Dissertations / Theses on the topic 'Alignment'
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Starrett, Dean. "Optimal Alignment of Multiple Sequence Alignments." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194840.
Full textAbstract:
An essential tool in biology is the alignment of multiple sequences. Biologists use multiple sequence alignments for tasks such as predicting protein structure and function, reconstructing phylogenetic trees, and finding motifs. Constructing high-quality multiple alignments is computationally hard, both in theory and in practice, and is typically done using heuristic methods. The majority of state-of-the-art multiple alignment programs employ a form and polish strategy, where in the construction phase, an initial multiple alignment is formed by progressively merging smaller alignments, starting with single sequences. Then in a local-search phase, the resulting alignment is polished by repeatedly splitting it into smaller alignments and re-merging. This merging of alignments, the basic computational problem in the construction and local-search phases of the best multiple alignment heuristics, is called the Aligning Alignments Problem. Under the sum-of-pairs objective for scoring multiple alignments, this problem may seem to be a simple extension of two-sequence alignment. It is proven here, however, that with affine gap costs (which are recognized as necessary to get biologically-informative alignments) the problem is NP-complete when gaps are counted exactly. Interestingly, this form of multiple alignment is polynomial-time solvable when we relax the exact count, showing that exact gap counts themselves are inherently hard in multiple sequence alignment. Unlike general multiple alignment however, we show that Aligning Alignments with affine gap costs and exact counts is tractable in practice, by demonstrating an effective algorithm and a fast implementation. Our software AlignAlign is both time- and space-efficient on biological data. Computational experiments on biological data show instances derived from standard benchmark suites can be optimally aligned with surprising efficiency, and experiments on simulated data show the time and space both scale well.
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Floden, Evan 1985. "Alignment uncertainty, regressive alignment and large scale deployment." Doctoral thesis, Universitat Pompeu Fabra, 2018. http://hdl.handle.net/10803/665300.
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A multiple sequence alignment (MSA) provides a description of the relationship between biological sequences where columns represent a shared ancestry through an implied set of evolutionary events. The majority of research in the field has focused on improving the accuracy of alignments within the progressive alignment framework and has allowed for powerful inferences including phylogenetic reconstruction, homology modelling and disease prediction. Notwithstanding this, when applied to modern genomics datasets - often comprising tens of thousands of sequences - new challenges arise in the construction of accurate MSA. These issues can be generalised to form three basic problems. Foremost, as the number of sequences increases, progressive alignment methodologies exhibit a dramatic decrease in alignment accuracy. Additionally, for any given dataset many possible MSA solutions exist, a problem which is exacerbated with an increasing number of sequences due to alignment uncertainty. Finally, technical difficulties hamper the deployment of such genomic analysis workflows - especially in a reproducible manner - often presenting a high barrier for even skilled practitioners. This work aims to address this trifecta of problems through a web server for fast homology extension based MSA, two new methods for improved phylogenetic bootstrap supports incorporating alignment uncertainty, a novel alignment procedure that improves large scale alignments termed regressive MSA and finally a workflow framework that enables the deployment of large scale reproducible analyses across clusters and clouds titled Nextflow. Together, this work can be seen to provide both conceptual and technical advances which deliver substantial improvements to existing MSA methods and the resulting inferences.Un alineament de seqüència múltiple (MSA) proporciona una descripció de la relació entre seqüències biològiques on les columnes representen una ascendència compartida a través d'un conjunt implicat d'esdeveniments evolutius. La majoria de la investigació en el camp s'ha centrat a millorar la precisió dels alineaments dins del marc d'alineació progressiva i ha permès inferències poderoses, incloent-hi la reconstrucció filogenètica, el modelatge d'homologia i la predicció de malalties. Malgrat això, quan s'aplica als conjunts de dades de genòmica moderns, que sovint comprenen desenes de milers de seqüències, sorgeixen nous reptes en la construcció d'un MSA precís. Aquests problemes es poden generalitzar per formar tres problemes bàsics. En primer lloc, a mesura que augmenta el nombre de seqüències, les metodologies d'alineació progressiva presenten una disminució espectacular de la precisió de l'alineació. A més, per a un conjunt de dades, existeixen molts MSA com a possibles solucions un problema que s'agreuja amb un nombre creixent de seqüències a causa de la incertesa d'alineació. Finalment, les dificultats tècniques obstaculitzen el desplegament d'aquests fluxos de treball d'anàlisi genòmica, especialment de manera reproduïble, sovint presenten una gran barrera per als professionals fins i tot qualificats. Aquest treball té com a objectiu abordar aquesta trifecta de problemes a través d'un servidor web per a l'extensió ràpida d'homologia basada en MSA, dos nous mètodes per a la millora de l'arrencada filogenètica permeten incorporar incertesa d'alineació, un nou procediment d'alineació que millora els alineaments a gran escala anomenat MSA regressivu i, finalment, un marc de flux de treball permet el desplegament d'anàlisis reproduïbles a gran escala a través de clústers i computació al núvol anomenat Nextflow. En conjunt, es pot veure que aquest treball proporciona tant avanços conceptuals com tècniques que proporcionen millores substancials als mètodes MSA existents i les conseqüències resultants.
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SUBRAMANIAN, SUCHITHA. "PROTEIN STRUCTURE ALIGNMENT USING A GENERALIZED ALIGNMENT MODEL." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1191966691.
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Chia, Nicholas Lee-Ping. "Sequence alignment." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1154616122.
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Wagner, Katharina. "Image Alignment." Bachelor's thesis, Universitätsbibliothek Chemnitz, 2009. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-200901305.
Full textAbstract:
Aligning two images by point to point correspondence is a hard optimization problem. It
can be solved using t-Extremal Optimization or with a modification of this method called
Fitness threshold accepting. In this work these two methods are tested and compared to
see whether one of the methods should be preferred for image alignment. Since real image
data is almost always noisy the performance of the methods under conditions like noisy and
outlying data is analyzed too.
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Ivanova, Valentina. "Fostering User Involvement in Ontology Alignment and Alignment Evaluation." Doctoral thesis, Linköpings universitet, Databas och informationsteknik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-143034.
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The abundance of data at our disposal empowers data-driven applications and decision making. The knowledge captured in the data, however, has not been utilized to full potential, as it is only accessible to human interpretation and data are distributed in heterogeneous repositories. Ontologies are a key technology unlocking the knowledge in the data by providing means to model the world around us and infer knowledge implicitly captured in the data. As data are hosted by independent organizations we often need to use several ontologies and discover the relationships between them in order to support data and knowledge transfer. Broadly speaking, while ontologies provide formal representations and thus the basis, ontology alignment supplies integration techniques and thus the means to turn the data kept in distributed, heterogeneous repositories into valuable knowledge. While many automatic approaches for creating alignments have already been developed, user input is still required for obtaining the highest-quality alignments. This thesis focuses on supporting users during the cognitively intensive alignment process and makes several contributions. We have identified front- and back-end system features that foster user involvement during the alignment process and have investigated their support in existing systems by user interface evaluations and literature studies. We have further narrowed down our investigation to features in connection to the, arguably, most cognitively demanding task from the users’ perspective—manual validation—and have also considered the level of user expertise by assessing the impact of user errors on alignments’ quality. As developing and aligning ontologies is an error-prone task, we have focused on the benefits of the integration of ontology alignment and debugging. We have enabled interactive comparative exploration and evaluation of multiple alignments at different levels of detail by developing a dedicated visual environment—Alignment Cubes—which allows for alignments’ evaluation even in the absence of reference alignments. Inspired by the latest technological advances we have investigated and identified three promising directions for the application of large, high-resolution displays in the field: improving the navigation in the ontologies and their alignments, supporting reasoning and collaboration between users.
