Alignment Algorithm Research Articles

Multiplet-Assisted Peak Alignment for 1H NMR-Based Metabolomics.

NMR-based metabolomics aims at recovering biological information by comparing spectral data from samples of biological interest and appropriate controls. Any statistical analysis performed on the data matrix relies on the proper peak alignment to produce meaningful results. Through the last decades, several peak alignment algorithms have been proposed, as well as alternatives like spectral binning or strategies for annotation and quantification, the latter depending on reference databases. Most of the alignment algorithms, mainly based on segmentation of the spectra, present limitations for regions with peak overlap or cases of frequency order exchange. Here, we present our multiplet-assisted peak alignment algorithm, a new methodology that consists of aligning peaks by matching multiplet profiles of f1 traces from J-resolved spectra. A correspondence matrix with the linked f1 traces is built, and multivariate data analysis can be performed on it to obtain useful information from the data, overcoming the issues of peak overlap and frequency crossovers. Statistical total correlation spectroscopy can be applied on the matrix as well, toward a better identification of molecules of interest. The results can be queried on one-dimensional (1D) 1H databases or can be directly coupled to our previously published Chemical Shift Multiplet Database.

A novel local alignment algorithm for Multilayer networks

Multilayer Network (MN) is a complex network comprising a set of graphs (also referred to as layers) interconnected by edges or interlayer edges (or inter-edges) linking the nodes of different layers. In biology, a MN may model interactions among diseases, genes, and drugs, only using its structure. Recently, there has been a growing interest in comparing two MNs by revealing local regions of similarity as a counterpart of Network Alignment algorithms (NA) for simple networks. However, classical algorithms for NA such as Local NA (LNA) cannot be applied on multilayer networks, since they are not able to deal with interlayer edges. Therefore, there is a need for the introduction of novel algorithms. In this paper, we present MuLan, an algorithm for the local alignment of multilayer networks. MuLan is based on the building of a multilayer alignment graph starting from a set of seed nodes. Then it analyses such a graph by revealing conserved regions. We first show as proof of concept the performances of MuLaN on a set of synthetic multilayer networks. Then, we used as a case study a real multilayer network in the biomedical domain. Our results show that MuLaN can build high-quality alignments and can extract knowledge about the aligned multilayer networks. MuLaN is available at https://github.com/pietrocinaglia/mulan.

Ultra-wide field and new wide field composite retinal image registration with AI-enabled pipeline and 3D distortion correction algorithm

PurposeThis study aimed to compare a new Artificial Intelligence (AI) method to conventional mathematical warping in accurately overlaying peripheral retinal vessels from two different imaging devices: confocal scanning laser ophthalmoscope (cSLO) wide-field images and SLO ultra-wide field images.MethodsImages were captured using the Heidelberg Spectralis 55-degree field-of-view and Optos ultra-wide field. The conventional mathematical warping was performed using Random Sample Consensus—Sample and Consensus sets (RANSAC-SC). This was compared to an AI alignment algorithm based on a one-way forward registration procedure consisting of full Convolutional Neural Networks (CNNs) with Outlier Rejection (OR CNN), as well as an iterative 3D camera pose optimization process (OR CNN + Distortion Correction [DC]). Images were provided in a checkerboard pattern, and peripheral vessels were graded in four quadrants based on alignment to the adjacent box.ResultsA total of 660 boxes were analysed from 55 eyes. Dice scores were compared between the three methods (RANSAC-SC/OR CNN/OR CNN + DC): 0.3341/0.4665/4784 for fold 1-2 and 0.3315/0.4494/4596 for fold 2-1 in composite images. The images composed using the OR CNN + DC have a median rating of 4 (out of 5) versus 2 using RANSAC-SC. The odds of getting a higher grading level are 4.8 times higher using our OR CNN + DC than RANSAC-SC (p < 0.0001).ConclusionPeripheral retinal vessel alignment performed better using our AI algorithm than RANSAC-SC. This may help improve co-localizing retinal anatomy and pathology with our algorithm.

