| 1. |
- Galindo-Prieto, Beatriz, et al.
(författare)
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A new approach for variable influence on projection (VIP) in O2PLS models
- 2017
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier. - 0169-7439 .- 1873-3239. ; 160, s. 110-124
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Tidskriftsartikel (refereegranskat)abstract
- A novel variable influence on projection approach for O2PLS® models, named VIPO2PLS, is presented in this paper. VIPO2PLS is a model-based method for judging the importance of variables. Its cornerstone is the 2-way formalism of the O2PLS models; i.e. the use of both predictive and orthogonal normalized loadings of the two modelled data matrices, and also a new weighting system based on the sum of squares of both data blocks (X, Y). The VIPO2PLS algorithm has been tested in one synthetic data set and two real cases, and the outcomes have been compared to the PLS-VIP, VIPOPLS, and i-PLS methods. The purpose is to achieve a sharper and enhanced model interpretation of O2PLS models by using the new VIPO2PLS method for assessing the importance of both X- and Y- variables.
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| 2. |
- Malmberg, Filip, et al.
(författare)
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An efficient algorithm for exact evaluation of stochastic watersheds
- 2014
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Ingår i: Pattern Recognition Letters. - : Elsevier BV. - 0167-8655 .- 1872-7344. ; 47, s. 80-84
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Tidskriftsartikel (refereegranskat)abstract
- The stochastic watershed is a method for unsupervised image segmentation proposed by Angulo and Jeulin (2007). The method first computes a probability density function (PDF), assigning to each piece of contour in the image the probability to appear as a segmentation boundary in seeded watershed segmentation with randomly selected seeds. Contours that appear with high probability are assumed to be more important. This PDF is then post-processed to obtain a final segmentation. The main computational hurdle with the stochastic watershed method is the calculation of the PDF. In the original publication by Angulo and Jeulin, the PDF was estimated by Monte Carlo simulation, i.e., repeatedly selecting random markers and performing seeded watershed segmentation. Meyer and Stawiaski (2010) showed that the PDF can be calculated exactly, without performing any Monte Carlo simulations, but do not provide any implementation details. In a naive implementation, the computational cost of their method is too high to make it useful in practice. Here, we extend the work of Meyer and Stawiaski by presenting an efficient (quasi-linear) algorithm for exact computation of the PDF. We demonstrate that in practice, the proposed method is faster than any previously reported method by more than two orders of magnitude. The algorithm is formulated for general undirected graphs, and thus trivially generalizes to images with any number of dimensions.
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| 3. |
- Ahmad, M. Rauf, et al.
(författare)
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Tests for high-dimensional covariance matrices using the theory of U-statistics
- 2015
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Ingår i: Journal of Statistical Computation and Simulation. - : Informa UK Limited. - 0094-9655 .- 1563-5163. ; 85:13, s. 2619-2631
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Tidskriftsartikel (refereegranskat)abstract
- Test statistics for sphericity and identity of the covariance matrix are presented, when the data are multivariate normal and the dimension, p, can exceed the sample size, n. Under certain mild conditions mainly on the traces of the unknown covariance matrix, and using the asymptotic theory of U-statistics, the test statistics are shown to follow an approximate normal distribution for large p, also when p >> n. The accuracy of the statistics is shown through simulation results, particularly emphasizing the case when p can be much larger than n. A real data set is used to illustrate the application of the proposed test statistics.
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| 4. |
- Nzabanita, Joseph, et al.
(författare)
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Bilinear regression model with Kronecker and linear structures for the covariance matrix
- 2015
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Ingår i: Afrika Statistika. - : Statistics and Probability African Society (SPAS). - 2316-090X. ; 10:2, s. 827-837
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, the bilinear regression model based on normally distributed random matrix is studied. For these models, the dispersion matrix has the so called Kronecker product structure and they can be used for example to model data with spatio-temporal relationships. The aim is to estimate the parameters of the model when, in addition, one covariance matrix is assumed to be linearly structured. On the basis of n independent observations from a matrix normal distribution, estimating equations in a flip-flop relation are established and the consistency of estimators is studied.
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| 5. |
- Mischenko, Kateryna, et al.
(författare)
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Assessing a multiple QTL search using the variance component model
- 2010
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Ingår i: Computational biology and chemistry (Print). - : Elseiver. - 1476-9271 .- 1476-928X. ; 34:1, s. 34-41
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Tidskriftsartikel (refereegranskat)abstract
- Development of variance component algorithms in genetics has previously mainly focused on animal breeding models or problems in human genetics with a simple data structure. We study alternative methods for constrained likelihood maximization in quantitative trait loci (QTL) analysis for large complex pedigrees. We apply a forward selection scheme to include several QTL and interaction effects, as well as polygenic effects, with up to five variance components in the model. We show that the implemented active set and primal-dual schemes result in accurate solutions and that they are robust. In terms of computational speed, a comparison of two approaches for approximating the Hessian of the log-likelihood shows that the method using an average information matrix is the method of choice for the five-dimensional problem. The active set method, with the average information method for Hessian computation, exhibits the fastest convergence with an average of 20 iterations per tested position, where the change in variance components <0.0001 was used as convergence criterion.