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Maezawa, Akira. "Bayesian Music Alignment." 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/199430.
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Sanchez, Alejandro Gonzalez. "Cosmological alignment effects." Thesis, University of Sussex, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.385966.
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Bhuta, Asim. "Shoulder implant alignment." Thesis, Imperial College London, 2015. http://hdl.handle.net/10044/1/60079.
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Total shoulder arthroplasty (TSA) is used to treat patients with glenohumeral joint osteoarthritis. Despite high success rates, complications occur and many patients undergo revision surgeries. The top three most frequent complications are: instability/dislocation of the joint, glenoid loosening and rotator cuff insufficiency. It is believed that these complications occur in most part due to alignment of the implant. In this thesis a two part investigation was conducted to test the effects of joint replacement humeral head version (-15° to 15°) and tilt (-10° to 10°) and glenoid version and tilt (-15° to 15°). The first part investigates the effect of the humeral head alignment on range of motion and activities of daily living using a collision detection modelling method. The second part investigates the effect of both humeral head and glenoid variations on the joint reaction and muscle forces to describe the risk of the three most frequent complications using the United Kingdom National Shoulder Model. This thesis shows that increasing humeral head posterior version decreased the ability to perform activities of daily living (up to 32% at 15°) mostly due to bone-implant collision, increased the risk of the rocking-horse mechanism (by up to 37% at 15°) and increased subscapularis activity (by up to 14% at 15°). Similarly, increasing inferior tilt of the glenoid to 10° produced the best outcomes: vertical rocking-horse mechanism decreased by 19% and no significant differences in muscle forces were observed. In conclusion, normal alignment of the humeral head following surgical guidelines is recommended to increase the chances of implant survival. Posterior versions of the humeral head should be avoided more so than other small mal-alignments. Increasing glenoid inferior tilt to 10° produced favourable results but after combining the results from this thesis and from the literature, it is concluded that all glenoid mal-alignments should be avoided and highlights the need for more effective surgical tools to accurately position the shoulder replacement.
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Kraft, Adam Davis. "Vision by alignment." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/115632.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 127-134).
Human visual intelligence is robust. Vision is versatile in its variety of tasks and operating conditions, it is flexible, adapting facilely to new tasks, and it is introspective, providing compositional explanations for its findings. Vision is fundamentally underdetermined, but it exists in a world that abounds with constraints and regularities perceived not only through vision but through other senses as well. These observations suggest that the imperative of vision is to exploit all sources of information to resolve ambiguity. I propose an alignment model for vision, in which computational specialists eagerly share state with their neighbors during ongoing computations, availing themselves of neighbors' partial results in order to ll gaps in evolving descriptions. Connections between specialists extend across sensory modalities, so that the computational machinery of many senses may be brought to bear on problems with strictly-visual inputs. I anticipate that this alignment process accounts for vision's robust attributes, and I call this prediction the alignment hypothesis. In this document I lay the groundwork for evaluating the hypothesis. I then demonstrate progress toward that goal, by way of the following contributions: -- I performed an experiment to investigate and characterize the ways that high-performing computer-vision models fall short of robust perception, and evaluated whether alignment models can address the shortcomings. The experiment, which relied on a procedure to remove signal energy from natural images while preserving high classication condence by a neural network, revealed that the type of object depicted in the original image is a strong predictor of whether humans recognize the reduced-energy image. -- I implemented an alignment model based on a network of propagators. The model can use constraints to infer locations and heights of pedestrians and locations of occluding objects in an outdoor urban scene. I used the results of the effort to refine the requirements of mechanisms to use in building alignment models. -- I implemented an alignment model based on neural networks. Alignment-motivated design empowers the model, trained to estimate depth maps from single images, to perform the additional task of depth super-resolution without retraining. The design thus demonstrates flexibility, a property of robust vision systems.
by Adam Davis Kraft.
Ph. D.
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Gomes, Luís Manuel dos Santos. "Parallel texts alignment." Master's thesis, FCT - UNL, 2009. http://hdl.handle.net/10362/2051.
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Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia InformáticaAlignment of parallel texts (texts that are translation of each other) is a required step for many applications that use parallel texts, including statistical machine translation, automatic extraction of translation equivalents, automatic creation of concordances, etc. This dissertation presents a new methodology for parallel texts alignment that departs from previous work in several ways. One important departure is a shift of goals concerning the use of lexicons for obtaining correspondences between the texts. Previous methods try to infer a bilingual lexicon as part of the alignment process and use it to obtain correspondences between the texts. Some of those methods can use external lexicons to complement the inferred one, but they tend to consider them as secondary. This dissertation presents several arguments supporting the thesis that lexicon inference should not be embedded in the alignment process. The method described complies with this statement and relies exclusively on externally managed lexicons to obtain correspondences. Moreover, the algorithms presented can handle very large lexicons containing terms of arbitrary length. Besides the exclusive use of external lexicons, this dissertation presents a new method for obtaining correspondences between translation equivalents found in the texts. It uses a decision criteria based on features that have been overlooked by prior work. The proposed method is iterative and refines the alignment at each iteration. It uses the alignment obtained in one iteration as a guide to obtaining new correspondences in the next iteration, which in turn are used to compute a finer alignment. This iterative scheme allows the method to correct correspondence errors from previous iterations in face of new information.
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Carleton, Kristin Rose. "Out of Alignment." Thesis, Virginia Tech, 2014. http://hdl.handle.net/10919/24813.
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This thesis is an exploration of relationships made between angular elements for the purpose of discovering the spatial results that those explorations create. The media used to develop this thesis are two dimensional linear compositions, three dimensional modeling, and photography.Master of Architecture
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Lee, Kevin F. Corkum Paul. "Controlling molecular alignment." *McMaster only, 2006.
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Wheelan, Sarah J. "The alignment manager." Available to US Hopkins community, 2003. http://wwwlib.umi.com/dissertations/dlnow/3080794.
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Al, Ghamdi Manal. "Video sequence alignment." Thesis, University of Sheffield, 2015. http://etheses.whiterose.ac.uk/9056/.
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The task of aligning multiple audio visual sequences with similar contents needs careful synchronisation in both spatial and temporal domains. It is a challenging task due to a broad range of contents variations, background clutter, occlusions, and other factors. This thesis is concerned with aligning video contents by characterising the spatial and temporal information embedded in the high-dimensional space. To that end a three- stage framework is developed, involving space-time representation of video clips with local linear coding, followed by their alignment in the manifold embedded space. The first two stages present a video representation techniques based on local feature extraction and linear coding methods. Firstly, the scale invariant feature transform (SIFT) is extended to extract interest points not only from the spatial plane but also from the planes along the space-time axis. Locality constrained coding is then incorporated to project each descriptor into a local coordinate system produced by a pooling technique. Human action classification benchmarks are adopted to evaluate these two stages, comparing their performance against existing techniques. The results shows that space-time extension of SIFT with a linear coding scheme outperforms most of the state-of-the-art approaches on the action classification task owing to its ability to represent complex events in video sequences. The final stage presents a manifold learning algorithm with spatio-temporal constraints to embed a video clip in a lower dimensional space while preserving the intrinsic geometry of the data. The similarities observed between frame sequences are captured by defining two types of correlation graphs: an intra-correlation graph within a single video sequence and an inter-correlation graph between two sequences. A video retrieval and ranking tasks are designed to evaluate the manifold learning stage. The experimental outcome shows that the approach outperforms the conventional techniques in defining similar video contents and capture the spatio-temporal correlations between them.
