<div> <div> <div> <p>Nowadays, the pace of coordinated cyber security crimes has become drastically more rapid, and network attacks have become more advanced and diversified. The explosive growth of network security threats poses serious challenges for building secure Cyber-based Systems (CBS). Existing studies have addressed a breadth of challenges related to detecting network attacks. However, there is still a lack of studies on the detection of sophisticated Multi-stage Attacks (MSAs). </p> <p>The objective of this dissertation is to address the challenges of modeling and detecting sophisticated network attacks, such as multiple interleaved MSAs. We present the interleaving concept and investigate how interleaving multiple MSAs can deceive intrusion detection systems. Using one of the important statistical machine learning (ML) techniques, Hidden Markov Models (HMM), we develop three architectures that take into account the stealth nature of the interleaving attacks, and that can detect and track the progress of these attacks. These architectures deploy a set of HMM templates of known attacks and exhibit varying performance and complexity. </p> <p>For performance evaluation, various metrics are proposed which include (1) attack risk probability, (2) detection error rate, and (3) the number of correctly detected stages. Extensive simulation experiments are conducted to demonstrate the efficacy of the proposed architecture in the presence of multiple multi-stage attack scenarios, and in the presence of false alerts with various rates. </p> </div> </div> </div>

This dissertation addresses the development of a telemanipulation system using intelligent mapping from a haptic user interface to a remote manipulator to assist in maximizing the manipulation capabilities of persons with disabilities. This mapping, referred to as assistance function, is determined on the basis of environmental model or real-time sensory data to guide the motion of a telerobotic manipulator while performing a given task. Human input is enhanced rather than superseded by the computer. This is particularly useful when the user has restricted range of movements due to certain disabilities such as muscular dystrophy, a stroke, or any form of pathological tremor. In telemanipulation system, assistance of variable position/velocity mapping or virtual fixture can improve manipulation capability and dexterity. Conventionally, these assistances are based on the environment information, without knowing user's motion intention. In this dissertation, user's motion intention is combined with real-time environment information for applying appropriate assistance. If the current task is following a path, a virtual fixture orthogonal to the path is applied. Similarly, if the task is to align the end-effector with a target, an attractive force field is generated. In order to successfully recognize user's motion intention, a Hidden Markov Model (HMM) is developed. This dissertation describes the HMM based skill learning and its application in a motion therapy system in which motion along a labyrinth is controlled using a haptic interface. Two persons with disabilities on upper limb are trained using this virtual therapist. The performance measures before and after the therapy training, including the smoothness of the trajectory, distance ratio, time taken, tremor and impact forces are presented. The results demonstrate that the forms of assistance provided reduced the execution times and increased the performance of the chosen tasks for the disabled individuals. In addition, these results suggest that the introduction of the haptic rendering capabilities, including the force feedback, offers special benefit to motion-impaired users by augmenting their performance on job related tasks.

Die Identifikation der Bindungsspezifitäten von Proteininteraktionsdomänen und damit letztlich auch ‎die Fähigkeit potentielle Bindungspartner dieser in vivo vorherzusagen bildet ein grundlegendes ‎Element für das Verständnis der biologischen Funktionen dieser Domänen. In dieser Arbeit wurde ‎untersucht, inwieweit solche Vorhersagen bezüglich der SH3-Domäne – als Beispiel für eine ‎Proteininteraktionsdomäne – mithilfe von Support-Vector-Machines (SVMs) möglich sind, wenn ‎diesen als Informationsquelle ausschließlich die innerhalb der Aminosäuresequenz der Domäne ‎konservierten Informationen zur Verfügung stehen. Um den SVM-basierten Klassifikator zu ‎trainieren und zu validieren, wurde ein Satz aus 51 SH3-Domänen verwendet, die zuvor ‎entsprechend ihrer Ligandenpräferenz in ein System aus acht verschiedenen Klassen eingeteilt ‎worden waren. Da die innerhalb der Aminosäuresequenzen konservierten Informationen in ‎abstrakte Zahlenwerte konvertiert werden mussten (Voraussetzung für mathematisch basierte ‎Klassifikatoren wie SVMs), wurde jede Aminosäuresequenz durch ihren jeweiligen Fisher-Score-‎Vektor ausgedrückt. Die Ergebnisse erbrachten einen Klassifikationserror, welcher weit unterhalb des ‎Zufallsniveaus lag, was darauf hindeutet, dass sich die Bindungsspezifität (Klasse) einer SH3-Domäne ‎in der Tat von seiner Aminosäuresequenz ableiten lassen dürfte. Mithilfe klassenspezifisch ‎emittierter, artifizieller Sequenzen, implementiert in den Trainingsprozess des Klassifikators, um ‎etwaigen nachteiligen Auswirkungen von Overfitting zu entgegenzuwirken, sowie durch ‎Berücksichtigung taxonomischer Informationen des Klassensystems während Training und ‎Validierung, ließ sich der Klassifikationserror sogar noch weiter senken und lag schließlich bei lediglich ‎‎35,29% (vergleiche Zufall: 7/8 = 87.50%). Auch die Nutzung von Feature Selections zur Abmilderung ‎Overfitting-bedingter, negativer Effekte lieferte recht vielversprechende Ergebnisse, wenngleich ihr ‎volles Potential aufgrund von Software-Beschränkungen nicht ausgenutzt werden konnte.‎ Die Analyse der Positionen im Sequence-Alignment, welche für den SVM- basierten Klassifikator am ‎relevantesten waren, zeigte, dass diese häufig mit Positionen korrelierten, von denen angenommen ‎wird auch in vivo eine Schlüsselrolle bei der Determination der Bindungsspezifität (Klasse) zu spielen. ‎Dies unterstreicht nicht nur die Reliabilität des präsentierten Klassifikators, es gibt auch Grund zur ‎Annahme, dass das Verfahren möglicherweise auch als Supplement anderer Ansätze genutzt werden ‎könnte, welche zum Ziel haben die Positionen zu identifizieren, die die Ligandenpräferenz in vivo ‎determinieren. Informationen, die nicht nur für ein besseres Verständnis der SH3-Domäne (und ‎möglicherweise auch anderer Proteininteraktionsdomänen) von grundlegender Bedeutung sind, ‎sondern auch aus pharmakologischer Sicht von großem Interesse sein dürften.‎ / Regarding protein-interaction-domains the identification of their binding specificities and ‎eventually ‎also the ability to predict potential binding partners for them in vivo constitutes a fundamental ‎element for the understanding of the biological functions of these domains. In this study it ‎was ‎investigated to what extent such predictions could be made for the SH3-domain – as an ‎example ‎for a protein-interaction-domain – when using support-vector-machines (SVMs) trained ‎exclusively ‎with the information conserved within the amino-acid-sequence of the domain. A set of ‎‎51 SH3-‎domains, pre-classified into a system of eight different classes according to their ligand ‎preference, was used to train and cross-validate the SVM-based classifier. To convert the ‎information ‎conserved within the amino-acid-sequences into abstract numeric values (a ‎prerequisite for a ‎mathematics-based classifier like SVMs) each sequence was represented by its ‎respective Fisher-‎score-vector. The results revealed a classification error level way below chance ‎level, indicating the ‎binding specificity (class) of an SH3-domain can indeed be inferred from its ‎amino-acid-sequence. ‎With the help of class-specific emitted, artificial sequences introduced into ‎the training process of the ‎classifier to counter adverse overfitting effects and by additionally ‎considering taxonomic ‎information of the class system during training and cross-validation, the ‎classification error level of ‎the classifier could be lowered even farther, eventually reaching a level ‎as low as 35.29% (compare ‎chance level: 7/8 = 87.50%). The use feature selections to counter ‎overfitting returned quite ‎promising results, too, however couldn't be exploited to its full potential ‎due to software limitations. ‎ The analysis of those positions in the sequence-alignment being most relevant for the SVM-‎based ‎classifier showed, they frequently correlated with positions considered to also play in vivo a ‎pivotal ‎role in binding specificity (class) determination of the SH3-domain. Not only does this ‎underline the ‎reliability of the presented classifier, it also gives reason to believe, the method could ‎possibly be ‎used as a supplement for other approaches trying to identify positions that determine ‎ligand ‎preference in vivo. Information, not only fundamental for a better understanding of the SH3-‎‎domain (and maybe also other protein-interaction-domains), but also likely to be of great interest ‎from a pharmacological point of view.‎

Modeling patterns in temporal data has arisen as an important problem in engineering and science. This has led to the popularity of several dynamic models, in particular the renowned hidden Markov model (HMM) [Rabiner, 1989]. Despite its widespread success in many cases, the standard HMM often fails to model more complex data whose elements are correlated hierarchically or over a long period. Such problems are, however, frequently encountered in practice. Existing efforts to overcome this weakness often address either one of these two aspects separately, mainly due to computational intractability. Motivated by this modeling challenge in many real world problems, in particular, for video surveillance and segmentation, this thesis aims to develop tractable probabilistic models that can jointly model duration and hierarchical information in a unified framework. We believe that jointly