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

Geometric combinatorics and computational molecular biology: branching polytopes for RNA sequences

Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the parameters used in the objective functions. The goal of a parametric analysis is to elucidate such dependencies, especially as they pertain to the accuracy and robustness of the optimal solutions. Techniques from geometric combinatorics, including polytopes and their normal fans, have been used previously to give parametric analyses of simple models for DNA sequence alignment and RNA branching configurations. Here, we present a new computational framework, and proof-of-principle results, which give the first complete parametric analysis of the branching portion of the nearest neighbor thermodynamic model for secondary structure prediction for real RNA sequences.Comment: 17 pages, 8 figure

Survey propagation at finite temperature: application to a Sourlas code as a toy model

In this paper we investigate a finite temperature generalization of survey propagation, by applying it to the problem of finite temperature decoding of a biased finite connectivity Sourlas code for temperatures lower than the Nishimori temperature. We observe that the result is a shift of the location of the dynamical critical channel noise to larger values than the corresponding dynamical transition for belief propagation, as suggested recently by Migliorini and Saad for LDPC codes. We show how the finite temperature 1-RSB SP gives accurate results in the regime where competing approaches fail to converge or fail to recover the retrieval state

An Output-sensitive Algorithm for Computing Projections of Resultant Polytopes

We develop an incremental algorithm to compute the Newton polytope of the resultant, aka resultant polytope, or its projection along a given direction. The resultant is fundamental in algebraic elimination and in implicitization of parametric hypersurfaces. Our algorithm exactly computes vertex- and halfspace-representations of the desired polytope using an oracle producing resultant vertices in a given direction. It is output-sensitive as it uses one oracle call per vertex. We overcome the bottleneck of determinantal predicates by hashing, thus accelerating execution from $18$ to $100$ times. We implement our algorithm using the experimental CGAL package {\tt triangulation}. A variant of the algorithm computes successively tighter inner and outer approximations: when these polytopes have, respectively, 90\% and 105\% of the true volume, runtime is reduced up to $25$ times. Our method computes instances of $5$-, $6$- or $7$-dimensional polytopes with $35$K, $23$K or $500$ vertices, resp., within $2$hr. Compared to tropical geometry software, ours is faster up to dimension $5$ or $6$, and competitive in higher dimensions

Enumeration of non-orientable 3-manifolds using face pairing graphs and union-find

Drawing together techniques from combinatorics and computer science, we improve the census algorithm for enumerating closed minimal P^2-irreducible 3-manifold triangulations. In particular, new constraints are proven for face pairing graphs, and pruning techniques are improved using a modification of the union-find algorithm. Using these results we catalogue all 136 closed non-orientable P^2-irreducible 3-manifolds that can be formed from at most ten tetrahedra.Comment: 37 pages, 34 figure

Correlating Cell Behavior with Tissue Topology in Embryonic Epithelia

Measurements on embryonic epithelial tissues in a diverse range of organisms have shown that the statistics of cell neighbor numbers are universal in tissues where cell proliferation is the primary cell activity. Highly simplified non-spatial models of proliferation are claimed to accurately reproduce these statistics. Using a systematic critical analysis, we show that non-spatial models are not capable of robustly describing the universal statistics observed in proliferating epithelia, indicating strong spatial correlations between cells. Furthermore we show that spatial simulations using the Subcellular Element Model are able to robustly reproduce the universal histogram. In addition these simulations are able to unify ostensibly divergent experimental data in the literature. We also analyze cell neighbor statistics in early stages of chick embryo development in which cell behaviors other than proliferation are important. We find from experimental observation that cell neighbor statistics in the primitive streak region, where cell motility and ingression are also important, show a much broader distribution. A non-spatial Markov process model provides excellent agreement with this broader histogram indicating that cells in the primitive streak may have significantly weaker spatial correlations. These findings show that cell neighbor statistics provide a potentially useful signature of collective cell behavior.Comment: PLoS one 201