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Anthonisz, Angela Jean. "Strategic alignment or non-alignment : the management of human capital in Dubai." Thesis, University of Derby, 2018. http://hdl.handle.net/10545/623047.
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This thesis focuses on the international hotel industry as part of the global economy and examines the implications that the strategic management of human capital has within the five-star sector of the hotel industry in Dubai, an emirate of the United Arab Emirates, and an economy based on the service sector. It examines the macro environmental factors influencing the potential strategic directions of two recognized international five-star hotel brands and considers the challenges this creates for the alignment of strategy, and the implications this has for management of human capital(people) as a key determinant of success that enhances organisational outcomes. In selecting this area of research, the author has adopted a grounded theory approach to the generation of new knowledge, allowing the literature to be guided by concerns raised by hotel managers and industry consultants working in the context of Dubai. This approach led to the employment of a case study method, through which the key influences of organisational culture and ownership are considered. Two international hotel chains were identified to represent the two strategic modes of entry into the destination. The first case being a locally owned and managed chain with 7 hotels in Dubai. The second case is a European chain operating 6 hotel properties under management contract in Dubai, with 6 different owners from the Middle East. Both companies operate within the luxury five-star market that is so prevalent in Dubai. The hospitality industry, by definition, relies heavily on human capital, both as a resource and a capability that may allow for the development of competitive advantage. However, the dynamics of the Dubai hotel environment, the strength of the Arab cultural values and the organisational conditions that exist in Dubai present HR managers with a number of unique challenges, including high levels of pastoral care, and approaches to managing the workforce that may be at odds with traditional ‘Western’ ideals. This thesis adds to the existing debate on the value and utilisation of existing theoretical frameworks attached to the alignment of strategy and the implications for managing human capital in the face of globalisation and presents a model of their application in a city that is characterised by power and control, predictability and change aversion.
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Sammeth, Michael. "Integrated multiple sequence alignment." [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=98148767X.
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Powell, David Richard 1973. "Algorithms for sequence alignment." Monash University, School of Computer Science and Software Engineering, 2001. http://arrow.monash.edu.au/hdl/1959.1/8051.
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Shokri, Razaghi Hazhir. "Study of Interference Alignment." Thesis, KTH, Kommunikationsteori, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-120502.
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The concept of interference alignment has recently become one of the importanttools to analyze the capacity of many multiuser communication networks,e.g. K-user interference channel, wireless X networks, multi hop interferencenetworks, etc. The idea is to consolidate the interference into smallerdimensions of signal space at each receiver and use the remaining dimensionsto transmit the desired signals. Furthermore, most progress in understandingof the wireless networks capacity has been made on the single hop schemes andmulti-hop multi-cast networks. However, there has not been as much progressin multi-hop multi-flow networks where all messages are not required by alldestination nodes. One of the basic problems in this area, is the capacity of2 × 2 × 2 interference channel. It is proved that the upper bound value of 2degrees of freedom (DoF) for this channel can be achieved using the so called“aligned interference neutralization” method.In the proposed interference alignment schemes for network problems whichwe mentioned in the above, including 2 × 2 × 2 interference channel, there aresome theoretical assumptions which seem to be difficult to apply in practice,e.g. high transmit power, asymptotic symbol extension of the channel, globaland perfect channel state information (CSI), etc. Among these assumptionsthe availability of CSI specially at transmitter, is crucial for performing theinterference alignment technique. The CSI at transmitter (CSIT) is usuallyavailable through feedback from receiver and it is used to estimate the currentchannel state, given that the channel coherence-time is long enough. However,it has been shown recently that the delayed CSIT, which is assumed to be independentof current channel state, still can be used to increase DoF of somespecific network settings.In this work, we consider the 2 × 2 × 2 interference channel where twosource nodes communicate with corresponding destination nodes via two relaynodes. We investigated the degrees of freedom of 2×2×2 interference channelwith delayed CSIT and we derived the upper bound on the degrees of freedomof the channel under this condition. Furthermore, we showed that this upperbound can be achieved using interference alignment technique. We also showedthat this completely out-of-date information of the channel can still be usefulto achieve higher rate compared to the situation where no CSIT is availableat the source nodes. Moreover, we observed that using relay nodes in interferencechannel can improve DoF compared to one hop interference channelwhere transmitters and receivers directly communicate with each other.
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Drayer, Benjamin [Verfasser], and Thomas [Akademischer Betreuer] Brox. "Object alignment and detection." Freiburg : Universität, 2017. http://d-nb.info/1156532620/34.
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Plüschke, Mareike. "Peak alignment in Estonian." Diss., Ludwig-Maximilians-Universität München, 2013. http://nbn-resolving.de/urn:nbn:de:bvb:19-158743.
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Earlier studies of Estonian showed that vowel quantity words (i.e. words dif-
fering only in vowel quantity) produced with an H*+L pitch accent differed
in their peak alignment: While words with a short and a long vowel had a
peak late in the vowel of the stressed syllable, words with an overlong vowel
were characterised by a peak earlier in the vowel (e.g. Asu et al., 2009; Lippus
et al., 2013). The main aim of this dissertation is to shed light on these peak
alignment differences: firstly, whether these alignment differences can be ex-
plained with the help of a segmental anchor; secondly, whether alignment is
similarily affected by quantity differences in consonants and vowels; thirdly,
whether such alignment differences are stable in regard to the prosodic con-
text, more precisely in regard to the number of post-focal unstressed syllables
(i.e. the vicinity to the sentence boundary) and a variation of the speaking
rate. Additionally, not only the peak alignment in regard to the vicinity
of an upcoming sentence boundary was investigated, but also the influence
of the sentence boundary on segment durations (phrase-final lengthening -
PFL). Previous studies (e.g. Krull, 1997; Asu et al., 2009) showed that PFL
occurs in Estonian, but it was not studied yet whether PFL affects vowel
and consonant quantity words differently. Furthermore no attempt made to
explain PFL in Estonian with the help of abstract phonological models. The
purpose of this dissertation is to fill this gap.
This dissertation contains three different experiments which are presented
in one chapter each. The first experiment (chapter 2) explored the influence
of the upcoming sentence boundary and its interaction with vowel (VQ)
and consonant (CQ) quantity on the peak alignment of falling nuclear H*+L
pitch accents. Disyllabic target words (C 1 V 1 C 2 V 2 ) only differing in either the
quantity of V 1 (VQ-words) or C 2 (CQ-words) were embedded in two different
carrier sentences: in one carrier sentence the target word was followed by two
unstressed syllables (long tail context) and in the other by none (short tail
ixcontext). All target words occured in three quantity degrees: short (Q1),
long (Q2) and overlong (Q3). There were two main results: (1) In the short
tail context the peak was aligned earlier. (2) The peak alignment of VQ- and
CQ-words was similar. Quantity degree differences of both VQ- and CQ-
words were cued by the peak alignment in proportion to the V 1 C 2 -duration.
