Convex Hulls, Oracles, and Homology

This paper presents a new algorithm for the convex hull problem, which is based on a reduction to a combinatorial decision problem POLYTOPE-COMPLETENESS-COMBINATORIAL, which in turn can be solved by a simplicial homology computation. Like other convex hull algorithms, our algorithm is polynomial (in the size of input plus output) for simplicial or simple input. We show that the ``no''-case of POLYTOPE-COMPLETENESS-COMBINATORIAL has a certificate that can be checked in polynomial time (if integrity of the input is guaranteed).Comment: 11 pages, 2 figure

Three-dimensional alpha shapes

Frequently, data in scientific computing is in its abstract form a finite point set in space, and it is sometimes useful or required to compute what one might call the ``shape'' of the set. For that purpose, this paper introduces the formal notion of the family of $\alpha$-shapes of a finite point set in \Real^3. Each shape is a well-defined polytope, derived from the Delaunay triangulation of the point set, with a parameter \alpha \in \Real controlling the desired level of detail. An algorithm is presented that constructs the entire family of shapes for a given set of size $n$ in time $O(n^2)$, worst case. A robust implementation of the algorithm is discussed and several applications in the area of scientific computing are mentioned.Comment: 32 page

Pruning Algorithms for Pretropisms of Newton Polytopes

Pretropisms are candidates for the leading exponents of Puiseux series that represent solutions of polynomial systems. To find pretropisms, we propose an exact gift wrapping algorithm to prune the tree of edges of a tuple of Newton polytopes. We prefer exact arithmetic not only because of the exact input and the degrees of the output, but because of the often unpredictable growth of the coordinates in the face normals, even for polytopes in generic position. We provide experimental results with our preliminary implementation in Sage that compare favorably with the pruning method that relies only on cone intersections.Comment: exact, gift wrapping, Newton polytope, pretropism, tree pruning, accepted for presentation at Computer Algebra in Scientific Computing, CASC 201

Parametric Inference for Biological Sequence Analysis

One of the major successes in computational biology has been the unification, using the graphical model formalism, of a multitude of algorithms for annotating and comparing biological sequences. Graphical models that have been applied towards these problems include hidden Markov models for annotation, tree models for phylogenetics, and pair hidden Markov models for alignment. A single algorithm, the sum-product algorithm, solves many of the inference problems associated with different statistical models. This paper introduces the \emph{polytope propagation algorithm} for computing the Newton polytope of an observation from a graphical model. This algorithm is a geometric version of the sum-product algorithm and is used to analyze the parametric behavior of maximum a posteriori inference calculations for graphical models.Comment: 15 pages, 4 figures. See also companion paper "Tropical Geometry of Statistical Models" (q-bio.QM/0311009

Design of Combined Coverage Area Reporting and Geo-casting of Queries for Wireless Sensor Networks

In order to efficiently deal with queries or other location dependent information, it is key that the wireless sensor network informs gateways what geographical area is serviced by which gateway. The gateways are then able to e.g. efficiently route queries which are only valid in particular regions of the deployment. The proposed algorithms combine coverage area reporting and geographical routing of queries which are injected by gateways.\u