Fast Alignment Research Articles

Fast and accurate short-read alignment with hybrid hash-tree data structure

Rapidly increasing the amount of short-read data generated by NGSs (new-generation sequencers) calls for the development of fast and accurate read alignment programs. The programs based on the hash table (BLAST) and Burrows-Wheeler transform (bwa-mem) are used, and the latter is known to give superior performance. We here present a new algorithm, a hybrid of hash table and suffix tree, which we designed to speed up the alignment of short reads against large reference sequences such as the human genome. The total turnaround time for processing one human genome sample (read depth of 30) is just 31 min with our system while that was more than 25 h with bwa-mem/gatk. The time for the aligner alone is 28 min for our system but around 2 h for bwa-mem. Our new algorithm is 4.4 times faster than bwa-mem while achieving similar accuracy. Variant calling and other downstream analyses after the alignment can be done with open-source tools such as SAMtools and Genome Analysis Toolkit (gatk) packages, as well as our own fast variant caller, which is well parallelized and much faster than gatk.

A Fast and Robust Range Alignment Method for ISAR Imaging Based on a Deep Learning Network and Regional Multi-Scale Minimum Entropy Method

In inverse synthetic aperture radar (ISAR) imaging, range alignment (RA) is crucial for translational compensation. To address the need for rapidity and accuracy in the RA process, a fast and robust range alignment method is proposed based on a deep learning network and minimum entropy (ME) method. The proposed method consists primarily of two components: the CNN-RNN attention mechanism network (CRAN) architecture and the regional multi-scale minimum entropy (RMSME) method. The main distinction of this method from existing approaches lies in its utilization of a deep learning network for rapid coarse alignment, followed by the search for minimum entropy within local regions at multiple scales. The integration strategy effectively addresses the current challenges of poor generalization in deep learning networks and low efficiency in the traditional ME method. The experimental results of simulation data indicate that the proposed method achieves the best range alignment performance compared to RNN, CRAN, and the traditional ME method. The experimental results of the measured data further validate the practicality of the proposed method. This research provides reference significance for the joint application of deep learning and traditional methods in the RA process.

Adaptive positioning of large-scale aircraft components using a simplified image-based visual servoing via online measurement of ball-head center

In digital alignment systems, ensuring fast and accurate alignment between the ball head on large aircraft components and the ball socket of the positioner is the key to aircraft assembly efficiency and quality. Image-based visual servoing is one of the most advanced techniques with high efficiency and positioning accuracy, but it does not account for measuring the ball-head position. Moreover, variable target positions, similar feature interference, and poor lighting conditions pose great challenges to the fast and robust visual measurement of ball-head position. Hence, an online visual measurement method is introduced to measure the absolute position of the ball head in real time. An adaptive region of interest extraction algorithm and an improved edge following method are introduced to extract the elliptical contour from the ball-head image, and ellipse detection is achieved through a simple triplet selection algorithm. A geometric model based on the perspective projection of the sphere is established for estimating the ball-head center. Then, the simplified image-based visual servoing method is developed by constantizing the image Jacobian matrix. Next, an adaptive positioning method of large-scale aircraft components with multiple ball heads is proposed from a holistic perspective. Finally, experiments show that the final positioning accuracy of each ball head in the X/Y plane is less than ± 0.05 mm, with an efficiency almost ten times that of the conventional method. After adaptive adjustment, the position and angle errors of the simulated component are reduced within 0.6 mm and 0.3°, respectively.

In-motion fine alignment algorithm for AUV based on improved extended state observer and Kalman filter

Abstract Achieving fast initial alignment has always been a major challenge for autonomous underwater vehicle navigation, especially in motion. During the fine alignment process, traditional algorithms often face the slow convergence of the azimuth misalignment angle. To solve this problem, this paper proposes a fast alignment algorithm based on the improved extended state observer (ESO) and Kalman filter. Specifically, since the application potential of ESO in fine alignment has not been fully explored by previous studies, this paper introduces the improved ESO through the in-depth research of traditional ESO. The obtained improved ESO is then combined with Kalman filter to constitute the proposed fast alignment algorithm. The algorithm first uses Kalman filter to estimate the two horizontal misalignment angles. Once the horizontal angles estimation of Kalman filter tends to be stable, the improved ESO is used to estimate the azimuth misalignment angle. Simulation and lake test show the proposed algorithm has excellent performance of in-motion alignment. The comparative analysis shows that the algorithm significantly improves the convergence speed of azimuth alignment angle.