The proportional peak alignment had the order Q3 < Q2 < Q1, where <
denotes that the peak of Q3-words was proportionally timed earlier than the
peak of Q2-words and so on.
The second experiment (chapter 3) analysed the influence of the sentence
boundary, i.e. phrase-final lengthening (PFL), on the segment durations of
VQ- and CQ-words. The data used for the analysis was the same as in the
first experiment. There were two main results: (1) The domain of PFL in
Estonian was the main bearer of the quantity contrast, i.e. V 1 in VQ-words
and C 2 in CQ-words and can be best accounted for in terms of a Structure-
based model for explaining PFL (Turk and Shattuck-Hufnagel, 2007). (2)
Progressive lengthening, i.e. the nearer a segment is to the final boundary
the more it is lengthened, occured in the data if the lengthened segments
were not in adjacent word-final position.
The third experiment (chapter 4) investigated whether speaking rate in-
fluences the alignment of the peak. VQ- and CQ-words were embedded in
carrier sentences with one unstressed syllable following the target word. They
were read in normal and fast speaking rate. There were two main results:
(1) In both VQ- and CQ-words the peak alignment in proportion to the
V 1 C 2 -duration had the order Q3 < Q2 < Q1, where < denotes that the
peak of Q3-words was aligned earlier than the peak of Q2-words and so on.
(2) Speaking rate did not influence the peak alignment in proportion to the
V 1 C 2 -duration.
The results of this dissertation favour in interpretation in the sense of the
segmental anchoring hypothesis (see e.g. Ladd et al., 1999, 2000; Schepman
et al., 2006) that tonal targets are anchored with specific points of the seg-
mental string. The results of the current dissertation created the impression
that in Estonian the offset of the first mora could be the anchorpoint for the
peak - regardless of quantity degree and type. Differences in the proportional
peak alignment emerge because the anchorpoint interacts with the temporal
correlates of the quantity contrast. Compatibly with Ladd (2008), the results
of the dissertation also show that peak alignment in Estonian is influenced
by phonologically-induced (an increase in the number of post-focal syllables)
but not phonetically-induced (faster speaking rate) time pressure.
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Willoughby, Patrick (Patrick John) 1978. "Elastically averaged precision alignment." Thesis, Massachusetts Institute of Technology, 2005. http://hdl.handle.net/1721.1/30361.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references (p. 107-110).
One of the most important steps in designing a machine is the consideration of the effect of interfaces between components. A badly designed interface can vary from costly difficulties such as additional control or calibration to machine failure. For precision assemblies such as automobile engines, robotics, and many measurement devices, exact constraint techniques have been used to align removable components. Exact constraint typically requires controlled precision machining to allow an interface to be repeatable and interchangeable. Elastic averaging techniques can be used instead of exact constraint to create less repeatable interfaces with more generous machining requirements. Elastic averaging represents a subset of coupling types where improved accuracy is derived from the averaging of errors over a large number of relatively compliant contacting members. Repeatability and accuracy obtained through elastic averaging can be nearly as high as in deterministic systems, elastic averaging design allows for higher stiffness and lower local stress when compared to kinematic couplings. In this thesis, a model of elastic averaging has been developed to predict the effects of manufacturing variations on design. To demonstrate the capabilities of this model, a new fiber optic connector has been designed with elastic averaging and precision injection molding in mind. Simulations predict repeatability of approximately 5 micrometers for a 5X scale version, which agreed with experimental measurements. Fidelity parts were produced using the Silicon Insert Molded Plastics process (SIMP). SIMP uses microfabricated silicon inserts in a traditional injection mold to create parts with micro-scale features.
(cont.) The SIMP fidelity parts were measured to estimate manufacturing repeatability of approximately 5 micrometers. Using this repeatability, simulations predict that the actual scale version has repeatability of approximately 0.5 micrometers
by Patrick Willoughby.
Ph.D.
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Birney, Ewan. "Sequence alignment in bioinformatics." Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.621653.
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Raglianti, Felipe. "The alignment of screens." Thesis, Lancaster University, 2016. http://eprints.lancs.ac.uk/83056/.
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This thesis makes a distinction between screen and surface. It proposes that an inquiry into screens includes, but is not limited to, the study of surfaces. Screens and screening practices are about doing both divisions and vision. The habit of reducing screens to the display neglects their capacity to emplace separations (think of folding screens). In this thesis an investigation of screens becomes a matter of asking how surfaces and the gaps in between them articulate alignments of people and things with displays that, in practice, always leave something out of sight. Rather than losing touch with screens by reducing them to surfaces, in other words, I am interested in alternative screen configurations. For this task I sketch an approach that touches on screens through the figures of lines, surfaces, textures, folds, knots and cuts. Lines help me to make the case for thinking about screens as alignments. I then ask what kinds of observers emerge from reducing screens to single or digital surfaces. I trace that concern with Google Glass, a pair of “smartglasses” with a transparent display. To distinguish between screen and surface I suggest, through a study of biodetection and assistance dogs, how to qualify or texture screens within webs of relations. I further outline, with snapshots of my workplace and two screens named Vig and Ben, two modes of touching or un/en/folding their locations. Finally, with knots and cuts, I underline the unfolding of self checkouts in supermarkets, and the enfolding of automated tellers outside banks. All of these reconfigurations experiment with screens by moving sideways in order to approach their displays laterally, and make visible their (ab)use by those in power. This method is a way of grasping the embodiment and the materiality of screens, while responding to the practices, agencies, and affects aligned around, through, and away from their displays.
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Shen, Wenzhuo. "EXPLAIN SINO-RUSSIAN ALIGNMENT." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1037975753.
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Huang, Hung-Jin, Rachel Mandelbaum, Peter E. Freeman, Yen-Chi Chen, Eduardo Rozo, and Eli Rykoff. "Intrinsic alignment in redMaPPer clusters – II. Radial alignment of satellites towards cluster centres." OXFORD UNIV PRESS, 2018. http://hdl.handle.net/10150/627131.
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We study the orientations of satellite galaxies in redMaPPer clusters constructed from the Sloan Digital Sky Survey at 0.1 < z < 0.35 to determine whether there is any preferential tendency for satellites to point radially towards cluster centres. We analyse the satellite alignment (SA) signal based on three shape measurement methods (re-Gaussianization, de Vaucouleurs, and isophotal shapes), which trace galaxy light profiles at different radii. The measured SA signal depends on these shape measurement methods. We detect the strongest SA signal in isophotal shapes, followed by de Vaucouleurs shapes. While no net SA signal is detected using re-Gaussianization shapes across the entire sample, the observed SA signal reaches a statistically significant level when limiting to a subsample of higher luminosity satellites. We further investigate the impact of noise, systematics, and real physical isophotal twisting effects in the comparison between the SA signal detected via different shape measurement methods. Unlike previous studies, which only consider the dependence of SA on a few parameters, here we explore a total of 17 galaxy and cluster properties, using a statistical model averaging technique to naturally account for parameter correlations and identify significant SA predictors. We find that the measured SA signal is strongest for satellites with the following characteristics: higher luminosity, smaller distance to the cluster centre, rounder in shape, higher bulge fraction, and distributed preferentially along the major axis directions of their centrals. Finally, we provide physical explanations for the identified dependences and discuss the connection to theories of SA.