exploiting statistical strength from both properties will lead to more accurate and robust models for the needed task. To tackle the modeling aspect, we base our work on an intersection between dynamic graphical models and statistics of lifetime modeling. Realizing that the key bottleneck found in the existing works lies in the choice of the distribution for a state, we have successfully integrated the discrete Coxian distribution [Cox, 1955], a special class of phase-type distributions, into the HMM to form a novel and powerful stochastic model termed as the Coxian Hidden Semi-Markov Model (CxHSMM). We show that this model can still be expressed as a dynamic Bayesian network, and inference and learning can be derived analytically. / Most importantly, it has four superior features over existing semi-Markov modelling: the parameter space is compact, computation is fast (almost the same as the HMM), close-formed estimation can be derived, and the Coxian is flexible enough to approximate a large class of distributions. Next, we exploit hierarchical decomposition in the data by borrowing analogy from the hierarchical hidden Markov model in [Fine et al., 1998, Bui et al., 2004] and introduce a new type of shallow structured graphical model that combines both duration and hierarchical modelling into a unified framework, termed the Coxian Switching Hidden Semi-Markov Models (CxSHSMM). The top layer is a Markov sequence of switching variables, while the bottom layer is a sequence of concatenated CxHSMMs whose parameters are determined by the switching variable at the top. Again, we provide a thorough analysis along with inference and learning machinery. We also show that semi-Markov models with arbitrary depth structure can easily be developed. In all cases we further address two practical issues: missing observations to unstable tracking and the use of partially labelled data to improve training accuracy. Motivated by real-world problems, our application contribution is a framework to recognize complex activities of daily livings (ADLs) and detect anomalies to provide better intelligent caring services for the elderly. / Coarser activities with self duration distributions are represented using the CxHSMM. Complex activities are made of a sequence of coarser activities and represented at the top level in the CxSHSMM. Intensive experiments are conducted to evaluate our solutions against existing methods. In many cases, the superiority of the joint modeling and the Coxian parameterization over traditional methods is confirmed. The robustness of our proposed models is further demonstrated in a series of more challenging experiments, in which the tracking is often lost and activities considerably overlap. Our final contribution is an application of the switching Coxian model to segment education-oriented videos into coherent topical units. Our results again demonstrate such segmentation processes can benefit greatly from the joint modeling of duration and hierarchy.

In this thesis, we consider a robust state estimation problem for discrete-time, homogeneous, first-order, finite-state finite-alphabet hidden Markov models (HMMs). Based on Kolmogorov's Theorem on the existence of a process, we first present the Kolmogorov model for the HMMs under consideration. A new change of measure is introduced. The statistical properties of the Kolmogorov representation of an HMM are discussed on the canonical probability space. A special Kolmogorov measure is constructed. Meanwhile, the ergodicity of two expanded Markov chains is investigated. In order to describe the uncertainty of HMMs, we study probability distance problems based on the Kolmogorov model of HMMs. Using a change of measure technique, the relative entropy and the relative entropy rate as probability distances between HMMs, are given in terms of the HMM parameters. Also, we obtain a new expression for a probability distance considered in the existing literature such that we can use an information state method to calculate it. Furthermore, we introduce regular conditional relative entropy as an a posteriori probability distance to measure the discrepancy between HMMs when a realized observation sequence is given. A representation of the regular conditional relative entropy is derived based on the Radon-Nikodym derivative. Then a recursion for the regular conditional relative entropy is obtained using an information state method. Meanwhile, the well-known duality relationship between free energy and relative entropy is extended to the case of regular conditional relative entropy given a sub-[special character]-algebra. Finally, regular conditional relative entropy constraints are defined based on the study of the probability distance problem. Using a Lagrange multiplier technique and the duality relationship for regular conditional relative entropy, a finite horizon robust state estimator for HMMs with regular conditional relative entropy constraints is derived. A complete characterization of the solution to the robust state estimation problem is also presented.

