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Staritzbichler, René, Edoardo Sarti, Emily Yaklich, Antoniya Aleksandrova, Marcus Stamm, Kamil Khafizov e Lucy R. Forrest. "Refining pairwise sequence alignments of membrane proteins by the incorporation of anchors". PLOS ONE 16, n. 4 (30 aprile 2021): e0239881. http://dx.doi.org/10.1371/journal.pone.0239881.
Testo completoAbstract (sommario):
The alignment of primary sequences is a fundamental step in the analysis of protein structure, function, and evolution, and in the generation of homology-based models. Integral membrane proteins pose a significant challenge for such sequence alignment approaches, because their evolutionary relationships can be very remote, and because a high content of hydrophobic amino acids reduces their complexity. Frequently, biochemical or biophysical data is available that informs the optimum alignment, for example, indicating specific positions that share common functional or structural roles. Currently, if those positions are not correctly matched by a standard pairwise sequence alignment procedure, the incorporation of such information into the alignment is typically addressed in an ad hoc manner, with manual adjustments. However, such modifications are problematic because they reduce the robustness and reproducibility of the aligned regions either side of the newly matched positions. Previous studies have introduced restraints as a means to impose the matching of positions during sequence alignments, originally in the context of genome assembly. Here we introduce position restraints, or “anchors” as a feature in our alignment tool AlignMe, providing an aid to pairwise global sequence alignment of alpha-helical membrane proteins. Applying this approach to realistic scenarios involving distantly-related and low complexity sequences, we illustrate how the addition of anchors can be used to modify alignments, while still maintaining the reproducibility and rigor of the rest of the alignment. Anchored alignments can be generated using the online version of AlignMe available at www.bioinfo.mpg.de/AlignMe/.
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Wheeler, Travis J., e John D. Kececioglu. "Multiple alignment by aligning alignments". Bioinformatics 23, n. 13 (1 luglio 2007): i559—i568. http://dx.doi.org/10.1093/bioinformatics/btm226.
Testo completo
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WANG, YI, e KUO-BIN LI. "MULTIPLE SEQUENCE ALIGNMENT USING AN EXHAUSTIVE AND GREEDY ALGORITHM". Journal of Bioinformatics and Computational Biology 03, n. 02 (aprile 2005): 243–55. http://dx.doi.org/10.1142/s021972000500103x.
Testo completoAbstract (sommario):
We describe an exhaustive and greedy algorithm for improving the accuracy of multiple sequence alignment. A simple progressive alignment approach is employed to provide initial alignments. The initial alignment is then iteratively optimized against an objective function. For any working alignment, the optimization involves three operations: insertions, deletions and shuffles of gaps. The optimization is exhaustive since the algorithm applies the above operations to all eligible positions of an alignment. It is also greedy since only the operation that gives the best improving objective score will be accepted. The algorithms have been implemented in the EGMA (Exhaustive and Greedy Multiple Alignment) package using Java programming language, and have been evaluated using the BAliBASE benchmark alignment database. Although EGMA is not guaranteed to produce globally optimized alignment, the tests indicate that EGMA is able to build alignments with high quality consistently, compared with other commonly used iterative and non-iterative alignment programs. It is also useful for refining multiple alignments obtained by other methods.
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Sampson, Jennifer, John Krogstie e Csaba Veres. "Ontology Alignment Quality". International Journal of Information System Modeling and Design 2, n. 3 (luglio 2011): 1–23. http://dx.doi.org/10.4018/jismd.2011070101.
Testo completoAbstract (sommario):
Recently semantic web technologies, such as ontologies, have been proposed as key enablers for integrating heterogeneous data schemas in business and governmental systems. Algorithms designed to align different but related ontologies have become necessary as differing ontologies proliferate. The process of ontology alignment seeks to find corresponding entities in a second ontology with the same or the closest meaning for each entity in a single ontology. This research is motivated by the need to provide tools and techniques to support the task of validating ontology alignment statements, since it cannot be guaranteed that the results from automated tools are accurate. The authors present a framework for understanding ontology alignment quality and describe how AlViz, a tool for visual ontology alignment, may be used to improve the quality of alignment results. An experiment was undertaken to test the claim that AlViz supports the task of validating ontology alignments. A promising result found that the tool has potential for identifying missing alignments and for rejecting false alignments.
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Bigvand, Anahita Mansouri, Te Bu e Anoop Sarkar. "Joint Prediction of Word Alignment with Alignment Types". Transactions of the Association for Computational Linguistics 5 (dicembre 2017): 501–14. http://dx.doi.org/10.1162/tacl_a_00076.
Testo completoAbstract (sommario):
Current word alignment models do not distinguish between different types of alignment links. In this paper, we provide a new probabilistic model for word alignment where word alignments are associated with linguistically motivated alignment types. We propose a novel task of joint prediction of word alignment and alignment types and propose novel semi-supervised learning algorithms for this task. We also solve a sub-task of predicting the alignment type given an aligned word pair. In our experimental results, the generative models we introduce to model alignment types significantly outperform the models without alignment types.
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González Laffitte, Marcos E., e Peter F. Stadler. "Progressive Multiple Alignment of Graphs". Algorithms 17, n. 3 (11 marzo 2024): 116. http://dx.doi.org/10.3390/a17030116.
Testo completoAbstract (sommario):
The comparison of multiple (labeled) graphs with unrelated vertex sets is an important task in diverse areas of applications. Conceptually, it is often closely related to multiple sequence alignments since one aims to determine a correspondence, or more precisely, a multipartite matching between the vertex sets. There, the goal is to match vertices that are similar in terms of labels and local neighborhoods. Alignments of sequences and ordered forests, however, have a second aspect that does not seem to be considered for graph comparison, namely the idea that an alignment is a superobject from which the constituent input objects can be recovered faithfully as well-defined projections. Progressive alignment algorithms are based on the idea of computing multiple alignments as a pairwise alignment of the alignments of two disjoint subsets of the input objects. Our formal framework guarantees that alignments have compositional properties that make alignments of alignments well-defined. The various similarity-based graph matching constructions do not share this property and solve substantially different optimization problems. We demonstrate that optimal multiple graph alignments can be approximated well by means of progressive alignment schemes. The solution of the pairwise alignment problem is reduced formally to computing maximal common induced subgraphs. Similar to the ambiguities arising from consecutive indels, pairwise alignments of graph alignments require the consideration of ambiguous edges that may appear between alignment columns with complementary gap patterns. We report a simple reference implementation in Python/NetworkX intended to serve as starting point for further developments. The computational feasibility of our approach is demonstrated on test sets of small graphs that mimimc in particular applications to molecular graphs.
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SALEM, SAEED, MOHAMMED J. ZAKI e CHRISTOPHER BYSTROFF. "ITERATIVE NON-SEQUENTIAL PROTEIN STRUCTURAL ALIGNMENT". Journal of Bioinformatics and Computational Biology 07, n. 03 (giugno 2009): 571–96. http://dx.doi.org/10.1142/s0219720009004205.
Testo completoAbstract (sommario):
Structural similarity between proteins gives us insights into their evolutionary relationships when there is low sequence similarity. In this paper, we present a novel approach called SNAP for non-sequential pair-wise structural alignment. Starting from an initial alignment, our approach iterates over a two-step process consisting of a superposition step and an alignment step, until convergence. We propose a novel greedy algorithm to construct both sequential and non-sequential alignments. The quality of SNAP alignments were assessed by comparing against the manually curated reference alignments in the challenging SISY and RIPC datasets. Moreover, when applied to a dataset of 4410 protein pairs selected from the CATH database, SNAP produced longer alignments with lower rmsd than several state-of-the-art alignment methods. Classification of folds using SNAP alignments was both highly sensitive and highly selective. The SNAP software along with the datasets are available online at
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Erkomaishvili, David. "Alliance Index: Measuring Alignments in International Relations". International Studies 56, n. 1 (gennaio 2019): 28–45. http://dx.doi.org/10.1177/0020881718825079.