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Jansson, Daniel, and Joel Karlsson. "Strategic Alignment and its influence on Purchasers : Propositions for constructing the strategic alignment." Thesis, Högskolan i Jönköping, Internationella Handelshögskolan, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:hj:diva-30811.
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Purpose The purpose of this research is to contribute towards a deeper understanding of the strategic alignments influence on the purchaser and how the alignment can be constructed to be more supportive for the purchaser. Methodology The empirical data were collected through interviews and document studies. A qualitative approach was used to get an in-depth understanding of the strategic alignment and its influence on the purchaser. The conclusions drawn in this study are based on the empirical findings and the constructed theoretical framework. Findings The authors identify 12 enablers/disablers that influence the purchaser’s ability to make strategically aligned decisions. Furthermore, the authors have conducted five propositions on what firms should consider when constructing their strategic alignment in order to enable the purchaser to make strategically aligned decisions Research limitations This research will be limited to the purchasing function and it will only embrace the internal integration connected to purchase. Thereby, the external orientation e.g. the effects from the supply-chain on the purchasing function and other effecting contexts will be outside the scope of this research. Implications This research provides a model that illustrates the areas connected to strategic alignment and enables both managers and researchers to map the construction of the strategic alignment in an easy and visualized manner. Together with the enablers/disablers and propositions managers and researchers will be able to recognize potential pitfalls and opportunities regarding the construction of firm’s strategic alignment. Originality / value To the researchers knowledge this is the first research that provides an in-depth understanding of how the strategic alignment influences the purchasers ability to make strategically aligned decisions.
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Nguyen, Ken D. "Multiple Biolgical Sequence Alignment: Scoring Functions, Algorithms, and Evaluations." Digital Archive @ GSU, 2011. http://digitalarchive.gsu.edu/cs_diss/62.
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Aligning multiple biological sequences such as protein sequences or DNA/RNA sequences is a fundamental task in bioinformatics and sequence analysis. These alignments may contain invaluable information that scientists need to predict the sequences' structures, determine the evolutionary relationships between them, or discover drug-like compounds that can bind to the sequences. Unfortunately, multiple sequence alignment (MSA) is NP-Complete. In addition, the lack of a reliable scoring method makes it very hard to align the sequences reliably and to evaluate the alignment outcomes.
In this dissertation, we have designed a new scoring method for use in multiple sequence alignment. Our scoring method encapsulates stereo-chemical properties of sequence residues and their substitution probabilities into a tree-structure scoring scheme. This new technique provides a reliable scoring scheme with low computational complexity.
In addition to the new scoring scheme, we have designed an overlapping sequence clustering algorithm to use in our new three multiple sequence alignment algorithms. One of our alignment algorithms uses a dynamic weighted guidance tree to perform multiple sequence alignment in progressive fashion. The use of dynamic weighted tree allows errors in the early alignment stages to be corrected in the subsequence stages. Other two algorithms utilize sequence knowledge-bases and sequence consistency to produce biological meaningful sequence alignments. To improve the speed of the multiple sequence alignment, we have developed a parallel algorithm that can be deployed on reconfigurable computer models. Analytically, our parallel algorithm is the fastest progressive multiple sequence alignment algorithm.
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Isa, Mohammad Nazrin. "High performance reconfigurable architectures for biological sequence alignment." Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/7721.
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Bioinformatics and computational biology (BCB) is a rapidly developing multidisciplinary field which encompasses a wide range of domains, including genomic sequence alignments. It is a fundamental tool in molecular biology in searching for homology between sequences. Sequence alignments are currently gaining close attention due to their great impact on the quality aspects of life such as facilitating early disease diagnosis, identifying the characteristics of a newly discovered sequence, and drug engineering. With the vast growth of genomic data, searching for a sequence homology over huge databases (often measured in gigabytes) is unable to produce results within a realistic time, hence the need for acceleration. Since the exponential increase of biological databases as a result of the human genome project (HGP), supercomputers and other parallel architectures such as the special purpose Very Large Scale Integration (VLSI) chip, Graphic Processing Unit (GPUs) and Field Programmable Gate Arrays (FPGAs) have become popular acceleration platforms. Nevertheless, there are always trade-off between area, speed, power, cost, development time and reusability when selecting an acceleration platform. FPGAs generally offer more flexibility, higher performance and lower overheads. However, they suffer from a relatively low level programming model as compared with off-the-shelf microprocessors such as standard microprocessors and GPUs. Due to the aforementioned limitations, the need has arisen for optimized FPGA core implementations which are crucial for this technology to become viable in high performance computing (HPC). This research proposes the use of state-of-the-art reprogrammable system-on-chip technology on FPGAs to accelerate three widely-used sequence alignment algorithms; the Smith-Waterman with affine gap penalty algorithm, the profile hidden Markov model (HMM) algorithm and the Basic Local Alignment Search Tool (BLAST) algorithm. The three novel aspects of this research are firstly that the algorithms are designed and implemented in hardware, with each core achieving the highest performance compared to the state-of-the-art. Secondly, an efficient scheduling strategy based on the double buffering technique is adopted into the hardware architectures. Here, when the alignment matrix computation task is overlapped with the PE configuration in a folded systolic array, the overall throughput of the core is significantly increased. This is due to the bound PE configuration time and the parallel PE configuration approach irrespective of the number of PEs in a systolic array. In addition, the use of only two configuration elements in the PE optimizes hardware resources and enables the scalability of PE systolic arrays without relying on restricted onboard memory resources. Finally, a new performance metric is devised, which facilitates the effective comparison of design performance between different FPGA devices and families. The normalized performance indicator (speed-up per area per process technology) takes out advantages of the area and lithography technology of any FPGA resulting in fairer comparisons. The cores have been designed using Verilog HDL and prototyped on the Alpha Data ADM-XRC-5LX card with the Virtex-5 XC5VLX110-3FF1153 FPGA. The implementation results show that the proposed architectures achieved giga cell updates per second (GCUPS) performances of 26.8, 29.5 and 24.2 respectively for the acceleration of the Smith-Waterman with affine gap penalty algorithm, the profile HMM algorithm and the BLAST algorithm. In terms of speed-up improvements, comparisons were made on performance of the designed cores against their corresponding software and the reported FPGA implementations. In the case of comparison with equivalent software execution, acceleration of the optimal alignment algorithm in hardware yielded an average speed-up of 269x as compared to the SSEARCH 35 software. For the profile HMM-based sequence alignment, the designed core achieved speed-up of 103x and 8.3x against the HMMER 2.0 and the latest version of HMMER (version 3.0) respectively. On the other hand, the implementation of the gapped BLAST with the two-hit method in hardware achieved a greater than tenfold speed-up compared to the latest NCBI BLAST software. In terms of comparison against other reported FPGA implementations, the proposed normalized performance indicator was used to evaluate the designed architectures fairly. The results showed that the first architecture achieved more than 50 percent improvement, while acceleration of the profile HMM sequence alignment in hardware gained a normalized speed-up of 1.34. In the case of the gapped BLAST with the two-hit method, the designed core achieved 11x speed-up after taking out advantages of the Virtex-5 FPGA. In addition, further analysis was conducted in terms of cost and power performances; it was noted that, the core achieved 0.46 MCUPS per dollar spent and 958.1 MCUPS per watt. This shows that FPGAs can be an attractive platform for high performance computation with advantages of smaller area footprint as well as represent economic ‘green’ solution compared to the other acceleration platforms. Higher throughput can be achieved by redeploying the cores on newer, bigger and faster FPGAs with minimal design effort.