Two new spatio-temporal hidden Markov models (HMM) are introduced in this thesis, with the purpose of capturing the persistent, spatially non-homogeneous nature of climate influence on annual rainfall series observed in Australia. The models extend the two-state HMM applied by Thyer (2001) by relaxing the assumption that all sites are under the same climate control. The Switch HMM (SHMM) allows at-site anomalous states, whilst still maintaining a regional control. The Regional HMM (RHMM), on the other hand, allows sites to be partitioned into different Markovian state regions. The analyses were conducted using a Bayesian framework to explicitly account for parameter uncertainty and select between competing hypotheses. Bayesian model averaging was used for comparison of the HMM and its generalisations. The HMM, SHMM and RHMM were applied to four groupings of four sites located on the Eastern coast of Australia, an area that has previously shown evidence of interannual persistence. In the majority of case studies, the RHMM variants showed greatest posterior weight, indicating that the data favoured the multiple region RHMM over the single region HMM or the SHMM variants. In no cases does the HMM produce the maximum marginal likelihood when compared to the SHMM and RHMM. The HMM state series and preferred model variants were sensitive to the parameterisation of the small-scale site-to-site correlation structure. Several parameterisations of the small-scale Gaussian correlation were trialled, namely Fitted Correlation, Exponential Decay Correlation, Empirical and Zero Correlation. Significantly, it was shown that annual rainfall data outliers can have a large effect on inference for a model that uses Gaussian distributions. The practical value of this modelling is demonstrated by the conditioning of the event based point rainfall model DRIP on the hidden state series of the HMM variants. Short timescale models typically underestimate annual variability because there is no explicit structure to incorporate long-term persistence. The two-state conditioned DRIP model was shown to reproduce the annual variability observed to a greater degree than the single state DRIP. / PhD Doctorate

Human activity analysis has attracted great interest from computer vision researchers due to its promising applications in many areas such as automated visual surveillance, computer-human interactions, and motion-based identification and diagnosis. This dissertation presents work in two areas: general human activity recognition from video, and human activity analysis for the purpose of identifying pathological gait from both 3D captured data and from video. Even though the research in human activity recognition has been going on for many years, still there are many issues that need more research. This includes the effective representation and modeling of human activities and the segmentation of sequences of continuous activities. In this thesis we present an algorithm that combines shape and motion features to represent human activities. In order to handle the activity recognition from any viewing angle we quantize the viewing direction and build a set of Hidden Markov Models (HMMs), where each model represents the activity from a given view. Finally, a voting based algorithm is used to segment and recognize a sequence of human activities from video. Our method of representing activities has good attributes and is suitable for both low resolution and high resolution video. The voting based algorithm performs the segmentation and recognition simultaneously. Experiments on two sets of video clips of different activities show that our method is effective. Our work on identifying pathological gait is based on the assumption of gait symmetry. Previous work on gait analysis measures the symmetry of gait based on Ground Reaction Force data, stance time, swing time or step length. Since the trajectories of the body parts contain information about the whole body movement, we measure the symmetry of the gait based on the trajectories of the body parts. Two algorithms, which can work with different data sources, are presented. The first algorithm works on 3D motion-captured data and the second works on video data. Both algorithms use support vector machine (SVM) for classification. Each of the two methods has three steps: the first step is data preparation, i.e., obtaining the trajectories of the body parts; the second step is gait representation based on a measure of gait symmetry; and the last step is SVM based classification. For 3D motion-captured data, a set of features based on Discrete Fourier Transform (DFT) is used to represent the gait. We demonstrate the accuracy of the classification by a set of experiments that shows that the method for 3D motion-captured data is highly effective. For video data, a model based tracking algorithm for human body parts is developed for preparing the data. Then, a symmetry measure that works on the sequence of 2D data, i.e. sequence of video frames, is derived to represent the gait. We performed experiments on both 2D projected data and real video data to examine this algorithm. The experimental results on 2D projected data showed that the presented algorithm is promising for identifying pathological gait from video. The experimental results on the real video data are not good as the results on 2D projected data. We believe that better results could be obtained if the accuracy of the tracking algorithm is improved.

