Bayesian classification of forest ecological type from satellite data

The main objective of this study was todo a statistical analysis of ecological type from optical satellite data, using Tipping's sparse Bayesian algorithm. This thesis uses "the Relevence Vector Machine" algorithm in ecological classification betweenforestland and wetland. Further this bi-classification technique was used to do classification of many other different species of trees and produces hierarchical classification of entire subclasses given as a target class. Also, we carried out an attempt to use airborne image of same forest area. Combining it with image analysis, using different image processing operation, we tried to extract good features and later used them to perform classification of forestland and wetland.

Visual Measurement and Modelling of Tool Wear in Rough Turning

Huolimatta korkeasta automaatioasteesta sorvausteollisuudessa, muutama keskeinen ongelma estää sorvauksen täydellisen automatisoinnin. Yksi näistä ongelmista on työkalun kuluminen. Tämä työ keskittyy toteuttamaan automaattisen järjestelmän kulumisen, erityisesti viistekulumisen, mittaukseen konenäön avulla. Kulumisen mittausjärjestelmä poistaa manuaalisen mittauksen tarpeen ja minimoi ajan, joka käytetään työkalun kulumisen mittaukseen. Mittauksen lisäksi tutkitaan kulumisen mallinnusta sekä ennustamista. Automaattinen mittausjärjestelmä sijoitettiin sorvin sisälle ja järjestelmä integroitiin onnistuneesti ulkopuolisten järjestelmien kanssa. Tehdyt kokeet osoittivat, että mittausjärjestelmä kykenee mittaamaan työkalun kulumisen järjestelmän oikeassa ympäristössä. Mittausjärjestelmä pystyy myös kestämään häiriöitä, jotka ovat konenäköjärjestelmille yleisiä. Työkalun kulumista mallinnusta tutkittiin useilla eri menetelmillä. Näihin kuuluivat muiden muassa neuroverkot ja tukivektoriregressio. Kokeet osoittivat, että tutkitut mallit pystyivät ennustamaan työkalun kulumisasteen käytetyn ajan perusteella. Parhaan tuloksen antoivat neuroverkot Bayesiläisellä regularisoinnilla.

Demographic Modelling of Human Population Growth

This work presents models and methods that have been used in producing forecasts of population growth. The work is intended to emphasize the reliability bounds of the model forecasts. Leslie model and various versions of logistic population models are presented. References to literature and several studies are given. A lot of relevant methodology has been developed in biological sciences. The Leslie modelling approach involves the use of current trends in mortality,fertility, migration and emigration. The model treats population divided in age groups and the model is given as a recursive system. Other group of models is based on straightforward extrapolation of census data. Trajectories of simple exponential growth function and logistic models are used to produce the forecast. The work presents the basics of Leslie type modelling and the logistic models, including multi- parameter logistic functions. The latter model is also analysed from model reliability point of view. Bayesian approach and MCMC method are used to create error bounds of the model predictions.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Modelling of potentiometric ion sensors

Potentiometric ion sensors are a very important subgroup of electrochemical sensors, very attractive for practical applications due to their small size, portability, low-energy consumption, relatively low cost and not changing the sample composition. They are investigated by the researchers from many fields of science. The continuous development of this field creates the necessity for a detailed description of sensor response and the electrochemical processes important in the practical applications of ion sensors. The aim of this thesis is to present the existing models available for the description of potentiometric ion sensors as well as their applicability and limitations. This includes the description of the diffusion potential occurring at the reference electrodes. The wide range of existing models, from most idealised phase boundary models to most general models, including migration, is discussed. This work concentrates on the advanced modelling of ion sensors, namely the Nernst-Planck-Poisson (NPP) model, which is the most general of the presented models, therefore the most widely applicable. It allows the modelling of the transport processes occurring in ion sensors and generating the potentiometric response. Details of the solution of the NPP model (including the numerical methods used) are shown. The comparisons between NPP and the more idealized models are presented. The applicability of the model to describe the formation of diffusion potential in reference electrode, the lower detection limit of both ion-exchanger and neutral carrier electrodes and the effect of the complexation in the membrane are discussed. The model was applied for the description of both types of electrodes, i.e. with the inner filling solution and solidcontact electrodes. The NPP model allows the electrochemical methods other than potentiometry to be described. Application of this model in Electrochemical Impedance Spectroscopy is discussed and a possible use in chrono-potentiometry is indicated. By combining the NPP model with evolutionary algorithms, namely Hierarchical Genetic Strategy (HGS), a novel method allowing the facilitation of the design of ion sensors was created. It is described in detail in this thesis and its possible applications in the field of ion sensors are indicated. Finally, some interesting effects occurring in the ion sensors (i.e. overshot response and influence of anionic sites) as well as the possible applications of NPP in biochemistry are described.