Testo completoAbstract (sommario):
Orthodox approaches developed by Alliance Theory to study alliances are characterized by static and state-centric focus, which exposes theory’s logical limitations. In contrast, modern alignments are marked by continuous oscillations. Alignment stability—according to orthodox Alliance Theory—may be altogether misleading for the explanation of behaviour in alignment. This article theoretically re-conceptualizes the key notion of the orthodox Alliance Theory—the concept of alliance. Building on the basis of isolated but significant fragments of advanced research, the theoretical essence of the Alliance Theory is adjusted to encompass alignment process. Importantly, such a re-calibration bears in on an overlooked element common to all alignments—fluidity. Theoretical modification resulted in two important outcomes. First, the change of the vantage point in explaining alignments theoretically extends the orthodox Alliance Theory’s traditionally limited applicability, which excluded subnational and non-state actors. Second, the change allowed reviewing the essence of alignments focusing on a persistently evolving process, rather than on alignments’ institutional image. Sustained realignment, upgrading or downgrading of cooperative relations between actors and concurrent alignment to rival parties is no more confusing in explaining alignments. The article develops an alignment index and calculates it for the post-Soviet space.
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Chen, Zhenxian, Yongchang Gao, Shibin Chen, Qida Zhang, Zhifeng Zhang, Jing Zhang, Xuan Zhang e Zhongmin Jin. "Biomechanics and wear comparison between mechanical and kinematic alignments in total knee arthroplasty". Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine 232, n. 12 (21 novembre 2018): 1209–18. http://dx.doi.org/10.1177/0954411918811855.
Testo completoAbstract (sommario):
The uses of mechanical and kinematic alignments in total knee arthroplasty are under debate in recent clinical investigations. In this study, the differences in short-term biomechanics and long-term wear volume between mechanical and kinematic alignments in total knee arthroplasty were investigated, based on a subject-specific musculoskeletal multi-body dynamics model during walking gait simulation. An increase of 8.2% in the peak tibiofemoral medial contact force, a posterior contact translation by maximum 4.7 mm and a decrease of 5.5% in the wear volume after a 10-million-cycle simulation were predicted in the kinematic alignment, compared with the mechanical alignment. Nevertheless, the tibiofemoral contact mechanics, the range of motions and the long-term wear were not markedly different between mechanical and kinematic alignments. Furthermore, the mechanical alignment with a posterior tibial slope similar to that under the kinematic alignment was found to produce similar anterior–posterior translation and the range of motion, and an approximate wear volume, compared with the kinematic alignment. The ligament forces under the kinematic alignment were influenced markedly by as much as 25%, 50% and 77% for the medial collateral ligament, lateral collateral ligament and posterior cruciate ligament forces, respectively. And, a maximum increase of 40% for patellofemoral contact force was predicted under the kinematic alignment. These findings suggest that the kinematic alignment is an alternative alignment principle but no marked advantages in biomechanics and wear to the mechanical alignment. The adverse effects of the kinematic alignment on patella loading and soft tissue forces should be noticed.
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Li, Wanli, Wenqi Wu, Jinling Wang e Liangqing Lu. "A Fast SINS Initial Alignment Scheme for Underwater Vehicle Applications". Journal of Navigation 66, n. 2 (30 luglio 2012): 181–98. http://dx.doi.org/10.1017/s0373463312000318.
Testo completoAbstract (sommario):
To achieve high Strapdown Inertial Navigation System (SINS) alignment accuracy within a short period of time is still a challenging issue for underwater vehicles. In this paper, a new SINS initial alignment scheme aided by the velocity derived from Doppler Velocity Log (DVL) is proposed to solve this problem. In the stage of the coarse alignment, the velocity of DVL is employed to reduce the impact of the linear motion. With a backtracking framework, the fine alignment runs with the data recorded during the process of the coarse alignment and thus will speed up the overall alignment process. In addition, by using this new scheme, it is equivalent to length the alignment time for both coarse and fine alignments, so the accuracy of the alignments will be improved. In order to reduce the volume of the data that has to be recorded, a new model for SINS fine alignment is derived in the inertial reference frame which makes it feasible for real time applications. The experimental results are presented for both unaided static and in-motion alignment using DVL aiding. It is clearly shown that the proposed method meets the requirement of SINS alignment for underwater vehicles.
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Schmidtbauer, Kelly A., E. Russell Esposito e Jason M. Wilken. "Ankle–foot orthosis alignment affects running mechanics in individuals with lower limb injuries". Prosthetics and Orthotics International 43, n. 3 (14 febbraio 2019): 316–24. http://dx.doi.org/10.1177/0309364619826386.
Testo completoAbstract (sommario):
Background: Individuals with severe lower extremity injuries often require ankle–foot orthoses to return to normal activities. Ankle–foot orthoses alignment is a key consideration during the clinical fitting process and may be particularly important during dynamic activities such as running. Objective: To investigate how 3° changes in sagittal plane ankle–foot orthoses alignment affect running mechanics. Study design: Controlled laboratory study. Methods: Twelve participants with unilateral lower limb injury ran overground and lower extremity running mechanics were assessed. Participants wore their passive-dynamic ankle–foot orthoses in three alignments: clinically fit neutral, 3° plantarflexed from clinically fit neutral, and 3° dorsiflexed from clinically fit neutral. Results: The 3° changes in sagittal alignment significantly influenced ankle mechanics during running. The plantarflexed alignment significantly decreased the peak ankle plantarflexor moment, peak knee extensor moment, and peak ankle and knee power absorption and generation compared to more dorsiflexed alignments. Alignment also altered footstrike angle, with dorsiflexed alignments associated with a more dorsiflexed footstrike pattern and plantarflexed alignments toward a more plantarflexed footstrike pattern. However, alignment did not influence loading rate. Conclusion: Small changes in ankle–foot orthoses alignment significantly altered running mechanics, including footstrike angle, and knee extensor moments. Understanding how ankle–foot orthoses design parameters affect running mechanics may aid the development of evidence-based prescription guidelines and improve function for ankle–foot orthoses users who perform high-impact activities. Clinical relevance Understanding how ankle–foot orthoses alignment impacts biomechanics should be a consideration when fitting passive-dynamic devices for higher impact activities, such as running. Individual running styles, including footstrike patterns, may be affected by small changes in alignment.
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Och, Franz Josef, e Hermann Ney. "A Systematic Comparison of Various Statistical Alignment Models". Computational Linguistics 29, n. 1 (marzo 2003): 19–51. http://dx.doi.org/10.1162/089120103321337421.
Testo completoAbstract (sommario):
We present and compare various methods for computing word alignments using statistical or heuristic models. We consider the five alignment models presented in Brown, Della Pietra, Della Pietra, and Mercer (1993), the hidden Markov alignment model, smoothing techniques, and refinements. These statistical models are compared with two heuristic models based on the Dice coefficient. We present different methods for combining word alignments to perform a symmetrization of directed statistical alignment models. As evaluation criterion, we use the quality of the resulting Viterbi alignment compared to a manually produced reference alignment. We evaluate the models on the German-English Verbmobil task and the French-English Hansards task. We perform a detailed analysis of various design decisions of our statistical alignment system and evaluate these on training corpora of various sizes. An important result is that refined alignment models with a first-order dependence and a fertility model yield significantly better results than simple heuristic models. In the Appendix, we present an efficient training algorithm for the alignment models presented.
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Zhan, Qing, Yilei Fu, Qinghua Jiang, Bo Liu, Jiajie Peng e Yadong Wang. "SpliVert: A Protein Multiple Sequence Alignment Refinement Method Based on Splitting-Splicing Vertically". Protein & Peptide Letters 27, n. 4 (17 marzo 2020): 295–302. http://dx.doi.org/10.2174/0929866526666190806143959.
