| 1. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models : Red Atoms, White Lies and Black Boxes in a Yellow Book
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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| 2. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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| 3. |
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| 4. |
- Baresel, Christian, et al.
(författare)
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Uncertainty-Accounting Environmental Policy and Management of Water Systems
- 2007
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Ingår i: Environmental Science & Technology. - : American Chemical Society (ACS). - 0013-936X .- 1520-5851. ; 41:10, s. 3653–3659-
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Tidskriftsartikel (refereegranskat)abstract
- Environmental policies for water quality and ecosystemmanagement do not commonly require explicit stochasticaccounts of uncertainty and risk associated with thequantification and prediction of waterborne pollutant loadsand abatement effects. In this study, we formulate andinvestigate a possible environmental policy that does requirean explicit stochastic uncertainty account. We compareboth the environmental and economic resource allocationperformance of such an uncertainty-accounting environmentalpolicy with that of deterministic, risk-prone and riskaverseenvironmental policies under a range of differenthypothetical, yet still possible, scenarios. The comparisonindicates that a stochastic uncertainty-accountingpolicy may perform better than deterministic policies overa range of different scenarios. Even in the absence ofreliable site-specific data, reported literature values appearto be useful for such a stochastic account of uncertainty.
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| 5. |
- Sabahno, Hamed, et al.
(författare)
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Variable parameters memory-type control charts for simultaneous monitoring of the mean and variability of multivariate multiple linear regression profiles
- 2024
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Variable parameters (VP) schemes are the most effective adaptive schemes in increasing control charts' sensitivity to detect small to moderate shift sizes. In this paper, we develop four VP adaptive memory-type control charts to monitor multivariate multiple linear regression profiles. All the proposed control charts are single-chart (single-statistic) control charts, two use a Max operator and two use an SS (squared sum) operator to create the final statistic. Moreover, two of the charts monitor the regression parameters, and the other two monitor the residuals. After developing the VP control charts, we developed a computer algorithm with which the charts' time-to-signal and run-length-based performances can be measured. Then, we perform extensive numerical analysis and simulation studies to evaluate the charts’ performance and the result shows significant improvements by using the VP schemes. Finally, we use real data from the national quality register for stroke care in Sweden, Riksstroke, to illustrate how the proposed control charts can be implemented in practice.
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| 6. |
- Mejia, A. F., et al.
(författare)
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A Bayesian General Linear Modeling Approach to Cortical Surface fMRI Data Analysis
- 2020
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Ingår i: Journal of the American Statistical Association. - : Informa UK Limited. - 0162-1459 .- 1537-274X.
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Tidskriftsartikel (refereegranskat)abstract
- Cortical surface functional magnetic resonance imaging (cs-fMRI) has recently grown in popularity versus traditional volumetric fMRI. In addition to offering better whole-brain visualization, dimension reduction, removal of extraneous tissue types, and improved alignment of cortical areas across subjects, it is also more compatible with common assumptions of Bayesian spatial models. However, as no spatial Bayesian model has been proposed for cs-fMRI data, most analyses continue to employ the classical general linear model (GLM), a "massive univariate" approach. Here, we propose a spatial Bayesian GLM for cs-fMRI, which employs a class of sophisticated spatial processes to model latent activation fields. We make several advances compared with existing spatial Bayesian models for volumetric fMRI. First, we use integrated nested Laplacian approximations, a highly accurate and efficient Bayesian computation technique, rather than variational Bayes. To identify regions of activation, we utilize an excursions set method based on the joint posterior distribution of the latent fields, rather than the marginal distribution at each location. Finally, we propose the first multi-subject spatial Bayesian modeling approach, which addresses a major gap in the existing literature. The methods are very computationally advantageous and are validated through simulation studies and two task fMRI studies from the Human Connectome Project. for this article, including a standardized description of the materials available for reproducing the work, are available as an online supplement.
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| 7. |
- Sabahno, Hamed, et al.