Aufgrund seiner nahezu kontinuierlichen eruptiven Aktivität zählt der Merapi zu den gefährlichsten Vulkanen der Welt. Der Merapi befindet sich im Zentralteil der dicht bevölkerten Insel Java (Indonesien). Selbst kleinere Ausbrüche des Merapi stellen deswegen eine große Gefahr für die ansässige Bevölkerung in der Umgebung des Vulkans dar. Die am Merapi beobachtete enge Korrelation zwischen seismischer und vulkanischer Aktivität erlaubt es, mit Hilfe der Überwachung der seismischen Aktivität Veränderungen des Aktivitätszustandes des Merapi zu erkennen. Ein System zur automatischen Detektion und Klassifizierung seismischer Ereignisse liefert einen wichtigen Beitrag für die schnelle Analyse der seismischen Aktivität. Im Falle eines bevorstehenden Ausbruchszyklus bedeutet dies ein wichtiges Hilfsmittel für die vor Ort ansässigen Wissenschaftler.<br /> In der vorliegenden Arbeit wird ein Mustererkennungsverfahren verwendet, um die Detektion und Klassifizierung seismischer Signale vulkanischen Urprunges aus den kontinuierlich aufgezeichneten Daten in Echtzeit zu bewerkstelligen. Der hier verwendete A nsatz der hidden Markov Modelle (HMM) wird motiviert durch die große Ähnlichkeit von seismischen Signalen vulkanischen Ursprunges und Sprachaufzeichnungen und den großen Erfolg, den HMM-basierte Erkennungssysteme in der automatischen Spracherkennung erlangt haben. <br /> Für eine erfolgreiche Implementierung eines Mustererkennungssytems ist es notwendig, eine geeignete Parametrisierung der Rohdaten vorzunehmen. Basierend auf den Erfahrungswerten seismologischer Observatorien wird ein Vorgehen zur Parametrisierung des seismischen Wellenfeldes auf Grundlage von robusten Analyseverfahren vorgeschlagen. Die Wellenfeldparameter werden pro Zeitschritt in einen reell-wertigen Mustervektor zusammengefasst. Die aus diesen Mustervektoren gebildete Zeitreihe ist dann Gegenstand des HMM-basierten Erkennungssystems. Um diskrete hidden Markov Modelle (DHMM) verwenden zu können, werden die Mustervektoren durch eine lineare Transformation und nachgeschaltete Vektor Quantisierung in eine diskrete Symbolsequenz überführt. Als Klassifikator kommt eine Maximum-Likelihood Testfunktion zwischen dieser Sequenz und den, in einem überwachten Lernverfahren trainierten, DHMMs zum Einsatz.<br /> Die am Merapi kontinuierlich aufgezeichneten seismischen Daten im Zeitraum vom 01.07. und 05.07.1998 sind besonders für einen Test dieses Klassifikationssystems geeignet. In dieser Zeit zeigte der Merapi einen rapiden Anstieg der Seismizität kurz bevor dem Auftreten zweier Eruptionen am 10.07. und 19.07.1998. Drei der bekannten, vom Vulkanologischen Dienst in Indonesien beschriebenen, seimischen Signalklassen konnten in diesem Zeitraum beobachtet werden. Es handelt sich hierbei um flache vulkanisch-tektonische Beben (VTB, h < 2.5 km), um sogenannte MP-Ereignisse, die in direktem Zusammenhang mit dem Wachstum des aktiven Lavadoms gebracht werden, und um seismische Ereignisse, die durch Gesteinslawinen erzeugt werden (lokaler Name: Guguran).<br /> Die spezielle Geometrie des digitalen seismischen Netzwerkes am Merapi besteht aus einer Kombination von drei Mini-Arrays an den Flanken des Merapi. Für die Parametrisierung des Wellenfeldes werden deswegen seismische Array-Verfahren eingesetzt. Die individuellen Wellenfeld Parameter wurden hinsichtlich ihrer Relevanz für den Klassifikationsprozess detailliert analysiert. Für jede der drei Signalklassen wurde ein Satz von DHMMs trainiert. Zusätzlich wurden als Ausschlussklassen noch zwei Gruppen von Noise-Modellen unterschieden.<br /> Insgesamt konnte mit diesem Ansatz eine Erkennungsrate von 67 % erreicht werden. Im Mittel erzeugte das automatische Klassifizierungssystem 41 Fehlalarme pro Tag und Klasse. Die Güte der Klassifikationsergebnisse zeigt starke Variationen zwischen den individuellen Signalklassen. Flache vulkanisch-tektonische Beben (VTB) zeigen sehr ausgeprägte Wellenfeldeigenschaften und, zumindest im untersuchten Zeitraum, sehr stabile Zeitmuster der individuellen Wellenfeldparameter. Das DHMM-basierte Klassifizierungssystem erlaubte für diesen Ereignistyp nahezu 89% richtige Entscheidungen und erzeugte im Mittel 2 Fehlalarme pro Tag.<br /> Ereignisse der Klassen MP und Guguran sind mit dem automatischen System schwieriger zu erkennen. 