Testo completoAbstract (sommario):
Background: Multiple Sequence Alignment (MSA) is a fundamental task in bioinformatics and is required for many biological analysis tasks. The more accurate the alignments are, the more credible the downstream analyses. Most protein MSA algorithms realign an alignment to refine it by dividing it into two groups horizontally and then realign the two groups. However, this strategy does not consider that different regions of the sequences have different conservation; this property may lead to incorrect residue-residue or residue-gap pairs, which cannot be corrected by this strategy. Objective: In this article, our motivation is to develop a novel refinement method based on splitting- splicing vertically. Method: Here, we present a novel refinement method based on splitting-splicing vertically, called SpliVert. For an alignment, we split it vertically into 3 parts, remove the gap characters in the middle, realign the middle part alone, and splice the realigned middle parts with the other two initial pieces to obtain a refined alignment. In the realign procedure of our method, the aligner will only focus on a certain part, ignoring the disturbance of the other parts, which could help fix the incorrect pairs. Results: We tested our refinement strategy for 2 leading MSA tools on 3 standard benchmarks, according to the commonly used average SP (and TC) score. The results show that given appropriate proportions to split the initial alignment, the average scores are increased comparably or slightly after using our method. We also compared the alignments refined by our method with alignments directly refined by the original alignment tools. The results suggest that using our SpliVert method to refine alignments can also outperform direct use of the original alignment tools. Conclusion: The results reveal that splitting vertically and realigning part of the alignment is a good strategy for the refinement of protein multiple sequence alignments.
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Cefalo, Raffaela, Tatiana Sluga, Giulio Ossich e Roberto Roberti. "Assessment of Design Consistency for Two-Lane Rural Highways with Low Tortuosity Alignment". Sustainability 16, n. 3 (23 gennaio 2024): 987. http://dx.doi.org/10.3390/su16030987.
Testo completoAbstract (sommario):
One technique employed to enhance road safety involves assessing the alignment’s consistency. A prevalent measure of consistency is evaluating speed variations along the alignment. A key consideration in this assessment is determining the speed upon which the road alignment should be based. This research reveals that on two-lane rural highways with low tortuosity alignments, operating speeds on horizontal curves and tangents consistently exceeded not only the design speeds but also the maximum permissible design speed for the road category. Consequently, using the design speed to assess consistency on these roads is deemed impractical, and utilizing operating speed poses challenges due to speeds exceeding the maximum permissible limit. The objectives of this paper are twofold: to explore the relationship between design consistency and safety levels on two-lane rural highways with low tortuosity alignments (which have been insufficiently covered in research) and to propose speed-control measures to limit the maximum operating speed to the maximum permissible speed. The study findings suggest that on roads with a low tortuosity alignment, operating speeds depend much more on the general characteristics of the alignment (evaluated in the operating speed models through the desired speed). Further, assessing speed consistency is feasible only with a rigorous control of the maximum operating speed (desired speed). Additionally, a specific type of speed control is recommended, achieved by limiting the curvature change rate (CCR) of the road section based on the desired speed (environmental speed), whose evaluation becomes a crucial factor.
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Shu, Jian-Jun, Kian Yan Yong e Weng Kong Chan. "An Improved Scoring Matrix for Multiple Sequence Alignment". Mathematical Problems in Engineering 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/490649.
Testo completoAbstract (sommario):
The way for performing multiple sequence alignment is based on the criterion of the maximum-scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading to ambiguities in selecting the best alignment. This paper addresses this issue by introducing the concept of joint weight matrix to eliminate the randomness in selecting the best multiple sequence alignment. Alignments with equal scores are iteratively rescored with the joint weight matrix of increasing level (nucleotide pairs, triplets, and so on) until one single best alignment is eventually found. This method for resolving ambiguity in multiple sequence alignment can be easily implemented by use of the improved scoring matrix.
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Hung, Che-Lun, e Yaw-Ling Lin. "Implementation of a Parallel Protein Structure Alignment Service on Cloud". International Journal of Genomics 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/439681.
Testo completoAbstract (sommario):
Protein structure alignment has become an important strategy by which to identify evolutionary relationships between protein sequences. Several alignment tools are currently available for online comparison of protein structures. In this paper, we propose a parallel protein structure alignment service based on the Hadoop distribution framework. This service includes a protein structure alignment algorithm, a refinement algorithm, and a MapReduce programming model. The refinement algorithm refines the result of alignment. To process vast numbers of protein structures in parallel, the alignment and refinement algorithms are implemented using MapReduce. We analyzed and compared the structure alignments produced by different methods using a dataset randomly selected from the PDB database. The experimental results verify that the proposed algorithm refines the resulting alignments more accurately than existing algorithms. Meanwhile, the computational performance of the proposed service is proportional to the number of processors used in our cloud platform.
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David, Steven R. "Explaining Third World Alignment". World Politics 43, n. 2 (gennaio 1991): 233–56. http://dx.doi.org/10.2307/2010472.
Testo completoAbstract (sommario):
Many argue that balance of power theory is as applicable to the Third World as it is to other states. Without substantial modification, however, balance of power theory cannot explain Third World alignments, because it ignores key characteristics of Third World states that determine alignment. The author develops a theory, “omnibalancing,” that is relevant to the Third World and that repairs these defects. Rather than balance of power's emphasis on states seeking to resist threats from other states, omnibalancing explains Third World alignments as a consequence of leaders seeking to counter internal and external threats to their rule. The superiority of omnibalancing over balance of power in making Third World alignments understandable is related to the Third World in general and to the alignment decisions of two key Third World states in particular. The author concludes by discussing why an understanding of the Third World, including Third World alignment, is central to the study of international relations.
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Lustig, Sébastien, Elliot Sappey-Marinier, Camdon Fary, Elvire Servien, Sébastien Parratte e Cécile Batailler. "Personalized alignment in total knee arthroplasty: current concepts". SICOT-J 7 (2021): 19. http://dx.doi.org/10.1051/sicotj/2021021.
Testo completoAbstract (sommario):
Traditionally in total knee arthroplasty (TKA), a post-operative neutral alignment was the gold standard. This principle has been contested as functional outcomes were found to be inconsistent. Analysis of limb alignment in the non-osteoarthritic population reveals variations from neutral alignment and consideration of a personalized or patient-specific alignment in TKA is challenging previous concepts. The aim of this review was to clarify the variations of current personalized alignments and to report their results. Current personalized approaches of alignment reported are: kinematic, inverse kinematic, restricted kinematic, and functional. The principle of “kinematic alignment” is knee resurfacing with restitution of pre-arthritic anatomy. The aim is to resurface the femur maintaining the native femoral joint line obliquity. The flexion and extension gaps are balanced with the tibial resection. The principle of the “inverse kinematic alignment” is to resurface the tibia with similar medial and lateral bone resections in order to keep the native tibial joint line obliquity. Gap balancing is performed by adjusting the femoral resections. To avoid reproducing extreme anatomical alignments there is “restricted kinematic alignment” which is a compromise between mechanical alignment and true kinematic alignment with a defined safe zone of alignment. Finally, there is the concept of “functional alignment” which is an evolution of kinematic alignment as enabling technology has progressed. This is obtained by manipulating alignment, bone resections, soft tissue releases, and/or implant positioning with a robotic-assisted system to optimize TKA function for a patient’s specific alignment, bone morphology, and soft tissue envelope. The aim of personalizing alignment is to restore native knee kinematics and improve functional outcomes after TKA. A long-term follow-up remains crucial to assess both outcomes and implant survivorship of these current concepts.
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Thorndike, Tony. "Non-alignment in an age of alignments". International Affairs 64, n. 2 (1988): 262–63. http://dx.doi.org/10.2307/2621852.
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Vedder, C. J. G., e N. E. Chisari. "Galaxy clusters as intrinsic alignment tracers: present and future". Monthly Notices of the Royal Astronomical Society 500, n. 4 (26 novembre 2020): 5561–69. http://dx.doi.org/10.1093/mnras/staa3633.
