Abstract Monitoring regional variation in the survival of cancer patients is an important tool for assessing realisation of regional equity in cancer care. When regions are small or sparsely populated, the random component in the total variation across the regions becomes prominent. The broad aim of this doctoral thesis is to develop methods for assessing regional variation in the cause-specific and relative survival of cancer patients in a country and for quantifying the public health impact of the regional variation in the presence of competing hazards of death using summary measures that are interpretable also for policy-makers and other stakeholders. Methods for summarising the survival of a patient population with incomplete follow-up in terms of the mean and median survival times are proposed. A cure fraction model with two sets of random effects for regional variation is fitted to cause-specific survival data in a Bayesian framework using Markov chain Monte Carlo simulation. This hierarchical model is extended to the estimation of relative survival where the expected survival is estimated by region and considered as a random quantity. The public health impact of regional variation is quantified by the extra survival time and the number of avoidable deaths that would be gained if the patients achieved the most favourable level of relative survival. The methods proposed were applied to real data sets from the Finnish Cancer Registry. Estimates of the mean and the median survival times of colon and thyroid cancer patients, respectively, were corrected for the bias that was caused by the inherent selection of patients during the period of diagnosis with respect to their age at diagnosis. The cure fraction model allowed estimation of regional variation in cause-specific and relative survival of breast and colon cancer patients, respectively, with a parsimonious number of parameters yielding reasonable estimates also for sparsely populated hospital districts. / Tiivistelmä Syöpäpotilaiden elossaolon alueellisen vaihtelun seuraaminen on tärkeää arvioitaessa syövänhoidon oikeudenmukaista jakautumista alueittain. Kun alueet ovat pieniä tai harvaan asuttuja, alueellisen kokonaisvaihtelun satunnainen osa kasvaa merkittäväksi. Tämän väitöstutkimuksen tavoitteena on kehittää menetelmiä, joilla pystytään arvioimaan maan sisäistä alueellista vaihtelua lisäkuolleisuudessa, jonka itse syöpä potilaille aiheuttaa, ja tiivistämään alueellisen vaihtelun kansanterveydellinen merkitys mittalukuihin, jotka ottavat kilpailevan kuolleisuuden huomioon ja ovat myös päättäjien tulkittavissa. Ehdotetuilla menetelmillä voidaan potilaiden ennustetta kuvailla käyttäen elossaolo-ajan keskiarvoa ja mediaania, vaikka potilaiden seuruu olisi keskeneräinen. Potilaiden syykohtaiselle kuolleisuudelle sovitetaan bayesiläisittäin MCMC-simulaatiota hyödyntäen malli, jossa parantuneiden potilaiden osuuden kuvaamisen lisäksi alueellinen vaihtelu esitetään kahden satunnaisefektijoukon avulla. Tämä hierarkkinen malli laajennetaan suhteellisen elossaolon estimointiin, jossa potilaiden odotettu elossaolo estimoidaan alueittain ja siihen liittyvä satunnaisvaihtelu otetaan huomioon. Alueellisen vaihtelun kansanterveydellistä merkitystä mitataan elossaoloajan keskimääräisellä pidentymällä sekä vältettävien kuolemien lukumäärällä, jotka voitaisiin saavuttaa, mikäli suotuisin suhteellisen elossaolon taso saavutettaisiin kaikilla alueilla. Kehitettyjä menetelmiä käytettiin Suomen Syöpärekisterin aineistojen analysointiin. Paksusuoli- ja kilpirauhassyöpäpotilaiden elinaikojen keskiarvojen ja mediaanien estimaatit oikaistiin harhasta, joka aiheutui potilaiden luontaisesta valikoitumisesta diagnosointijakson aikana iän suhteen. Parantuneiden osuuden satunnaisefektimalli mahdollisti rintasyöpäpotilaiden syykohtaisen kuolleisuuden ja paksusuolisyöpäpotilaiden suhteellisen elossaolon kuvaamisen vähäisellä määrällä parametreja ja antoi järkeenkäyvät estimaatit myös harvaan asutuille sairaanhoitopiireille.