Multidata inverse problems and Bayesian solution methods in astronomy

Statistical analyses of measurements that can be described by statistical models are of essence in astronomy and in scientific inquiry in general. The sensitivity of such analyses, modelling approaches, and the consequent predictions, is sometimes highly dependent on the exact techniques applied, and improvements therein can result in significantly better understanding of the observed system of interest. Particularly, optimising the sensitivity of statistical techniques in detecting the faint signatures of low-mass planets orbiting the nearby stars is, together with improvements in instrumentation, essential in estimating the properties of the population of such planets, and in the race to detect Earth-analogs, i.e. planets that could support liquid water and, perhaps, life on their surfaces. We review the developments in Bayesian statistical techniques applicable to detections planets orbiting nearby stars and astronomical data analysis problems in general. We also discuss these techniques and demonstrate their usefulness by using various examples and detailed descriptions of the respective mathematics involved. We demonstrate the practical aspects of Bayesian statistical techniques by describing several algorithms and numerical techniques, as well as theoretical constructions, in the estimation of model parameters and in hypothesis testing. We also apply these algorithms to Doppler measurements of nearby stars to show how they can be used in practice to obtain as much information from the noisy data as possible. Bayesian statistical techniques are powerful tools in analysing and interpreting noisy data and should be preferred in practice whenever computational limitations are not too restrictive.

Bayesian analysis of SEIR epidemic models

This thesis concerns the analysis of epidemic models. We adopt the Bayesian paradigm and develop suitable Markov Chain Monte Carlo (MCMC) algorithms. This is done by considering an Ebola outbreak in the Democratic Republic of Congo, former Zaïre, 1995 as a case of SEIR epidemic models. We model the Ebola epidemic deterministically using ODEs and stochastically through SDEs to take into account a possible bias in each compartment. Since the model has unknown parameters, we use different methods to estimate them such as least squares, maximum likelihood and MCMC. The motivation behind choosing MCMC over other existing methods in this thesis is that it has the ability to tackle complicated nonlinear problems with large number of parameters. First, in a deterministic Ebola model, we compute the likelihood function by sum of square of residuals method and estimate parameters using the LSQ and MCMC methods. We sample parameters and then use them to calculate the basic reproduction number and to study the disease-free equilibrium. From the sampled chain from the posterior, we test the convergence diagnostic and confirm the viability of the model. The results show that the Ebola model fits the observed onset data with high precision, and all the unknown model parameters are well identified. Second, we convert the ODE model into a SDE Ebola model. We compute the likelihood function using extended Kalman filter (EKF) and estimate parameters again. The motivation of using the SDE formulation here is to consider the impact of modelling errors. Moreover, the EKF approach allows us to formulate a filtered likelihood for the parameters of such a stochastic model. We use the MCMC procedure to attain the posterior distributions of the parameters of the SDE Ebola model drift and diffusion parts. In this thesis, we analyse two cases: (1) the model error covariance matrix of the dynamic noise is close to zero , i.e. only small stochasticity added into the model. The results are then similar to the ones got from deterministic Ebola model, even if methods of computing the likelihood function are different (2) the model error covariance matrix is different from zero, i.e. a considerable stochasticity is introduced into the Ebola model. This accounts for the situation where we would know that the model is not exact. As a results, we obtain parameter posteriors with larger variances. Consequently, the model predictions then show larger uncertainties, in accordance with the assumption of an incomplete model.