Terrestrial Laser Scanning for Heliostat Surface Shape Determination and Canting Errors Correction

Canting errors, resulting from misalignments of heliostat facets, pose a significant challenge to solar power plants' efficiency. Traditional methods of alignment are time-consuming and costly. This paper presents an innovative approach utilizing Terrestrial Laser Scanning (TLS) technology for precise and fast heliostat alignment. The method involves point cloud processing, paraboloid fitting, and heliostat facet’s screw adjustments. A case study at Thémis solar tower demonstrates the effectiveness, resulting in a significant improvement in optical quality and power output.

Novel metagenomics analysis of stony coral tissue loss disease.

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.

Fast multiple sequence alignment via multi-armed bandits.

Multiple sequence alignment is an important problem in computational biology with applications that include phylogeny and the detection of remote homology between protein sequences. UPP is a popular software package that constructs accurate multiple sequence alignments for large datasets based on ensembles of hidden Markov models (HMMs). A computational bottleneck for this method is a sequence-to-HMM assignment step, which relies on the precise computation of probability scores on the HMMs. In this work, we show that we can speed up this assignment step significantly by replacing these HMM probability scores with alternative scores that can be efficiently estimated. Our proposed approach utilizes a multi-armed bandit algorithm to adaptively and efficiently compute estimates of these scores. This allows us to achieve similar alignment accuracy as UPP with a significant reduction in computation time, particularly for datasets with long sequences. The code used to produce the results in this paper is available on GitHub at: https://github.com/ilanshom/adaptiveMSA.

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.

Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

Current Sheet Alignment in Oblique Black Hole Magnetospheres: A Black Hole Pulsar?

We study the magnetospheric evolution of a nonaccreting spinning black hole (BH) with an initially inclined split monopole magnetic field by means of 3D general relativistic magnetohydrodynamic simulations. This serves as a model for a neutron star (NS) collapse or a BH–NS merger remnant after the inherited magnetosphere has settled into a split monopole field creating a striped wind. We show that the initially inclined split monopolar current sheet aligns over time with the BH equatorial plane. The inclination angle evolves exponentially toward alignment, with an alignment timescale that is inversely proportional to the square of the BH angular velocity, where higher spin results in faster alignment. Furthermore, magnetic reconnection in the current sheet leads to exponential decay of event-horizon-penetrating magnetic flux with nearly the same timescale for all considered BH spins. In addition, we present relations for the BH mass and spin in terms of the period and alignment timescale of the striped wind. The explored scenario of a rotating, aligning, and reconnecting current sheet can potentially lead to multimessenger electromagnetic counterparts to a gravitational-wave event due to the acceleration of particles powering high-energy radiation, plasmoid mergers resulting in coherent radio signals, and pulsating emission due to the initial misalignment of the BH magnetosphere.

An optimized multisource acquisition and registration workflow for imaging guided ventricular tachycardia ablation