Testo completoAbstract (sommario):
ABSTRACT Galaxies and clusters embedded in the large-scale structure of the Universe are observed to align in preferential directions. Galaxy alignment has been established as a potential probe for cosmological information, but the application of cluster alignments for these purposes remains unexplored. Clusters are observed to have a higher alignment amplitude than galaxies, but because galaxies are much more numerous, the trade-off in detectability between the two signals remains unclear. We present forecasts comparing cluster and galaxy alignments for two extragalactic survey set-ups: a currently available low-redshift survey (Sloan Digital Sky Survey, SDSS) and an upcoming higher redshift survey (Legacy Survey of Space and Time, LSST). For SDSS, we rely on the publicly available redmapper catalogue to describe the cluster sample. For LSST, we perform estimations of the expected number counts while we extrapolate the alignment measurements from SDSS. Clusters in SDSS have typically higher alignment signal-to-noise ratio (S/N) than galaxies. For LSST, the cluster alignment signals quickly wash out with redshift due to a relatively low number count and a decreasing alignment amplitude. Nevertheless, a potential strong suit of clusters is in their interplay with weak lensing: intrinsic alignments can be more easily isolated for clusters than for galaxies. The S/N of cluster alignment can in general be improved by isolating close pairs along the line of sight.
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Knowles, Thea, Meghan Clayards e Morgan Sonderegger. "Examining Factors Influencing the Viability of Automatic Acoustic Analysis of Child Speech". Journal of Speech, Language, and Hearing Research 61, n. 10 (26 ottobre 2018): 2487–501. http://dx.doi.org/10.1044/2018_jslhr-s-17-0275.
Testo completoAbstract (sommario):
Purpose Heterogeneous child speech was force-aligned to investigate whether (a) manipulating specific parameters could improve alignment accuracy and (b) forced alignment could be used to replicate published results on acoustic characteristics of /s/ production by children. Method In Part 1, child speech from 2 corpora was force-aligned with a trainable aligner (Prosodylab-Aligner) under different conditions that systematically manipulated input training data and the type of transcription used. Alignment accuracy was determined by comparing hand and automatic alignments as to how often they overlapped (%-Match) and absolute differences in duration and boundary placements. Using mixed-effects regression, accuracy was modeled as a function of alignment conditions, as well as segment and child age. In Part 2, forced alignments derived from a subset of the alignment conditions in Part 1 were used to extract spectral center of gravity of /s/ productions from young children. These findings were compared to published results that used manual alignments of the same data. Results Overall, the results of Part 1 demonstrated that using training data more similar to the data to be aligned as well as phonetic transcription led to improvements in alignment accuracy. Speech from older children was aligned more accurately than younger children. In Part 2, /s/ center of gravity extracted from force-aligned segments was found to diverge in the speech of male and female children, replicating the pattern found in previous work using manually aligned segments. This was true even for the least accurate forced alignment method. Conclusions Alignment accuracy of child speech can be improved by using more specific training and transcription. However, poor alignment accuracy was not found to impede acoustic analysis of /s/ produced by even very young children. Thus, forced alignment presents a useful tool for the analysis of child speech. Supplemental Material https://doi.org/10.23641/asha.7070105
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Li, Wei, Hao Pu, Hai Feng Zhao e Wei Liu. "Bidirectional Dynamic Programming Approach for Highway Alignment Optimization". Advanced Materials Research 779-780 (settembre 2013): 700–704. http://dx.doi.org/10.4028/www.scientific.net/amr.779-780.700.
Testo completoAbstract (sommario):
In order to automatically generate the optimal highway alignment and avoid omitting valuable scenarios, a bidirectional dynamic programming approach for alignment optimization was put forward. Firstly we established a three-dimensional search grid in the study area. Then dynamic programming was used to find the best alignments within the vast study area. A double-direction searching strategy was proposed to obtain a group of scenarios ranking by their corresponding comprehensive cost. The alignments were then refined with Powell method so that the resulting alignments could deviate from the grid points to reach better solutions. Examples demonstrated that this approach can obtain global optimal alignment with good diversity.
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Darby, Charlotte A., Ravi Gaddipati, Michael C. Schatz e Ben Langmead. "Vargas: heuristic-free alignment for assessing linear and graph read aligners". Bioinformatics 36, n. 12 (22 aprile 2020): 3712–18. http://dx.doi.org/10.1093/bioinformatics/btaa265.
Testo completoAbstract (sommario):
Abstract Motivation Read alignment is central to many aspects of modern genomics. Most aligners use heuristics to accelerate processing, but these heuristics can fail to find the optimal alignments of reads. Alignment accuracy is typically measured through simulated reads; however, the simulated location may not be the (only) location with the optimal alignment score. Results Vargas implements a heuristic-free algorithm guaranteed to find the highest-scoring alignment for real sequencing reads to a linear or graph genome. With semiglobal and local alignment modes and affine gap and quality-scaled mismatch penalties, it can implement the scoring functions of commonly used aligners to calculate optimal alignments. While this is computationally intensive, Vargas uses multi-core parallelization and vectorized (SIMD) instructions to make it practical to optimally align large numbers of reads, achieving a maximum speed of 456 billion cell updates per second. We demonstrate how these ‘gold standard’ Vargas alignments can be used to improve heuristic alignment accuracy by optimizing command-line parameters in Bowtie 2, BWA-maximal exact match and vg to align more reads correctly. Availability and implementation Source code implemented in C++ and compiled binary releases are available at https://github.com/langmead-lab/vargas under the MIT license. Supplementary information Supplementary data are available at Bioinformatics online.
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Kuchaiev, Oleksii, Tijana Milenković, Vesna Memišević, Wayne Hayes e Nataša Pržulj. "Topological network alignment uncovers biological function and phylogeny". Journal of The Royal Society Interface 7, n. 50 (24 marzo 2010): 1341–54. http://dx.doi.org/10.1098/rsif.2010.0063.
Testo completoAbstract (sommario):
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology and disease. Comparison and alignment of biological networks will probably have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments. Topology-based alignments have the potential to provide a completely new, independent source of phylogenetic information. Our alignment of the protein–protein interaction networks of two very different species—yeast and human—indicate that even distant species share a surprising amount of network topology, suggesting broad similarities in internal cellular wiring across all life on Earth.
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Farid, Muhammad Rifqiawan, Andri Irfan Rifai e Mohamad Taufik. "The Alignment Horizontal Design of Alternative Road: A Case of Jalan Subang – Cikamurang, West Java". Indonesian Journal of Multidisciplinary Science 1, n. 1 (17 gennaio 2023): 344–56. http://dx.doi.org/10.55324/ijoms.v1i1.393.
Testo completoAbstract (sommario):
Horizontal alignment belongs to the aspect of the geometric design of the road. Jalan Subang - Cikamurang, located in Indramayu, West Java, is planned to have three horizontal alignments. This design aims to connect Subang and Cikamurang to shorten the travel time for the surrounding community's needs. This research uses the Bina Marga method, referring to the 2021 Road Geometric Design Guidelines. First, road traffic data is obtained from the google earth application and then processed with a manual method to determine the coordinates of the road traffic and the location of horizontal alignment. Then the data obtained is processed by referring to the Bina Marga method to design horizontal alignment. Jalan Subang - Cikamurang is a Primary Local Road (Arterial Road), Primary Collector, and class III C road type. Three horizontal alignments with Spiral-Circle-Spiral (SCS) type, the first horizontal alignment is at STA 0+544.018 – 0+819.445, the second horizontal alignment is at STA 1+224.778 – 1+474.695, and the third horizontal alignment is at STA 1+763 – 2+164.390.
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Xu, Kun, Linfeng Song, Yansong Feng, Yan Song e Dong Yu. "Coordinated Reasoning for Cross-Lingual Knowledge Graph Alignment". Proceedings of the AAAI Conference on Artificial Intelligence 34, n. 05 (3 aprile 2020): 9354–61. http://dx.doi.org/10.1609/aaai.v34i05.6476.