Modelling software quality : a multidimensional approach

Les sociétés modernes dépendent de plus en plus sur les systèmes informatiques et ainsi, il y a de plus en plus de pression sur les équipes de développement pour produire des logiciels de bonne qualité. Plusieurs compagnies utilisent des modèles de qualité, des suites de programmes qui analysent et évaluent la qualité d'autres programmes, mais la construction de modèles de qualité est difficile parce qu'il existe plusieurs questions qui n'ont pas été répondues dans la littérature. Nous avons étudié les pratiques de modélisation de la qualité auprès d'une grande entreprise et avons identifié les trois dimensions où une recherche additionnelle est désirable : Le support de la subjectivité de la qualité, les techniques pour faire le suivi de la qualité lors de l'évolution des logiciels, et la composition de la qualité entre différents niveaux d'abstraction. Concernant la subjectivité, nous avons proposé l'utilisation de modèles bayésiens parce qu'ils sont capables de traiter des données ambiguës. Nous avons appliqué nos modèles au problème de la détection des défauts de conception. Dans une étude de deux logiciels libres, nous avons trouvé que notre approche est supérieure aux techniques décrites dans l'état de l'art, qui sont basées sur des règles. Pour supporter l'évolution des logiciels, nous avons considéré que les scores produits par un modèle de qualité sont des signaux qui peuvent être analysés en utilisant des techniques d'exploration de données pour identifier des patrons d'évolution de la qualité. Nous avons étudié comment les défauts de conception apparaissent et disparaissent des logiciels. Un logiciel est typiquement conçu comme une hiérarchie de composants, mais les modèles de qualité ne tiennent pas compte de cette organisation. Dans la dernière partie de la dissertation, nous présentons un modèle de qualité à deux niveaux. Ces modèles ont trois parties: un modèle au niveau du composant, un modèle qui évalue l'importance de chacun des composants, et un autre qui évalue la qualité d'un composé en combinant la qualité de ses composants. L'approche a été testée sur la prédiction de classes à fort changement à partir de la qualité des méthodes. Nous avons trouvé que nos modèles à deux niveaux permettent une meilleure identification des classes à fort changement. Pour terminer, nous avons appliqué nos modèles à deux niveaux pour l'évaluation de la navigabilité des sites web à partir de la qualité des pages. Nos modèles étaient capables de distinguer entre des sites de très bonne qualité et des sites choisis aléatoirement. Au cours de la dissertation, nous présentons non seulement des problèmes théoriques et leurs solutions, mais nous avons également mené des expériences pour démontrer les avantages et les limitations de nos solutions. Nos résultats indiquent qu'on peut espérer améliorer l'état de l'art dans les trois dimensions présentées. En particulier, notre travail sur la composition de la qualité et la modélisation de l'importance est le premier à cibler ce problème. Nous croyons que nos modèles à deux niveaux sont un point de départ intéressant pour des travaux de recherche plus approfondis.

Modelling structural zeros in compositional data

This analysis was stimulated by the real data analysis problem of household expenditure data. The full dataset contains expenditure data for a sample of 1224 households. The expenditure is broken down at 2 hierarchical levels: 9 major levels (e.g. housing, food, utilities etc.) and 92 minor levels. There are also 5 factors and 5 covariates at the household level. Not surprisingly, there are a small number of zeros at the major level, but many zeros at the minor level. The question is how best to model the zeros. Clearly, models that try to add a small amount to the zero terms are not appropriate in general as at least some of the zeros are clearly structural, e.g. alcohol/tobacco for households that are teetotal. The key question then is how to build suitable conditional models. For example, is the sub-composition of spending excluding alcohol/tobacco similar for teetotal and non-teetotal households? In other words, we are looking for sub-compositional independence. Also, what determines whether a household is teetotal? Can we assume that it is independent of the composition? In general, whether teetotal will clearly depend on the household level variables, so we need to be able to model this dependence. The other tricky question is that with zeros on more than one component, we need to be able to model dependence and independence of zeros on the different components. Lastly, while some zeros are structural, others may not be, for example, for expenditure on durables, it may be chance as to whether a particular household spends money on durables within the sample period. This would clearly be distinguishable if we had longitudinal data, but may still be distinguishable by looking at the distribution, on the assumption that random zeros will usually be for situations where any non-zero expenditure is not small. While this analysis is based on around economic data, the ideas carry over to many other situations, including geological data, where minerals may be missing for structural reasons (similar to alcohol), or missing because they occur only in random regions which may be missed in a sample (similar to the durables)

Skill Rating by Bayesian Inference

Systems Engineering often involves computer modelling the behaviour of proposed systems and their components. Where a component is human, fallibility must be modelled by a stochastic agent. The identification of a model of decision-making over quantifiable options is investigated using the game-domain of Chess. Bayesian methods are used to infer the distribution of players’ skill levels from the moves they play rather than from their competitive results. The approach is used on large sets of games by players across a broad FIDE Elo range, and is in principle applicable to any scenario where high-value decisions are being made under pressure.

Bayesian estimation of willingness-to-pay where respondents mis-report their preferences

We introduce a modified conditional logit model that takes account of uncertainty associated with mis-reporting in revealed preference experiments estimating willingness-to-pay (WTP). Like Hausman et al. [Journal of Econometrics (1988) Vol. 87, pp. 239-269], our model captures the extent and direction of uncertainty by respondents. Using a Bayesian methodology, we apply our model to a choice modelling (CM) data set examining UK consumer preferences for non-pesticide food. We compare the results of our model with the Hausman model. WTP estimates are produced for different groups of consumers and we find that modified estimates of WTP, that take account of mis-reporting, are substantially revised downwards. We find a significant proportion of respondents mis-reporting in favour of the non-pesticide option. Finally, with this data set, Bayes factors suggest that our model is preferred to the Hausman model.