Uncertainty in rainfall forecasts affects the level of quality and assurance for decisions made to manage water resource-based systems. However, eliminating uncertainty in a complete manner could be difficult, decision-makers thus are challenged to make decisions in the light of uncertainty. This study provides statistical models as an approach to cope with uncertainty, including: a) a statistical method relying on a Gaussian mixture (GM) model to assist in better characterize uncertainty in climate model projections and evaluate their performance in matching observations; b) a stochastic model that incorporates the El Niño–Southern Oscillation (ENSO) cycle to narrow uncertainty in seasonal rainfall forecasts; and c) a statistical approach to determine to what extent drought events forecasted using ENSO information could be utilized in the water resources decision-making process. This study also investigates the relationship between calibration and lead time on the ability to narrow the interannual uncertainty of forecasts and the associated usefulness for decision making. These objectives are demonstrated for the northwest region of Costa Rica as a case study of a developing country in Central America. This region of Costa Rica is under an increasing risk of future water shortages due to climate change, increased demand, and high variability in the bimodal cycle of seasonal rainfall. First, the GM model is shown to be a suitable approach to compare and characterize long-term projections of climate models. The GM representation of seasonal cycles is then employed to construct detailed comparison tests for climate models with respect to observed rainfall data. Three verification metrics demonstrate that an acceptable degree of predictability can be obtained by incorporating ENSO information in reducing error and interannual variability in the forecast of seasonal rainfall. The predictability of multicategory rainfall forecasts in the late portion of the wet season surpasses that in the early portion of the wet season. Later, the value of drought forecast information for coping with uncertainty in making decisions on water management is determined by quantifying the reduction in expected losses relative to a perfect forecast. Both the discrimination ability and the relative economic value of drought-event forecasts are improved by the proposed forecast method, especially after calibration. Positive relative economic value is found only for a range of scenarios of the cost-loss ratio, which indicates that the proposed forecast could be used for specific cases. Otherwise, taking actions (no-actions) is preferred as the cost-loss ratio approaches zero (one). Overall, the approach of incorporating ENSO information into seasonal rainfall forecasts would provide useful value to the decision-making process - in particular at lead times of one year ahead.

Les modèles latents sont très utilisés en pratique, comme en génomique, économétrie, reconnaissance de parole... Comme la modélisation paramétrique des densités d’émission, c’est-à-dire les lois d’une observation sachant l’état latent, peut conduire à de mauvais résultats en pratique, un récent intérêt pour les modèles latents non paramétriques est apparu dans les applications. Or ces modèles ont peu été étudiés en théorie. Dans cette thèse je me suis intéressée aux propriétés asymptotiques des estimateurs (dans le cas fréquentiste) et de la loi a posteriori (dans le cadre Bayésien) dans deux modèles latents particuliers : les modèles de Markov caché et les modèles de mélange. J’ai tout d’abord étudié la concentration de la loi a posteriori dans les modèles non paramétriques de Markov caché. Plus précisément, j’ai étudié la consistance puis la vitesse de concentration de la loi a posteriori. Enfin je me suis intéressée à l’estimation efficace du paramètre de mélange dans les modèles semi paramétriques de mélange. / Latent models have been widely used in diverse fields such as speech recognition, genomics, econometrics. Because parametric modeling of emission distributions, that is the distributions of an observation given the latent state, may lead to poor results in practice, in particular for clustering purposes, recent interest in using non parametric latent models appeared in applications. Yet little thoughts have been given to theory in this framework. During my PhD I have been interested in the asymptotic behaviour of estimators (in the frequentist case) and the posterior distribution (in the Bayesian case) in two particuliar non parametric latent models: hidden Markov models and mixture models. I have first studied the concentration of the posterior distribution in non parametric hidden Markov models. More precisely, I have considered posterior consistency and posterior concentration rates. Finally, I have been interested in efficient estimation of the mixture parameter in semi parametric mixture models.

Nous nous intéressons, dans cette thèse, à l'étude des modèles de mélange et des modèles linéaires généralisés, avec une application aux données de co-infection entre les arbovirus et les parasites du paludisme. Après une première partie consacrée à l'étude de la co-infection par un modèle logistique multinomial, nous proposons dans une deuxième partie l'étude des mélanges de modèles linéaires généralisés. La méthode proposée pour estimer les paramètres du mélange est une combinaison d'une méthode des moments et d'une méthode spectrale. Nous proposons à la fin une dernière partie consacrée aux mélanges de valeurs extrêmes en présence de censure. La méthode d'estimation proposée dans cette partie se fait en deux étapes basées sur la maximisation d'une vraisemblance. / We are interested, in this thesis, to the study of mixture models and generalized linear models, with an application to co-infection data between arboviruses and malaria parasites. After a first part dedicated to the study of co-infection using a multinomial logistic model, we propose in a second part to study the mixtures of generalized linear models. The proposed method to estimate the parameters of the mixture is a combination of a moment method and a spectral method. Finally, we propose a final section for studing extreme value mixtures under random censoring. The estimation method proposed in this section is done in two steps based on the maximization of a likelihood.