64% aller MP-Ereignisse und 74% aller Guguran-Ereignisse wurden korrekt erkannt. Im Mittel kam es bei MP-Ereignissen zu 87 Fehlalarmen und bei Guguran Ereignissen zu 33 Fehlalarmen pro Tag. Eine Vielzahl der Fehlalarme und nicht detektierten Ereignisse entstehen jedoch durch eine Verwechslung dieser beiden Signalklassen im automatischen Erkennnungsprozess. Dieses Ergebnis konnte aufgrund der ähnlichen Wellenfeldeigenschaften beider Signalklassen erklärt werden, deren Ursache vermutlich in den bekannt starken Einflüssen des Mediums entlang des Wellenausbreitungsweges in vulkanischen Gebieten liegen. <br /> Insgesamt ist die Erkennungsleistung des entwickelten automatischen Klassifizierungssystems als sehr vielversprechend einzustufen. Im Gegensatz zu Standardverfahren, bei denen in der Seismologie üblicherweise nur der Startzeitpunkt eines seismischen Ereignisses detektiert wird, werden in dem untersuchten Verfahren seismische Ereignisse in ihrer Gesamtheit erfasst und zudem im selben Schritt bereits klassifiziert. / Merapi volcano is one of the most active and dangerous volcanoes of the earth. Located in central part of Java island (Indonesia), even a moderate eruption of Merapi poses a high risk to the highly populated area. Due to the close relationship between the volcanic unrest and the occurrence of seismic events at Mt. Merapi, the monitoring of Merapi's seismicity plays an important role for recognizing major changes in the volcanic activity. An automatic seismic event detection and classification system, which is capable to characterize the actual seismic activity in near real-time, is an important tool which allows the scientists in charge to take immediate decisions during a volcanic crisis. <br /> In order to accomplish the task of detecting and classifying volcano-seismic signals automatically in the continuous data streams, a pattern recognition approach has been used. It is based on the method of hidden Markov models (HMM), a technique, which has proven to provide high recognition rates at high confidence levels in classification tasks of similar complexity (e.g. speech recognition). Any pattern recognition system relies on the appropriate representation of the input data in order to allow a reasonable class-decision by means of a mathematical test function. Based on the experiences from seismological observatory practice, a parametrization scheme of the seismic waveform data is derived using robust seismological analysis techniques. The wavefield parameters are summarized into a real-valued feature vector per time step. The time series of this feature vector build the basis for the HMM-based classification system. In order to make use of discrete hidden Markov (DHMM) techniques, the feature vectors are further processed by applying a de-correlating and prewhitening transformation and additional vector quantization. The seismic wavefield is finally represented as a discrete symbol sequence with a finite alphabet. This sequence is subject to a maximum likelihood test against the discrete hidden Markov models, learned from a representative set of training sequences for each seismic event type of interest.<br /> A time period from July, 1st to July, 5th, 1998 of rapidly increasing seismic activity prior to the eruptive cycle between July, 10th and July, 19th, 1998 at Merapi volcano is selected for evaluating the performance of this classification approach. Three distinct types of seismic events according to the established classification scheme of the Volcanological Survey of Indonesia (VSI) have been observed during this time period. Shallow volcano-tectonic events VTB (h < 2.5 km), very shallow dome-growth related seismic events MP (h < 1 km) and seismic signals connected to rockfall activity originating from the active lava dome, termed Guguran.<br /> The special configuration of the digital seismic station network at Merapi volcano, a combination of small-aperture array deployments surrounding Merapi's summit region, allows the use of array methods to parametrize the continuously recorded seismic wavefield. The individual signal parameters are analyzed to determine their relevance for the discrimination of seismic event classes. For each of the three observed event types a set of DHMMs has been trained using a selected set of seismic events with varying signal to noise ratios and signal durations. Additionally, two sets of discrete hidden Markov models have been derived for the seismic noise, incorporating the fact, that the wavefield properties of the ambient vibrations differ considerably during working hours and night time. <br /> A total recognition accuracy of 67% is obtained. The mean false alarm (FA) rate can be given by 41 FA/class/day. However, variations in the recognition capabilities for the individual seismic event classes are significant. Shallow volcano-tectonic signals (VTB) show very distinct wavefield properties and (at least in the selected time period) a stable time pattern of wavefield attributes. The DHMM-based classification performs therefore best for VTB-type events, with almost 89% recognition accuracy and 2 FA/day. <br /> Seismic signals of the MP- and Guguran-classes are more difficult to detect and classify. Around 64% of MP-events and 74% of Guguran signals are recognized correctly. The average false alarm rate for MP-events is 87 FA/day, whereas for Guguran signals 33 FA/day