Testo completoAbstract (sommario):
Existing entity alignment methods mainly vary on the choices of encoding the knowledge graph, but they typically use the same decoding method, which independently chooses the local optimal match for each source entity. This decoding method may not only cause the “many-to-one” problem but also neglect the coordinated nature of this task, that is, each alignment decision may highly correlate to the other decisions. In this paper, we introduce two coordinated reasoning methods, i.e., the Easy-to-Hard decoding strategy and joint entity alignment algorithm. Specifically, the Easy-to-Hard strategy first retrieves the model-confident alignments from the predicted results and then incorporates them as additional knowledge to resolve the remaining model-uncertain alignments. To achieve this, we further propose an enhanced alignment model that is built on the current state-of-the-art baseline. In addition, to address the many-to-one problem, we propose to jointly predict entity alignments so that the one-to-one constraint can be naturally incorporated into the alignment prediction. Experimental results show that our model achieves the state-of-the-art performance and our reasoning methods can also significantly improve existing baselines.
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Peter, Jan-Thorsten, Arne Nix e Hermann Ney. "Generating Alignments Using Target Foresight in Attention-Based Neural Machine Translation". Prague Bulletin of Mathematical Linguistics 108, n. 1 (1 giugno 2017): 27–36. http://dx.doi.org/10.1515/pralin-2017-0006.
Testo completoAbstract (sommario):
AbstractNeural machine translation (NMT) has shown large improvements in recent years. The currently most successful approach in this area relies on the attention mechanism, which is often interpreted as an alignment, even though it is computed without explicit knowledge of the target word. This limitation is the most likely reason that the quality of attention-based alignments is inferior to the quality of traditional alignment methods. Guided alignment training has shown that alignments are still capable of improving translation quality. In this work, we propose an extension of the attention-based NMT model that introduces target information into the attention mechanism to produce high-quality alignments. In comparison to the conventional attention-based alignments, our model halves the Aer with an absolute improvement of 19.1% Aer. Compared to GIZA++ it shows an absolute improvement of 2.0% Aer.
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Raghuwanshi, Pankaj, Dr Rajeev Jain, Prof Sanjay Saraswat e Deepti Gangele. "Improvements in the Horizontal Alignment and Vertical Profile of Balampur Ghat Section in Bhopal-Vidisha State Highway Road (SH-18) using MXRoad Software". International Journal for Research in Applied Science and Engineering Technology 11, n. 8 (31 agosto 2023): 2008–33. http://dx.doi.org/10.22214/ijraset.2023.55502.
Testo completoAbstract (sommario):
Abstract: Geometric design of highway deals with designing of physical visible features of highway those comprise of horizontal alignment, vertical profile, circular and transition curves, superelevation, Summit and valley curves, cross sectional elements, sight distances and other features. From the safety point of view, road geometric features should be well designed as per the IRC recommendation. In this research work, the horizontal alignment and vertical profile have designed of Balampur Ghat section in the Bhopal-Vidisha Road which is in the Madhya Pradesh State of India. The objective of this research work is “Improvements in the Horizontal alignment and Vertical profile of Balampur Ghat Section in Bhopal-Vidisha State Highway Road (SH-18) using MX Road Software”. The design of horizontal alignment and vertical profile have been done for Balampur ghat section approx. 2.0 km in length of State highway no. 18 (SH-18) of Madhya Pradesh. SH-18 is connected to Vidisha from Bhopal in the state of Madhya Pradesh and having heavy commercial traffic. Balampur ghat section is hilly terrain and have two improper horizontal curves along with 6.5% of vertical gradient and because of this reason that section is not safe for deriving therefore it has become an accident-prone area and the accident-prone area have the human and economical losses so it should be improved and re design of the horizontal and vertical alignment for safe design speed. The proposed methodology is on the basis of inventory survey (preliminary survey), topographic survey and MX Road software. In inventory survey take the data of existing road and find the suitable route of alternative alignment if re-alignment is required in the road. Then the topographic survey done on the existing road and alternative alignment. Import the topographic data of the road in MX Road software for generate existing surface of the road for design of horizontal alignment and vertical profile. As per IRC recommendations, there are two alternative alignments designed of the existing ghat section. As per the outputs of this research work, the length of both improved alignments is short as compare to existing road. There are no improper curves at improved alignment and maximum gradient is 4.2% which is less than the existing gradient (6.5%). The minimum design speed is 40-50 kmph which was 20 kmph in existing road. The both two improved alignments are safer as compare to existing alignment and the design speed of the vehicle has been increased. The improved alignment 2 is straighter than the improved alignment The improved alignment has also reduced the human and economic losses.
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Andito, Ilham Rafid, Andri Irfan Rifai e Adinda Fajarika Akhir. "The Design of Alignment Horizontal Using Indonesia Highway Design Standard: A Case of Jalan Babat – Tapen, East Java". Indonesian Journal of Multidisciplinary Science 1, n. 1 (17 gennaio 2023): 199–210. http://dx.doi.org/10.55324/ijoms.v1i1.383.
Testo completoAbstract (sommario):
Horizontal alignment is included in the aspect of the geometric design of the road. Jalan Babat – Tapen in Jombang, East Java, is planned to have three horizontal alignments. This design aims to connect Jalan Babat and Jalan Tapen to shorten the travel time for the surrounding community's needs. This research uses the Bina Marga method, which refers to the Highway Design Standard of Indonesia 2021. First, road traffic data is obtained from the google earth application. The global mapper is then processed in AutoCAD to determine the coordinates of the road trace and the location of horizontal alignment. Then the data obtained is processed by referring to the Bina Marga method to design horizontal alignment. Jalan Tapen – Babat is a Secondary SJJ (Urban Road), Secondary Collector, and medium road, and the minor type of road 2/2 is not separate (TT). It has a flat terrain in design with a planned speed of 40 km / h. Three horizontal alignments with Spiral-Circle-Spiral (SCS) type, the first horizontal alignment is at STA 0+700 – 0+864, the second horizontal alignment is at STA 1+383 – 1+558, and the third horizontal alignment is at STA 2+132 – 2+304.
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Pervez, Muhammad Tariq, Hayat Ali Shah, Masroor Ellahi Babar, Nasir Naveed e Muhammad Shoaib. "SAliBASE: A Database of Simulated Protein Alignments". Evolutionary Bioinformatics 15 (gennaio 2019): 117693431882108. http://dx.doi.org/10.1177/1176934318821080.
Testo completoAbstract (sommario):
Simulated alignments are alternatives to manually constructed multiple sequence alignments for evaluating performance of multiple sequence alignment tools. The importance of simulated sequences is recognized because their true evolutionary history is known, which is very helpful for reconstructing accurate phylogenetic trees and alignments. However, generating simulated alignments require expertise to use bioinformatics tools and consume several hours for reconstructing even a few hundreds of simulated sequences. It becomes a tedious job for an end user who needs a few datasets of variety of simulated sequences. Currently, there is no databank available which may help researchers to download simulated sequences/alignments for their study. Major focus of our study was to develop a database of simulated protein sequences (SAliBASE) based on different varying parameters such as insertion rate, deletion rate, sequence length, number of sequences, and indel size. Each dataset has corresponding alignment as well. This repository is very useful for evaluating multiple alignment methods.
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Zhai, Yixiao, Jiannan Chao, Yizheng Wang, Pinglu Zhang, Furong Tang e Quan Zou. "TPMA: A two pointers meta-alignment tool to ensemble different multiple nucleic acid sequence alignments". PLOS Computational Biology 20, n. 4 (1 aprile 2024): e1011988. http://dx.doi.org/10.1371/journal.pcbi.1011988.
