ACTS Wideband Channel

Satellite communications channels are susceptible to various sources of interference. Wideband channels have a proportionally greater probability of receiving interference than narrowband channels. NASA's Advanced Communications Technology Satellite (ACTS) includes a 900 MHz bandwidth hardlimiting transponder which has provided an opportunity for the study of interference effects of wideband channels. A series of interference tests using two independent ACTS ground terminals measured the effects of continuous-wave (CW) uplink interference on the bit-error rate of a 220 Mbps digitally modulated carrier. These results indicate the susceptibility of high data rate transmissions to CW interference and are compared to results obtained with a laboratory hardware-based system simulation and a computer simulation.

Kerczewski, Robert J.↗