The Value and Realization of Choral Conducting Talent Cultivation for Music Teachers in the Context of Deep Learning

Abstract Focusing on virtual chorus, this paper analyzes the training process of VR technology and music choral conductor talents. After the construction of the online data platform, the image splicing, image alignment and image fusion algorithms of VR technology are integrated with the Harris corner detection improvement algorithm to realize the virtual chorus in the context of deep learning. The influence of family support and school aesthetic education on various dimensions of psychological needs for talent cultivation was modeled using structural equation modeling. Based on the data of music teachers using VR technology, mediated effect analysis and total effect analysis were conducted to analyze the factors influencing the use of imagery with VR technology. ANOVA was utilized to compare the data on the four dimensions of rhythmic memory, pitch, melodic memory, and listening ability to verify the effectiveness of VR technology on music teachers’ talent cultivation. The total effect analysis showed that the order of the influence of each influencing factor on the intention to use was 0.361&gt;social influence 0.263&gt;perceived usefulness 0.263&gt;perceived ease of use 0.251&gt;computer self-efficacy 0.169&gt;convenience conditions 0.162&gt;job relevance 0.134&gt;simulation 0.075.

Lambda CI Binding to Related Phage Operator Sequences Validates Alignment Algorithm and Highlights the Importance of Overlooked Bonds.

Bacteriophage λ's CI repressor protein controls a genetic switch between the virus's lysogenic and lytic lifecycles, in part, by selectively binding to six different DNA sequences within the phage genome-collectively referred to as operator sites. However, the minimal level of information needed for CI to recognize and specifically bind these six unique-but-related sequences is unclear. In a previous study, we introduced an algorithm that extracts the minimal direct readout information needed for λ-CI to recognize and bind its six binding sites. We further revealed direct readout information shared among three evolutionarily related lambdoid phages: λ-phage, Enterobacteria phage VT2-Sakai, and Stx2 converting phage I, suggesting that the λ-CI protein could bind to the operator sites of these other phages. In this study, we show that λ-CI can indeed bind the other two phages' cognate binding sites as predicted using our algorithm, validating the hypotheses from that paper. We go on to demonstrate the importance of specific hydrogen bond donors and acceptors that are maintained despite changes to the nucleobase itself, and another that has an important role in recognition and binding. This in vitro validation of our algorithm supports its use as a tool to predict alternative binding sites for DNA-binding proteins.

SAMNA: accurate alignment of multiple biological networks based on simulated annealing.

Proteins are important parts of the biological structures and encode a lot of biological information. Protein-protein interaction network alignment is a model for analyzing proteins that helps discover conserved functions between organisms and predict unknown functions. In particular, multi-network alignment aims at finding the mapping relationship among multiple network nodes, so as to transfer the knowledge across species. However, with the increasing complexity of PPI networks, how to perform network alignment more accurately and efficiently is a new challenge. This paper proposes a new global network alignment algorithm called Simulated Annealing Multiple Network Alignment (SAMNA), using both network topology and sequence homology information. To generate the alignment, SAMNA first generates cross-network candidate clusters by a clustering algorithm on a k-partite similarity graph constructed with sequence similarity information, and then selects candidate cluster nodes as alignment results and optimizes them using an improved simulated annealing algorithm. Finally, the SAMNA algorithm was experimented on synthetic and real-world network datasets, and the results showed that SAMNA outperformed the state-of-the-art algorithm in biological performance.

A deep learning approach to the automatic detection of alignment errors in cryo-electron tomographic reconstructions

Electron tomography is an imaging technique that allows for the elucidation of three-dimensional structural information of biological specimens in a very general context, including cellular in situ observations. The approach starts by collecting a set of images at different projection directions by tilting the specimen stage inside the microscope. Therefore, a crucial preliminary step is to precisely define the acquisition geometry by aligning all the tilt images to a common reference. Errors introduced in this step will lead to the appearance of artifacts in the tomographic reconstruction, rendering them unsuitable for the sample study. Focusing on fiducial-based acquisition strategies, this work proposes a deep-learning algorithm to detect misalignment artifacts in tomographic reconstructions by analyzing the characteristics of these fiducial markers in the tomogram. In addition, we propose an algorithm designed to detect fiducial markers in the tomogram with which to feed the classification algorithm in case the alignment algorithm does not provide the location of the markers. This open-source software is available as part of the Xmipp software package inside of the Scipion framework, and also through the command-line in the standalone version of Xmipp.

Experimental Study on Wave Motion Response Characteristics of Large Amphibious Aircraft

To master the motion response of an amphibious aircraft under regular waves of drifting and anchoring, a 1:8.5 scaled model test of an amphibious aircraft under regular waves was carried out, and the test device and acquisition method were designed. Through experiments, the wave response characteristics of the drifting and anchoring states were obtained, which provided technical support for the design of the IRS initial alignment algorithm for large amphibious aircraft.

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.

Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0.