are obtained. However, the majority of missed events and false alarms for both MP and Guguran events are due to confusion errors between these two event classes in the recognition process. <br /> The confusion of MP and Guguran events is interpreted as being a consequence of the selected parametrization approach for the continuous seismic data streams. The observed patterns of the analyzed wavefield attributes for MP and Guguran events show a significant amount of similarity, thus providing not sufficient discriminative information for the numerical classification. The similarity of wavefield parameters obtained for seismic events of MP and Guguran type reflect the commonly observed dominance of path effects on the seismic wave propagation in volcanic environments.<br /> The recognition rates obtained for the five-day period of increasing seismicity show, that the presented DHMM-based automatic classification system is a promising approach for the difficult task of classifying volcano-seismic signals. Compared to standard signal detection algorithms, the most significant advantage of the discussed technique is, that the entire seismogram is detected and classified in a single step.

Membrane proteins comprise around 20-30% of a typical proteome and play crucial roles in a wide variety of biochemical pathways. Apart from their general biological significance, membrane proteins are of particular interest to the pharmaceutical industry, being targets for more than half of all available drugs. This thesis focuses on prediction methods for membrane proteins that ultimately rely on their amino acid sequence only. By identifying soluble protein domains in membrane protein sequences, we were able to constrain and improve prediction of membrane protein topology, i.e. what parts of the sequence span the membrane and what parts are located on the cytoplasmic and extra-cytoplasmic sides. Using predicted topology as input to a profile-profile based alignment protocol, we managed to increase sensitivity to detect distant membrane protein homologs. Finally, experimental measurements of the level of membrane integration of systematically designed transmembrane helices in vitro were used to derive a scale of position-specific contributions to helix insertion efficiency for all 20 naturally occurring amino acids. Notably, position within the helix was found to be an important factor for the contribution to helix insertion efficiency for polar and charged amino acids, reflecting the highly anisotropic environment of the membrane. Using the scale to predict natural transmembrane helices in protein sequences revealed that, whereas helices in single-spanning proteins are typically hydrophobic enough to insert by themselves, a large part of the helices in multi-spanning proteins seem to require stabilizing helix-helix interactions for proper membrane integration. Implementing the scale to predict full transmembrane topologies yielded results comparable to the best statistics-based topology prediction methods.

This thesis presents work in the area of automatic speech recognition (ASR). The thesis focuses on methods for increasing the efficiency of speech recognition systems and on techniques for efficient representation of different types of knowledge in the decoding process. In this work, several decoding algorithms and recognition systems have been developed, aimed at various recognition tasks. The thesis presents the KTH large vocabulary speech recognition system. The system was developed for online (live) recognition with large vocabularies and complex language models. The system utilizes weighted transducer theory for efficient representation of different knowledge sources, with the purpose of optimizing the recognition process. A search algorithm for efficient processing of hidden Markov models (HMMs) is presented. The algorithm is an alternative to the classical Viterbi algorithm for fast computation of shortest paths in HMMs. It is part of a larger decoding strategy aimed at reducing the overall computational complexity in ASR. In this approach, all HMM computations are completely decoupled from the rest of the decoding process. This enables the use of larger vocabularies and more complex language models without an increase of HMM-related computations. Ace is another speech recognition system developed within this work. It is a platform aimed at facilitating the development of speech recognizers and new decoding methods. A real-time system for low-latency online speech transcription is also presented. The system was developed within a project with the goal of improving the possibilities for hard-of-hearing people to use conventional telephony by providing speech-synchronized multimodal feedback. This work addresses several additional requirements implied by this special recognition task. / QC 20100811