8,986 research outputs found
Hierarchical image simplification and segmentation based on Mumford-Shah-salient level line selection
Hierarchies, such as the tree of shapes, are popular representations for
image simplification and segmentation thanks to their multiscale structures.
Selecting meaningful level lines (boundaries of shapes) yields to simplify
image while preserving intact salient structures. Many image simplification and
segmentation methods are driven by the optimization of an energy functional,
for instance the celebrated Mumford-Shah functional. In this paper, we propose
an efficient approach to hierarchical image simplification and segmentation
based on the minimization of the piecewise-constant Mumford-Shah functional.
This method conforms to the current trend that consists in producing
hierarchical results rather than a unique partition. Contrary to classical
approaches which compute optimal hierarchical segmentations from an input
hierarchy of segmentations, we rely on the tree of shapes, a unique and
well-defined representation equivalent to the image. Simply put, we compute for
each level line of the image an attribute function that characterizes its
persistence under the energy minimization. Then we stack the level lines from
meaningless ones to salient ones through a saliency map based on extinction
values defined on the tree-based shape space. Qualitative illustrations and
quantitative evaluation on Weizmann segmentation evaluation database
demonstrate the state-of-the-art performance of our method.Comment: Pattern Recognition Letters, Elsevier, 201
Unifying Parsimonious Tree Reconciliation
Evolution is a process that is influenced by various environmental factors,
e.g. the interactions between different species, genes, and biogeographical
properties. Hence, it is interesting to study the combined evolutionary history
of multiple species, their genes, and the environment they live in. A common
approach to address this research problem is to describe each individual
evolution as a phylogenetic tree and construct a tree reconciliation which is
parsimonious with respect to a given event model. Unfortunately, most of the
previous approaches are designed only either for host-parasite systems, for
gene tree/species tree reconciliation, or biogeography. Hence, a method is
desirable, which addresses the general problem of mapping phylogenetic trees
and covering all varieties of coevolving systems, including e.g., predator-prey
and symbiotic relationships. To overcome this gap, we introduce a generalized
cophylogenetic event model considering the combinatorial complete set of local
coevolutionary events. We give a dynamic programming based heuristic for
solving the maximum parsimony reconciliation problem in time O(n^2), for two
phylogenies each with at most n leaves. Furthermore, we present an exact
branch-and-bound algorithm which uses the results from the dynamic programming
heuristic for discarding partial reconciliations. The approach has been
implemented as a Java application which is freely available from
http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on
Algorithms in Bioinformatics (WABI2013
Probabilistic Graphical Model Representation in Phylogenetics
Recent years have seen a rapid expansion of the model space explored in
statistical phylogenetics, emphasizing the need for new approaches to
statistical model representation and software development. Clear communication
and representation of the chosen model is crucial for: (1) reproducibility of
an analysis, (2) model development and (3) software design. Moreover, a
unified, clear and understandable framework for model representation lowers the
barrier for beginners and non-specialists to grasp complex phylogenetic models,
including their assumptions and parameter/variable dependencies.
Graphical modeling is a unifying framework that has gained in popularity in
the statistical literature in recent years. The core idea is to break complex
models into conditionally independent distributions. The strength lies in the
comprehensibility, flexibility, and adaptability of this formalism, and the
large body of computational work based on it. Graphical models are well-suited
to teach statistical models, to facilitate communication among phylogeneticists
and in the development of generic software for simulation and statistical
inference.
Here, we provide an introduction to graphical models for phylogeneticists and
extend the standard graphical model representation to the realm of
phylogenetics. We introduce a new graphical model component, tree plates, to
capture the changing structure of the subgraph corresponding to a phylogenetic
tree. We describe a range of phylogenetic models using the graphical model
framework and introduce modules to simplify the representation of standard
components in large and complex models. Phylogenetic model graphs can be
readily used in simulation, maximum likelihood inference, and Bayesian
inference using, for example, Metropolis-Hastings or Gibbs sampling of the
posterior distribution
Using numerical plant models and phenotypic correlation space to design achievable ideotypes
Numerical plant models can predict the outcome of plant traits modifications
resulting from genetic variations, on plant performance, by simulating
physiological processes and their interaction with the environment.
