| 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. |
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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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| 5. |
- 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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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- 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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| 10. |
- Moradi, M. Mehdi, et al.
(författare)
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Resample-smoothing of Voronoi intensity estimators
- 2019
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Ingår i: Statistics and computing. - : Springer. - 0960-3174 .- 1573-1375. ; 29:5, s. 995-1010
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Tidskriftsartikel (refereegranskat)abstract
- Voronoi estimators are non-parametric and adaptive estimators of the intensity of a point process. The intensity estimate at a given location is equal to the reciprocal of the size of the Voronoi/Dirichlet cell containing that location. Their major drawback is that they tend to paradoxically under-smooth the data in regions where the point density of the observed point pattern is high, and over-smooth where the point density is low. To remedy this behaviour, we propose to apply an additional smoothing operation to the Voronoi estimator, based on resampling the point pattern by independent random thinning. Through a simulation study we show that our resample-smoothing technique improves the estimation substantially. In addition, we study statistical properties such as unbiasedness and variance, and propose a rule-of-thumb and a data-driven cross-validation approach to choose the amount of smoothing to apply. Finally we apply our proposed intensity estimation scheme to two datasets: locations of pine saplings (planar point pattern) and motor vehicle traffic accidents (linear network point pattern).
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| 11. |
- Löfgren, Stefan, et al.
(författare)
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Water chemistry in 179 randomly selected Swedish headwaterstreams related to forest production, clear-felling and climate
- 2014
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Ingår i: Environmental Monitoring & Assessment. - : Springer Berlin/Heidelberg. - 0167-6369 .- 1573-2959. ; 186:12, s. 8907-8928
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Tidskriftsartikel (refereegranskat)abstract
- From a policy perspective, it is important to understand forestry effects on surface waters from a landscape perspective. The EU Water Framework Directive demands remedial actions if not achieving good ecological status. In Sweden, 44 % of the surface water bodies have moderate ecological status or worse. Many of these drain catchments with a mosaic of managed forests. It is important for the forestry sector and water authorities to be able to identify where, in the forested landscape, special precautions are necessary. The aim of this study was to quantify the relations between forestry parameters and headwater stream concentrations of nutrients, organic matter and acid-base chemistry. The results are put into the context of regional climate, sulphur and nitrogen deposition, as well as marine influences. Water chemistry was measured in 179 randomly selected headwater streams from two regions in southwest and central Sweden, corresponding to 10 % of the Swedish land area. Forest status was determined from satellite images and Swedish National Forest Inventory data using the probabilistic classifier method, which was used to model stream water chemistry with Bayesian model averaging. The results indicate that concentrations of e.g. nitrogen, phosphorus and organic matter are related to factors associated with forest production but that it is not forestry per se that causes the excess losses. Instead, factors simultaneously affecting forest production and stream water chemistry, such as climate, extensive soil pools and nitrogen deposition, are the most likely candidates The relationships with clear-felled and wetland areas are likely to be direct effects.
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| 12. |
- Almquist, Joachim, 1980
(författare)
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Kinetic Models in Life Science — Contributions to Methods and Applications
- 2017
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Kinetic models in life science combine mathematics and biology to answer questions from areas such as cell biology, physiology, biotechnology, and drug development. The idea of kinetic models is to represent a biological system by a number of biochemical reactions together with mathematical expressions for the reaction kinetics, i.e., how fast the reactions occur. This defines a set of mass balance differential equations for the modeled biochemical variables, whose solution determines the variables' temporal dynamics. Good kinetic models describe, predict, and enable understanding of biological systems, and provide answers to questions which are otherwise technically challenging, unethical, or expensive to obtain directly from experiments. This thesis investigates the workflow for building and using kinetic models. Briefly, the model question determines a suitable mathematical framework for the mass balance equations, prior knowledge informs selection of relevant reactions and kinetics, and unknown parameters are estimated from experimental data. A validated model is used for simulation and analysis, which is interpreted to gain biological insights. Three kinetic models were created to illustrate the workflow. First, a model of the antiplatelet drug ticagrelor and the investigational antidote MEDI2452 was developed for the mouse. The model unraveled the biological mechanisms of the pharmacokinetic interaction and predicted free ticagrelor plasma concentration, thereby contributing to the pharmaceutical development of MEDI2452. Second, a model of the Kv1.5 potassium ion channel was integrated within an existing electrophysiological model of a canine atrial cell. The effect of Kv1.5 block on the action potential was simulated, which improved understanding of blocking mechanisms and enabled assessing pharmacological treatment of atrial fibrillation. Third, a nonlinear mixed effects (NLME) model, with population-level distributions of kinetic parameters, was successfully used to describe cell-to-cell variability of the yeast transcription factor Mig1. This model demonstrated the innovative idea of applying NLME modeling to single cell data.Two studies of kinetic model-building methods are also presented. First, a novel parameter estimation algorithm for NLME models is explained. It computes exact gradients using sensitivity-equations, and represents a substantial advancement over its predecessor. Second, a modeling framework is proposed that combines stochastic differential equations with NLME modeling. This promising framework extends the current scope of NLME models by considering uncertainty in the model dynamics.
