| 1. |
- Calatayud, Joaquín, et al.
(författare)
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Exploring the solution landscape enables more reliable network community detection
- 2019
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Ingår i: Physical review. E. - 2470-0045 .- 2470-0053. ; 100:5
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Tidskriftsartikel (refereegranskat)abstract
- To understand how a complex system is organized and functions, researchers often identify communities in the system's network of interactions. Because it is practically impossible to explore all solutions to guarantee the best one, many community-detection algorithms rely on multiple stochastic searches. But for a given combination of network and stochastic algorithms, how many searches are sufficient to find a solution that is good enough? The standard approach is to pick a reasonably large number of searches and select the network partition with the highest quality or derive a consensus solution based on all network partitions. However, if different partitions have similar qualities such that the solution landscape is degenerate, the single best partition may miss relevant information, and a consensus solution may blur complementary communities. Here we address this degeneracy problem with coarse-grained descriptions of the solution landscape. We cluster network partitions based on their similarity and suggest an approach to determine the minimum number of searches required to describe the solution landscape adequately. To make good use of all partitions, we also propose different ways to explore the solution landscape, including a significance clustering procedure. We test these approaches on synthetic networks and a real-world network using two contrasting community-detection algorithms: The algorithm that can identify more general structures requires more searches, and networks with clearer community structures require fewer searches. We also find that exploring the coarse-grained solution landscape can reveal complementary solutions and enable more reliable community detection.
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| 2. |
- Calatayud, Joaquín, et al.
(författare)
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Positive associations among rare species and their persistence in ecological assemblages
- 2020
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Ingår i: Nature Ecology & Evolution. - : Nature Publishing Group. - 2397-334X. ; 4:1, s. 40-45
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Tidskriftsartikel (refereegranskat)abstract
- According to the competitive exclusion principle, species with low competitive abilities should be excluded by more efficient competitors; yet, they generally remain as rare species. Here, we describe the positive and negative spatial association networks of 326 disparate assemblages, showing a general organization pattern that simultaneously supports the primacy of competition and the persistence of rare species. Abundant species monopolize negative associations in about 90% of the assemblages. On the other hand, rare species are mostly involved in positive associations, forming small network modules. Simulations suggest that positive interactions among rare species and microhabitat preferences are the most probable mechanisms underpinning this pattern and rare species persistence. The consistent results across taxa and geography suggest a general explanation for the maintenance of biodiversity in competitive environments. Analysing spatial association networks among >300 terrestrial and aquatic assemblages, the authors find that the majority of negative associations involve abundant species. In contrast, rare species form mostly positive associations, potentially explaining their persistence in natural communities.
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| 3. |
- Calatayud, Joaquín, et al.
(författare)
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Regularities in species’ niches reveal the world’s climate regions
- 2021
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Ingår i: eLIFE. - : eLife Sciences Publications Ltd.. - 2050-084X. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Climate regions form the basis of many ecological, evolutionary, and conservation studies. However, our understanding of climate regions is limited to how they shape vegetation: They do not account for the distribution of animals. Here we develop a network-based framework to identify important climates worldwide based on regularities in realized niches of about 26,000 tetrapods. We show that high-energy climates, including deserts, tropical savannas, and steppes, are consistent across animal-and plant-derived classifications, indicating similar underlying climatic determinants. Conversely, temperate climates differ across all groups, suggesting that these climates allow for idiosyncratic adaptations. Finally, we show how the integration of niche classifications with geographical information enables the detection of climatic transition zones and the signal of geographic and historical processes. Our results identify the climates shaping the distribution of tetrapods and call for caution when using general climate classifications to study the ecology, evolution, or conservation of specific taxa.
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| 4. |
- Edstrom, Per, et al.
(författare)
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Geometry Related Inter-Instrument Differences in Spectrophotometric Measurements
- 2010
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Ingår i: Nordic Pulp & Paper Research Journal. - : Walter de Gruyter GmbH. - 0283-2631 .- 2000-0669. ; 25:2, s. 221-232
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Tidskriftsartikel (refereegranskat)abstract
- The L&W Elrepho d/0 and the Spectrolino 45/0 instruments are examined using paper samples with different properties. External factors that influence the measurements such as the sample background, the instrument calibration and the sample inhomogeneity are studied, and a methodology for their minimization is presented. Experimental measurements show that such external factors, if not minimized by proper routines, affect the inter-instrument differences far more (up to 4-5 Delta E-ab(star)) than the instrument geometry (the effect of which is small and of order 0.1 Delta E-ab(star)). The DORT2002 radiative transfer model is used to simulate differences caused by instrument geometry. The simulated and measured differences are found to agree in magnitude, and the differences are mapped against sample properties. It is observed that the 45/0 instrument detects higher reflectance from paper samples with negligible absorption and transmittance. When there is considerable absorption (dyed samples) or transmittance (thin samples), the d/0 instrument detects higher reflectance. The physical mechanism behind this behavior is studied and explained using DORT2002, and the instrument differences are shown to depend on the anisotropy of the reflected light. The model/measurement agreement is satisfactory as the characteristic behavior is captured in almost all cases studied. This new understanding is important for facilitating accurate data exchange between the paper and graphic arts industries, but also for interpretation of reflectance measurements in general.