(författare)
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New statistical and machine learning based control charts with variable parameters for monitoring generalized linear model profiles
- 2023
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Ingår i: Computers & industrial engineering. - : Elsevier. - 0360-8352 .- 1879-0550. ; 184
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Tidskriftsartikel (refereegranskat)abstract
- In this research, we develop three statistical based control charts: the Hotelling’s T2, MEWMA (multivariate exponentially weighted moving average), and LRT (likelihood ratio test) as well as three machine learning (ML) based control charts: the ANN (artificial neural network), SVR (support vector regression), and RFR (random forest regression), for monitoring generalized linear model (GLM) profiles. We train these ML models with two different training methods to get a linear (regression) output and then apply our classification technique to see if the process is in-control or out-of-control, at each sampling time. In addition to developing the FP (fixed parameters) schemes, for the first time in GLM profiles, we design an adaptive VP (variable parameters) scheme for each control chart as well to increase the charts’ sensitivity in detecting shifts. We develop some algorithms with which the values of the control chart parameters in both FP and VP schemes can be obtained. Then, we develop two algorithms to measure the charts’ performance in both FP and VP schemes, by using the run-length and time-to-signal based performance measures. This is also the first control chart-related research that develops an algorithm to compute the performance measures that applies to any VP adaptive control scheme. After designing the control charts as well as performance measures, we perform extensive simulation studies and evaluate and compare all our control charts under different shift sizes and scenarios, and in three different simulation environments. Finally, we present a numerical example regarding a drug dose-response study to show how the proposed control charts can be implemented in real practice.
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| 8. |
- Pavlenko, Tatjana
(författare)
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Feature Informativeness, Curse-of-Dimensionality and Error Probability in Discriminant Analysis
- 2001
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is based on four papers on high-dimensional discriminant analysis. Throughout, the curse-of-dimensionality effect on the precision of the discrimination performance is emphasized. A growing dimension asymptotic approach is used for assessing this effect and the limiting error probability are taken as the performance criteria. A combined effect of a high dimensionality and feature informativeness on the discrimination performance is evaluated.
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| 9. |
- Casarino, V., et al.
(författare)
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On the variation operator for the Ornstein-Uhlenbeck semigroup in dimension one
- 2024
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Ingår i: Annali Di Matematica Pura Ed Applicata. - 0373-3114 .- 1618-1891. ; 203:1, s. 205-219
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Tidskriftsartikel (refereegranskat)abstract
- Consider the variation seminorm of the Ornstein-Uhlenbeck semigroup Ht in dimension one, taken with respect to t. We show that this seminorm defines an operator of weak type (1, 1) for the relevant Gaussian measure. The analogous Lp estimates for 1 < p < 8 were already known.
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| 10. |
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Modern Problems in Insurance Mathematics
- 2014
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Samlingsverk (redaktörskap) (refereegranskat)abstract
- The boook is a compilation of 21 of the papers presented at the International Cramér Symposium on Insurance Mathematics (ICSIM) held at Stockholm University 0n 11-14 June, 2013.
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| 11. |
- Gu, Irene Yu-Hua, 1953, et al.
(författare)
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Grassmann Manifold Online Learning and Partial Occlusion Handling for Visual Object Tracking under Bayesian Formulation
- 2012
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Ingår i: Proceedings - International Conference on Pattern Recognition. - 1051-4651. - 9784990644109 ; , s. 1463-1466
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Konferensbidrag (refereegranskat)abstract
- This paper addresses issues of online learning and occlusion handling in video object tracking. Although manifold tracking is promising, large pose changes and long term partial occlusions of video objects remain challenging.We propose a novel manifold tracking scheme that tackles such problems, with the following main novelties: (a) Online estimation of object appearances on Grassmann manifolds; (b) Optimal criterion-based occlusion handling during online learning; (c) Nonlinear dynamic model for appearance basis matrix and its velocity; (b) Bayesian formulations separately for the tracking and the online learning process. Two particle filters are employed: one is on the manifold for generating appearance particles and another on the linear space for generating affine box particles. Tracking and online updating are performed in alternative fashion to mitigate the tracking drift. Experiments on videos have shown robust tracking performance especially when objects contain significantpose changes accompanied with long-term partial occlusions. Evaluations and comparisons with two existing methods provide further support to the proposed method.
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| 12. |
- Bayisa, Fekadu, et al.