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| 13. |
- Miller, Frank, et al.
(författare)
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A decision theoretical modeling for Phase III investments and drug licensing
- 2018
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Ingår i: Journal of Biopharmaceutical Statistics. - : Informa UK Limited. - 1054-3406 .- 1520-5711. ; 28:4, s. 698-721
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Tidskriftsartikel (refereegranskat)abstract
- For a new candidate drug to become an approved medicine, several decision points have to be passed. In this article, we focus on two of them: First, based on Phase II data, the commercial sponsor decides to invest (or not) in Phase III. Second, based on the outcome of Phase III, the regulator determines whether the drug should be granted market access. Assuming a population of candidate drugs with a distribution of true efficacy, we optimize the two stakeholders' decisions and study the interdependence between them. The regulator is assumed to seek to optimize the total public health benefit resulting from the efficacy of the drug and a safety penalty. In optimizing the regulatory rules, in terms of minimal required sample size and the Type I error in Phase III, we have to consider how these rules will modify the commercial optimization made by the sponsor. The results indicate that different Type I errors should be used depending on the rarity of the disease.
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| 14. |
- Lundengård, Karl, 1987-
(författare)
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Generalized Vandermonde matrices and determinants in electromagnetic compatibility
- 2017
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Matrices whose rows (or columns) consists of monomials of sequential powers are called Vandermonde matrices and can be used to describe several useful concepts and have properties that can be helpful for solving many kinds of problems. In this thesis we will discuss this matrix and some of its properties as well as a generalization of it and how it can be applied to curve fitting discharge current for the purpose of ensuring electromagnetic compatibility.In the first chapter the basic theory for later chapters is introduced. This includes the Vandermonde matrix and some of its properties, history, applications and generalizations, interpolation and regression problems, optimal experiment design and modelling of electrostatic discharge currents with the purpose to ensure electromagnetic compatibility.The second chapter focuses on finding the extreme points for the determinant for the Vandermonde matrix on various surfaces including spheres, ellipsoids, cylinders and tori. The extreme points are analysed in three dimensions or more.The third chapter discusses fitting a particular model called the p-peaked Analytically Extended Function (AEF) to data taken either from a standard for electromagnetic compatibility or experimental measurements. More specifically the AEF will be fitted to discharge currents from the IEC 62305-1 and IEC 61000-4-2 standards for lightning protection and electrostatic discharge immunity as well as some experimentally measured data of similar phenomena.
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| 15. |
- Avelin, Benny, 1984-, et al.
(författare)
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Boundary estimates for solutions to operators of p-Laplace type with lower order terms
- 2011
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Ingår i: Journal of Differential Equations. - : Elsevier BV. - 0022-0396 .- 1090-2732. ; 250:1, s. 264-291
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we study the boundary behavior of solutions to equations of the form∇⋅A(x,∇u)+B(x,∇u)=0, in a domain Ω⊂Rn, assuming that Ω is a δ-Reifenberg flat domain for δ sufficiently small. The function A is assumed to be of p-Laplace character. Concerning B, we assume that |∇ηB(x,η)|⩽c|η|p−2, |B(x,η)|⩽c|η|p−1, for some constant c, and that B(x,η)=|η|p−1B(x,η/|η|), whenever x∈Rn, η∈Rn∖{0}. In particular, we generalize the results proved in J. Lewis et al. (2008) [12] concerning the equation ∇⋅A(x,∇u)=0, to equations including lower order terms.
