Ribonucleic acid (RNA) sometimes occurs in a complex structure called pseudoknots. Prediction of RNA secondary structures has drawn much attention from both biologists and computer scientists. Consequently, many useful tools have been developed for RNA secondary structure prediction, with or without pseudoknots. These tools have their individual strength and weakness. As a result, we propose a hybrid feature extraction method which integrates two prediction tools pknotsRG and NUPACK with a support vector machine (SVM). We first extract some useful features from the target RNA sequence, and then decide its prediction tool preference with SVM classification. Our test data set contains 723 RNA sequences, where 202 pseudoknotted RNA sequences are obtained from PseudoBase, and 521 nested RNA sequences are obtained from RNA SSTRAND. Experimental results show that our method improves not only the overall accuracy but also the sensitivity and the selectivity of the target sequences. Our method serves as a preprocessing process in analyzing RNA sequences before employing the RNA secondary structure prediction tools. The ability to combine the existing methods and make the prediction tools more accurate is our main contribution.

<p>This licentiate thesis presents a software architecture for inductive labeled dependency parsing of unrestricted natural language text, which achieves a strict modularization of parsing algorithm, feature model and learning method such that these parameters can be varied independently. The architecture is based on the theoretical framework of inductive dependency parsing by Nivre \citeyear{nivre06c} and has been realized in MaltParser, a system that supports several parsing algorithms and learning methods, for which complex feature models can be defined in a special description language. Special attention is given in this thesis to learning methods based on support vector machines (SVM).</p><p>The implementation is validated in three sets of experiments using data from three languages (Chinese, English and Swedish). First, we check if the implementation realizes the underlying architecture. The experiments show that the MaltParser system outperforms the baseline and satisfies the basic constraints of well-formedness. Furthermore, the experiments show that it is possible to vary parsing algorithm, feature model and learning method independently. Secondly, we focus on the special properties of the SVM interface. It is possible to reduce the learning and parsing time without sacrificing accuracy by dividing the training data into smaller sets, according to the part-of-speech of the next token in the current parser configuration. Thirdly, the last set of experiments present a broad empirical study that compares SVM to memory-based learning (MBL) with five different feature models, where all combinations have gone through parameter optimization for both learning methods. The study shows that SVM outperforms MBL for more complex and lexicalized feature models with respect to parsing accuracy. There are also indications that SVM, with a splitting strategy, can achieve faster parsing than MBL. The parsing accuracy achieved is the highest reported for the Swedish data set and very close to the state of the art for Chinese and English.</p> / <p>Denna licentiatavhandling presenterar en mjukvaruarkitektur för</p><p>datadriven dependensparsning, dvs. för att automatiskt skapa en</p><p>syntaktisk analys i form av dependensgrafer för meningar i texter</p><p>på naturligt språk. Arkitekturen bygger på idén att man ska kunna variera parsningsalgoritm, särdragsmodell och inlärningsmetod oberoende av varandra. Till grund för denna arkitektur har vi använt det teoretiska ramverket för induktiv dependensparsning presenterat av Nivre \citeyear{nivre06c}. Arkitekturen har realiserats i programvaran MaltParser, där det är möjligt att definiera komplexa särdragsmodeller i ett speciellt beskrivningsspråk. I denna avhandling kommer vi att lägga extra tyngd vid att beskriva hur vi har integrerat inlärningsmetoden supportvektor-maskiner (SVM).</p><p>MaltParser valideras med tre experimentserier, där data från tre språk används (kinesiska, engelska och svenska). I den första experimentserien kontrolleras om implementationen realiserar den underliggande arkitekturen. Experimenten visar att MaltParser utklassar en trivial metod för dependensparsning (\emph{eng}. baseline) och de grundläggande kraven på välformade dependensgrafer uppfylls. Dessutom visar experimenten att det är möjligt att variera parsningsalgoritm, särdragsmodell och inlärningsmetod oberoende av varandra. Den andra experimentserien fokuserar på de speciella egenskaperna för SVM-gränssnittet. Experimenten visar att det är möjligt att reducera inlärnings- och parsningstiden utan att förlora i parsningskorrekthet genom att dela upp träningsdata enligt ordklasstaggen för nästa ord i nuvarande parsningskonfiguration. Den tredje och sista experimentserien presenterar en empirisk undersökning som jämför SVM med minnesbaserad inlärning (MBL). Studien använder sig av fem särdragsmodeller, där alla kombinationer av språk, inlärningsmetod och särdragsmodell</p><p>har genomgått omfattande parameteroptimering. Experimenten visar att SVM överträffar MBL för mer komplexa och lexikaliserade särdragsmodeller med avseende på parsningskorrekthet. Det finns även vissa indikationer på att SVM, med en uppdelningsstrategi, kan parsa en text snabbare än MBL. För svenska kan vi rapportera den högsta parsningskorrektheten hittills och för kinesiska och engelska är resultaten nära de bästa som har rapporterats.</p>

Thesis (M.S.)--University of North Carolina at Wilmington, 2003. / Includes bibliographical references (leaves : [44]).

Thesis (Ph. D.)--School of Industrial and Systems Engineering, Georgia Institute of Technology, 2004. Directed by Joel S. Sokol. / Vita. Includes bibliographical references (leaves 114-116).

Thesis (Ph. D.)--University of Texas at Austin, 1999. / Vita. Includes bibliographical references (leaves 160-162). Available also in a digital version from Dissertation Abstracts.

Thesis (Ph. D.)--University of California, San Diego, 2003. / Vita. Includes bibliographical references.

Thesis (M. Phil.)--University of Hong Kong, 2010. / Includes bibliographical references (p. 67-[70]). Also available in print.

Thesis (Ph. D.)--University of Hong Kong, 2002. / Includes bibliographical references (leaves 171-191).

A new ensemble method for cluster analysis is introduced, which can be interpreted in two different ways: As complexity-reducing preprocessing stage for hierarchical clustering and as combination procedure for several partitioning results. The basic idea is to locate and combine structurally stable cluster centers and/or prototypes. Random effects of the training set are reduced by repeatedly training on resampled sets (bootstrap samples). We discuss the algorithm both from a more theoretical and an applied point of view and demonstrate it on several data sets. (author's abstract) / Series: Working Papers SFB "Adaptive Information Systems and Modelling in Economics and Management Science"

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