Testo completoAbstract (sommario):
Accurate multiple sequence alignment (MSA) is imperative for the comprehensive analysis of biological sequences. However, a notable challenge arises as no single MSA tool consistently outperforms its counterparts across diverse datasets. Users often have to try multiple MSA tools to achieve optimal alignment results, which can be time-consuming and memory-intensive. While the overall accuracy of certain MSA results may be lower, there could be local regions with the highest alignment scores, prompting researchers to seek a tool capable of merging these locally optimal results from multiple initial alignments into a globally optimal alignment. In this study, we introduce Two Pointers Meta-Alignment (TPMA), a novel tool designed for the integration of nucleic acid sequence alignments. TPMA employs two pointers to partition the initial alignments into blocks containing identical sequence fragments. It selects blocks with the high sum of pairs (SP) scores to concatenate them into an alignment with an overall SP score superior to that of the initial alignments. Through tests on simulated and real datasets, the experimental results consistently demonstrate that TPMA outperforms M-Coffee in terms of aSP, Q, and total column (TC) scores across most datasets. Even in cases where TPMA’s scores are comparable to M-Coffee, TPMA exhibits significantly lower running time and memory consumption. Furthermore, we comprehensively assessed all the MSA tools used in the experiments, considering accuracy, time, and memory consumption. We propose accurate and fast combination strategies for small and large datasets, which streamline the user tool selection process and facilitate large-scale dataset integration. The dataset and source code of TPMA are available on GitHub (https://github.com/malabz/TPMA).
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Mahr, Tristan J., Visar Berisha, Kan Kawabata, Julie Liss e Katherine C. Hustad. "Performance of Forced-Alignment Algorithms on Children's Speech". Journal of Speech, Language, and Hearing Research 64, n. 6S (18 giugno 2021): 2213–22. http://dx.doi.org/10.1044/2020_jslhr-20-00268.
Testo completoAbstract (sommario):
Purpose Acoustic measurement of speech sounds requires first segmenting the speech signal into relevant units (words, phones, etc.). Manual segmentation is cumbersome and time consuming. Forced-alignment algorithms automate this process by aligning a transcript and a speech sample. We compared the phoneme-level alignment performance of five available forced-alignment algorithms on a corpus of child speech. Our goal was to document aligner performance for child speech researchers. Method The child speech sample included 42 children between 3 and 6 years of age. The corpus was force-aligned using the Montreal Forced Aligner with and without speaker adaptive training, triphone alignment from the Kaldi speech recognition engine, the Prosodylab-Aligner, and the Penn Phonetics Lab Forced Aligner. The sample was also manually aligned to create gold-standard alignments. We evaluated alignment algorithms in terms of accuracy (whether the interval covers the midpoint of the manual alignment) and difference in phone-onset times between the automatic and manual intervals. Results The Montreal Forced Aligner with speaker adaptive training showed the highest accuracy and smallest timing differences. Vowels were consistently the most accurately aligned class of sounds across all the aligners, and alignment accuracy increased with age for fricative sounds across the aligners too. Conclusion The best-performing aligner fell just short of human-level reliability for forced alignment. Researchers can use forced alignment with child speech for certain classes of sounds (vowels, fricatives for older children), especially as part of a semi-automated workflow where alignments are later inspected for gross errors. Supplemental Material https://doi.org/10.23641/asha.14167058
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Krivozubov, Mikhail, Florian Goebels e Sergei Spirin. "Estimation of relative effectiveness of phylogenetic programs by machine learning". Journal of Bioinformatics and Computational Biology 12, n. 02 (aprile 2014): 1441004. http://dx.doi.org/10.1142/s0219720014410042.
Testo completoAbstract (sommario):
Reconstruction of phylogeny of a protein family from a sequence alignment can produce results of different quality. Our goal is to predict the quality of phylogeny reconstruction basing on features that can be extracted from the input alignment. We used Fitch–Margoliash (FM) method of phylogeny reconstruction and random forest as a predictor. For training and testing the predictor, alignments of orthologous series (OS) were used, for which the result of phylogeny reconstruction can be evaluated by comparison with trees of corresponding organisms. Our results show that the quality of phylogeny reconstruction can be predicted with more than 80% precision. Also, we tried to predict which phylogeny reconstruction method, FM or UPGMA, is better for a particular alignment. With the used set of features, among alignments for which the obtained predictor predicts a better performance of UPGMA, 56% really give a better result with UPGMA. Taking into account that in our testing set only for 34% alignments UPGMA performs better, this result shows a principal possibility to predict the better phylogeny reconstruction method basing on features of a sequence alignment.
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Steenwyk, Jacob L., Thomas J. Buida, Yuanning Li, Xing-Xing Shen e Antonis Rokas. "ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference". PLOS Biology 18, n. 12 (2 dicembre 2020): e3001007. http://dx.doi.org/10.1371/journal.pbio.3001007.
Testo completoAbstract (sommario):
Highly divergent sites in multiple sequence alignments (MSAs), which can stem from erroneous inference of homology and saturation of substitutions, are thought to negatively impact phylogenetic inference. Thus, several different trimming strategies have been developed for identifying and removing these sites prior to phylogenetic inference. However, a recent study reported that doing so can worsen inference, underscoring the need for alternative alignment trimming strategies. Here, we introduce ClipKIT, an alignment trimming software that, rather than identifying and removing putatively phylogenetically uninformative sites, instead aims to identify and retain parsimony-informative sites, which are known to be phylogenetically informative. To test the efficacy of ClipKIT, we examined the accuracy and support of phylogenies inferred from 14 different alignment trimming strategies, including those implemented in ClipKIT, across nearly 140,000 alignments from a broad sampling of evolutionary histories. Phylogenies inferred from ClipKIT-trimmed alignments are accurate, robust, and time saving. Furthermore, ClipKIT consistently outperformed other trimming methods across diverse datasets, suggesting that strategies based on identifying and retaining parsimony-informative sites provide a robust framework for alignment trimming.
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Arenas-Díaz, Edgar D., Helga Ochoterena e Katya Rodríguez-Vázquez. "Multiple Sequence Alignment Using a Genetic Algorithm and GLOCSA". Journal of Artificial Evolution and Applications 2009 (27 agosto 2009): 1–10. http://dx.doi.org/10.1155/2009/963150.
Testo completoAbstract (sommario):
Algorithms that minimize putative synapomorphy in an alignment cannot be directly implemented since trivial cases with concatenated sequences would be selected because they would imply a minimum number of events to be explained (e.g., a single insertion/deletion would be required to explain divergence among two sequences). Therefore, indirect measures to approach parsimony need to be implemented. In this paper, we thoroughly present a Global Criterion for Sequence Alignment (GLOCSA) that uses a scoring function to globally rate multiple alignments aiming to produce matrices that minimize the number of putative synapomorphies. We also present a Genetic Algorithm that uses GLOCSA as the objective function to produce sequence alignments refining alignments previously generated by additional existing alignment tools (we recommend MUSCLE). We show that in the example cases our GLOCSA-guided Genetic Algorithm (GGGA) does improve the GLOCSA values, resulting in alignments that imply less putative synapomorphies.
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Ji, Yukai, Tao Huang, Chunlai Ma, Chao Hu, Zhanfeng Wang e Anmin Fu. "IMCSA: Providing Better Sequence Alignment Space for Industrial Control Protocol Reverse Engineering". Security and Communication Networks 2022 (24 novembre 2022): 1–9. http://dx.doi.org/10.1155/2022/8026280.
Testo completoAbstract (sommario):
Nowadays, with the wide application of industrial control facilities, industrial control protocol reverse engineering has significant security implications. The reverse method of industrial protocol based on sequence alignment is the current mainstream method because of its high accuracy. However, this method will incur a huge time overhead due to unnecessary alignments during the sequence alignment process. In this paper, we optimize the traditional sequence alignment method by combining the characteristics of industrial control protocols. We improve the frequent sequence mining algorithm, Apriori, to propose a more efficient Bag-of-Words generation algorithm for finding keywords. Then, we precluster the messages based on the generated Bag-of-Words to improve the similarity of the message within a cluster. Finally, we propose an industrial control protocol message preclustering model for sequence alignment, namely, IMCSA. We evaluate it over five industrial control protocols, and the results show that IMCSA can generate clusters with higher message similarity, which will greatly reduce the invalid alignments existing in the sequence alignment stage and ultimately improve the overall efficiency.