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| 16. |
- Jonsson, Viktor, 1987, et al.
(författare)
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Modelling of zero-inflation improves inference of metagenomic gene count data
- 2019
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Ingår i: Statistical Methods in Medical Research. - : SAGE Publications. - 0962-2802 .- 1477-0334. ; 28:12, s. 3712-3728
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Tidskriftsartikel (refereegranskat)abstract
- Metagenomics enables the study of gene abundances in complex mixtures of microorganisms and has become a standard methodology for the analysis of the human microbiome. However, gene abundance data is inherently noisy and contains high levels of biological and technical variability as well as an excess of zeros due to non-detected genes. This makes the statistical analysis challenging. In this study, we present a new hierarchical Bayesian model for inference of metagenomic gene abundance data. The model uses a zero-inflated overdispersed Poisson distribution which is able to simultaneously capture the high gene-specific variability as well as zero observations in the data. By analysis of three comprehensive datasets, we show that zero-inflation is common in metagenomic data from the human gut and, if not correctly modelled, it can lead to substantial reductions in statistical power. We also show, by using resampled metagenomic data, that our model has, compared to other methods, a higher and more stable performance for detecting differentially abundant genes. We conclude that proper modelling of the gene-specific variability, including the excess of zeros, is necessary to accurately describe gene abundances in metagenomic data. The proposed model will thus pave the way for new biological insights into the structure of microbial communities.
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| 17. |
- Cronie, Ottmar, 1979, et al.
(författare)
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Some edge correction methods for marked spatio-temporal point process models
- 2011
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Ingår i: Computational Statistics & Data Analysis. - : Elsevier BV. - 0167-9473 .- 1872-7352. ; 55:7, s. 2209-2220
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Tidskriftsartikel (refereegranskat)abstract
- Three edge correction methods for (marked) spatio-temporal point processes are proposed. They are all based on the idea of placing an approximated expected behaviour of the process at hand (simulated realisations) outside the study region which interacts with the data during the estimation. These methods are applied to the so-called growth-interaction model. The specific choices of growth function and interaction function made are purely motivated by the forestry applications considered. The parameters of the growth and interaction functions, i.e. the parameters related to the development of the marks, are estimated using the least-squares approach together with the proposed edge corrections. Finally, the edge corrected estimation methods are applied to a data set of Swedish Scots pine.
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| 18. |
- Bartoszek, Krzysztof
(författare)
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Quantifying the effects of anagenetic and cladogenetic evolution
- 2014
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Ingår i: Mathematical Biosciences. - : Elsevier BV. - 0025-5564 .- 1879-3134. ; 254, s. 42-57
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Tidskriftsartikel (refereegranskat)abstract
- An ongoing debate in evolutionary biology is whether phenotypic change occurs predominantly around the time of speciation or whether it instead accumulates gradually over time. In this work I propose a general framework incorporating both types of change, quantify the effects of speciational change via the correlation between species and attribute the proportion of change to each type. I discuss results of parameter estimation of Hominoid body size in this light. I derive mathematical formulae related to this problem, the probability generating functions of the number of speciation events along a randomly drawn lineage and from the most recent common ancestor of two randomly chosen tip species for a conditioned Yule tree. Additionally I obtain in closed form the variance of the distance from the root to the most recent common ancestor of two randomly chosen tip species.
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| 19. |
- Sundberg, Rolf, 1942-
(författare)
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Statistical Modelling by Exponential Families
- 2019
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Bok (refereegranskat)abstract
- This book is a readable, digestible introduction to exponential families, encompassing statistical models based on the most useful distributions in statistical theory, including the normal, gamma, binomial, Poisson, and negative binomial. Strongly motivated by applications, it presents the essential theory and then demonstrates the theory's practical potential by connecting it with developments in areas like item response analysis, social network models, conditional independence and latent variable structures, and point process models. Extensions to incomplete data models and generalized linear models are also included. In addition, the author gives a concise account of the philosophy of Per Martin-Löf in order to connect statistical modelling with ideas in statistical physics, including Boltzmann's law. Written for graduate students and researchers with a background in basic statistical inference, the book includes a vast set of examples demonstrating models for applications and exercises embedded within the text as well as at the ends of chapters.