(författare)
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Large-scale modelling and forecasting of ambulance calls in northern Sweden using spatio-temporal log-Gaussian Cox processes
- 2020
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Ingår i: Spatial Statistics. - : Elsevier BV. - 2211-6753. ; 39
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Tidskriftsartikel (refereegranskat)abstract
- Although ambulance call data typically come in the form of spatio-temporal point patterns, point process-based modelling approaches presented in the literature are scarce. In this paper, we study a unique set of Swedish spatio-temporal ambulance call data, which consist of the spatial (GPS) locations of the calls (within the four northernmost regions of Sweden) and the associated days of occurrence of the calls (January 1, 2014-December 31, 2018). Motivated by the nature of the data, we here employ log-Gaussian Cox processes (LGCPs) for the spatiotemporal modelling and forecasting of the calls. To this end, we propose a K-means clustering based bandwidth selection method for the kernel estimation of the spatial component of the separable spatio-temporal intensity function. The temporal component of the intensity function is modelled by means of Poisson regression, using different calendar covariates, and the spatiotemporal random field component of the random intensity of the LGCP is fitted using the Metropolis-adjusted Langevin algorithm. Spatial hot-spots have been found in the south-eastern part of the study region, where most people in the region live and our fitted model/forecasts manage to capture this behaviour quite well. Also, there is a significant association between the expected number of calls and the day-of-the-week, and the season-ofthe-year. A non-parametric second-order analysis indicates that LGCPs seem to be reasonable models for the data. Finally, we find that the fitted forecasts generate simulated future spatial event patterns which quite well resemble the actual future data. (C) 2020 The Author(s). Published by Elsevier B.V.
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| 13. |
- Fedosova, K., et al.
(författare)
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High energy asymptotics for the perturbed anharmonic oscillator
- 2021
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Ingår i: Complex Variables and Elliptic Equations. - : Informa UK Limited. - 1747-6933 .- 1747-6941.
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we study the spectral properties of the perturbation of the generalized anharmonic oscillator. We consider a piecewise Holder continuous perturbation and investigate how the Holder constant can affect the eigenvalues. More precisely, we derive several first terms in the asymptotic expansion for the eigenvalues.
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| 14. |
- Tapani, Sofia, 1982
(författare)
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Stochastic modelling and analysis of early mouse development
- 2011
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this thesis is to model and describe dynamical events for biological cells using statistical and mathematical tools. The thesis includes five papers that all relate to stochastic modelling of cells. In order to understand the development and patterning of the early mammalian embryo, stochastic modelling has become a more important tool than ever. It allows for studying the processes that mediate the transition from pluripotency of the embryonic cells to their differentiation. It is still unclear whether the positions of cells determine their future fates. One alternative possibility is that cells are pre-specified at random positions and then sort according to a already set fate. Mouse embryonic cells are thought to be equivalent in their developmental properties until approaching the eight-cell stage. Some biological studies show, in comparison, that patterning can be present already at sperm entry and in the pronuclei migration. We investigate in Paper I the dynamics of the pronuclei migration by analysing their trajectories and find that not only do the pronuclei follow a noise corrupted path towards the centre of the egg but they also have some attraction to each other which affects their dynamics. Continuing in Paper II and III, we use these results to model this behaviour with a coupled stochastic differential equation model. This enables us to simulate distributions that describe the meeting plane between pronuclei which in turn can be related to the orientation of the first cleavage of the egg. Our results show that adding randomness in sperm entry point is different from the randomness added through the environment of the egg. We are also able to show that data sets with normal eggs and eggs treated with an actin growth inhibitor give rise to considerably different model dynamics, suggesting that the treatment is affecting the migration in an invasive way. Altering the pronuclei dynamics can alter the polarity of the egg and may transfer into the later axis-formation process. Invasiveness of experimental procedures is a difficult issue to handle. The alternative to invasive procedures is not appealing since it means that important developmental features may not be discovered because of individual variability and noise, leading to guesswork of the underlying mechanisms. The embryonic cells are easily affected by treatments performed to make the measuring, made by hand, easier or by the light exposure of the microscope. Treatments as such are used for example for producing flourescent proteins in membranes or slowing processes down. Paper IV and Paper V serve to analyse how light induced stress affects yeast cells and we employ a method for analysing the noisy non-stationary time series, which are a result of the yeast experiments, using wavelet decomposition.
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| 15. |
- Gulliksson, Mårten, 1963-, et al.
(författare)
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An Iterative Approach to Ill-Conditioned Optimal Portfolio Selection
- 2020
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Ingår i: Computational Economics. - : Springer. - 0927-7099 .- 1572-9974. ; 56, s. 773-794
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Tidskriftsartikel (refereegranskat)abstract
- Covariance matrix of the asset returns plays an important role in the portfolioselection. A number of papers is focused on the case when the covariance matrixis positive definite. In this paper, we consider portfolio selection with a singu-lar covariance matrix. We describe an iterative method based on a second orderdamped dynamical systems that solves the linear rank-deficient problem approxi-mately. Since the solution is not unique, we suggest one numerical solution that canbe chosen from the iterates that balances the size of portfolio and the risk. The nu-merical study confirms that the method has good convergence properties and givesa solution as good as or better than the constrained least norm Moore-Penrose solu-tion. Finally, we complement our result with an empirical study where we analyzea portfolio with actual returns listed in S&P 500 index.