Parmi les diverses modalités biométriques qui permettent l'identification des personnes, l'iris est considéré comme très fiable, avec un taux d'erreur remarquablement faible. Toutefois, ce niveau élevé de performances est obtenu en contrôlant la qualité des images acquises et en imposant de fortes contraintes à la personne (être statique et à proximité de la caméra). Cependant, dans de nombreuses applications de sécurité comme les contrôles d'accès, ces contraintes ne sont plus adaptées. Les images résultantes souffrent alors de diverses dégradations (manque de résolution, artefacts...) qui affectent négativement les taux de reconnaissance. Pour contourner ce problème, il est possible d’exploiter la redondance de l’information découlant de la disponibilité de plusieurs images du même œil dans la séquence enregistrée. Cette thèse se concentre sur la façon de fusionner ces informations, afin d'améliorer les performances. Dans la littérature, diverses méthodes de fusion ont été proposées. Cependant, elles s’accordent sur le fait que la qualité des images utilisées dans la fusion est un facteur crucial pour sa réussite. Plusieurs facteurs de qualité doivent être pris en considération et différentes méthodes ont été proposées pour les quantifier. Ces mesures de qualité sont généralement combinées pour obtenir une valeur unique et globale. Cependant, il n'existe pas de méthode de combinaison universelle et des connaissances a priori doivent être utilisées, ce qui rend le problème non trivial. Pour faire face à ces limites, nous proposons une nouvelle manière de mesurer et d'intégrer des mesures de qualité dans un schéma de fusion d'images, basé sur une approche de super-résolution. Cette stratégie permet de remédier à deux problèmes courants en reconnaissance par l'iris: le manque de résolution et la présence d’artefacts dans les images d'iris. La première partie de la thèse consiste en l’élaboration d’une mesure de qualité pertinente pour quantifier la qualité d’image d’iris. Elle repose sur une mesure statistique locale de la texture de l’iris grâce à un modèle de mélange de Gaussienne. L'intérêt de notre mesure est 1) sa simplicité, 2) son calcul ne nécessite pas d'identifier a priori les types de dégradations, 3) son unicité, évitant ainsi l’estimation de plusieurs facteurs de qualité et un schéma de combinaison associé et 4) sa capacité à prendre en compte la qualité intrinsèque des images mais aussi, et surtout, les défauts liés à une mauvaise segmentation de la zone d’iris. Dans la deuxième partie de la thèse, nous proposons de nouvelles approches de fusion basées sur des mesures de qualité. Tout d’abord, notre métrique est utilisée comme une mesure de qualité globale de deux façons différentes: 1) comme outil de sélection pour détecter les meilleures images de la séquence et 2) comme facteur de pondération au niveau pixel dans le schéma de super-résolution pour donner plus d'importance aux images de bonnes qualités. Puis, profitant du caractère local de notre mesure de qualité, nous proposons un schéma de fusion original basé sur une pondération locale au niveau pixel, permettant ainsi de prendre en compte le fait que les dégradations peuvent varier d’une sous partie à une autre. Ainsi, les zones de bonne qualité contribueront davantage à la reconstruction de l'image fusionnée que les zones présentant des artéfacts. Par conséquent, l'image résultante sera de meilleure qualité et pourra donc permettre d'assurer de meilleures performances en reconnaissance. L'efficacité des approches proposées est démontrée sur plusieurs bases de données couramment utilisées: MBGC, Casia-Iris-Thousand et QFIRE à trois distances différentes. Nous étudions séparément l'amélioration apportée par la super-résolution, la qualité globale, puis locale dans le processus de fusion. Les résultats montrent une amélioration importante apportée par l'utilisation de la qualité globale, amélioration qui est encore augmentée en utilisant la qualité locale / Among the large number of biometric modalities, iris is considered as a very reliable biometrics with a remarkably low error rate. The excellent performance of iris recognition systems are obtained by controlling the quality of the captured images and by imposing certain constraints on users, such as standing at a close fixed distance from the camera. However, in many real-world applications such as control access and airport boarding these constraints are no longer suitable. In such non ideal conditions, the resulting iris images suffer from diverse degradations which have a negative impact on the recognition rate. One way to try to circumvent this bad situation is to use some redundancy arising from the availability of several images of the same eye in the recorded sequence. Therefore, this thesis focuses on how to fuse the information available in the sequence in order to improve the performance. In the literature, diverse schemes of fusion have been proposed. However, they agree on the fact that the quality of the used images in the fusion process is an important factor for its success in increasing the recognition rate. Therefore, researchers concentrated their efforts in the estimation of image quality to weight each image in the fusion process according to its quality. There are various iris quality factors to be considered and diverse methods have been proposed for quantifying these criteria. These quality measures are generally combined to one unique value: a global quality. However, there is no universal combination scheme to do so and some a priori knowledge has to be inserted, which is not a trivial task. To deal with these drawbacks, in this thesis we propose of a novel way of measuring and integrating quality measures in a super-resolution approach, aiming at improving the performance. This strategy can handle two types of issues for iris recognition: the lack of resolution and the presence of various artifacts in the captured iris images. The first part of the doctoral work consists in elaborating a relevant quality metric able to quantify locally the quality of the iris images. Our measure relies on a Gaussian Mixture Model estimation of clean iris texture distribution. The interest of our quality measure is 1) its simplicity, 2) its computation does not require identifying in advance the type of degradations that can occur in the iris image, 3) its uniqueness, avoiding thus the computation of several quality metrics and associated combination rule and 4) its ability to measure the intrinsic quality and to specially detect segmentation errors. In the second part of the thesis, we propose two novel quality-based fusion schemes. Firstly, we suggest using our quality metric as a global measure in the fusion process in two ways: as a selection tool for detecting the best images and as a weighting factor at the pixel-level in the super-resolution scheme. In the last case, the contribution of each image of the sequence in final fused image will only depend on its overall quality. Secondly, taking advantage of the localness of our quality measure, we propose an original fusion scheme based on a local weighting at the pixel-level, allowing us to take into account the fact that degradations can be different in diverse parts of the iris image. This means that regions free from occlusions will contribute more in the image reconstruction than regions with artefacts. Thus, the quality of the fused image will be optimized in order to improve the performance. The effectiveness of the proposed approaches is shown on several databases commonly used: MBGC, Casia-Iris-Thousand and QFIRE at three different distances: 5, 7 and 11 feet. We separately investigate the improvement brought by the super-resolution, the global quality and the local quality in the fusion process. In particular, the results show the important improvement brought by the use of the global quality, improvement that is even increased using the local quality