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| 20. |
- Vanhatalo, Erik, et al.
(författare)
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Towards improved analysis methods for two-level factorial experiments with time series responses
- 2013
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Ingår i: Quality and Reliability Engineering International. - : Wiley. - 0748-8017 .- 1099-1638. ; 29:5, s. 725-741
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic processes exhibit a time delay between the disturbances and the resulting process response. Therefore, one has to acknowledge process dynamics, such as transition times, when planning and analyzing experiments in dynamic processes. In this article, we explore, discuss, and compare different methods to estimate location effects for two-level factorial experiments where the responses are represented by time series. Particularly, we outline the use of intervention-noise modeling to estimate the effects and to compare this method by using the averages of the response observations in each run as the single response. The comparisons are made by simulated experiments using a dynamic continuous process model. The results show that the effect estimates for the different analysis methods are similar. Using the average of the response in each run, but removing the transition time, is found to be a competitive, robust, and straightforward method, whereas intervention-noise models are found to be more comprehensive, render slightly fewer spurious effects, find more of the active effects for unreplicated experiments and provide the possibility to model effect dynamics. Copyright © 2012 John Wiley & Sons, Ltd. Copyright © 2012 John Wiley & Sons, Ltd.
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| 21. |
- Fagerström, Cecilia, Docent, 1973-, et al.
(författare)
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Factorial validity and invariance of the Life Satisfaction Index in older people across groups and time: Addressing the heterogeneity of age, functional ability, and depression.
- 2012
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Ingår i: Archives of gerontology and geriatrics (Print). - : Elsevier BV. - 0167-4943 .- 1872-6976. ; 55:2, s. 349-356
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Tidskriftsartikel (refereegranskat)abstract
- In the last decades, extensive research efforts have been directed at exploring life satisfaction in old age, and the Life Satisfaction Index A scale (LSIA), developed by Neugarten et al. in the 1960s, is one of the most commonly used instruments. However, studies have focused on predicting and comparing changes in people’s life satisfaction without testing if the LSIA instrument is equally valid for different subgroups of people. The present study investigated the underlying dimensions of the LSIA in a Swedish population (n=1402) of people 60−96 years of age. The study also examined factorial invariance across age, gender, functional ability and depression during a six-year period. The results showed that while a five-factor solution of the LSIA did not exhibit an acceptable fit to the data, a three-factor solution did show a close fit. The two three-factor models that demonstrated the best fit showed invariance across gender and across time, but noninvariance across groups with different levels of reduced functional ability, depressive symptoms and age. These findings suggest that the psychometric properties of life satisfaction instruments like the LSIA need to be taken into consideration before drawing conclusions about life satisfaction when comparing older people of different ages and with different depression and function levels.
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| 22. |
- Willighagen, Egon, 1974-, et al.
(författare)
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Linking the Resource Description Framework to cheminformatics and proteochemometrics
- 2011
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Ingår i: Journal of Biomedical Semantics. - 2041-1480. ; 2:Suppl 1, s. 6-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND :Semantic web technologies are finding their way into the life sciences. Ontologies and semantic markup have already been used for more than a decade in molecular sciences, but have not found widespread use yet. The semantic web technology Resource Description Framework (RDF) and related methods show to be sufficiently versatile to change that situation.RESULTS :The work presented here focuses on linking RDF approaches to existing molecular chemometrics fields, including cheminformatics, QSAR modeling and proteochemometrics. Applications are presented that link RDF technologies to methods from statistics and cheminformatics, including data aggregation, visualization, chemical identification, and property prediction. They demonstrate how this can be done using various existing RDF standards and cheminformatics libraries. For example, we show how IC50 and Ki values are modeled for a number of biological targets using data from the ChEMBL database.CONCLUSIONS :We have shown that existing RDF standards can suitably be integrated into existing molecular chemometrics methods. Platforms that unite these technologies, like Bioclipse, makes this even simpler and more transparent. Being able to create and share workflows that integrate data aggregation and analysis (visual and statistical) is beneficial to interoperability and reproducibility. The current work shows that RDF approaches are sufficiently powerful to support molecular chemometrics workflows.