Transcatheter aortic valve implantation with commissural alignment

Transcatheter aortic valve implantation (TAVI) is commonly accepted method of treatment of aortic stenosis in most patients with currently increasing number of TAVI procedures. Patients after TAVI frequently have indications for percutaneous coronary intervention (PCI) that might be technically challenging due to the presence of transcatheter valve. Compromising coronary ostia involves such issues as design of the prosthesis and its position in the aortic root with respect to the commissures of native aortic valve. Since TAVI with commissural alignment can mitigate risk of compromising coronary ostia, this option should be considered while planning TAVI, especially in younger patients with coronary atherosclerosis and relatively high probability of PCI in the future. The algorithm of commissural alignment in clinical practice of TAVI up to date has been proposed only for several transcatheter heart valves reported in this paper.

WFA-GPU: gap-affine pairwise read-alignment using GPUs.

Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic programming (DP), impose impractical computational requirements to align long and noisy sequences like those produced by PacBio and Nanopore technologies. The recently proposed wavefront alignment (WFA) algorithm paves the way for more efficient alignment tools, improving time and memory complexity over previous methods. However, high-performance computing (HPC) platforms require efficient parallel algorithms and tools to exploit the computing resources available on modern accelerator-based architectures. This paper presents WFA-GPU, a GPU (graphics processing unit)-accelerated tool to compute exact gap-affine alignments based on the WFA algorithm. We present the algorithmic adaptations and performance optimizations that allow exploiting the massively parallel capabilities of modern GPU devices to accelerate the alignment computations. In particular, we propose a CPU-GPU co-design capable of performing inter-sequence and intra-sequence parallel sequence alignment, combining a succinct WFA-data representation with an efficient GPU implementation. As a result, we demonstrate that our implementation outperforms the original multi-threaded WFA implementation by up to 4.3× and up to 18.2× when using heuristic methods on long and noisy sequences. Compared to other state-of-the-art tools and libraries, the WFA-GPU is up to 29× faster than other GPU implementations and up to four orders of magnitude faster than other CPU implementations. Furthermore, WFA-GPU is the only GPU solution capable of correctly aligning long reads using a commodity GPU. WFA-GPU code and documentation are publicly available at https://github.com/quim0/WFA-GPU.

Automatic Recognition of Blood Cell Images with Dense Distributions Based on a Faster Region-Based Convolutional Neural Network

In modern clinical medicine, the important information of red blood cells, such as shape and number, is applied to detect blood diseases. However, the automatic recognition problem of single cells and adherent cells always exists in a densely distributed medical scene, which is difficult to solve for both the traditional detection algorithms with lower recognition rates and the conventional networks with weaker feature extraction capabilities. In this paper, an automatic recognition method of adherent blood cells with dense distribution is proposed. Based on the Faster R-CNN, the balanced feature pyramid structure, deformable convolution network, and efficient pyramid split attention mechanism are adopted to automatically recognize the blood cells under the conditions of dense distribution, extrusion deformation, adhesion and overlap. In addition, the Align algorithm for region of interest also contributes to improving the accuracy of recognition results. The experimental results show that the mean average precision of cell detection is 0.895, which is 24.5% higher than that of the original network model. Compared with the one-stage mainstream networks, the presented network has a stronger feature extraction capability. The proposed method is suitable for identifying single cells and adherent cells with dense distribution in the actual medical scene.

G-Aligner: a graph-based feature alignment method for untargeted LC–MS-based metabolomics

BackgroundLiquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature alignment algorithms to observe the intensity variations across runs. However, most of the existing feature alignment methods focus more on accurate retention time correction, while underestimating the importance of feature matching. None of the existing methods can comprehensively consider feature correspondences among all runs and achieve optimal matching.ResultsTo comprehensively analyze feature correspondences among runs, we propose G-Aligner, a graph-based feature alignment method for untargeted LC–MS data. In the feature matching stage, G-Aligner treats features and potential correspondences as nodes and edges in a multipartite graph, considers the multi-run feature matching problem an unbalanced multidimensional assignment problem, and provides three combinatorial optimization algorithms to find optimal matching solutions. In comparison with the feature alignment methods in OpenMS, MZmine2 and XCMS on three public metabolomics benchmark datasets, G-Aligner achieved the best feature alignment performance on all the three datasets with up to 9.8% and 26.6% increase in accurately aligned features and analytes, and helped all comparison software obtain more accurate results on their self-extracted features by integrating G-Aligner to their analysis workflow. G-Aligner is open-source and freely available at https://github.com/CSi-Studio/G-Aligner under a permissive license. Benchmark datasets, manual annotation results, evaluation methods and results are available at https://doi.org/10.5281/zenodo.8313034ConclusionsIn this study, we proposed G-Aligner to improve feature matching accuracy for untargeted metabolomics LC–MS data. G-Aligner comprehensively considered potential feature correspondences between all runs, converting the feature matching problem as a multidimensional assignment problem (MAP). In evaluations on three public metabolomics benchmark datasets, G-Aligner achieved the highest alignment accuracy on manual annotated and popular software extracted features, proving the effectiveness and robustness of the algorithm.