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Blanco, García Enrique. "Meta-alignment of biological sequences." Doctoral thesis, Universitat Politècnica de Catalunya, 2006. http://hdl.handle.net/10803/6654.
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Les seqüències són una de les estructures de dades més versàtils que existeixen. De forma relativament senzilla, en una seqüència de símbols es pot emmagatzemar informació de qualsevol tipus. L'anàlisi sistemàtic de seqüències es un àrea molt rica de l'algorísmica amb numeroses aproximacions desenvolupades amb éxit. En concret, la comparació de seqüències mitjançant l'alineament d'aquestes és una de les eines més potents. Una de les aproximacions més populars i eficients per alinear dues seqüències es l'ús de la programació dinàmica. Malgrat la seva evident utilitat, un alineament de dues seqüències no és sempre la millor opció per a caracteritzar la seva funció. Moltes vegades, les seqüències codifiquen la informació en diferents nivells (meta-informació). És llavors quan la comparació directa entre dues seqüències no es capaç de revelar aquelles estructures d'ordre superior que podrien explicar la relació establerta entre aquestes seqüències.
Amb aquest treball hem contribuït a millorar la forma en que dues seqüències poden ser comparades, desenvolupant una família d'algorismes d'alineament de la informació d'alt nivell codificada en seqüències biològiques (meta-alineaments). Inicialment, hem redissenyat un antic algorisme, basat en programació dinàmica, que és capaç d'alinear dues seqüències de meta-informació, procedint després a introduir-hi vàries millores per accelerar la seva velocitat. A continuació hem desenvolupat un algorisme de meta-aliniament capaç d'alinear un número múltiple de seqüències, combinant l'algorisme general amb un esquema de clustering jeràrquic. A més, hem estudiat les propietats dels meta-alineaments produïts, modificant l'algorisme per tal d'identificar alineaments amb una configuració no necessàriament col.lineal, el que permet llavors la detecció de permutacions en els resultats.
La vida molecular és un exemple paradigmátic de la versatilitat de les seqüències. Les comparaciones entre genomes, ara que la seva seqüència està disponible, permeten identificar numerosos elements biològicament funcionals. La seqüència de nucleòtids de molts gens, per exemple, es troba acceptablement conservada entre diferents espècies. En canvi, les seqüències que regulen la activació dels propis gens són més curtes i variables. Així l'activació simultànea d'un conjunt de gens es pot explicar només a partir de la conservació de configuracions comunes d'elements reguladors d'alt nivell i no pas a partir de la simple conservació de les seves seqüències. Per tant, hem entrenat els nostres programes de meta-alineament en una sèrie de conjunts de regions reguladores recopilades per nosaltres mateixos de la literatura i desprès, hem provat la utilitat biològica de la nostra aproximació, caracteritzant automàticament de forma exitosa les regions activadores de gens humans conservats en altres espècies.
The sequences are very versatile data structures. In a straightforward manner, a sequence of symbols can store any type of information. Systematic analysis of sequences is a very rich area of algorithmics, with lots of successful applications. The comparison by sequence alignment is a very powerful analysis tool. Dynamic programming is one of the most popular and efficient approaches to align two sequences. However, despite their utility, alignments are not always the best option for characterizing the function of two sequences. Sequences often encode information in different levels of organization (meta-information). In these cases, direct sequence comparison is not able to unveil those higher-order structures that can actually explain the relationship between the sequences.
We have contributed with the work presented here to improve the way in which two sequences can be compared, developing a new family of algorithms that align high level information encoded in biological sequences (meta-alignment). Initially, we have redesigned an existent algorithm, based in dynamic programming, to align two sequences of meta-information, introducing later several improvements for a better performance. Next, we have developed a multiple meta-alignment algorithm, by combining the general algorithm with the progressive schema. In addition, we have studied the properties of the resulting meta-alignments, modifying the algorithm to identify non-collinear or permuted configurations.
Molecular life is a great example of the sequence versatility. Comparative genomics provide the identification of numerous biologically functional elements. The nucleotide sequence of many genes, for example, is relatively well conserved between different species. In contrast, the sequences that regulate the gene expression are shorter and weaker. Thus, the simultaneous activation of a set of genes only can be explained in terms of conservation between configurations of higher-order regulatory elements, that can not be detected at the sequence level. We, therefore, have trained our meta-alignment programs in several datasets of regulatory regions collected from the literature. Then, we have tested the accuracy of our approximation to successfully characterize the promoter regions of human genes and their orthologs in other species.
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Fleissner, Roland. "Sequence alignment and phylogenetic inference." Berlin : Logos Verlag, 2004. http://diss.ub.uni-duesseldorf.de/ebib/diss/file?dissid=769.
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Fleissner, Roland. "Sequence alignment and phylogenetic inference." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=971844704.
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Auer, Jens. "Metaheuristic Multiple Sequence Alignment Optimisation." Thesis, University of Skövde, School of Humanities and Informatics, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-899.
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The ability to tackle NP-hard problems has been greatly extended by the introduction of Metaheuristics (see Blum & Roli (2003)) for a summary of most Metaheuristics, general problem-independent optimisation algorithms extending the hill-climbing local search approach to escape local minima. One of these algorithms is Iterated Local Search (ILS) (Lourenco et al., 2002; Stützle, 1999a, p. 25ff), a recent easy to implement but powerful algorithm with results comparable or superior to other state-of-the-art methods for many combinatorial optimisation problems, among them the Traveling Salesman (TSP) and Quadratic Assignment Problem (QAP). ILS iteratively samples local minima by modifying the current local minimum and restarting
a local search porcedure on this modified solution. This thesis will show how ILS can be implemented for MSA. After that, ILS will be evaluated and compared to other MSA algorithms by BAliBASE (Thomson et al., 1999), a set of manually refined alignments used in most recent publications of algorithms and in at least two MSA algorithm surveys. The runtime-behaviour will be evaluated using runtime-distributions.
The quality of alignments produced by ILS is at least as good as the best algorithms available and significantly superiour to previously published Metaheuristics for MSA, Tabu Search and Genetic Algorithm (SAGA). On the average, ILS performed best in five out of eight test cases, second for one test set and third for the remaining two. A drawback of all iterative methods for MSA is the long runtime needed to produce good alignments. ILS needs considerably less runtime than Tabu Search and SAGA, but can not compete with progressive or consistency based methods, e. g. ClustalW or T-COFFEE.
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Arvestad, Lars. "Algorithms for biological sequence alignment." Doctoral thesis, KTH, Numerisk analys och datalogi, NADA, 1999. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-2905.
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Zhang, Liang, and Guido Brunnett. "Efficient Dynamic Alignment of Motions." Universitätsbibliothek Chemnitz, 2018. http://nbn-resolving.de/urn:nbn:de:bsz:ch1-qucosa-233521.
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We consider the computation of optimal alignments between sub-sequences of given motion clips based on dynamic programming. To avoid redundant computations in multiple alignment queries, we introduced the concept of a guideboard matrix. Using this data structure, the existence inquiry for an alignment is answered in O(1) time and the extraction of the alignment is done in O(n+m) time where n and m denote the numbers of frames in the considered motions.
