329,620 research outputs found
Measuring hidden phenotype:Quantifying the shape of barley seeds using the Euler characteristic transform
Shape plays a fundamental role in biology. Traditional phenotypic analysis methods measure some features but fail to measure the information embedded in shape comprehensively. To extract, compare and analyse this information embedded in a robust and concise way, we turn to topological data analysis (TDA), specifically the Euler characteristic transform. TDA measures shape comprehensively using mathematical representations based on algebraic topology features. To study its use, we compute both traditional and topological shape descriptors to quantify the morphology of 3121 barley seeds scanned with X-ray computed tomography (CT) technology at 127 μm resolution. The Euler characteristic transform measures shape by analysing topological features of an object at thresholds across a number of directional axes. A Kruskal-Wallis analysis of the information encoded by the topological signature reveals that the Euler characteristic transform picks up successfully the shape of the crease and bottom of the seeds. Moreover, while traditional shape descriptors can cluster the seeds based on their accession, topological shape descriptors can cluster them further based on their panicle. We then successfully train a support vector machine to classify 28 different accessions of barley based exclusively on the shape of their grains. We observe that combining both traditional and topological descriptors classifies barley seeds better than using just traditional descriptors alone. This improvement suggests that TDA is thus a powerful complement to traditional morphometrics to comprehensively describe a multitude of 'hidden' shape nuances which are otherwise not detected.</p
Parallel Algorithms for Geometric Graph Problems
We give algorithms for geometric graph problems in the modern parallel models
inspired by MapReduce. For example, for the Minimum Spanning Tree (MST) problem
over a set of points in the two-dimensional space, our algorithm computes a
-approximate MST. Our algorithms work in a constant number of
rounds of communication, while using total space and communication proportional
to the size of the data (linear space and near linear time algorithms). In
contrast, for general graphs, achieving the same result for MST (or even
connectivity) remains a challenging open problem, despite drawing significant
attention in recent years.
We develop a general algorithmic framework that, besides MST, also applies to
Earth-Mover Distance (EMD) and the transportation cost problem. Our algorithmic
framework has implications beyond the MapReduce model. For example it yields a
new algorithm for computing EMD cost in the plane in near-linear time,
. We note that while recently Sharathkumar and Agarwal
developed a near-linear time algorithm for -approximating EMD,
our algorithm is fundamentally different, and, for example, also solves the
transportation (cost) problem, raised as an open question in their work.
Furthermore, our algorithm immediately gives a -approximation
algorithm with space in the streaming-with-sorting model with
passes. As such, it is tempting to conjecture that the
parallel models may also constitute a concrete playground in the quest for
efficient algorithms for EMD (and other similar problems) in the vanilla
streaming model, a well-known open problem
MM Algorithms for Geometric and Signomial Programming
This paper derives new algorithms for signomial programming, a generalization
of geometric programming. The algorithms are based on a generic principle for
optimization called the MM algorithm. In this setting, one can apply the
geometric-arithmetic mean inequality and a supporting hyperplane inequality to
create a surrogate function with parameters separated. Thus, unconstrained
signomial programming reduces to a sequence of one-dimensional minimization
problems. Simple examples demonstrate that the MM algorithm derived can
converge to a boundary point or to one point of a continuum of minimum points.
Conditions under which the minimum point is unique or occurs in the interior of
parameter space are proved for geometric programming. Convergence to an
interior point occurs at a linear rate. Finally, the MM framework easily
accommodates equality and inequality constraints of signomial type. For the
most important special case, constrained quadratic programming, the MM
algorithm involves very simple updates.Comment: 16 pages, 1 figur
Subsumption Algorithms for Three-Valued Geometric Resolution
In our implementation of geometric resolution, the most costly operation is
subsumption testing (or matching): One has to decide for a three-valued,
geometric formula, if this formula is false in a given interpretation. The
formula contains only atoms with variables, equality, and existential
quantifiers. The interpretation contains only atoms with constants. Because the
atoms have no term structure, matching for geometric resolution is hard. We
translate the matching problem into a generalized constraint satisfaction
problem, and discuss several approaches for solving it efficiently, one direct
algorithm and two translations to propositional SAT. After that, we study
filtering techniques based on local consistency checking. Such filtering
techniques can a priori refute a large percentage of generalized constraint
satisfaction problems. Finally, we adapt the matching algorithms in such a way
that they find solutions that use a minimal subset of the interpretation. The
adaptation can be combined with every matching algorithm. The techniques
presented in this paper may have applications in constraint solving independent
of geometric resolution.Comment: This version was revised on 18.05.201
Faster Geometric Algorithms via Dynamic Determinant Computation
The computation of determinants or their signs is the core procedure in many
important geometric algorithms, such as convex hull, volume and point location.
As the dimension of the computation space grows, a higher percentage of the
total computation time is consumed by these computations. In this paper we
study the sequences of determinants that appear in geometric algorithms. The
computation of a single determinant is accelerated by using the information
from the previous computations in that sequence.
We propose two dynamic determinant algorithms with quadratic arithmetic
complexity when employed in convex hull and volume computations, and with
linear arithmetic complexity when used in point location problems. We implement
the proposed algorithms and perform an extensive experimental analysis. On one
hand, our analysis serves as a performance study of state-of-the-art
determinant algorithms and implementations. On the other hand, we demonstrate
the supremacy of our methods over state-of-the-art implementations of
determinant and geometric algorithms. Our experimental results include a 20 and
78 times speed-up in volume and point location computations in dimension 6 and
11 respectively.Comment: 29 pages, 8 figures, 3 table
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