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| 16. |
- Laksman, Efraim, 1983, et al.
(författare)
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The stochastic opportunistic replacement problem, part III: improved bounding procedures
- 2020
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Ingår i: Annals of Operations Research. - : Springer Science and Business Media LLC. - 1572-9338 .- 0254-5330. ; 292:2, s. 711-733
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Tidskriftsartikel (refereegranskat)abstract
- We consider the problem to find a schedule for component replacement in a multi-component system, whose components possess stochastic lives and economic dependencies, such that the expected costs for maintenance during a pre-defined time period are minimized. The problem was considered in Patriksson et al. (Ann Oper Res 224:51–75, 2015), in which a two-stage approximation of the problem was optimized through decomposition (denoted the optimization policy). The current paper improves the effectiveness of the decomposition approach by establishing a tighter bound on the value of the recourse function (i.e., the second stage in the approximation). A general lower bound on the expected maintenance cost is also established. Numerical experiments with 100 simulation scenarios for each of four test instances show that the tighter bound yields a decomposition generating fewer optimality cuts. They also illustrate the quality of the lower bound. Contrary to results presented earlier, an age-based policy performs on par with the optimization policy, although most simple policies perform worse than the optimization policy.
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| 17. |
- Arkeryd, Leif, 1940, et al.
(författare)
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Stationary solutions to the two-dimensional Broadwell model
- 2020
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Ingår i: Documenta Mathematica. - 1431-0643 .- 1431-0635. ; 25, s. 2023-2048
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Tidskriftsartikel (refereegranskat)abstract
- Existence of renormalized solutions to the two-dimensional stationary Broadwell model in a square with given indata in L-1 is proven. Averaging techniques from the continuous velocity case being unavailable when the velocities are discrete, the approach is based on direct L-1-compactness arguments using the Kolmogorov-Riesz theorem.
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| 18. |
- Pihlsgård, Mats
(författare)
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Two-Barrier Problems in Applied Probability: Algorithms and Analysis
- 2005
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis consists of five papers (A-E). In Paper A, we study transient properties of the queue length process in various queueing settings. We focus on computing the mean and the Laplace transform of the time required for the queue length starting at $x0. We define the loss rate due to the reflection. The main result is sharp asymptotics for the loss rate as $K$ tends to infinity. As a major example, we consider the case where the increments of the random walk may be written as the difference between two phase-type distributed random variables. In this example we perform an explicit comparison between asymptotic and exact results for the loss rate. Paper C deals with queues and insurance risk processes where a generic service time, respectively generic claim, has a truncated heavy-tailed distribution. We study the compound Poisson ruin probability (or, equivalently, the tail of the M/G/1 steady-state waiting time) numerically. Furthermore, we investigate the asymptotics of the asymptotic exponential decay rate as the truncation level tends to infinity in a more general truncated Lévy process set-up. Paper D is a sequel of Paper B. We consider a Lévy process reflected at 0 and $K$>0 and define the loss rate. The first step is to identify the loss rate, which is non-trivial in the Lévy process case. The technique we use is based on optional stopping of the Kella-Whitt martingale for the reflected process. Once the identification is performed, we derive asymptotics for the loss rate in the case of a light-tailed Lévy measure. Paper E is also a sequel of Paper B. We present an algorithm for simulating the loss rate for a reflected random walk. The algorithm is efficient in the sense of bounded relative error. Key words: many-server queues, quasi birth-death processes, Kella-Whitt martingale, optional stopping, heterogeneous servers, reflected random walks, loss rate, Lundberg's equation, Cramér-Lundberg approximation, Wiener-Hopf factorization, asymptotics, phase-type distributions, reflected Lévy processes, light tails, efficient simulation.