Abstract Background Catheter ablation is a cornerstone treatment for scar-related ventricular arrhythmias arising in patients affected by structural heart disease. Imaging integration with electroanatomical mapping (EAM) suites for ventricular tachycardia (VT) ablation procedural guidance is an established step for advanced substrate characterization and treatment. Purpose To compare and validate different approaches for intraprocedural multisource imaging registration and integration with EAM suites for VT ablation guidance. Methods Thirty consecutive patients prospectively enrolled in the ongoing VOYAGE clinical trial for imaging guided/aided VT ablation at our center were retrospectively analyzed. Multidetector computed tomography (MDCT) and late gadolinium enhancement cardiac magnetic resonance (LGE-CMR) imaging was performed before procedure. MDCT and LGE-CMR images were both acquired during end-expiratory breath hold. Same cardiac cycle phase images were used. Wide band LGE-CMR was acquired in case of a cardiac implantable electronic device was present to reduce artifacts. Images were imported in ADAS3D software. MDCT and CMR images were manually registered using established anatomical landmarks (left ventricle outflow tract, left ventricle apex, papillary muscles, left and right ventricle junction), were then respectively processed for aortic/ventricular anatomical reconstruction and myocardial characterization and then imported in CARTO3 electroanatomical mapping suite for procedural guidance. Registration between EAM and imaging was either performed with ascending aorta fast anatomical mapping (FAM) and 3D landmark alignment with aortic MDCT or via intracardiac echocardiography (ICE) left ventricle (LV) chamber segmentation and 3D landmark alignment with ventricular MDCT. ICE segmentation was also obtained for every case regardless of aortic FAM. Surface match between ICE and MDCT LV chamber reconstructions was calculated for method comparison. Results All 30 patients had an ICE segmentation of the LV, with a mean of 15,66±4,89 contours. Aortic FAM was obtained and used for aortic MDCT registration in 10 subjects. LV ICE was instead used for imaging alignment in 20 subjects. When compared to aortic FAM, LV ICE to LV MDCT alignment achieved lower average surface distance (3,86±1,41 mm vs 8,884±6,77 mm; p<0,001), lower minimum surface distance (0,002±0,03 vs 0,07±0,06; p= 0,001) and lower maximum surface distance (14,16±4,37 vs 22,93±11,10; p<0,001). Conclusion An optimized workflow consisting of ICE LV chamber segmentation was superior in terms of 3D surface distance to aortic FAM reconstruction to obtain reliable multisource imaging registration for MDCT/CMR guided/aided VT ablation.

An Improved Initial Alignment Method Based on SE2(3)/EKF for SINS/GNSS Integrated Navigation System with Large Misalignment Angles.

This paper proposes an improved initial alignment method for a strap-down inertial navigation system/global navigation satellite system (SINS/GNSS) integrated navigation system with large misalignment angles. Its methodology is based on the three-dimensional special Euclidean group and extended Kalman filter (SE2(3)/EKF) and aims to overcome the challenges of achieving fast alignment under large misalignment angles using traditional methods. To accurately characterize the state errors of attitude, velocity, and position, these elements are constructed as elements of a Lie group. The nonlinear error on the Lie group can then be well quantified. Additionally, a group vector mixed error model is developed, taking into account the zero bias errors of gyroscopes and accelerometers. Using this new error definition, a GNSS-assisted SINS dynamic initial alignment algorithm is derived, which is based on the invariance of velocity and position measurements. Simulation experiments demonstrate that the alignment method based on SE2(3)/EKF can achieve a higher accuracy in various scenarios with large misalignment angles, while the attitude error can be rapidly reduced to a lower level.

Fast Alignment and Calibration of Rotational Inertial System Based on Bilinear Embedding

Fast Alignment and Calibration of Rotational Inertial System Based on Bilinear Embedding

Dynamic rail wear measurement: integration of RTK GNSS, IMU, and laser

Currently, laser sensors are widely utilized in railway systems for monitoring rail wear. However, the lack or insufficiency of rail waist data poses a challenge to accurately match profiles and calculate wear. In this paper, we propose a novel approach for dynamic rail wear monitoring that comprises three major modules: a filtering methodology to smooth rail profile data, fine compensation to calibrate the angle distortion, and fast profile alignment. Initially, the AF technique and Kalman filter are applied to reconstruct the profile. This is followed by integrating real-time kinematic global navigation satellite system, inertial measurement unit, and laser to precisely correct the rail profile dynamic distortion. Additionally, genetic algorithms-least squares method is used for rapid determination of the R20mm center of the profile. Rigorous testing and trials have demonstrated that our proposed approach achieves precision as low as 0.03 mm with significant potential in dynamic rail wear monitoring.

A fast photometric image alignment algorithm with row and column means

This paper introduces an astronomical image alignment algorithm. This algorithm uses the means of the rows and columns of the original image for alignment, and finds the optimal offset corresponding to the maximum similarity by comparing different offsets between images. The similarity is evaluated by the standard deviation of the quotient divided by the means. This paper also discusses the theoretical feasibility of this algorithm. Through practical testing, it has been confirmed that the algorithm is fast and robust.