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SHIN, Kilho. "Alignment Kernels Based on a Generalization of Alignments". IEICE Transactions on Information and Systems E97.D, n. 1 (2014): 1–10. http://dx.doi.org/10.1587/transinf.e97.d.1.
Testo completo
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Bucka-Lassen, K., O. Caprani e J. Hein. "Combining many multiple alignments in one improved alignment". Bioinformatics 15, n. 2 (1 febbraio 1999): 122–30. http://dx.doi.org/10.1093/bioinformatics/15.2.122.
Testo completo
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Lee, Hyeonseok, Semo Kim, Dohun Lim, Seoung-Hun Bae, Lae-Hyong Kang e Sungchan Kim. "Two-Step Approach toward Alignment of Spatiotemporal Wide-Area Unmanned Aerial Vehicle Imageries". Drones 7, n. 2 (12 febbraio 2023): 131. http://dx.doi.org/10.3390/drones7020131.
Testo completoAbstract (sommario):
Recently, analysis and decision-making based on spatiotemporal unmanned aerial vehicle (UAV) high-resolution imagery are gaining significant attention in smart agriculture. Constructing a spatiotemporal dataset requires multiple UAV image mosaics taken at different times. Because the weather or a UAV flight trajectory is subject to change when the images are taken, the mosaics are typically unaligned. This paper proposes a two-step approach, composed of global and local alignments, for spatiotemporal alignment of two wide-area UAV mosaics of high resolution. The first step, global alignment, finds a projection matrix that initially maps keypoints in the source mosaic onto matched counterparts in the target mosaic. The next step, local alignment, refines the result of the global alignment. The proposed method splits input mosaics into patches and applies individual transformations to each patch to enhance the remaining local misalignments at patch level. Such independent local alignments may result in new artifacts at patch boundaries. The proposed method uses a simple yet effective technique to suppress those artifacts without harming the benefit of the local alignment. Extensive experiments validate the proposed method by using several datasets for highland fields and plains in South Korea. Compared with a recent work, the proposed method improves the accuracy of alignment by up to 13.21% over the datasets.
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Zemla, Adam T., e Carol L. Ecale Zhou. "Structural Re-Alignment in an Immunogenic Surface Region of Ricin a Chain". Bioinformatics and Biology Insights 2 (gennaio 2008): BBI.S437. http://dx.doi.org/10.4137/bbi.s437.
Testo completoAbstract (sommario):
We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connecting the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e. alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments: http://as2ts.llnl.gov/AS2TS/LGA/lga_pdblist_plots.html .
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Samuroff, S., J. Blazek, M. A. Troxel, N. MacCrann, E. Krause, C. D. Leonard, J. Prat et al. "Dark Energy Survey Year 1 results: constraints on intrinsic alignments and their colour dependence from galaxy clustering and weak lensing". Monthly Notices of the Royal Astronomical Society 489, n. 4 (16 agosto 2019): 5453–82. http://dx.doi.org/10.1093/mnras/stz2197.
Testo completoAbstract (sommario):
Abstract We perform a joint analysis of intrinsic alignments and cosmology using tomographic weak lensing, galaxy clustering, and galaxy–galaxy lensing measurements from Year 1 (Y1) of the Dark Energy Survey. We define early- and late-type subsamples, which are found to pass a series of systematics tests, including for spurious photometric redshift error and point spread function correlations. We analyse these split data alongside the fiducial mixed Y1 sample using a range of intrinsic alignment models. In a fiducial non-linear alignment model analysis, assuming a flat Λ cold dark matter cosmology, we find a significant difference in intrinsic alignment amplitude, with early-type galaxies favouring $A_\mathrm{IA} = 2.38^{+0.32}_{-0.31}$ and late-type galaxies consistent with no intrinsic alignments at $0.05^{+0.10}_{-0.09}$. The analysis is repeated using a number of extended model spaces, including a physically motivated model that includes both tidal torquing and tidal alignment mechanisms. In multiprobe likelihood chains in which cosmology, intrinsic alignments in both galaxy samples and all other relevant systematics are varied simultaneously, we find the tidal alignment and tidal torquing parts of the intrinsic alignment signal have amplitudes $A_1 = 2.66 ^{+0.67}_{-0.66}$, $A_2=-2.94^{+1.94}_{-1.83}$, respectively, for early-type galaxies and $A_1 = 0.62 ^{+0.41}_{-0.41}$, $A_2 = -2.26^{+1.30}_{-1.16}$ for late-type galaxies. In the full (mixed) Y1 sample the best constraints are $A_1 = 0.70 ^{+0.41}_{-0.38}$, $A_2 = -1.36 ^{+1.08}_{-1.41}$. For all galaxy splits and IA models considered, we report cosmological parameter constraints consistent with the results of the main DES Y1 cosmic shear and multiprobe cosmology papers.
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Lu, Jing, e Qikai Gai. "Multi-grained alignment method based on stable topics in cross-social networks". PeerJ Computer Science 10 (28 febbraio 2024): e1892. http://dx.doi.org/10.7717/peerj-cs.1892.
Testo completoAbstract (sommario):
The user alignment of cross-social networks is divided into user and group alignments, respectively. Obtaining users’ full features is difficult due to social network privacy protection policies in user alignment mode. In contrast, the alignment accuracy is low due to the large number of edge users in the group alignment mode. To resolve this issue, First, stable topics are obtained from user-generated content (UGC) based on embedded topic jitter time, and the weight of user edges is updated by using vector distances. An improved Louvain algorithm, called Stable Topic-Louvain (ST-L), is designed to accomplish multi-level community detection without predetermined tags. It aims to obtain fuzzy topic features of the community and finalize the community alignment across social networks. Furthermore, iterative alignment is executed from coarse-grained communities to fine-grained sub-communities until user-level alignment occurs. The process can be terminated at any layer to achieve multi-granularity alignment, which resolves the low accuracy issue of edge user alignment at a single granularity and improves the accuracy of user alignment. The effectiveness of the proposed method is shown by implementing real datasets.
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Huang, Yan, Tianyuan Zhang e Huidong Zhu. "Improving Word Alignment by Adding Gromov-Wasserstein into Attention Neural Network". Journal of Physics: Conference Series 2171, n. 1 (1 gennaio 2022): 012043. http://dx.doi.org/10.1088/1742-6596/2171/1/012043.
Testo completoAbstract (sommario):
Abstract Statistical machine translation systems usually break the translation task into two or more subtasks and an important one is finding word alignments over a parallel sentence bilingual corpus. We address the problem of introducing word alignment for language pairs by developing a novel neural network model that can applied to other generative alignment models. We use Multi-layer attention model and multi-layer model with multi-head-attention mechanism on each layer provides superior translation quality. It can be trained on bilingual data without relying on word alignment. In this paper, we cast the correspondence problem directly as an optimal distance problem. We use the Gromov-Wasserstein distance to calculated how similarities between word pairs are related across languages. The resulting alignments dramatically outperform the GIZA++ and FastAlign approach, these alignments are comparable on public data sets.
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Ishizuka, K., e K. Shirota. "Voltage-center COMA-free alignment for high-resolution Electron Microscopy". Proceedings, annual meeting, Electron Microscopy Society of America 52 (1994): 410–11. http://dx.doi.org/10.1017/s042482010016978x.
