| 1. |
- Lu, Xin, et al.
(författare)
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Respondent-driven sampling on directed networks
- 2013
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Ingår i: Electronic Journal of Statistics. - 1935-7524. ; 7, s. 292-322
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Tidskriftsartikel (refereegranskat)abstract
- Respondent-driven sampling (RDS) is a widely used method for generating chain-referral samples from hidden populations. It is an extension of the snowball sampling method and can, given that some assumptions are met, generate unbiased population estimates. One key assumption, not likely to be met, is that the acquaintance network in which the recruitment process takes place is undirected, meaning that all recruiters should have the potential to be recruited by the person they recruit. Using a mean-field approach, we develop an estimator which is based on prior information about the average indegrees of estimated variables. When the indegree is known, such as for RDS studies over internet social networks, the estimator can greatly reduce estimate error and bias as compared with current methods; when the indegree is not known, which is most common for interview-based RDS studies, the estimator can through sensitivity analysis be used as a tool to account for uncertainties of network directedness and error in self-reported degree data. The performance of the new estimator, together with previous RDS estimators, is investigated thoroughly by simulations on networks with varying structures. We have applied the new estimator on an empirical RDS study for injecting drug users in New York City.
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| 2. |
- Öktem, Ozan, 1969-, et al.
(författare)
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A component-wise iterated relative entropy regularization method with updated prior and regularization parameter
- 2007
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Ingår i: Inverse Problems. - : Institute of Physics (IOP). - 0266-5611 .- 1361-6420. ; 23:5, s. 2121-2139
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Tidskriftsartikel (refereegranskat)abstract
- We present a componentwise iterated relative entropy regularization method (COMET) where the prior and regularization parameter could be updated in the iterates. Such a reconstruction method could be useful for multicomponent inverse problems, such as the one occurring in electron tomography. The paper also contains a brief introduction to regularization theory with emphasis on variational based regularization methods, and we rigorously prove that the tolerance-based entropy reconstruction method that occurs in the COMET iterates is a regularization method. We conclude by showing examples of COMET applied to electron tomography data.
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| 3. |
- Iftimi, Adina, et al.
(författare)
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Second-order analysis of marked inhomogeneous spatio-temporal point processes : applications to earthquake data
- 2019
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Ingår i: Scandinavian Journal of Statistics. - : Wiley. - 0303-6898 .- 1467-9469. ; 46:3, s. 661-685
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Tidskriftsartikel (refereegranskat)abstract
- To analyse interactions in marked spatio-temporal point processes (MSTPPs), we introduce marked second-order reduced moment measures and K-functions for inhomogeneous second-order intensity reweighted stationary MSTPPs. These summary statistics, which allow us to quantify dependence between different mark-based classifications of the points, are depending on the specific mark space and mark reference measure chosen. Unbiased and consistent minus-sampling estimators are derived for all statistics considered and a test for random labelling is indicated. In addition, we treat Voronoi intensity estimators for MSTPPs. These new statistics are finally employed to analyse an Andaman sea earthquake data set.
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| 4. |
- Cooray, Vernon, 1952-, et al.
(författare)
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A Novel Interpretation of the Electromagnetic Fields of Lightning Return Strokes
- 2019
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Ingår i: Atmosphere. - : MDPI. - 2073-4433 .- 2073-4433. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Electric and/or magnetic fields are generated by stationary charges, uniformly moving charges and accelerating charges. These field components are described in the literature as static fields, velocity fields (or generalized Coulomb field) and radiation fields (or acceleration fields), respectively. In the literature, the electromagnetic fields generated by lightning return strokes are presented using the field components associated with short dipoles, and in this description the one-to-one association of the electromagnetic field terms with the physical process that gives rise to them is lost. In this paper, we have derived expressions for the electromagnetic fields using field equations associated with accelerating (and moving) charges and separated the resulting fields into static, velocity and radiation fields. The results illustrate how the radiation fields emanating from the lightning channel give rise to field terms varying as 1/r and 1/r2, the velocity fields generating field terms varying as 1/r2, and the static fields generating field components varying as 1/r2 and 1/r3. These field components depend explicitly on the speed of propagation of the current pulse. However, the total field does not depend explicitly on the speed of propagation of the current pulse. It is shown that these field components can be combined to generate the field components pertinent to the dipole technique. However, in this conversion process the connection of the field components to the physical processes taking place at the source that generate these fields (i.e., static charges, uniformly moving charges and accelerating charges) is lost.
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| 5. |
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| 6. |
- Lu, Xin, et al.
(författare)
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Finding the shortest paths by node combination
- 2011
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Ingår i: Applied Mathematics and Computation. - : Elsevier BV. - 0096-3003 .- 1873-5649. ; 217:13, s. 6401-6408
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Tidskriftsartikel (refereegranskat)abstract
- By repeatedly combining the source node's nearest neighbor, we propose a node combination (NC) method to implement the Dijkstra's algorithm. The NC algorithm finds the shortest paths with three simple iterative steps: find the nearest neighbor of the source node, combine that node with the source node, and modify the weights on edges that connect to the nearest neighbor. The NC algorithm is more comprehensible and convenient for programming as there is no need to maintain a set with the nodes' distances. Experimental evaluations on various networks reveal that the NC algorithm is as efficient as Dijkstra's algorithm. As the whole process of the NC algorithm can be implemented with vectors, we also show how to find the shortest paths on a weight matrix.