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Kulkarni, Dattatraya H. "CDA, computation decomposition and alignment." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape16/PQDD_0008/NQ27983.pdf.
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Raum, Christopher Richard. "Fibre optic alignment using micromachines." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk3/ftp04/mq30540.pdf.
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Holmes, Christopher J. "Surface alignment control of nematodynamics." Thesis, University of Exeter, 2012. http://hdl.handle.net/10036/4009.
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The primary study of this thesis is the response of the nematic director to pressure driven flow. Dynamic flow experiments using optical conoscopy and pressure gradient measurements are used to explore the physics behind the flow alignment seen to occur for some nematic liquid crystals. New research into the techniques and methods for aligning the director at a glass interface is also presented, the results of which are used towards the latter end of this thesis in the production of a highly novel flow cell. A bespoke technique for fabricating robust liquid crystal flow cells is also presented. The observation of flow alignment for the nematic liquid crystal 5CB is detailed for pressure driven flow via optical conoscopy when the director is initially aligned planar homogeneously at 45◦ to the direction of flow. The results of this experiment are compared to the theory of Ericksen and Leslie through a one dimensional dynamic model that provides simulated director profiles and corresponding simulated conoscopic images. Good agreement between the data and simulation is observed, whereby the director is seen to rotate to become parallel to the flow direction whilst exhibiting no net tilt distortion at all flow rates. The presence of small surface pretilt from a rubbed planar aligning polyimide layer and its effect on director rotation is also examined for cells that are rubbed in both the parallel and anti-parallel directions. The result observed is a striking difference in the mean director rotation when initially aligned close to normal to the direction of flow. The results of these experiments are also compared to the theory of Ericksen and Leslie through the one dimensional dynamic model. Good agreement is seen, highlighting the dramatic effect that a small amount of surface pretilt can have on the overall director orientation, whilst also demonstrating the need for caution when assuming that rubbed conventional alignment techniques provide true planar orientation. Two methods for producing intermediate or large pretilt angles at liquid crystal align- ment surfaces are also examined. Here, two recipes involving the commercial polyimides Nissan SE-1211, Nissan SE-130 and Nissan SE-4811 are experimentally investigated, with results showing the ability to tune the director pretilt angle as a function of the rubbing strength used to align the sample. The results also show an interesting depen- dance on the material upon which the aligning layer is deposited for the recipe involving Nissan SE-1211. Here, vastly different pretilt angles are observed for cells constructed with glass and indium tin oxide (ITO) layers. Finally, the large pretilt angles produced from the recipes mentioned above are also used to fabricate pressure driven flow cells exhibiting large pretilt angles on both sur- faces, constraining the director to align in a splayed state. When aligned parallel to the flow direction, experiments examining the valve-like nature of the director profile suggest that a preferential flow direction exists in what here is termed the ‘diode cell’. Measurements of the pressure gradient required to achieve a constant volumetric flow rate through the cell are compared for flow in both directions relative to the splayed di- rector profile. A striking difference is observed for flow ‘with’ the splay and ‘against’ the splay, leading to the realisation of a cell exhibiting a preferential flow direction through surface treatment. Again, results are compared to the theory of Ericksen and Leslie through the one dimensional dynamic model, showing good agreement.
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Ishihara, Takeshi. "Tonal alignment in Tokyo Japanese." Thesis, University of Edinburgh, 2006. http://hdl.handle.net/1842/1469.
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A large amount of evidence for regularities of tonal alignment in various languages has been accumulated recently. However, there is still much disagreement on the characterisation and modelling of these alignment regularities. This thesis investigates tonal alignment in Tokyo Japanese with two objectives. One is to provide a thorough description of tonal alignment in Tokyo Japanese, including a well-known phenomenon, ososagari ('peak delay'); the other is to contribute to the current understanding of tonal alignment, based on empirical data of tonal alignment in Tokyo Japanese. Three speech production experiments were performed. The first experiment examined the alignment of the F0 targets at the beginning of initial-accented words, varying the syllable/mora structures of the accented syllable. The results showed that both the F0 valley and peak were consistently aligned with specific segmental landmarks, and that the alignment of the F0 peak depended on the syllable/mora structure of the accented syllable. The second experiment explored how the alignment patterns found in the first experiment were influenced in different speaking modes; the speaking modes of interest were fast speech rate, raised voice, and local emphasis. The results showed that the orderly alignment behaviour found in the first experiment remained intact irrespective of different speaking modes, although different kinds of small effects were found. The third experiment compared the F0 peak alignment of unaccented and non-initial-accented words to those of initial-accented words. The results of unaccented words demonstrated consistent alignment of the F0 peak with a specific landmark, which is comparable to those of initial-accented words. On the other hand, the results of non-initial-accented words showed earlier alignment of the F0 peak for the pitch accent than those of initial-accented words. The results of the current study as a whole demonstrate consistent alignment of the F0 targets with specific places in the prosodic structure in a language-specific way, which are rather resistant to changes caused by differences of speaking mode. Further durational analyses, together with the alignment data, also suggest that segments and tones are mutually synchronised with each other. These findings provide further evidence that segmental anchoring is a necessary concept in accounting for alignment regularities.
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Ho, Ngai-lam, and 何毅林. "Algorithms on constrained sequence alignment." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30201949.
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Siu, Wing-yan, and 蕭穎欣. "Multiple structural alignment for proteins." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2008. http://hub.hku.hk/bib/B4068748X.
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Ho, Wai-cheong, and 何偉昌. "Business and information technology alignment." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1998. http://hub.hku.hk/bib/B31268833.
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Krishnamurthy, Sundar Rajan. "Interference Alignment| Beyond Generic Channels." Thesis, University of California, Irvine, 2014. http://pqdtopen.proquest.com/#viewpdf?dispub=3646739.
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Capacity characterization of communication networks is the most fundamental problem in Information Theory, that underlies the design of various wireless and wired networks. The radical idea of "Interference alignment" has enabled Capacity or Degrees of Freedom characterization (DoF, a first order approximation) for many interference networks. Various alignment schemes developed have provided new and fundamental insights into the number of accessible signal dimensions in communication networks where the output signals are linear functions of the input signals. Most of the prior art deal with generic channels wherein the channel coefficients are assumed to be independent and drawn from a continuous distribution, continuous alphabet with infinite diversity, and the network is often single-hop. These assumptions are challenged due to the following reasons: 1) In MIMO systems, poor scattering environment and network topology lead to spatial dependencies that are manifested as rank deficient channels, 2) Multi-hop dependencies arise due to the presence of relays, and 3) Linear network coding applications (as in wired networks) act as finite field counterparts of wireless networks, with limited diversity.