Development and Research of a System for Automatic Recognition of the Digits Yemeni Dialect of Arabic Speech Using Neural Networks

The article describes the results of research on the development and testing of an automatic speech recognition system (SAR) in Arabic numerals using artificial neural networks. Sound recordings (speech signals) of the Arabic Yemeni dialect recorded in the Republic of Yemen were used for the research. SAR is an isolated system of recognition of whole words, it is implemented in two modes: "speaker-dependent system" (the same speakers are used for training and testing the system) and "speaker-independent system" (the speakers used for training the system differ from those used for testing it). In the process of speech recognition, the speech signal is cleared of noise using filters, then the signal is pre-localized, processed and analyzed by the Hamming window (a time alignment algorithm is used to compensate for differences in pronunciation). Informative features are extracted from the speech signal using mel-frequency cepstral coefficients. The developed SAR provides high accuracy of the recognition of Arabic numerals of the Yemeni dialect – 96.2 % (for a speaker-dependent system) and 98.8 % (for a speaker-independent system).

Spatial-linked alignment tool (SLAT) for aligning heterogenous slices

Spatially resolved omics technologies reveal the spatial organization of cells in various biological systems. Here we propose SLAT (Spatially-Linked Alignment Tool), a graph-based algorithm for efficient and effective alignment of spatial slices. Adopting a graph adversarial matching strategy, SLAT is the first algorithm capable of aligning heterogenous spatial data across distinct technologies and modalities. Systematic benchmarks demonstrate SLAT’s superior precision, robustness, and speed over existing state-of-the-arts. Applications to multiple real-world datasets further show SLAT’s utility in enhancing cell-typing resolution, integrating multiple modalities for regulatory inference, and mapping fine-scale spatial-temporal changes during development. The full SLAT package is available at https://github.com/gao-lab/SLAT.

Low-variance Forward Gradients using Direct Feedback Alignment and momentum

Supervised learning in deep neural networks is commonly performed using error backpropagation. However, the sequential propagation of errors during the backward pass limits its scalability and applicability to low-powered neuromorphic hardware. Therefore, there is growing interest in finding local alternatives to backpropagation. Recently proposed methods based on forward-mode automatic differentiation suffer from high variance in large deep neural networks, which affects convergence. In this paper, we propose the Forward Direct Feedback Alignment algorithm that combines Activity-Perturbed Forward Gradients with Direct Feedback Alignment and momentum. We provide both theoretical proofs and empirical evidence that our proposed method achieves lower variance than forward gradient techniques. In this way, our approach enables faster convergence and better performance when compared to other local alternatives to backpropagation and opens a new perspective for the development of online learning algorithms compatible with neuromorphic systems.

Variable-Speed Frequency-Hopping Signal Sorting: Spectrogram Is Sufficient

In this paper, we present a novel signal sorting method aimed at reducing the impact of interference and noise while achieving blind detection and accurate sorting of a variable-speed frequency-hopping communication system. To achieve this, we combine spectrogram analysis with an innovative sorting approach. First, we generate the spectrogram of the received signal, and then employ a morphology filter to effectively eliminate noise and sweep frequency interference from the spectrogram. Subsequently, we identify and mark connected domains in the spectrogram, from which we extract the duration data to create a dataset specifically for separating fixed-frequency interference. Furthermore, we propose a specialized time alignment algorithm designed to accommodate the unique characteristics of variable-speed frequency-hopping signals, enabling precise sorting of variable-speed frequency-hopping signals. Through rigorous comparative evaluations against existing algorithms, we demonstrate that our proposed approach provides superior accuracy by offering a clearer representation of the time–frequency situation of the received signals. The proposed method provides a high correct sorting probability which is equal to 0.8 when signal-to-noise ratio is 0 dB and reaches 1 when signal-to-noise ratio reaches over 12 dB. In comparison, the correct sorting probability of the comparison algorithm is far inferior to the proposed algorithm.

GCNA-Cluster: A Gene Co-Expression Network Alignment to Cluster Cancer Patients Algorithm for Identifying Subtypes of Pancreatic Ductal Adenocarcinoma.