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| 7. |
- Mahmudi, Owais, et al.
(författare)
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Genome-wide probabilistic reconciliation analysis across vertebrates
- 2013
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 14:Suppl 15, s. S10-
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Tidskriftsartikel (refereegranskat)abstract
- Gene duplication is considered to be a major driving force in evolution that enables the genome of a species to acquire new functions. A reconciliation - a mapping of gene tree vertices to the edges or vertices of a species tree explains where gene duplications have occurred on the species tree. In this study, we sample reconciliations from a posterior over reconciliations, gene trees, edge lengths and other parameters, given a species tree and gene sequences. We employ a Bayesian analysis tool, based on the probabilistic model DLRS that integrates gene duplication, gene loss and sequence evolution under a relaxed molecular clock for substitution rates, to obtain this posterior. By applying these methods, we perform a genome-wide analysis of a nine species dataset, OPTIC, and conclude that for many gene families, the most parsimonious reconciliation (MPR) - a reconciliation that minimizes the number of duplications - is far from the correct explanation of the evolutionary history. For the given dataset, we observe that approximately 19% of the sampled reconciliations are different from MPR. This is in clear contrast with previous estimates, based on simpler models and less realistic assumptions, according to which 98% of the reconciliations can be expected to be identical to MPR. We also generate heatmaps showing where in the species trees duplications have been most frequent during the evolution of these species.
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| 8. |
- Marco Salas, Sergio, et al.
(författare)
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De novo spatiotemporal modelling of cell-type signatures in the developmental human heart using graph convolutional neural networks
- 2022
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Ingår i: PloS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18:8
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Tidskriftsartikel (refereegranskat)abstract
- With the emergence of high throughput single cell techniques, the understanding of the molecular and cellular diversity of mammalian organs have rapidly increased. In order to understand the spatial organization of this diversity, single cell data is often integrated with spatial data to create probabilistic cell maps. However, targeted cell typing approaches relying on existing single cell data achieve incomplete and biased maps that could mask the true diversity present in a tissue slide. Here we applied a de novo technique to spatially resolve and characterize cellular diversity of in situ sequencing data during human heart development. We obtained and made accessible well defined spatial cell-type maps of fetal hearts from 4.5 to 9 post conception weeks, not biased by probabilistic cell typing approaches. With our analysis, we could characterize previously unreported molecular diversity within cardiomyocytes and epicardial cells and identified their characteristic expression signatures, comparing them with specific subpopulations found in single cell RNA sequencing datasets. We further characterized the differentiation trajectories of epicardial cells, identifying a clear spatial component on it. All in all, our study provides a novel technique for conducting de novo spatial-temporal analyses in developmental tissue samples and a useful resource for online exploration of cell-type differentiation during heart development at sub-cellular image resolution.
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| 9. |
- Zeebari, Zangin, et al.
(författare)
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Regularized conditional estimators of unit inefficiency in stochastic frontier analysis, with application to electricity distribution market
- 2022
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Ingår i: Journal of Productivity Analysis. - New York, NY : Springer. - 0895-562X .- 1573-0441. ; 59:1, s. 79-97
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Tidskriftsartikel (refereegranskat)abstract
- In stochastic frontier analysis, the conventional estimation of unit inefficiency is based on the mean/mode of the inefficiency, conditioned on the composite error. It is known that the conditional mean of inefficiency shrinks towards the mean rather than towards the unit inefficiency. In this paper, we analytically prove that the conditional mode cannot accurately estimate unit inefficiency, either. We propose regularized estimators of unit inefficiency that restrict the unit inefficiency estimators to satisfy some a priori assumptions, and derive the closed form regularized conditional mode estimators for the three most commonly used inefficiency densities. Extensive simulations show that, under common empirical situations, e.g., regarding sample size and signal-to-noise ratio, the regularized estimators outperform the conventional (unregularized) estimators when the inefficiency is greater than its mean/mode. Based on real data from the electricity distribution sector in Sweden, we demonstrate that the conventional conditional estimators and our regularized conditional estimators provide substantially different results for highly inefficient companies. © 2022, The Author(s).
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| 10. |
- Öktem, Ozan, 1969-, et al.
(författare)
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Electron Lambda-tomography
- 2009
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy Press. - 0027-8424 .- 1091-6490. ; 106:51, s. 21842-21847
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Tidskriftsartikel (refereegranskat)abstract
- Filtered back-projection and weighted back-projection have long been the methods of choice within the electron microscopy com- munity for reconstructing the structure of macromolecular assem- blies from electron tomography data. Here, we describe electron lambda-tomography, a reconstruction method that enjoys the ben- efits of the above mentioned methods, namely speed and ease of implementation, but also addresses some of their shortcomings. In particular, compared to these standard methods, electron lambda- tomography is less sensitive to artifacts that come from structures outside the region that is being reconstructed, and it can sharpen boundaries.
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