Clustering machine learning algorithms have existed for a long time and there are a multitude of variations of them available to implement. Each of them has its advantages and disadvantages, which makes it challenging to select one for a particular problem and application. This study focuses on comparing two algorithms, the K-Means and Gaussian Mixture Model algorithms for outlier detection within public travel data from the travel planning mobile application MobiTime1[1]. The purpose of this study was to compare the two algorithms against each other, to identify differences between their outlier detection results. The comparisons were mainly done by comparing the differences in number of outliers located for each model, with respect to outlier threshold and number of clusters. The study found that the algorithms have large differences regarding their capabilities of detecting outliers. These differences heavily depend on the type of data that is used, but one major difference that was found was that K-Means was more restrictive then Gaussian Mixture Model when it comes to classifying data points as outliers. The result of this study could help people determining which algorithms to implement for their specific application and use case.

Pterins belong to an important group of compounds, acting as inhibitors, sensiziters, enzymes, coenzymes, pigments etc. and together with carotenoids and anthraquinones are responsible for characteristic coloration of bugs. This work was focused on the development of a capillary electrophoretic separation method for the analysis of six pterine derivatives, namely biopterine, neopterine, isoxanthopterine, leukopterine, xanthopterine and erythropterine and on their identification in the real samples. Separation was conducted in an uncoated fused-silica capillary termostated at 30 řC. Separation electrolyte contained boric acid, tris(hydroxymethyl)aminomethane and disodium salt of ethylenediaminetetraacetic acid. The effects of buffer pH, concentration of electrolyte components, separation voltage and wavelength of UV detection on electromigration behavior and detection sensitivity were studied. Under the optimized separation conditions, organic extracts of the three forms of Graphosoma semipunctatum bugs were analyzed.