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| 6. |
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| 7. |
- Skarin, Anna
(författare)
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Modeling interdependent animal movement in continuous time
- 2016
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Ingår i: Biometrics. - : Wiley. - 0006-341X .- 1541-0420. ; 72, s. 315-324
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Tidskriftsartikel (refereegranskat)abstract
- This article presents a new approach to modeling group animal movement in continuous time. The movement of a group of animals is modeled as a multivariate Ornstein Uhlenbeck diffusion process in a high-dimensional space. Each individual of the group is attracted to a leading point which is generally unobserved, and the movement of the leading point is also an Ornstein Uhlenbeck process attracted to an unknown attractor. The Ornstein Uhlenbeck bridge is applied to reconstruct the location of the leading point. All movement parameters are estimated using Markov chain Monte Carlo sampling, specifically a Metropolis Hastings algorithm. We apply the method to a small group of simultaneously tracked reindeer, Rangifer tarandus tarandus, showing that the method detects dependency in movement between individuals.
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| 8. |
- Andersson, R., et al.
(författare)
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Dose-response-time modelling: Second-generation turnover model with integral feedback control
- 2016
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Ingår i: European Journal of Pharmaceutical Sciences. - : Elsevier BV. - 0928-0987 .- 1879-0720. ; 81, s. 189-200
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Tidskriftsartikel (refereegranskat)abstract
- © 2015 Elsevier B.V. All rights reserved. This study presents a dose-response-time (DRT) analysis based on a large preclinical biomarker dataset on the interaction between nicotinic acid (NiAc) and free fatty acids (FFA). Data were collected from studies that examined different rates, routes, and modes of NiAc provocations on the FFA time course. All information regarding the exposure to NiAc was excluded in order to demonstrate the utility of a DRT model. Special emphasis was placed on the selection process of the biophase model. An inhibitory Imax-model, driven by the biophase amount, acted on the turnover rate of FFA. A second generation NiAc/FFA model, which encompasses integral (slow buildup of tolerance - an extension of the previously used NiAc/FFA turnover models) and moderator (rapid and oscillatory) feedback control, was simultaneously fitted to all time courses in normal rats. The integral feedback control managed to capture an observed 90% adaptation (i.e., almost a full return to baseline) when 10 days constant-rate infusion protocols of NiAc were used. The half-life of the adaptation process had a 90% prediction interval between 3.5-12 in the present population. The pharmacodynamic parameter estimates were highly consistent when compared to an exposure-driven analysis, partly validating the DRT modelling approach and suggesting the potential of DRT analysis in areas where exposure data are not attainable. Finally, new numerical algorithms, which rely on sensitivity equations to robustly and efficiently compute the gradients in the parameter optimization, were successfully used for the mixed-effects approach in the parameter estimation.
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| 9. |
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| 10. |
- Beier, Ulrika
(författare)
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Habitat use in fish communities : size- and environment-dependent mechanisms affecting biotic interactions and population regulation
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Through the influence of abiotic factors, the habitat use of organisms affects their metabolism as well as other species- and size-dependent individual-based rates. The habitat-specific performances of individuals interacting in different habitats thereby affect biotic interactions. Habitat use is thus central for the outcomes of biotic interactions that, in turn, regulate populations and communities. My aim is to investigate how individual processes are influenced by habitat-dependent abiotic factors, affecting biotic interactions to regulate habitat use and population structures in fish communities. I examined patterns of habitat distribution and population structures of perch (Perca fluviatilis L.), roach (Rutilus rutilus (L.)), and the zooplankton specialist vendace (Coregonus albula (L.)) using a database of standardised test fishing data in lakes. To clarify mechanisms, I experimentally studied predation from perch in pond enclosures as well as relative foraging abilities of the two competitors roach and vendace in aquaria with different temperature and light treatments. To test mechanisms in natural situations, I calculated species- and size-dependent net energy intake, incorporating temperature- and light-dependence, including metabolism, using field data from different habitats in lakes with and without vendace. I also developed and applied a stage-structured biomass model, considering a cold water species (vendace) using two habitats differing in temperature. I thereby studied how climate warming which acts differently on different lake habitats affected temperature-dependent individual-based processes, and results on the population level. Through multi-species studies, I found that a combination of size- and environment-dependent individual processes determining energy gain, rather than predation risk, could explain size- and species-specific habitat use. The single-species study showed that stage-specific intake rates in one habitat, altered by increased temperature, affected intraspecific competition in both habitats, through a mechanism of ‘inter-habitat subsidies’ which altered population structure through maturation and reproduction rates. My thesis shows how including size- and environment-dependent individual processes, and interactions across habitats, increases our understanding of population and community structure as well as effects of environmental change.
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