An illustration of the modelling of cost and efficacy data from a clinical trial

Health care providers, purchasers and policy makers need to make informed decisions regarding the provision of cost-effective care. When a new health care intervention is to be compared with the current standard, an economic evaluation alongside an evaluation of health benefits provides useful information for the decision making process. We consider the information on cost-effectiveness which arises from an individual clinical trial comparing the two interventions. Recent methods for conducting a cost-effectiveness analysis for a clinical trial have focused on the net benefit parameter. The net benefit parameter, a function of costs and health benefits, is positive if the new intervention is cost-effective compared with the standard. In this paper we describe frequentist and Bayesian approaches to cost-effectiveness analysis which have been suggested in the literature and apply them to data from a clinical trial comparing laparoscopic surgery with open mesh surgery for the repair of inguinal hernias. We extend the Bayesian model to allow the total cost to be divided into a number of different components. The advantages and disadvantages of the different approaches are discussed. In January 2001, NICE issued guidance on the type of surgery to be used for inguinal hernia repair. We discuss our example in the light of this information. Copyright © 2003 John Wiley & Sons, Ltd.

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

The rate at which a given site in a gene sequence alignment evolves over time may vary. This phenomenon-known as heterotachy-can bias or distort phylogenetic trees inferred from models of sequence evolution that assume rates of evolution are constant. Here, we describe a phylogenetic mixture model designed to accommodate heterotachy. The method sums the likelihood of the data at each site over more than one set of branch lengths on the same tree topology. A branch-length set that is best for one site may differ from the branch-length set that is best for some other site, thereby allowing different sites to have different rates of change throughout the tree. Because rate variation may not be present in all branches, we use a reversible-jump Markov chain Monte Carlo algorithm to identify those branches in which reliable amounts of heterotachy occur. We implement the method in combination with our 'pattern-heterogeneity' mixture model, applying it to simulated data and five published datasets. We find that complex evolutionary signals of heterotachy are routinely present over and above variation in the rate or pattern of evolution across sites, that the reversible-jump method requires far fewer parameters than conventional mixture models to describe it, and serves to identify the regions of the tree in which heterotachy is most pronounced. The reversible-jump procedure also removes the need for a posteriori tests of 'significance' such as the Akaike or Bayesian information criterion tests, or Bayes factors. Heterotachy has important consequences for the correct reconstruction of phylogenies as well as for tests of hypotheses that rely on accurate branch-length information. These include molecular clocks, analyses of tempo and mode of evolution, comparative studies and ancestral state reconstruction. The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data.

Efficient and cost-effective experimental determination of kinetic constants and data: the success of a Bayesian systematic approach to drug transport, receptor binding, continuous culture and cell transport kinetics

Details about the parameters of kinetic systems are crucial for progress in both medical and industrial research, including drug development, clinical diagnosis and biotechnology applications. Such details must be collected by a series of kinetic experiments and investigations. The correct design of the experiment is essential to collecting data suitable for analysis, modelling and deriving the correct information. We have developed a systematic and iterative Bayesian method and sets of rules for the design of enzyme kinetic experiments. Our method selects the optimum design to collect data suitable for accurate modelling and analysis and minimises the error in the parameters estimated. The rules select features of the design such as the substrate range and the number of measurements. We show here that this method can be directly applied to the study of other important kinetic systems, including drug transport, receptor binding, microbial culture and cell transport kinetics. It is possible to reduce the errors in the estimated parameters and, most importantly, increase the efficiency and cost-effectiveness by reducing the necessary amount of experiments and data points measured. (C) 2003 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A novel Bayesian approach to drug design with simple and complex enzymes: Use with lens aldehyde dehydrogenase and the glyoxalase pathway

Purpose: Acquiring details of kinetic parameters of enzymes is crucial to biochemical understanding, drug development, and clinical diagnosis in ocular diseases. The correct design of an experiment is critical to collecting data suitable for analysis, modelling and deriving the correct information. As classical design methods are not targeted to the more complex kinetics being frequently studied, attention is needed to estimate parameters of such models with low variance. Methods: We have developed Bayesian utility functions to minimise kinetic parameter variance involving differentiation of model expressions and matrix inversion. These have been applied to the simple kinetics of the enzymes in the glyoxalase pathway (of importance in posttranslational modification of proteins in cataract), and the complex kinetics of lens aldehyde dehydrogenase (also of relevance to cataract). Results: Our successful application of Bayesian statistics has allowed us to identify a set of rules for designing optimum kinetic experiments iteratively. Most importantly, the distribution of points in the range is critical; it is not simply a matter of even or multiple increases. At least 60 % must be below the KM (or plural if more than one dissociation constant) and 40% above. This choice halves the variance found using a simple even spread across the range.With both the glyoxalase system and lens aldehyde dehydrogenase we have significantly improved the variance of kinetic parameter estimation while reducing the number and costs of experiments. Conclusions: We have developed an optimal and iterative method for selecting features of design such as substrate range, number of measurements and choice of intermediate points. Our novel approach minimises parameter error and costs, and maximises experimental efficiency. It is applicable to many areas of ocular drug design, including receptor-ligand binding and immunoglobulin binding, and should be an important tool in ocular drug discovery.