The field of speech recognition has during the last decade left the re- search stage and found its way in to the public market. Most computers and mobile phones sold today support dictation and transcription in a number of chosen languages.  Swedish is often not one of them. In this thesis, which is executed on behalf of the Swedish Radio, an Automatic Speech Recognition model for Swedish is trained and the performance evaluated. The model is built using the open source toolkit Kaldi.  Two approaches of training the acoustic part of the model is investigated. Firstly, using Hidden Markov Model and Gaussian Mixture Models and secondly, using Hidden Markov Models and Deep Neural Networks. The later approach using deep neural networks is found to achieve a better performance in terms of Word Error Rate. / De senaste åren har olika tillämpningar inom människa-dator interaktion och främst taligenkänning hittat sig ut på den allmänna marknaden. Många system och tekniska produkter stöder idag tjänsterna att transkribera tal och diktera text. Detta gäller dock främst de större språken och sällan finns samma stöd för mindre språk som exempelvis svenskan. I detta examensprojekt har en modell för taligenkänning på svenska ut- vecklas. Det är genomfört på uppdrag av Sveriges Radio som skulle ha stor nytta av en fungerande taligenkänningsmodell på svenska. Modellen är utvecklad i ramverket Kaldi. Två tillvägagångssätt för den akustiska träningen av modellen är implementerade och prestandan för dessa två är evaluerade och jämförda. Först tränas en modell med användningen av Hidden Markov Models och Gaussian Mixture Models och slutligen en modell där Hidden Markov Models och Deep Neural Networks an- vänds, det visar sig att den senare uppnår ett bättre resultat i form av måttet Word Error Rate.

Exploring massive amount of user generated data with topics posits a new way to find useful information. The topics are assumed to be “hidden” and must be “uncovered” by statistical methods such as topic modeling. However, the user generated data is typically short and messy e.g. informal chat conversations, heavy use of slang words and “noise” which could be URL’s or other forms of pseudo-text. This type of data is difficult to process for most natural language processing methods, including topic modeling. This thesis attempts to find the approach that objectively give the better topics from short and messy text in a comparative study. The compared approaches are latent Dirichlet allocation (LDA), Re-organized LDA (RO-LDA), Gaussian Mixture Model (GMM) with distributed representation of words, and a new approach based on previous work named Neural Probabilistic Topic Modeling (NPTM). It could only be concluded that NPTM have a tendency to achieve better topics on short and messy text than LDA and RO-LDA. GMM on the other hand could not produce any meaningful results at all. The results are less conclusive since NPTM suffers from long running times which prevented enough samples to be obtained for a statistical test. / Att utforska enorma mängder användargenererad data med ämnen postulerar ett nytt sätt att hitta användbar information. Ämnena antas vara “gömda” och måste “avtäckas” med statistiska metoder såsom ämnesmodellering. Dock är användargenererad data generellt sätt kort och stökig t.ex. informella chattkonversationer, mycket slangord och “brus” som kan vara URL:er eller andra former av pseudo-text. Denna typ av data är svår att bearbeta för de flesta algoritmer i naturligt språk, inklusive ämnesmodellering. Det här arbetet har försökt hitta den metod som objektivt ger dem bättre ämnena ur kort och stökig text i en jämförande studie. De metoder som jämfördes var latent Dirichlet allocation (LDA), Re-organized LDA (RO-LDA), Gaussian Mixture Model (GMM) with distributed representation of words samt en egen metod med namnet Neural Probabilistic Topic Modeling (NPTM) baserat på tidigare arbeten. Den slutsats som kan dras är att NPTM har en tendens att ge bättre ämnen på kort och stökig text jämfört med LDA och RO-LDA. GMM lyckades inte ge några meningsfulla resultat alls. Resultaten är mindre bevisande eftersom NPTM har problem med långa körtider vilket innebär att tillräckligt många stickprov inte kunde erhållas för ett statistiskt test.

The field of speech recognition during the last decade has left the research stage and found its way into the public market, and today, speech recognition software is ubiquitous around us. An automatic speech recognizer understands human speech and represents it as text. Most of the current speech recognition software employs variants of deep neural networks. Before the deep learning era, the hybrid of hidden Markov model and Gaussian mixture model (HMM-GMM) was a popular statistical model to solve speech recognition. In this thesis, automatic speech recognition using HMM-GMM was trained on Somali data which consisted of voice recording and its transcription. HMM-GMM is a hybrid system in which the framework is composed of an acoustic model and a language model. The acoustic model represents the time-variant aspect of the speech signal, and the language model determines how probable is the observed sequence of words. This thesis begins with background about speech recognition. Literature survey covers some of the work that has been done in this field. This thesis evaluates how different language models and discounting methods affect the performance of speech recognition systems. Also, log scores were calculated for the top 5 predicted sentences and confidence measures of pre-dicted sentences. The model was trained on 4.5 hrs of voiced data and its corresponding transcription. It was evaluated on 3 mins of testing data. The performance of the trained model on the test set was good, given that the data was devoid of any background noise and lack of variability. The performance of the model is measured using word error rate(WER) and sentence error rate (SER). The performance of the implemented model is also compared with the results of other research work. This thesis also discusses why log and confidence score of the sentence might not be a good way to measure the performance of the resulting model. It also discusses the shortcoming of the HMM-GMM model, how the existing model can be improved, and different alternatives to solve the problem.