Accurate global and local 3D alignment of cryo-EM density maps using local spatial structural features.

Advances in cryo-electron microscopy (cryo-EM) imaging technologies have led to a rapidly increasing number of cryo-EM density maps. Alignment and comparison of density maps play a crucial role in interpreting structural information, such as conformational heterogeneity analysis using global alignment and atomic model assembly through local alignment. Here, we present a fast and accurate global and local cryo-EM density map alignment method called CryoAlign, that leverages local density feature descriptors to capture spatial structure similarities. CryoAlign is a feature-based cryo-EM map alignment tool, in which the employment of feature-based architecture enables the rapid establishment of point pair correspondences and robust estimation of alignment parameters. Extensive experimental evaluations demonstrate the superiority of CryoAlign over the existing methods in terms of both alignment accuracy and speed.

Simcryocluster: a semantic similarity clustering method of cryo-EM images by adopting contrastive learning

BackgroundCryo-electron microscopy (Cryo-EM) plays an increasingly important role in the determination of the three-dimensional (3D) structure of macromolecules. In order to achieve 3D reconstruction results close to atomic resolution, 2D single-particle image classification is not only conducive to single-particle selection, but also a key step that affects 3D reconstruction. The main task is to cluster and align 2D single-grain images into non-heterogeneous groups to obtain sharper single-grain images by averaging calculations. The main difficulties are that the cryo-EM single-particle image has a low signal-to-noise ratio (SNR), cannot manually label the data, and the projection direction is random and the distribution is unknown. Therefore, in the low SNR scenario, how to obtain the characteristic information of the effective particles, improve the clustering accuracy, and thus improve the reconstruction accuracy, is a key problem in the 2D image analysis of single particles of cryo-EM.ResultsAiming at the above problems, we propose a learnable deep clustering method and a fast alignment weighted averaging method based on frequency domain space to effectively improve the class averaging results and improve the reconstruction accuracy. In particular, it is very prominent in the feature extraction and dimensionality reduction module. Compared with the classification method based on Bayesian and great likelihood, a large amount of single particle data is required to estimate the relative angle orientation of macromolecular single particles in the 3D structure, and we propose that the clustering method shows good results.ConclusionsSimcryoCluster can use the contrastive learning method to perform well in the unlabeled high-noise cryo-EM single particle image classification task, making it an important tool for cryo-EM protein structure determination

Relaying Fast In-Flight Alignment Method Based on Adaptive Multiconstraints

Relaying Fast In-Flight Alignment Method Based on Adaptive Multiconstraints

TMP: Temporal Motion Propagation for Online Video Super-Resolution.

Online video super-resolution (online-VSR) highly relies on an effective alignment module to aggregate temporal information, while the strict latency requirement makes accurate and efficient alignment very challenging. Though much progress has been achieved, most of the existing online-VSR methods estimate the motion fields of each frame separately to perform alignment, which is computationally redundant and ignores the fact that the motion fields of adjacent frames are correlated. In this work, we propose an efficient Temporal Motion Propagation (TMP) method, which leverages the continuity of motion field to achieve fast pixel-level alignment among consecutive frames. Specifically, we first propagate the offsets from previous frames to the current frame, and then refine them in the neighborhood, significantly reducing the matching space and speeding up the offset estimation process. Furthermore, to enhance the robustness of alignment, we perform spatial-wise weighting on the warped features, where the positions with more precise offsets are assigned higher importance. Experiments on benchmark datasets demonstrate that the proposed TMP method achieves leading online-VSR accuracy as well as inference speed. The source code of TMP can be found at https://github.com/xtudbxk/TMP.

A Novel LOD Rendering Method with Multi-level Structure Keeping Mesh Simplification and Fast Texture Alignment for Realistic 3D Models

A Novel LOD Rendering Method with Multi-level Structure Keeping Mesh Simplification and Fast Texture Alignment for Realistic 3D Models

A Fast In-Motion Alignment Method for INS/DVL in Rough Sea Conditions

A Fast In-Motion Alignment Method for INS/DVL in Rough Sea Conditions