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| 5. |
- Edström, Per, et al.
(författare)
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Geometry Related Inter-Instrument Differences in Spectrophotometric Measurements
- 2010
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Ingår i: Nordic Pulp & Paper Research Journal. - 0283-2631 .- 2000-0669. ; 25:2, s. 221-232
-
Tidskriftsartikel (refereegranskat)abstract
- The L&W Elrepho d/0 and the Spectrolino 45/0 instruments are examined using paper samples with different properties. External factors that influence the measurements such as the sample background, the instrument calibration and the sample inhomogeneity are studied, and a methodology for their minimization is presented. Experimental measurements show that such external factors, if not minimized by proper routines, affect the inter-instrument differences far more (up to 4-5 Delta E-ab(star)) than the instrument geometry (the effect of which is small and of order 0.1 Delta E-ab(star)). The DORT2002 radiative transfer model is used to simulate differences caused by instrument geometry. The simulated and measured differences are found to agree in magnitude, and the differences are mapped against sample properties. It is observed that the 45/0 instrument detects higher reflectance from paper samples with negligible absorption and transmittance. When there is considerable absorption (dyed samples) or transmittance (thin samples), the d/0 instrument detects higher reflectance. The physical mechanism behind this behavior is studied and explained using DORT2002, and the instrument differences are shown to depend on the anisotropy of the reflected light. The model/measurement agreement is satisfactory as the characteristic behavior is captured in almost all cases studied. This new understanding is important for facilitating accurate data exchange between the paper and graphic arts industries, but also for interpretation of reflectance measurements in general.
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| 6. |
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| 7. |
- Edvardsson, Sverker, et al.
(författare)
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Solving equations through particle dynamics
- 2015
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Ingår i: Computer Physics Communications. - : Elsevier. - 0010-4655 .- 1879-2944. ; 197, s. 169-181
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Tidskriftsartikel (refereegranskat)abstract
- The present work evaluates a recently developed particle method (DFPM). The basic idea behind this method is to utilize a Newtonian system of interacting particles that through dissipation solves mathematical problems. We find that this second order dynamical system results in an algorithm that is among the best methods known. The present work studies large systems of linear equations. Of special interest is the wide eigenvalue spectrum. This case is common as the discretization of the continuous problem becomes dense. The convergence rate of DFPM is shown to be in parity with that of the conjugate gradient method, both analytically and through numerical examples. However, an advantage with DFPM is that it is cheaper per iteration. Another advantage is that it is not restricted to symmetric matrices only, as is the case for the conjugate gradient method. The convergence properties of DFPM are shown to be superior to the closely related approach utilizing only a first order dynamical system, and also to several other iterative methods in numerical linear algebra. The performance properties are understood and optimized by taking advantage of critically damped oscillators in classical mechanics. Just as in the case of the conjugate gradient method, a limitation is that all eigenvalues (spring constants) are required to be of the same sign. DFPM has no other limitation such as matrix structure or a spectral radius as is common among iterative methods. Examples are provided to test the particle algorithm’s merits and also various performance comparisons with existent numerical algorithms are provided.
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| 8. |
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| 9. |
- Gustafsson Coppel, Ludovic, 1973-, et al.
(författare)
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Angular dependence of fluorescence from turbid media
- 2015
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Ingår i: Optics Express. - : Optical Society of America. - 1094-4087. ; 23:15, s. 19552-19564
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Tidskriftsartikel (refereegranskat)abstract
- We perform Monte Carlo light scattering simulations to study the angular distribution of the fluorescence emission from turbid media and compare the results to measured angular distributions from fluorescing white paper samples. The angular distribution of fluorescence emission is significantly depending on the concentration of fluorophores. The simulations show also a dependence on the angle of incidence that is however not as evident in the measurements. A detailed analysis of the factors affecting this angular distribution indicates that it is strongly correlated to the mean depth of the fluorescence process. The findings can find applications in fluorescence spectroscopy and are of particular interest when optimizing the impact of fluorescence on e.g.the appearance of paper as the measured values are angle dependent.
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| 10. |
- Gustafsson Coppel, Ludovic, 1975-, et al.
(författare)
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Extension of the Stokes equation for layered constructions to fluorescent turbid media
- 2012
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Ingår i: Journal of the Optical Society of America A. - : Optical Society of America. - 1084-7529 .- 1520-8532. ; 29:4, s. 574-578
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Tidskriftsartikel (refereegranskat)abstract
- Expressions relating the bispectral reflectance of a stack of n fluorescinglayers to each individual layer's reflectance and transmittance arederived. This theoretical framework is used together with recentlyproposed extensions of the Kubelka--Munk model to study the fluorescencefrom layered turbid media. For one layer over a reflecting background,the model is shown to give the same results as a previous model.The extension to n layers with different optical properties allowssimulating the bispectral reflectance from a pad of layered turbidmedia. The applicability of the model is exemplified with an optimizationof fluorophore distribution in layered turbid media.
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