Optimization methods complement those models to design ideotypes, i.e. ideal
values of a set of plant traits resulting in optimal adaptation for given
combinations of environment and management, mainly through the maximization of
a performance criteria (e.g. yield, light interception). As use of simulation
models gains momentum in plant breeding, numerical experiments must be
carefully engineered to provide accurate and attainable results, rooting them
in biological reality. Here, we propose a multi-objective optimization
formulation that includes a metric of performance, returned by the numerical
model, and a metric of feasibility, accounting for correlations between traits
based on field observations. We applied this approach to two contrasting
models: a process-based crop model of sunflower and a functional-structural
plant model of apple trees. In both cases, the method successfully
characterized key plant traits and identified a continuum of optimal solutions,
ranging from the most feasible to the most efficient. The present study thus
provides successful proof of concept for this enhanced modeling approach, which
identified paths for desirable trait modification, including direction and
intensity.Comment: 25 pages, 5 figures, 2017, Plant, Cell and Environmen
Prioritizing Populations for Conservation Using Phylogenetic Networks
In the face of inevitable future losses to biodiversity, ranking species by conservation priority seems more than prudent. Setting conservation priorities within species (i.e., at the population level) may be critical as species ranges become fragmented and connectivity declines. However, existing approaches to prioritization (e.g., scoring organisms by their expected genetic contribution) are based on phylogenetic trees, which may be poor representations of differentiation below the species level. In this paper we extend evolutionary isolation indices used in conservation planning from phylogenetic trees to phylogenetic networks. Such networks better represent population differentiation, and our extension allows populations to be ranked in order of their expected contribution to the set. We illustrate the approach using data from two imperiled species: the spotted owl Strix occidentalis in North America and the mountain pygmy-possum Burramys parvus in Australia. Using previously published mitochondrial and microsatellite data, we construct phylogenetic networks and score each population by its relative genetic distinctiveness. In both cases, our phylogenetic networks capture the geographic structure of each species: geographically peripheral populations harbor less-redundant genetic information, increasing their conservation rankings. We note that our approach can be used with all conservation-relevant distances (e.g., those based on whole-genome, ecological, or adaptive variation) and suggest it be added to the assortment of tools available to wildlife managers for allocating effort among threatened populations
Return of the features. Efficient feature selection and interpretation for photometric redshifts
The explosion of data in recent years has generated an increasing need for
new analysis techniques in order to extract knowledge from massive datasets.
Machine learning has proved particularly useful to perform this task. Fully
automatized methods have recently gathered great popularity, even though those
methods often lack physical interpretability. In contrast, feature based
approaches can provide both well-performing models and understandable
causalities with respect to the correlations found between features and
physical processes. Efficient feature selection is an essential tool to boost
the performance of machine learning models. In this work, we propose a forward
selection method in order to compute, evaluate, and characterize better
performing features for regression and classification problems. Given the
importance of photometric redshift estimation, we adopt it as our case study.
We synthetically created 4,520 features by combining magnitudes, errors, radii,
and ellipticities of quasars, taken from the SDSS. We apply a forward selection
process, a recursive method in which a huge number of feature sets is tested
through a kNN algorithm, leading to a tree of feature sets. The branches of the
tree are then used to perform experiments with the random forest, in order to
validate the best set with an alternative model. We demonstrate that the sets
of features determined with our approach improve the performances of the
regression models significantly when compared to the performance of the classic
features from the literature. The found features are unexpected and surprising,
being very different from the classic features. Therefore, a method to
interpret some of the found features in a physical context is presented. The
methodology described here is very general and can be used to improve the
performance of machine learning models for any regression or classification
task.Comment: 21 pages, 11 figures, accepted for publication on A&A, final version
after language revisio
Radiative transfer on hierarchial grids
We present new methods for radiative transfer on hierarchial grids. We
develop a new method for calculating the scattered flux that employs the grid
structure to speed up the computation. We describe a novel subiteration
algorithm that can be used to accelerate calculations with strong dust
temperature self-coupling. We compute two test models, a molecular cloud and a
circumstellar disc, and compare the accuracy and speed of the new algorithms
against existing methods. An adaptive model of the molecular cloud with less
than 8 % of the cells in the uniform grid produced results in good agreement
with the full resolution model. The relative RMS error of the surface
brightness <4 % at all wavelengths, and in regions of high column density the
relative RMS error was only 10^{-4}. Computation with the adaptive model was
faster by a factor of ~5. The new method for calculating the scattered flux is
faster by a factor of ~4 in large models with a deep hierarchy structure, when
images of the scattered light are computed towards several observing
directions. The efficiency of the subiteration algorithm is highly dependent on
the details of the model. In the circumstellar disc test the speed-up was a
factor of two, but much larger gains are possible. The algorithm is expected to
be most beneficial in models where a large number of small, dense regions are
embedded in an environment with a lower mean density.Comment: Accepted to A&A; 13 pages, 8 figures; (v2: minor typos corrected
Polynomial Time Algorithms for Multi-Type Branching Processes and Stochastic Context-Free Grammars
We show that one can approximate the least fixed point solution for a
multivariate system of monotone probabilistic polynomial equations in time
polynomial in both the encoding size of the system of equations and in
log(1/\epsilon), where \epsilon > 0 is the desired additive error bound of the
solution. (The model of computation is the standard Turing machine model.)
We use this result to resolve several open problems regarding the
computational complexity of computing key quantities associated with some
classic and heavily studied stochastic processes, including multi-type
branching processes and stochastic context-free grammars
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