In this thesis, Capacity / DoF of linear communication networks are characterized for "Non-generic channels". One of the significant problems considered is the DoF of the K-user MIMO rank deficient interference channel, with different ranks for the direct and the cross channels. For this rank deficient interference channel, it is shown that the rank deficiency of direct channels does not help DoF and the rank-deficiency of cross-channels does not hurt DoF. The main challenge is to account for the spatial dependencies introduced by rank deficiencies in the interference alignment schemes that typically rely on the independence of channel coefficients. Another interesting problem is the DoF of Two-hop MIMO rank deficient interference channel with different channel ranks in the first and the second hops, for which a rank-matching principle is identified reminiscent of impedance matching in circuit theory. For this channel, the DoF loss is shown to be the rank-mismatch between the two hops. Finally, capacity results for the finite field counterparts of wireless networks are presented, exploring the implications of channels being from a finite alphabet with limited diversity. By characterizing the capacity of constant finite field channels over Fpn for 2-user X channel and 3-user interference channel, interesting parallels are drawn between p and SNR, and n and Channel Diversity.
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Hallam, Benjamin Thomas. "Grating alignment of liquid crystals." Thesis, University of Exeter, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.312444.
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Weber, Alexis Christian 1974. "Precision passive alignment of wafers." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/89364.
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Khohayting, Jerome S. (Jerome Suntay). "Automatic orthographic alignment of speech." Thesis, Massachusetts Institute of Technology, 1994. http://hdl.handle.net/1721.1/36447.
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Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994.Includes bibliographical references (leaves 86-87).
by Jerome S. Khohayting.
M.Eng.
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Fay, Matthew Paul. "Enabling imagination through story alignment." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/71281.
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Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2012.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student submitted PDF version of thesis.
Includes bibliographical references (p. 81-82).
Stories are an essential piece of human intelligence. They exist in countless forms and varieties seamlessly integrated into every facet of our lives. Stories fuel human understanding and our explanations of the world. Narrative acts as a Swiss army knife, simultaneously facilitating the transfer of knowledge, culture and beliefs while also powering our high level mental faculties. If we are to develop artificial intelligence with the cognitive capacities of humans, our systems must not only be able to understand stories but also to incorporate them into the thought process as humans do. In order to work towards the goal of computational story understanding, I developed a novel story comparison method. The techniques I present in this thesis enable efficient and effective story comparison through story alignment. My algorithms, implemented into the Genesis system, allow the comparison and combination of stories which is a step towards enabling imagination in artificial intelligence. This capability is made possible by reducing the runtime of a previously intractable computational problem to polynomial time. In the course of this research, these algorithms have been applied to a variety of story analysis problems. By comparing short, 10 sentence summaries of the Tet Offensive and the Yom Kippur War, the system predicts information omitted from both stories. In the analysis of a brief synopsis of Shakespeare's Macbeth, my algorithm is able to correctly match actors and events between two different variations of the tale by cutting down a search space of over 10³⁰ nodes to a mere 546 nodes. My techniques also demonstrate promise as a component of a larger video analysis system. The story alignment capabilities are used to fill in missing gaps in descriptions of videos, corresponding to missing video data, by comparing video feeds to an existing video corpus.
by Matthew Paul Fay.
S.M.
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Green-Petersen, Minna. "Mitochondrial alignment in ATP gradients." Thesis, KTH, Tillämpad fysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-189551.
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Liu, Zhonghao. "Interference Alignment through Propagation Delay." Thesis, University of North Texas, 2020. https://digital.library.unt.edu/ark:/67531/metadc1703337/.
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With the rapid development of wireless communication technology, the demands for higher communication rates are increasing. Higher communication rate corresponds to higher DoF. Interference alignment, which is an emerging interference management technique, is able to substantially increase the DoF of wireless communication systems. This thesis mainly studies the delay-based interference alignment technique. The key problem lies in the design of the transmission scheme and the appropriate allocation of the propagation delay, so as to achieve the desired DoF of different wireless networks. In addition, through delay-based interference alignment, the achievability of extreme points of the DoF region of different wireless networks can be proved.
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Korhonen, Daniel. "Wheel alignment method feasibility study." Thesis, KTH, Fordonsdynamik, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-280555.
Full textAbstract:
Throughout the history of motor vehicles, the tyres have always been consideredas one of the most important components of the vehicle due to their interactionwith the road. One important aspect is the wheel alignment, with the purposeto adjust the static wheel angles that are essential for many reasons, such assafety and fuel consumption for instance. Despite the numerous methods forwheel angle measurements, there seems to be no existing technical solutionbased on computer vision, that is suitable for residential use, regarding bothcost and size of the equipment. The study aims to investigate the feasibility ofsuch a system.The proposed system is based on planar fiducial markers called ArUco.From images or video frames of the marker, the pose of the marker can beestimated. Thus, by placing such markers on the ground, on the wheel andon the vehicle, the estimated pose of the markers can be used to measure andcalculate the wheel alignment parameters. Only toe and camber angles aremeasured within the scope of this thesis, even if the system has the potential tomeasure other wheel alignment parameters as well.After camera calibration, simplified ArUco marker tests were done by measuringthe known displacement and inclination of a marker with respect to areference marker. The mean absolute error was 030400 and 0:024mm for theinclination angle and displacement, respectively. Furthermore, the toe and camberangles of a vehicle were measured and compared to reference measurementsperformed with a commercial wheel alignment system, giving mean absoluteerrors of 0520 and 0280 for the camber and toe angles, respectively. Despitethe relatively large errors for the toe and camber angle measurements, theresults from the initial inclination and displacement tests show the potential ofthe system. In addition, several error sources and suggestions for improvementcan be identified.As a conclusion, the proposed system can be considered a working firstprototype, which after improvement and optimisation has the potential tobecome a feasible alternative, especially for residential use and for mobileworkshops due to the low cost, size and usability of the system.Inom fordonstekniken har däcken alltid betraktats som en av fordonets viktigastekomponenter på grund av deras interaktion med vägen. En viktig aspektär hjulinställning, med syftet att justera de statiska hjulvinklarna som är viktigaav många anledningar, som exempelvis säkerhet och bränsleförbrukning.Trots flera metoder för mätning av hjulvinklar verkar det inte finnas någonbefintlig teknisk lösning baserad på datorseende, som är lämplig för privat brukbåde gällande kostnad och storlek på utrustningen. Syftet med studien är attundersöka genomförbarheten för ett sådant system.Det föreslagna systemet är baserat på plana ArUco-markörer. Från bildereller bildrutor i en video av markören kan dess läge uppskattas. Genom attplacera sådana markörer på marken, på hjulet och på fordonet, kan såledesmarkörernas uppskattade lägen användas för att mäta och beräkna hjulvinklarna.Endast toe- och cambervinklar mäts inom ramen för detta examensarbete, ävenom systemet också kan mäta andra hjulvinklar.Efter kamerakalibrering utfördes enkla ArUco-markörtester genom att mätaden kända förskjutningen och vinkeln av en markör i förhållande till en referensmarkör.De genomsnittliga absoluta felen var 030400 och 0:024mm förvinkeln respektive förskjutningen. Vidare mättes toe- och cambervinklar påett fordon och jämfördes med referensmätningar utförda med ett kommersiellthjulinställningssystem. De genomsnittliga absoluta felen var 0520 och 0280för camber- respektive toevinkeln. Trots de relativt stora felen i mätningarnaav toe- och cambervinklar visar resultaten från de första testerna systemetspotential. Dessutom kan flera felkällor och förslag till förbättringar identifieras.Som en slutsats kan det föreslagna systemet betraktas som en fungerandeförsta prototyp, som efter förbättring och optimering har potential att bli ettmöjligt alternativ, särskilt för hemmabruk och för mobila verkstäder på grundav låga kostnader, systemets ringa storlek och användbarhet.