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| 19. |
- Westerberg, Marcus, 1990-
(författare)
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Prostate cancer incidence, treatment and mortality : Empirical longitudinal register-based studies and methods for handling missing data
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The diagnostic activity for prostate cancer has increased substantially in Sweden, primarily due to increased use of prostate-specific antigen (PSA) testing in asymptomatic men, and this has led to a large increase in diagnoses. There have also been changes in the diagnostic workup, guidelines, treatment strategies, and more effective treatments have been introduced in different phases of the disease. This thesis aims to increase the understanding of consequences of changes in diagnostic activity and treatment, with a focus on empirical studies, methodological development, and handling of missing data.In paper I, the survival of men with metastatic prostate cancer was investigated across calendar time periods by use of Kaplan-Meier analyses and Cox regression. The median survival from diagnosis increased with six months comparing men diagnosed 1998-2001 with men diagnosed 2010-2015, while median PSA decreased.In paper II, a discrete time multivariate longitudinal model was combined with a proxy for the unobserved level of diagnostic activity to produce prognoses of incidence and mortality. Simulations indicated that a higher diagnostic activity was associated with fewer men diagnosed with metastatic disease and fewer prostate cancer deaths.In paper III, we looked for clinical variables predictive of the survival of men with castration-resistant prostate cancer (CRPC). A new data base was created including longitudinal data on prescriptions of hormonal treatment, PSA, and cause of death. We found that PSA doubling time and PSA at time of CRCP were highly predictive and could be used for treatment decision.In paper IV, we estimated annual incidence of metastatic prostate cancer using different methods for handling missing data in metastatic status (M stage). Missing data in M stage was high and varied over calendar time and risk groups, yet each method indicated a downward trend in incidence. Although men with unknown metastatic status cannot be assumed to have nonmetastatic disease in general, this may be reasonable among those with tumour characteristics that indicate a low risk of metastases.In paper V, the estimation of multivariate longitudinal models was considered in a context where some events are observed on a coarser level (e.g. grouped) at some time points, causing gaps in the data. The likelihood function, score and observed information were derived under an independent coarsening mechanism. A simulation study was conducted comparing properties of several estimators including direct maximum likelihood and Monte Carlo Expectation Maximisation.
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| 20. |
- Sabahno, Hamed, et al.
(författare)
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New machine-learning control charts for simultaneous monitoring of multivariate normal process parameters with detection and identification
- 2023
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Ingår i: Mathematics. - : MDPI. - 2227-7390. ; 11:16
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Tidskriftsartikel (refereegranskat)abstract
- Simultaneous monitoring of the process parameters in a multivariate normal process has caught researchers’ attention during the last two decades. However, only statistical control charts have been developed so far for this purpose. On the other hand, machine-learning (ML) techniques have rarely been developed to be used in control charts. In this paper, three ML control charts are proposed using the concepts of artificial neural networks, support vector machines, and random forests techniques. These ML techniques are trained to obtain linear outputs, and then based on the concepts of memory-less control charts, the process is classified into in-control or out-of-control states. Two different input scenarios and two different training methods are used for the proposed ML structures. In addition, two different process control scenarios are utilized. In one, the goal is only the detection of the out-of-control situation. In the other one, the identification of the responsible variable (s)/process parameter (s) for the out-of-control signal is also an aim (detection–identification). After developing the ML control charts for each scenario, we compare them to one another, as well as to the most recently developed statistical control charts. The results show significantly better performance of the proposed ML control charts against the traditional memory-less statistical control charts in most compared cases. Finally, an illustrative example is presented to show how the proposed scheme can be implemented in a healthcare process.
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| 21. |
- Lindo, Alexey, 1987, et al.
(författare)
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General linear-fractional branching processes with discrete time.
- 2018
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Ingår i: Stochastics. - : Informa UK Limited. - 1744-2508 .- 1744-2516. ; 90:3, s. 364-378
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Tidskriftsartikel (refereegranskat)abstract
- We study a linear-fractional Bienayme-Galton-Watson process with a general type space. The corresponding tree contour process is described by an alternating random walk with the downward jumps having a geometric distribution. This leads to the linear-fractional distribution formula for an arbitrary observation time, which allows us to establish transparent limit theorems for the subcritical, critical and supercritical cases. Our results extend recent findings for the linear-fractional branching processes with countably many types.
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| 22. |
- Bolin, David, 1983, et al.
(författare)
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The Rational SPDE Approach for Gaussian Random Fields With General Smoothness
- 2020
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Ingår i: Journal of Computational and Graphical Statistics. - : Informa UK Limited. - 1061-8600 .- 1537-2715. ; 29:2, s. 274-85
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Tidskriftsartikel (refereegranskat)abstract
- A popular approach for modeling and inference in spatial statistics is to represent Gaussian random fields as solutions to stochastic partial differential equations (SPDEs) of the form , where is Gaussian white noise, L is a second-order differential operator, and is a parameter that determines the smoothness of u. However, this approach has been limited to the case , which excludes several important models and makes it necessary to keep beta fixed during inference. We propose a new method, the rational SPDE approach, which in spatial dimension is applicable for any , and thus remedies the mentioned limitation. The presented scheme combines a finite element discretization with a rational approximation of the function to approximate u. For the resulting approximation, an explicit rate of convergence to u in mean-square sense is derived. Furthermore, we show that our method has the same computational benefits as in the restricted case . Several numerical experiments and a statistical application are used to illustrate the accuracy of the method, and to show that it facilitates likelihood-based inference for all model parameters including beta. for this article are available online.