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| 23. |
- Ivarsson, Andreas, et al.
(författare)
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Are all predicted relationships linear by nature? : A note about quantile regression in sport and exercise psychology
- 2014
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Ingår i: Advances in Contemporary Sport Psychology. - New York : Nova Science Publishers, Inc.. - 9781633216730 - 9781633216655 ; 6:2, s. 115-123
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Data in sport and exercise psychology research are often analyzed based on the assumption that the relationships between two or more variables are linear in nature. But are all relationships in sport and exercise settings linear? The aim of this paper is to: a) discuss the potential shortcomings with using linear regression analysis, b) introduce quantile regression analysis (Q-regression) as an alternative to linear regression, and c) give examples of how to use Q-regression analysis in order to overcome some of the shortcomings of linear regression analysis. A comparison between the results from a linear regression analysis and a Q-regression analysis shows differences between the two methods. More specifically, the independent variables in the results of the Q-regression analysis were shown to have non-linear relationships with the dependent variable in given examples. Researchers are encouraged to consider using Q-regression analysis in studies where non-linear relationships could be expected.
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| 24. |
- Broman, Erik, 1977, et al.
(författare)
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Random cover times using the Poisson cylinder process
- 2019
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Ingår i: Alea-Latin American Journal of Probability and Mathematical Statistics. - : Institute for Applied and Pure Mathematics (IMPA). - 1980-0436. ; 16:2, s. 1165-1199
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we deal with the classical problem of random cover times. We investigate the distribution of the time it takes for a Poisson process of cylinders to cover a set A subset of R-d . This Poisson process of cylinders is invariant under rotations, reflections and translations, and in addition we add a time component so that cylinders are "raining from the sky" at unit rate. Our main results concerns the asymptotic of this cover time as the set A grows. If the set A is discrete and well separated, we show convergence of the cover time to a Gumbel distribution. If instead A has positive box dimension (and satisfies a weak additional assumption), we find the correct rate of convergence.
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| 25. |
- Chigansky, Pavel, et al.
(författare)
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Populations with interaction and environmental dependence: From few, (almost) independent, members into deterministic evolution of high densities
- 2019
-
Ingår i: Stochastic Models. - : Informa UK Limited. - 1532-6349 .- 1532-4214. ; 35:2, s. 108-118
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Tidskriftsartikel (refereegranskat)abstract
- Many populations, e.g. not only of cells, bacteria, viruses, or replicating DNA molecules, but also of species invading a habitat, or physical systems of elements generating new elements, start small, from a few lndividuals, and grow large into a noticeable fraction of the environmental carrying capacity K or some corresponding regulating or system scale unit. Typically, the elements of the initiating, sparse set will not be hampering each other and their number will grow from Z0 = z0 in a branching process or Malthusian like, roughly exponential fashion, Zt ~atW, where Z t is the size at discrete time t → ∞, a > 1 is the offspring mean per individual (at the low starting density of elements, and large K), and W a sum of z0 i.i.d. random variables. It will, thus, become detectable (i.e. of the same order as K) only after around K generations, when its density Xt := Z t /K will tend to be strictly positive. Typically, this entity will be random, even if the very beginning was not at all stochastic, as indicated by lower case z0 , due to variations during the early development. However, from that time onwards, law of large numbers effects will render the process deterministic, though inititiated by the random density at time log K, expressed through the variable W. Thus, W acts both as a random veil concealing the start and a stochastic initial value for later, deterministic population density development. We make such arguments precise, studying general density and also system-size dependent, processes, as K → ∞. As an intrinsic size parameter, K may also be chosen to be the time unit. The fundamental ideas are to couple the initial system to a branching process and to show that late densities develop very much like iterates of a conditional expectation operator. The “random veil”, hiding the start, was first observed in the very concrete special case of finding the initial copy number in quantitative PCR under Michaelis-Menten enzyme kinetics, where the initial individual replication variance is nil if and only if the efficiency is one, i.e. all molecules replicate.
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