Cancer heterogeneity makes it necessary to use different treatment strategies for patients with the same pathological features. Accurate identification of cancer subtypes is a crucial step in this approach. The current studies of pancreatic ductal adenocarcinoma (PDAC) subtypes mainly focus on single genes and ignore the synergistic effects of genes. Here we proposed a network alignment algorithm GCNA-cluster to cluster patients based on gene co-expression networks. We constructed weighted gene co-expression networks for patients and aligned the networks of two patients to estimate the similarity of patients and their cancer subtypes. A scoring function is defined to measure the network alignment result and the score can indicate the similarity between patients. Then, the patients are clustered based on their similarities. We validated the accuracy of the algorithm on the GEO-PDAC dataset with real labels, and the experimental results show that the GCNA-cluster algorithm has better results than classical cancer subtyping algorithms. In addition, the GCNA-cluster algorithm applied to the TCGA-PDAC dataset identified two subtypes based on the Silhouette Coefficient. Biomarkers identified for the PDAC subtypes hint to cell growth, cell cycle or apoptosis as targets for new therapeutic strategies.

Multi-Attribute Method (MAM) Analytical Workflow for Biotherapeutic Protein Characterization from Process Development to QC.

The multi-attribute method (MAM) has emerged significantly in recent years to support biotherapeutic protein characterization from process development to the QC environment. MAM is a liquid chromatography mass spectrometry (LC-MS) based peptide mapping approach, which combines the benefits from liquid chromatography coupled to high resolution accurate mass mass spectrometry (LC-HRAM MS), enabling direct assessment of protein sequence and product quality attributes with site specificity. These product quality attributes may impact efficacy, safety, stability, and process robustness. MAM is intended to replace conventional analytical approaches as it offers a more streamlined strategy for parallel monitoring of multiple attributes in a single analysis with high sensitivity and confidence, and ultimately supports more robust Quality by Design (QbD) approaches and faster decision cycles for biotherapeutic development. MAM consists of three main stages. The first stage is sample digestion, which typically entails proteolytic digestion of the protein. The second stage is reversed-phase chromatographic separation of the generated peptides and detection by HRAM MS in two phases. During MAM Phase I (discovery phase), data-dependent acquisition (DDA) MS/MS is performed to enable confident identification of peaks and development of a peptide workbook. During MAM Phase II (monitoring phase), full MS acquisition is only carried out for the monitoring of predefined product quality attributes (PQAs). The third stage is data processing, which entails analysis and reporting for each of the two phases including evaluation of sequence coverage, assessment of PQAs and peptide workbook creation during phase I, and targeted monitoring of predefined product attributes and new peak detection (NPD) during phase II. The latter is a comparative analysis that uses a base peak alignment algorithm to determine any non-monitored differences between the LC-MS chromatograms of a test sample and a reference standard. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: In-solution sample digestion Alternate Protocol: Automated sample digestion Basic Protocol 2: Reversed-phase chromatographic separation and detection by HRAM-MS (RPLC-HRAM MS) Basic Protocol 3: Data processing and reporting.

Deep learning-assisted construction of three-dimensional face midsagittal plane based on point clouds

Objective: To establish an intelligent registration algorithm under the framework of original-mirror alignment algorithm to construct three-dimensional(3D) facial midsagittal plane automatically. Dynamic Graph Registration Network (DGRNet) was established to realize the intelligent registration, in order to provide a reference for clinical digital design and analysis. Methods: Two hundred clinical patients without significant facial deformities were collected from October 2020 to October 2022 at Peking University School and Hospital of Stomatology. The DGRNet consists of constructing the feature vectors of key points in point original and mirror point clouds (X, Y), obtaining the correspondence of key points, and calculating the rotation and translation by singular value decomposition. Original and mirror point clouds were registrated and united. The principal component analysis (PCA) algorithm was used to obtain the DGRNet alignment midsagittal plane. The model was evaluated based on the coefficient of determination (R2) index for the translation and rotation matrix of test set. The angle error was evaluated on the 3D facial midsagittal plane constructed by the DGRNet alignment midsagittal plane and the iterative closet point(ICP) alignment midsagittal plane for 50 cases of clinical facial data. Results: The average angle error of the DGRNet alignment midsagittal plane and ICP alignment midsagittal plane was 1.05°±0.56°, and the minimum angle error was only 0.13°. The successful detection rate was 78%(39/50) within 1.50° and 90% (45/50)within 2.00°. Conclusions: This study proposes a new solution for the construction of 3D facial midsagittal plane based on the DGRNet alignment method with intelligent registration, which can improve the efficiency and effectiveness of treatment to some extent.