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| 23. |
- Lindgren, Petter, et al.
(författare)
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A likelihood ratio-based approach for improved source attribution in microbiological forensic investigations
- 2019
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Ingår i: Forensic Science International. - : Elsevier. - 0379-0738 .- 1872-6283. ; 302
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Tidskriftsartikel (refereegranskat)abstract
- A common objective in microbial forensic investigations is to identify the origin of a recovered pathogenic bacterium by DNA sequencing. However, there is currently no consensus about how degrees of belief in such origin hypotheses should be quantified, interpreted, and communicated to wider audiences. To fill this gap, we have developed a concept based on calculating probabilistic evidential values for microbial forensic hypotheses. The likelihood-ratio method underpinning this concept is widely used in other forensic fields, such as human DNA matching, where results are readily interpretable and have been successfully communicated in juridical hearings. The concept was applied to two case scenarios of interest in microbial forensics: (1) identifying source cultures among series of very similar cultures generated by parallel serial passage of the Tier 1 pathogen Francisella tularensis, and (2) finding the production facilities of strains isolated in a real disease outbreak caused by the human pathogen Listeria monocytogenes. Evidence values for the studied hypotheses were computed based on signatures derived from whole genome sequencing data, including deep-sequenced low-frequency variants and structural variants such as duplications and deletions acquired during serial passages. In the F. tularensis case study, we were able to correctly assign fictive evidence samples to the correct culture batches of origin on the basis of structural variant data. By setting up relevant hypotheses and using data on cultivated batch sources to define the reference populations under each hypothesis, evidential values could be calculated. The results show that extremely similar strains can be separated on the basis of amplified mutational patterns identified by high-throughput sequencing. In the L. monocytogenes scenario, analyses of whole genome sequence data conclusively assigned the clinical samples to specific sources of origin, and conclusions were formulated to facilitate communication of the findings. Taken together, these findings demonstrate the potential of using bacterial whole genome sequencing data, including data on both low frequency SNP signatures and structural variants, to calculate evidence values that facilitate interpretation and communication of the results. The concept could be applied in diverse scenarios, including both epidemiological and forensic source tracking of bacterial infectious disease outbreaks.
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| 24. |
- Eriksson, Kimmo, et al.
(författare)
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Bentley’s conjecture on popularity toplist turnover under random copying
- 2010
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Ingår i: The Ramanujan journal. - : Springer Science and Business Media LLC. - 1382-4090 .- 1572-9303. ; 23, s. 371-396
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Tidskriftsartikel (refereegranskat)abstract
- Bentley et al studied the turnover rate in popularity toplists in a ’random copying’ model of cultural evolution. Based on simulations of a model with population size N, list length ℓ and invention rate μ, they conjectured a remarkably simple formula for the turnover rate: ℓ√μ. Here we study an overlapping generations version of the random copying model, which can be interpreted as a random walk on the integer partitions of the population size. In this model we show that the conjectured formula, after a slight correction, holds asymptotically.
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| 25. |
- Kuronen, M., et al.
(författare)
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Hierarchical log Gaussian Cox process for regeneration in uneven-aged forests
- 2022
-
Ingår i: Environmental and Ecological Statistics. - : Springer Science and Business Media LLC. - 1352-8505 .- 1573-3009. ; 29:1, s. 185-205
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Tidskriftsartikel (refereegranskat)abstract
- We propose a hierarchical log Gaussian Cox process (LGCP) for point patterns, where a set of points x affects another set of points y but not vice versa. We use the model to investigate the effect of large trees on the locations of seedlings. In the model, every point in x has a parametric influence kernel or signal, which together form an influence field. Conditionally on the parameters, the influence field acts as a spatial covariate in the intensity of the model, and the intensity itself is a non-linear function of the parameters. Points outside the observationwindowmay affect the influence field inside the window. We propose an edge correction to account for this missing data. The parameters of the model are estimated in a Bayesian framework using Markov chain Monte Carlo where a Laplace approximation is used for the Gaussian field of the LGCP model. The proposed model is used to analyze the effect of large trees on the success of regeneration in uneven-aged forest stands in Finland.
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