Testo completoAbstract (sommario):
In a conventional alignment for high-resolution electron microscopy, the specimen point imaged at the viewing-screen center is made dispersion-free against a voltage fluctuation by adjusting the incident beam direction using the beam deflector. For high-resolution works the voltage-center alignment is important, since this alignment reduces the chromatic aberration. On the other hand, the coma-free alignment is also indispensable for high-resolution electron microscopy. This is because even a small misalignment of the incident beam direction induces wave aberrations and affects the appearance of high resolution electron micrographs. Some alignment procedures which cancel out the coma by changing the incident beam direction have been proposed. Most recently, the effect of a three-fold astigmatism on the coma-free alignment has been revealed, and new algorithms of coma-free alignment have been proposed.However, the voltage-center and the coma-free alignments as well as the current-center alignment in general do not coincide to each other because of beam deflection due to a leakage field within the objective lens, even if the main magnetic-field of the objective lens is rotationally symmetric. Since all the proposed procedures for the coma-free alignment also use the same beam deflector above the objective lens that is used for the voltage-center alignment, the coma-free alignment is only attained at the sacrifice of the voltage-center alignment.
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Pineda-Jaramillo, J., P. Salvador-Zuriaga, P. Martínez-Fernández e R. Insa-Franco. "Impact of Symmetric Vertical Sinusoid Alignments on Infrastructure Construction Costs: Optimizing Energy Consumption in Metropolitan Railway Lines Using Artificial Neural Networks". Urban Rail Transit 6, n. 3 (2 luglio 2020): 145–56. http://dx.doi.org/10.1007/s40864-020-00130-7.
Testo completoAbstract (sommario):
Abstract Minimizing energy consumption is a key issue from both an environmental and economic perspectives for railways systems; however, it is also important to reduce infrastructure construction costs. In the present work, an artificial neural network (ANN) was trained to estimate the energy consumption of a metropolitan railway line. This ANN was used to test hypothetical vertical alignments scenarios, proving that symmetric vertical sinusoid alignments (SVSA) can reduce energy consumption by up to 18.4% compared with a flat alignment. Finally, we analyzed the impact of SVSA application on infrastructure construction costs, considering different scenarios based on top–down excavation methods. When balancing reduction in energy consumption against infrastructure construction costs between SVSA and flat alignment, the extra construction costs due to SVSA have a return period of 25–300 years compared with a flat alignment, depending on the soil type and construction method used. Symmetric vertical sinusoid alignment layouts are thus suitable for scattered or soft soils, up to compacted intermediate geomaterials.
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Hansen, A. H., M. R. Meier, M. Sam, D. S. Childress e M. L. Edwards. "Alignment of transtibial prostheses based on rollover shape principles". Prosthetics and Orthotics International 27, n. 2 (agosto 2003): 89–99. http://dx.doi.org/10.1080/03093640308726664.
Testo completoAbstract (sommario):
The authors examined the rollover shape alignment hypothesis, which states that prosthetic feet are aligned by matching their rollover shapes with an “ideal” shape. The “ideal” shape was considered to be the rollover shape of the ablebodied footankle system. An alignment algorithm and computational alignment system were developed to set transtibial alignments based on this hypothesis. Three prosthetic feet with considerably different rollover shapes were either aligned using the alignment system or not aligned (i.e. used previous foot's alignment), and then were aligned by a team of prosthetists. No significant differences were found between rollover shapes aligned by the computational alignment system and those based on standard clinical techniques (p = 0.944). Significant differences were found between the “no alignment” shapes and the prosthetist alignment shapes (p = 0.006), and between the “no alignment” shapes and the computational alignment system shapes (p = 0.024). The results of the experiment support the hypothesis that the goal of alignment is to match the prosthetic foot's rollover shape, as closely as possible, with an “ideal” shape. The hypothesis is also supported by its ability to explain the results of previous studies. Using an “ideal” rollover shape or surface as a goal for prosthetic alignment could lead to a priori alignment, eliminating the need for alignment hardware in some cases. Being able to build the alignment into a prosthesis without special hardware could be beneficial in lowincome countries and in the fabrication of lightweight prostheses for the elderly.
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Lin, Tsung Hsien, e Wen Zheng Chen. "Photo-Alignment Effect in Liquid-Crystal Films Containing Nanoparticles and Azo-Dye". Key Engineering Materials 428-429 (gennaio 2010): 276–79. http://dx.doi.org/10.4028/www.scientific.net/kem.428-429.276.
Testo completoAbstract (sommario):
This work reports the photo-alignment effect in a liquid-crystal film doped with nanoparticles and azo-dye. Vertical alignment induced by the nanoparticles polyhedral oligomeric silsesquioxanes (POSS) can be switched to homogeneous alignment by the absorption of photo-excited azo-dye. Both electro-optical and surface properties are analyzed to verify this effect. Using this photo-alignment technique in nanoparticle- and azo-dye-doped liquid crystal, the phase grating is also demonstrated. The diffraction efficiency is related to the polarization of the probe light and can be controlled by applying voltage. Both nanoparticle- and azo-dye-induced vertical and homogeneous alignments are non-contact aligning methods. Thus, the technique based on dopant-induced alignment has potential for practical applications.
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DENG, YONGGANG, SHANKAR KUMAR e WILLIAM BYRNE. "Segmentation and alignment of parallel text for statistical machine translation". Natural Language Engineering 13, n. 3 (6 luglio 2006): 235–60. http://dx.doi.org/10.1017/s1351324906004293.
Testo completoAbstract (sommario):
We address the problem of extracting bilingual chunk pairs from parallel text to create training sets for statistical machine translation. We formulate the problem in terms of a stochastic generative process over text translation pairs, and derive two different alignment procedures based on the underlying alignment model. The first procedure is a now-standard dynamic programming alignment model which we use to generate an initial coarse alignment of the parallel text. The second procedure is a divisive clustering parallel text alignment procedure which we use to refine the first-pass alignments. This latter procedure is novel in that it permits the segmentation of the parallel text into sub-sentence units which are allowed to be reordered to improve the chunk alignment. The quality of chunk pairs are measured by the performance of machine translation systems trained from them. We show practical benefits of divisive clustering as well as how system performance can be improved by exploiting portions of the parallel text that otherwise would have to be discarded. We also show that chunk alignment as a first step in word alignment can significantly reduce word alignment error rate.
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Srivastava, Saurabh, e Derrick E. D’Souza. "Exploring patterns of organizational capability alignment: a contingency approach". Management Research Review 43, n. 3 (11 ottobre 2019): 311–31. http://dx.doi.org/10.1108/mrr-03-2019-0115.
Testo completoAbstract (sommario):
Purpose The purpose of the study is to investigate whether the alignment between organizational capabilities is idiosyncratic to an organization or a predictable pattern of alignments can be identified across organizations. Design/methodology/approach Survey design is used to collect data from upper- and mid-level managers of organizations operating in the software industry. A total of 219 responses are used to test the study hypotheses. Partial least squares structural equation modeling and regression analysis are used for data analysis and hypotheses testing. Findings Results suggest that the alignment between strategic thinking and absorptive capacity is different for organizations with a prospector-type strategic orientation compared to organizations with other types (defenders and analyzers) of strategic orientations. The study also finds that the pattern of alignment holds for each dimension of absorptive capacity. Originality/value There is limited research on the alignment between the three types of organizational capabilities (metaphysical, dynamic and ordinary). This may have transcended from arguments that if organizational capabilities are truly idiosyncratic, they should not be expected to follow a predictable pattern of alignments across organizations. To the best of the authors’ knowledge, this study is the first to empirically investigate and provide evidence that the alignment between organizational capabilities is contingent on the strategic orientation of the organizations. The findings offer hope for the development of a generalizable theory of organizational capability alignment in organizations.
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Catanach, Therese A., Andrew D. Sweet, Nam-phuong D. Nguyen, Rhiannon M. Peery, Andrew H. Debevec, Andrea K. Thomer, Amanda C. Owings et al. "Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus". PeerJ 7 (3 gennaio 2019): e6142. http://dx.doi.org/10.7717/peerj.6142.
Testo completoAbstract (sommario):
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected “by eye” prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.